From 3fa31b50af2861382fbe2c76406f5a04c3fefc93 Mon Sep 17 00:00:00 2001 From: SoloDShelby Date: Fri, 19 Jul 2024 14:41:40 +0300 Subject: Evaluation code for paper 1 --- .../data/datasets/old/full_general_dataset.json | 248 +++++++++++++++++++++ 1 file changed, 248 insertions(+) create mode 100644 gnqa/paper1_eval/src/data/datasets/old/full_general_dataset.json (limited to 'gnqa/paper1_eval/src/data/datasets/old/full_general_dataset.json') diff --git a/gnqa/paper1_eval/src/data/datasets/old/full_general_dataset.json b/gnqa/paper1_eval/src/data/datasets/old/full_general_dataset.json new file mode 100644 index 0000000..5e8a3b4 --- /dev/null +++ b/gnqa/paper1_eval/src/data/datasets/old/full_general_dataset.json @@ -0,0 +1,248 @@ +{ + "question": [ + "What is the most cited environmental factor for the onset of asthma.", + "What is apoptosis?", + "How would one extract the DNA, from say, mammals or plants?", + "What is a genetic marker?", + "Explain the process of finding a genetic marker followed by a quantitative trait loci.", + "Create a how-to guide for genetic sequencing.", + "What is the significance of the length of telomeres?", + "Once a sperm combines with an egg, what determines how traits are passed onto the resulting lifeform?", + "Why is genetic tracing matrilineal rather than patrilineal?", + "How does one tell the difference between X and Y DNA, with respect to DNA tracing and determining QTLs?" + ], + "answer": [ + "Air pollution is the most cited environmental factor for the onset of asthma.", + "Apoptosis, also known as cell suicide or programmed cell death, is a biological process in multicellular organisms that allows specific cells to be removed during the development of complex tissues, or potentially dangerous damaged cells to be destroyed for the benefit of the whole organism. It is characterized by a sequence of well-defined events resulting in cell destruction and is necessary for normal cell turnover. It is also essential to various other biological processes.", + "For mammals, DNA can be extracted using a DNA Isolation Kit for Mammalian Blood, following the manufacturer's instructions. This process typically involves mixing blood with lysis buffer and Proteinase K, followed by the addition of isopropanol and Inhibitor Removal Buffer. The DNA is then washed, centrifuged, and the supernatant discarded. The remaining pellet, which contains the purified genomic DNA, is diluted in TE buffer.\n\nFor plants, the mixed alkyl trimethyl ammonium bromide (MATAB) procedure can be used. This involves grinding plant material in liquid nitrogen, incubating it in extraction buffer, and then purifying it with chloroform:isoamylalcohol. The DNA extracts are then precipitated with isopropanol and resuspended in a buffer. The extracts are further purified on anion exchange columns.", + "A genetic marker is a measurable polymorphic sequence of DNA whose chromosomal location is known. They often have no known functional significance but are used as pointers to a particular chromosomal location. They are used to track the inheritance of genes and can be a gene or some section of DNA with no known function.", + "The process of finding a genetic marker followed by a quantitative trait loci (QTL) involves several steps. First, a population is developed for genetic mapping. This population can be a segregating population or a permanent population. The population is then genotyped using molecular markers. Next, the population is phenotyped for an interested trait. QTL analysis is then conducted using statistical procedures to find markers linked to the QTL. This involves single-marker regression across all chromosomes, where a hypothetical QTL is evaluated at the location of each marker locus. The significance of that QTL is estimated from a likelihood ratio statistic. A permutation test is then conducted to establish genome-wide significance criteria for the trait. The result is a list of marker loci that show a significant association with the trait. These loci are most likely to be near QTLs. The goal of QTL mapping is to identify regions of the genome that harbor genes relevant to a specified trait.", + "1. Start with an initial linkage or association: This is the first step in a genetic study where a trait or disease is linked to a specific region of the genome.\n\n2. Perform Laboratory Genotyping: This involves determining the genetic variation of an individual by examining their DNA sequence using biological assays and comparing it to a standard sequence.\n\n3. Use Genomic Sequence: The role of genomic sequence is crucial at every stage. It serves as a common thread that ties all the stages together.\n\n4. Establish True Orthology: Determine the true orthology between genes in different species. If two genes are truly orthologous, their evolution closely follows patterns of speciation.\n\n5. Apply Bioinformatics: Use bioinformatics tools and techniques to analyze the data. This can be applied to sequence data from any collection of organisms.\n\n6. Understand Genome Structure and Content: Provide an overview of genome structure and content to provide a context for subsequent discussions.\n\n7. Improve DNA Sequencing Methods: Constantly work on improving DNA sequencing methods with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000.\n\n8. Interpret the Information: The major challenge ahead is the interpretation of this information. Understand how our genes interact with each other, and how the environment contributes to the development of health and disease.\n\n9. Consider the Implications: Understand the individual and societal implications of knowing our genome sequence.\n\n10. Keep Up with Technological Advances: With further technological advances, other previously unimaginable research approaches will become real.", + "The length of telomeres is significant as it is associated with aging, disease, and mortality. Longer telomeres are generally associated with better health outcomes, including protection from age-related diseases, better cognitive function, and healthier lipid profiles. Shorter telomeres, on the other hand, have been linked to higher risks of heart disease, infection-related death, and other diseases. Telomere length can also be influenced by factors such as stress, with high-stress situations potentially leading to faster telomere shortening and premature aging.", + "The traits are determined by the combination of genes from both the sperm and the egg. This process involves meiosis, where each gamete (sperm and egg) contributes one chromosome to each pair, resulting in a zygote with a full complement of 23 chromosome pairs. The process of recombination or crossing over, where similar DNA sequences from the paired chromosomes swap genetic material, also plays a crucial role in determining the traits of the offspring. This results in a shuffling of genetic material and contributes to the genetic variation seen among offspring.", + "Genetic tracing is matrilineal due to the inheritance of mitochondrial DNA (mtDNA), which is passed from mother to all her children without any admixture from the father. This allows for a clear lineage tracing through the maternal line. In contrast, Y-DNA is passed from father to son, allowing for patrilineal tracing, but it does not provide information about the genetic contributions of other ancestors in a family tree.", + "The difference between X and Y DNA is not explicitly discussed in the context of determining QTLs in the provided text. However, in general, X and Y chromosomes are different in size and gene content, which can be identified through genetic sequencing. In the context of QTL studies, these differences could potentially influence the traits being studied. However, the specific process of how this is done in QTL mapping is not detailed in the provided text." + ], + "contexts": [ + [ + "INTRODUCTION Asthma is a chronic disease of the airways defined by its symptoms, which include reversible airflow obstruction, inflammation, and bronchial hyperresponsiveness.The ancient Egyptians, Greeks, and Romans made reference to the symptoms of asthma, and today the disease is estimated to affect 235-334 million people worldwide (44,53).", + " The atopic triad.Perhaps the most widely recognized pattern of co-occurrence is the one of asthma, atopic dermatitis (eczema), and allergic rhinitis (hay fever), which together are referred to as the atopic triad and characteristically present clinically in a temporal sequence known as the atopic march.Within this sequence, atopic dermatitis is typically the first component to manifest, with approximately 20-30% of individuals with mild disease and 70% of those with severe disease going on to develop asthma.Individuals who undergo this distinctive sequence of disease progression frequently exhibit a more severe and persistent phenotype, with increased risk of allergen sensitization.", + " Clinically, asthma is characterized by episodes of coughing, chest tightness, wheezing, dyspnea, or sputum production.Often, asthma sufferers experience a combination of these symptoms, or some symptoms more than others.Pulmonary breathing tests typically demonstrate variable airway obstruction and hyperreactivity, but may be normal, even in patients with severe and uncontrolled disease [8].Thus, the diagnosis of asthma, which is based on general clinical symptoms and variable lung function testing, is non-specific and heavily dependent on clinical history.Within the \"umbrella\" diagnosis of asthma there exists a diverse array of differing clinical phenotypes [9].For example, childhood asthma is often associated with personal and parental atopic diseases (i.e., atopic dermatitis, food allergy, eosinophilic esophagitis, allergic rhinitis), viral infections, and tobacco smoke exposure [10].Alternatively, adult-onset asthma is less associated with atopic disease [11,12], but more associated with female sex [13], sinus disease [14], and preceding respiratory infections such as pneumonia [15].In addition, adult-onset disease is often of higher severity [12,16] with a faster and more persistent decline in lung function [17].Moreover, although severe patients are found in every demographic and age group, the most common phenotype is an adult female that is older and obese [18].", + "Introduction An estimated 9% of children and 6% of adults in the United States have asthma [1].The total number of asthma sufferers worldwide is estimated to be over 300 million, with an additional 100 million expected to develop asthma by 2025 [2][3][4][5].Developed countries are the most affected, with some of the highest rates found in the United Kingdom, Australia, New Zealand and the Republic of Ireland [3].Asthma prevalence is rising significantly in developing countries in transition to a more Western lifestyle [3].In 2007, the cost of disease in the United States was estimated to be $56 billion in relation to medical expenses, missed days of work, and early deaths [1].The rate of asthma deaths has likely plateaued, but is still as high as 250,000 per year worldwide [6].Morbidity and mortality are particularly high in ethnic minorities living below or near the poverty line, and African American children had a death rate 10 times that of non-Hispanic white children in 2015 [7].Thus, asthma is a costly, growing health problem associated with high morbidity and mortality.", + "Getting accurate estimates of exposures is difficult, whether this is air pollution or toxins in our food and drink, but these are important questions. Rutter: That is an important point. From the twin study data it is clear that environmental effects account for quite a lot of the variance on all the multifactorial disorders. Yet the kinds of measures that are used aren\u2019t terribly solid. They include broad thing such as socio-economic status (SES). Even where there are good measures the care taken in testing for environmental mediation is usually poor.", + "Bronchiolitis, a disease that happens in the first year of life in many infants, is strongly associated with subsequent asthma. We ascertained it in the first years of life and have been following these people to age 25 now. For the people who had bronchiolitis and now have asthma, their parents recall much better that they had bronchiolitis than those who don\u2019t have asthma now. It is at least twice more. Extraordinarily, some of these latter parents don\u2019t recall that they took their child to the doctor in the fi rst year of life.", + "If you arrive in the USA when you are young you have almost the same prevalence of asthma as an adult as those who are born in the USA and who are not Mexican. But if you arrive at older ages you have less asthma. If you arrive at the age of 20 you have the same asthma risk as those born in Mexico (Eldeirawi et al 2005). Kotb: This is extremely interesting. There is a relationship between depression and the immune system. This especially applies to natural killer (NK) cells, which are the main cells that fight cancers.", + "A colleague of mine in Georgia found this may have a protective effect against later development of asthma (Ownby et al 2002). Martinez: We find significantly decreased likelihood of asthma if you have a dog in a home, but not if you have a cat. The reason for this is not that I hate cats, which I do, but most likely because cats are stealth hunters, and they have to be very clean. Dogs are collective hunters and they don\u2019t care if they smell.", + "; Guffey, S.E. Investigation into pedestrian exposure to near-vehicle exhaust emissions. Environ. Health 2009, 8, 13. [CrossRef] [PubMed] Our World in Data.org. 2017. Available online: https://ourworldindata.org/data-review-air-pollution-deaths (accessed on 10 January 2022). Pope, C.A. , III. Respiratory disease associated with community air pollution and a steel mill, Utah Valley. Am. J. Public Health 1989, 79, 623\u2013628. [CrossRef] [PubMed] Pope, C.A. , III. What do epidemiologic findings tell us about the health effects of environmental aerosols? J. Aerosol. Med. 2000, 13, 335\u2013354. [CrossRef] [PubMed] Pope, C.A. , III.", + "Case for Support BBSRC Grant Application September 2005 \u201cIntegrative Analysis of the Genetic Factors behind Asthma and Atopic Dermatitis\u201d Part I: Research Proposal Background A Introduction of topic of research and its academic and wider context Asthma is the most common disease of childhood, and affects one child in seven in the United Kingdom. Atopic Dermatitis (AD, eczema) affects similar numbers of children. About 60% of children with severe AD will have concomitant asthma. Treatments for both diseases are unsatisfactory. Abandonment of orthodox medical therapy for AD is common in many families who have children with the disease.", + "This is most common during the rainy season when aerosols are created, which results in repeated inhalation of Bp [43, 44]. Environmental sampling studies reveal there is a positive association between the prevalence of disease and the degree of environmental contamination [7]. In addition to environmental factors, data suggests that host factors play an important role in mounting an immune response against infectious diseases [45] such as melioidosis. While healthy persons can contract melioidosis, most patients in endemic regions have an underlying predisposition [28], which suggests that the immunological status of the patient can influence disease initiation and progression [15].", + "Sensitivity analysis We did two sets of post-hoc sensitivity analyses to assess the effects of potential poor recall of age of onset among individuals with adult-onset asthma, and the effects of misclassification of COPD as asthma among the adultonset cases, even with exclusion of cases with a reported diagnosis of COPD, emphysema, or chronic bronchitis.First, to assure that the adult-onset cases did not include a significant proportion of childhood-onset asthma in which symptoms remitted in early life but then relapsed in adulthood, we replaced adult-onset cases with increasing proportions of randomly selected childhood-onset cases, and then tested for association at the two most significant childhood onset-specific loci.This procedure was repeated 20 times for each proportion to quantify the sampling variability (appendix pp 7-8).Second, we did two analyses in which we removed either individuals with ages of asthma onset between 46 and 65 years or adult-onset cases and controls with FEV\u2081/FVC <0\u202270.For each, we compared p values and ORs with the GWAS including all adult-onset cases (appendix pp 8-9).", + " We used data for British white individuals from UK Biobank data release July 19, 2017. 8We extracted disease status (asthma, allergic rhinitis, atopic dermatitis, food allergy, chronic obstructive pulmonary disease (COPD), emphysema, and chronic bronchitis), age of on set of asthma, and sex from self-reported question naires and hospital records (International Classification of Diseases 10th revision [ICD-10] codes) by querying our in-house protected UK Biobank database server. 9For our main case analysis, we included individuals who self-reported that they had doctor-diagnosed asthma.Further details of our research approach are provided in the appendix (pp 4-7).", + "; Guffey, S.E. Investigation into pedestrian exposure to near-vehicle exhaust emissions. Environ. Health 2009, 8, 13. [CrossRef] [PubMed] Our World in Data.org. 2017. Available online: https://ourworldindata.org/data-review-air-pollution-deaths (accessed on 10 January 2022). Pope, C.A. , III. Respiratory disease associated with community air pollution and a steel mill, Utah Valley. Am. J. Public Health 1989, 79, 623\u2013628. [CrossRef] [PubMed] Pope, C.A. , III. What do epidemiologic findings tell us about the health effects of environmental aerosols? J. Aerosol. Med. 2000, 13, 335\u2013354. [CrossRef] [PubMed] Pope, C.A. , III.", + "8 The socio-ecologic framework posits that various aspects of a child\u2019s environment directly and indirectly impact the child\u2019s health and development.9 Drawing on this framework, Beck and colleagues10 examined several biologic, social and ecologic variables to provide a greater understanding of factors influencing asthma-related hospital readmissions for black children compared to their white counterparts. The study revealed that black children were over two times as likely to be readmitted for an asthma-related illness compared to white children; this resulted from significant differences in almost every socio-ecologic variable measured, including disease management practices and access to primary care.", + "Specific Aims Asthma is the most common chronic pediatric medical condition in the United States, with a prevalence over 9.6% in children under 18 years of age.1, 2 Low-income, urban children incur a disproportionate share of asthma prevalence and morbidity;2-4 13% of children living below the poverty threshold are diagnosed with asthma compared to 8% of non-poor (>200% poverty),3 and poverty is associated with higher rates of asthma attacks.1 Living in an urban area confers additional risk for asthma and increased ED utilization.4, 5 Implementation of the National Asthma Education and Prevention Program\u2019s (NAEPP) Guidelines has contributed to reductions in asthma morbidity and mortality rates, and these guidelines emphasize establishing a partnership between healthcare providers and patients/families to promote effective asthma management.6 The NAEPP expert panel states, \u201cbuilding a partnership requires that clinicians promote open communication and ensure that patients have a basic and accurate foundation of knowledge about asthma\u2026\u201d (p.124),6 yet care partnerships also require that the patient/parent effectively communicate issues such as emerging symptoms or response to medications.", + "Vital & health statistics Series 3, Analytical and epidemiological studies. 2012(35):1-58. CDC. Current Asthma Prevalence. https://www.cdc.gov/asthma/most_recent_data.htm. 2015. Updated June 2017. Accessed March 9, 2018. Northridge J, Ramirez OF, Stingone JA, Claudio L. The role of housing type and housing quality in urban children with asthma. Journal of urban health : bulletin of the New York Academy of Medicine. 2010;87(2):211-224. Flores G, Snowden-Bridon C, Torres S, et al. Urban minority children with asthma: substantial morbidity, compromised quality and access to specialists, and the importance of poverty and specialty care.", + "Asthma Prevalence and Disparities Asthma is the most common chronic pediatric medical condition in the United States,1 affecting an estimated 6.2 million children annually.2 Poorly controlled pediatric asthma contributes to over 700,000 visits a year to emergency departments (ED).1 Children living in impoverished, urban settings are disproportionately affected by asthma,3 and the disparate impact of asthma is even worse among black and Latino children, and children whose parents have limited English proficiency (LEP) in these urban low-income areas.4-6 A 2017 longitudinal study revealed that black race and Latino ethnicity are significantly associated with worse asthma outcomes including 1) asthma knowledge, 2) asthma-related quality of life, 3) asthma severity, and 4) asthma control.", + "The Journal of asthma : official journal of the Association for the Care of Asthma. 2017:16. Inkelas M, Garro N, McQuaid EL, Ortega AN. Race/ethnicity, language, and asthma care: findings from a 4-state survey. Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology. 2008;100(2):120-127. National Asthma Education and Prevention Program. Expert Panel Report 3: Guidelines for the Diagnosis and Management of Asthma Bethesda, MD: National Institutes of Health, National Heart, Lung, and Blood Institute; 2007. Publication no. 08-045.1. NIH Consensus Group. Video report: What is mHealth?", + "Contact PD/PI: Coker, Tumaini Rucker INTRODUCTION TO APPLICATION Research Plan Overview Childhood asthma is the most common pediatric medical condition in the United States, and disproportionately affects children living in low-income, urban settings. Many low-income, urban families rely on emergency department (ED) services as their source for sick care for their child. This is often due to not having a primary care provider or sufficient access to their primary care provider for asthma management." + ], + [ + " Apoptosis, or controlled cell death [62], is another major stressed-cell response, and was also represented in our results (Fig. 9e).A large body of direct evidence points to apoptosis as one of the main routes of RPE degeneration in AMD [63].Induction of apoptosis upon stress is dictated by the action of master regulator p53, and it was recently shown that aging increases the activity of p53 in RPE cells and the likelihood for apoptotic cell death [64].Consistent with this evidence, we found association with pathways in Transcriptional regulation by TP53 group (Fig. 9d).In particular, Regulation of TP53 activity through methylation was among the top pathway in our association analysis (Table 1), suggesting that p53 modification by methylation and the closely related histone modifications [Protein lysine methyltransferases (PKMTs) methylate histone lysine in Fig. 9e] play important roles in RPE apoptosis regulation.In the intrinsic apoptotic pathway induced by oxidative stress, cytochrome c is released from mitochondria into the cytosol, binding and activating caspases, the main proteases central to apoptotic action.We found association in pathways involving 'inhibitor of apoptosis' (IAP) and its negative regulator 'second mitochondrial activator of caspases' (SMAC) [65], which suggests that disruption to regulatory mechanisms preventing apoptosis in RPE cells may play roles in AMD.", + "Apoptosis Persistent DNA damage", + "42 ABSTRACT 18 A MODULARIZED MODEL OF APOPTOSIS HA Harrington, KHo, Sk Ghosh, KC Tung , CY Kao, and B Aguda Imperial College London, Courant Institute of Mathematical Sciences New York University, University of Texas at Arlington, University of Texas Southwestern Medical Center, Mathematical Biosciences Institute, and Department of Mathematics, The Ohio State University Columbus, OH, USA Background: One of the key physiological mechanisms employed by the cell (during development and for maintenance of homeostasis) in multi-cellular organism is apoptosis, which is characterized by a sequence of well-defined events resulting in cell destruction.", + "14 Apoptosis is caused by the activation of the caspase cascade, which is initiated by two signaling routes (stress-induced death and death-domain receptor-induced death) (Domen 2001). This process can be prevented by antiapoptotic molecules, such as Bcl-2 (Domen and Weissman 2000). Direct evidence for the involvement of apoptosis in HSC number regulation came from the findings that overexpression of the anti-apoptotic gene bcl-2 led to increased numbers of Thy-1.1low, Sca-1+, c-kit+, Lin- cells, a population with long-term multi-lineage repopulation potential (Domen et al. 2000).", + "Several lines of evidence have indicated that apoptosis acts as an important regulator of stem cells. First of all, expression of some apoptosisrelated genes were detected in human and/or murine HSCs (Domen 2001). Secondly, targeted disruption of some of these genes in null and dominant negative mutant mice interfered with normal apoptotic processes in HSCs. For example, overexpression of Bcl-2, a negative regulator of apoptosis, increased not only the numbers and competitive repopulation capabilities of HSCs, but also the resistance of HSCs to apoptosis induced by ionizing radiation (Domen and Weissman 2003).", + "Apoptosis Cell suicide, or apoptosis, is a well-studied biological phenomenon in multicellular organisms that allows specific cells to be removed during the development of complex tissues, or potentially dangerous damaged cells to be destroyed for the benefit of the whole organism.The lack of an apparent evolutionary benefit for such a process in a single-celled organism initially caused controversy about the presence of an apoptotic pathway in yeast.Today, however, a number of yeast orthologues to mammalian apoptosis genes have been discovered and apoptotic-like cell death has been linked to mating, colony formation, and aging (Buttner et al. 2006;Eisenberg et al. 2007;Frohlich et al. 2007).With respect to aging, both replicatively and chronologically aged cells that die have increased ROS and display apoptotic phenotypes (Fabrizio et al. 2004a;Herker et al. 2004;Laun et al. 2001).", + " The importance of apoptosis in yeast aging has yet to be fully characterized.At the very least, yeast apoptosis provides a useful pathway for studying genetic interactions for age-related diseases that affect humans, such as cancer.Readers interested in further information related to yeast apoptosis are referred to several in-depth reviews (Buttner et al. 2006;Eisenberg et al. 2007;Frohlich et al. 2007).", + "Early redistribution of plasma membrane phosphatidylserine is a general feature of apoptosis regardless of the initiating stimulus: inhibition by overexpression of Bcl-2 and Abl. J Exp Med 182: 1545-56. Mathew CG (2006). Fanconi anaemia genes and susceptibility to cancer. Oncogene 25: 5875-84. McBride MW, Carr FJ, Graham D, Anderson NH, Clark JS, Lee WK et al (2003). Microarray analysis of rat chromosome 2 congenic strains. Hypertension 41: 847-53. Merino-Trigo A, Kerr MC, Houghton F, Lindberg A, Mitchell C, Teasdale RD et al (2004).", + " When a cell harbors such severe DNA damage that it is beyond repair, it is disposed of through apoptosis.Alternatively, DNA damage can induce cellular senescence, the irreversible cessation of mitosis.Both processes are critically dependent on p53, which is known as the guardian of the genome [3] .DNA damage may also trigger autophagy, a cellular catabolic process that maintains homeostasis [4] .It should be noted that under normal conditions cells are rarely exposed to very high doses of DNAdamaging agents, which may be the explanation why we do not age and die because we run out of cells.However, aging is associated with some atrophy [1] and it is conceivable that at older ages bursts of DNA damage, for example from free radical reactions associated with inflammation, do occur and give rise to an increasingly high rate of apoptosis or cellular senescence.While there is some evidence for increased apoptosis and cellular senescence at old age, it is doubtful that under normal conditions this would lead to a significant loss of functional cells.", + " Apoptosis, or programmed cell death, literally eliminates cells at risk for neoplastic transformation.Senescence, by contrast, permanently arrests their growth.Both processes are controlled by the p53 tumor suppressor protein (Amundson, Myers, & Fornace, 1998;Bringold & Serrano, 2000;Hickman, Moroni, & Helin, 2002;Itahana, Dimri, & Campisi, 2001).p53 is a transcriptional regulator that both transactivates and transrepresses target genes in response to stress (Prives & Hall, 1999;Ryan, Phillips, & Voudsen, 2001).These target genes, in turn, stimulate DNA repair, transient cell cycle arrest, permanent cell cycle arrest (senescence) or cell death (apoptosis), depending on cell type, degree and type of damage, and other variables.In contrast, cells that lack normal p53 regulation or function -for example, tumor cells -tend to die in response to telomere dysfunction.Some normal human cells, on the other hand, undergo a senescence growth arrest.In either case, when present, p53 is crucial for mediating the cellular response to telomere dysfunction (Yaswen & Stampfer, 2002) (Fig. 4).", + "Cell death, and in particular apoptosis, can be caused by a number of mechanisms including loss of growth factors and excitotoxicity (e.g. , Bhutta and Anand, 2002; Nikolic\u0301 et al. , 2013). It is of interest therefore, that proximal to the region of the QTL there are several genes that are related to growth factors including the latent transforming growth factor protein 2 (ltbp2), placental growth factor (pgf), and transforming growth factor beta (Tgf beta).", + " Apoptosis-related gene expression profiles", + " Apoptosis.Programmed death of cells during embryogenesis and metamorphosis or during cell turnover in adult tissues.", + "14 Apoptosis is caused by the activation of the caspase cascade, which is initiated by two signaling routes (stress-induced death and death-domain receptor-induced death) (Domen 2001). This process can be prevented by antiapoptotic molecules, such as Bcl-2 (Domen and Weissman 2000). Direct evidence for the involvement of apoptosis in HSC number regulation came from the findings that overexpression of the anti-apoptotic gene bcl-2 led to increased numbers of Thy-1.1low, Sca-1+, c-kit+, Lin- cells, a population with long-term multi-lineage repopulation potential (Domen et al. 2000).", + "Several lines of evidence have indicated that apoptosis acts as an important regulator of stem cells. First of all, expression of some apoptosisrelated genes were detected in human and/or murine HSCs (Domen 2001). Secondly, targeted disruption of some of these genes in null and dominant negative mutant mice interfered with normal apoptotic processes in HSCs. For example, overexpression of Bcl-2, a negative regulator of apoptosis, increased not only the numbers and competitive repopulation capabilities of HSCs, but also the resistance of HSCs to apoptosis induced by ionizing radiation (Domen and Weissman 2003).", + " Fraction of cells displaying apoptosis", + " It has been known that mitochondria play a central role in the life and death of cells (Kroemer & Reed, 2000).Apoptosis was observed in developmentally arrested embryos by 72 h, but not at 24 h after FCCP treatment, despite considerable telomere attrition at this early stage, suggesting that telomere attrition occurs prior to apoptosis and may serve as an intermediate step between mitochondrial dysfunction and apoptosis.These results also suggest that telomere shortening may signal apoptosis (Lee et al ., 1998;Karlseder et al ., 1999).", + "Cell Death A form of programmed cell death, apoptosis is necessary for normal cell turnover and is essential to a plethora of other biological processes.Apoptosis can be executed via Bcl-2 activation of caspases, via signals from the death receptor on the plasma membrane, or via induction by granzyme B secreted from cytotoxic T cells (Tc cells) [35].Endonucleases and proteases are activated by active caspases, eventually leading to the death of the cell.With age, however, apoptotic activity changes.In heart [36], kidney [37], skeletal muscle [38], and Tc cells [39], increased apoptosis has been reported, perhaps contributing to loss of cellularity in these tissues.This escalation across various tissues may be attributed to the increased production of free radicals [40] and furthermore exacerbated by the accumulation of DNA damage in the aged cells [41].As the risk increases for cells to turn cancerous and dysfunctional with advancing age, increased apoptosis in aged cells is argued to be a defense strategy.In other tissues, such as the colon, apoptosis appears to decrease with age perhaps contributing to the accumulation of senescent cells and age-associated carcinogenesis [42].", + " The regulation and execution of apoptosis in endothelial cells is a complex process involving paracrine factors, membrane receptors, interaction of pro-and anti-apoptotic factors and cysteinyl aspartate-specific proteases (caspases).Recent studies suggest that in aging there is an imbalance in the expression of pro-and anti-apoptotic genes resulting in an enhanced apoptosis in the myocardium (19), central nervous system (24), skeletal muscle (10), lung (33), and liver (2,33).Yet, age-related alterations in the expression of pro-and anti-apoptotic genes in coronary arteries have not been elucidated.", + "Apoptosis modulating genes Apopotosis or programmed cell death is associated with alterations in cell morphology, particularly the nucleus, with endonucleatytic cleavage of DNA into nucleosomal length fragments.Apoptosis may result from withdrawal of growth signals." + ], + [ + "DNA and RNA extraction of tissues Genomic DNA was extracted from frozen placentae (n \u03ed 3/group) and liver (n \u03ed 9/group) using a modified version of an established protocol (28,29).Total RNA was extracted from the remaining tissue using TRIzol, as per the manufacturer's instructions (Invitrogen Canada Inc).Genomic DNA and RNA purity and concentration were assessed using spectrophotometric anal-ysis, and integrity was verified using agarose gel [1% (wt/vol)] electrophoresis.", + "Taxon Sampling and DNA Extractions We extracted DNA from 72 pinned specimens from the National Museum of Natural History (NMNH) Entomology collection for this study.We plucked middle legs from the pinned bees using a pair of sterilized forceps and washed the tissue in 95% ethanol to remove dust, pollen, and other forms of accumulated debris on the bee legs.After evaporation of the ethanol (by drying the tissue on a clean Kimwipe \u2122 ), the samples were placed in a freezer for several hours.DNA was then extracted destructively by grinding the frozen tissue with a sterile pestle, using a DNeasy Blood and TissueKit (Qiagen, Valencia, CA, USA) and following the manufacturer's protocol, except the DNA was eluted in 130\u03bcL ddH 2 O instead of the supplied buffer.We ran 10\u03bcL of each extract for 60 min at 100 volt on 1.5% agarose SB (sodium borate) gels, to estimate size of the genomic DNA.", + "DNA extraction DNA was extracted from PBMCs using the QIAamp DNA Mini kit (Qiagen, CA, USA), following the manufacturer's instructions for the spin protocol.The DNA was eluted in 60 \u03bcl of AE elution buffer and stored at -20\u00b0C.The concentration and quality of the DNA was assessed with the Qubit dsDNA HS Assay (Invitrogen, Eugene, OR, USA).", + "Methods Laboratory procedures.We initially screened 107 ancient samples (Supplementary Data 1) in dedicated clean facilities at the ancient DNA lab of Jilin University, China, following published protocols for DNA extraction and library preparation 36,37 .Prior to sampling, we wiped all skeletal elements with 5% bleach and irradiated with UV-light for 30 min from each side.We drilled teeth to obtain fine powder using a dental drill (Dremel, USA).We sampled the dense part of petrous bones around the cochlea by first removing the outer part using the sandblaster (Renfert, Germany), and then grinding the clean inner part into fine powder with the mixer mill (Retsch, Germany).We digested the powder (50-100 mg) in 900 \u03bcl 0.5 M EDTA (Sigma-Aldrich), 16.7 \u03bcl of Proteinase K (Sigma-Aldrich), and 83.3 \u03bcl ddH 2 O (Thermo Fisher, USA) at 37 \u00b0C for 18 h.Then we transferred the supernatant to a MinElute silica spin column (QIAGEN, Germany) after fully mixed with the 13 ml custom binding buffer [5 M guanidine hydrochloride (MW 95.53), 40% Isopropanol, 90 mM Sodium Acetate (3 M), and 0.05% Tween-20] followed by two washes with PE buffer (80% ethanol).Then we eluted the DNA with 100 \u03bcl TET buffer (QIAGEN, Germany).", + "DNA Extraction After blood was drawn into EDTA tubes, genomic DNA was extracted using a DNA Isolation Kit for Mammalian Blood Kit (Roche Applied Science, Indianapolis, IN, USA) according to the manufacturer's recommendations.Briefly, 300 \u03bcl of whole blood from each sample was mixed with 200 \u03bcl of lysis buffer (50 mM Tris pH 8.0, 100 mM EDTA, 100 mM NaCl, 1% SDS) and 40 \u03bcl of Proteinase K, followed by addition of 100 \u03bcl of isoproponal and 500 \u03bcl of Inhibitor Removal Buffer (5M guanidine-HCl, 20 mM Tris-HCl pH 6.6).The DNA was washed with a buffer (20 mM NaCl; 2 mM Tris-HCl; pH 7.5), centrifuged twice at 2000 rpm, washed using cold 70% ethanol and centrifuged at 3000 rpm.The supernatant was discarded and the pellet containing purified genomic DNA was diluted in TE buffer (1 mM EDTA; 10 mM Tris-HCl, pH 7.5) to a concentration of approximately 50 ng/\u03bcl.", + "Genomic DNA extraction Leukocytes were isolated from 5-ml peripheral blood samples.DNA was prepared by phenol extraction and chloroform extraction followed by isopropanol precipitation, washed with ethanol, and air-dried.Tris-EDTA buffer pH 8.0 was used to dissolve the final genomic DNA product.", + " The pulled down DNA fragments were extracted and purified using phenolchloroform extraction/ethanol precipitation.The samples were stored at -20 \u00b0C until use.", + "DNA extraction for genotyping For the majority of samples, DNA was extracted from either spleen or the exocrine fraction of the islet isolation using the Tissue DNA Purification Kit according to manufacturer's instructions on an automated Maxwell 16 system (both Promega, USA).When no other tissue was available, DNA was extracted from human islets using the Trizol fraction remaining after extraction of RNA (see above).To precipitate the DNA, 300\u03bcl 100% ethanol was added to the thawed solution.This mixture was incubated at room temperature for a minimum of 30 minutes.DNA was then pelleted by centrifugation at 4,000 x g for 5 minutes at 4\u00b0C.After removing the supernatant, the pellet was twice washed with 0.1M trisodium citrate (Sigma Aldrich, UK) in 10% ethanol and left at room temperature for 30 minutes, followed by another wash step with 75% ethanol.After the final wash step, pellets were air-dried for 10 minutes to remove residual ethanol and re-suspended in a minimum of 100 \u03bcL 8mM NaOH (Sigma Aldrich).Extracted DNA was stored at -20\u00b0C before further use.", + "DNA extraction Tissue samples were incubated at 50\u00b0C overnight with shaking in DNA extraction buffer (100 mM NaCl, 10 mM Tris.HCl pH8, 25 mM EDTA, 0.5% (w/v) SDS), containing 200 \u03bcg/ml proteinase K. DNA was isolated by two rounds of phenol:chloroform extraction, followed by RNAse A treatment, precipitation in absolute ethanol containing 10% (v/v) sodium acetate (3 M, pH 5.2), and resuspended in 100 \u03bcl nuclease-free water (Ambion, Austin, TX, USA) or using salting out method followed by purification with Qiagen blood and tissue kit (Qiagen, Mississauga, ON, USA).DNA was stored at -20\u00b0C.", + "Methods Human DNA samples DNA was extracted from human patient tissue samples acquired from the University of Minnesota Tissue Procurement Facility from BioNet (IRB#0805E32181).See Supplemental Table S4 for patient data.Briefly, 2 mg of tissue was digested overnight at 55\u00b0C on a rotating platform in 710 mL of digest buffer (1 M Tris at pH 8.0, 1 mM EDTA, 13 SSC, 1% SDS, 1 Mm NaCl, 10 mg/mL Proteinase K).Following digest, DNA was purified using phenolchloroform-isoamyl alcohol (Life Sciences) isolation protocol.", + "3.2.2 Isolation of genomic DNA Genomic DNA was isolated from frozen liver tissue. The isolation was conducted using the Qiagen DNeasy\uf8e8 Blood & Tissue Kit (Qiagen) according to the manufacturer\u2019s protocol. DNA concentration was evaluated photometrically at a wavelength of 260 nm using the FusionTM Universal Microplate Analyzer. For nucleic acid quantification, the Beer-Lambert (A = \u03b5 * b * c) equation is modified to use an extinction coefficient with units of M-1 cm-1.", + " Most typically, DNA is extracted from blood samples, dried blood spots, buccal swabs, saliva, tissue and even urine and stool samples.In forensic science, other sources have been validated e.g.bone, tooth pulp, dandruff and others.", + "DNA isolation High-molecular weight DNAs was isolated from the samples by organic solvent extraction method, followed by precipitation in cold ethanol [14].", + "Genomic DNA extraction DNA from MEF cultures or mouse liver was isolated by phenol/chloroform extraction, as described [11].", + "DNA is usually recovered from cells by methods that include cell rupture but that prevent the DNA from fragmenting by mechanical shearing. This is generally undertaken in the presence of EDTA, which chelates the magnesium ions needed as cofactors for enzymes that degrade DNA, termed DNase. Ideally, cell walls, if present, should be digested enzymatically (e.g. , lysozyme in the bacteria or bacterial cell). In addition the cell membrane should be solubilized using detergent.", + "DNA solutions can be stored frozen, although repeated freezing and thawing tends to damage long DNA molecules by shearing. A flow diagram summarizing the extraction of DNA is given in Fig. 1.2. The above-described procedure is suitable for total cellular DNA. If the DNA from a specific organelle or viral particle is needed, it is best to isolate the organelle or virus before extracting its DNA, because the recovery of a particular type of DNA from a mixture is usually rather difficult.", + "Genomic DNA extraction Genomic DNA was extracted by the mixed alkyl trimethyl ammonium bromide (MATAB) procedure.Briefly, 250 mg of plant material was ground in liquid nitrogen and immediately incubated in 2 ml of pre-warmed extraction buffer (100 mM Tris-HCl, pH 8, containing 20 mM EDTA, 1.4 M NaCl, 2% (w/v) MATAB, 1% (w/v) PEG6000 (polyethylene glycol), 0.5% (w/v) sodium sulfite, 20% (w/v) Igepal CA630, 20% (w/v) lithium dodecyl sulfate, and 20% (w/v) sodium deoxycholate) at 74 \u00b0C for 20 min.After purification with 2 ml of chloroform:isoamylalcohol (24:1, v/v), DNA extracts were precipitated with 1.6 ml of isopropanol then resuspended in 1 ml of buffer (50 mM Tris-HCl, pH 8, containing 10 mM EDTA and 0.7 M NaCl).The extracts were purified on anion exchange columns (QIAGEN-tip 20) following the manufacturer's instructions (QIAGEN, Valencia, CA).", + "DNA extraction and enzymatic digestion Total DNA was isolated from whole blood and separated blood subtypes using a Qiagen DNeasy Blood & Tissue Kit following the manufacturer instructions.After extraction, DNA was quantified by NanoDrop (Thermo Scientific NanoDrop products, Wilmington, DE).The isolated genomic DNA was enzymatically digested according to previously described method.Briefly, DNA (3 \u03bcg) was first denatured by heating at 95 \u00b0C for 5 min and then chilling on ice for 2 min.Then, 1/10 volume of S1 nuclease buffer (30 mM CH 3 COONa, pH 4.6, 280 mM NaCl, 1 mM ZnSO 4 ) and 100 units of S1 nuclease were added before the mixture (20 \u03bcL) was incubated at 37 \u00b0C for 16 h.Subsequently, after 1/10 volume of alkaline phosphatase buffer (50 mM Tris-HCl, 10 mM MgCl 2 , pH 9.0), 0.002 units of venom phosphodiesterase I, and 10 units of alkaline phosphatase were added, the solution was incubated at 37 \u00b0C for an additional 4 h followed by extraction with an equal volume of chloroform for twice.The aqueous layer was collected and lyophilized to dryness and then reconstituted in 100 \u03bcL water.About 30 \u03bcL of the obtained samples were then subjected to liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis.", + " The conventional DNA extraction procedure involved the homogenization of single D. magna in 400 l of sperm lysis buffer (100 mM Tris-HCl, pH 8; 500 mM NaCl; 10 mM ethylenediaminetetraacetic acid [EDTA], pH 8; 1% SDS; 2% mercaptoethanol) followed by RNase treatment (40 g, 37\u040aC for 1.5 h).The DNA was then extracted in phenol (pH 8) and chloroform:isoamyl alcohol (1:1).The DNA was finally precipitated by two volumes of ice-cold ethanol in the presence of 3 M sodium acetate (1/10 of the DNA volume) and was incubated at \u03ea80\u040aC overnight.Precipitated DNA was harvested by centrifugation, dried in air, and the final pellet dissolved in sterile analytic grade water.", + "DNA extraction and quantification DNA was extracted from whole organs by standard techniques (34) with emphasis on minimizing shearing or nicking of DNA as nicked DNA has been shown to be refractory to LX-PCR (35).DNA from the brain was extracted from the right hemisphere.Extracted DNA was resuspended in 10 mM Tris 1 mM EDTA (pH 8) (TE) and stored at 4_C.A number of samples were normalized for mtDNA content by dot blotting and hybridization with digoxigenin-labeled full-length mtDNA and densitometry.In cases where mtDNA quantification was not carried out, the DNAs were normalized by A 260 of total DNA." + ], + [ + "Using genetic markers, the pattern of inheritance can be tracked through families. For example, by analyzing a marker linked to the eye color gene in several generations, it is possible to determine from which grandparents a child has inherited its eye color alleles. More importantly, \ufb01nding a marker linked to a disease can lead to location of the faulty gene causing the disease. Finding the gene is very valuable in the search for the cure. The distance between two loci can be expressed either as physical or genetic distance.", + " It is well known, however, that not all genomic markers are independent (Frazer et al., 2007).Genetic variation is often inherited in contiguous segments of DNA, such that there tends to be correlation between the inheritance of alleles at markers close to each other on the same chromosome.This genetic correlation is called linkage disequilibrium (LD), and, as a result, the effective number of independent tests (M eff ) conducted is less than the total number of markers (M).By effective number of tests, we mean the number of independent tests that would have to be conducted to lead to a null distribution for the minimum P-values that was approximately the same as that obtained when conducting tests that are necessarily correlated due to LD.", + "Genetic mapping is a powerful strategy that exploits genomic information to dissect complex traits into Mendelian loci (quantitative trait loci or QTL) and identifies genetic * Correspondence: marioenrico.pe@sssup.it 1 Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy Full list of author information is available at the end of the article determinants that may lead to crop improvement. As marker density ceases to be a limiting factor [3], our ability to discover specific genetic determinants in a single mapping study depends upon the availability of populations with high genetic diversity and recombination density [4].", + "This capacity allows samples to be placed into meaningful genetic groups that reflect evolutionary relationships (more stable, lower diversity markers), while simultaneously permitting high levels of strain resolution (high diversity markers). From a clinical perspective, markers that accurately reflect broad evolutionary relationships are valuable for comparing the genetic similarity of an isolate to isolates on a regional or global scale, whereas high-resolution markers are valuable for detailed epidemiological tracking in an outbreak. Variable-number tandem repeats (VNTRs) are genetic markers that can span a range of variability and, therefore, can capture genetic relationships on multiple scales (18\u201319).", + "Identifying the genetic loci that modulate a trait based on correlation between variation in phenotype and variation in genotype is the essence of genetic mapping. This first involves systematically genotyping a genetically diverse population using microsatellite or SNP markers. The phenotype of interest is then measured and its variability in the population assessed. A statistical test is then carried out to identify chromosomal regions that segregate with the trait and show linkage with the trait, i.e. , 3 identify genetic regions that have the same genotype among individuals with similar trait values but differ between individuals with dissimilar trait values.", + "Using genetic markers, the pattern of inheritance can be tracked through families. For example, by analyzing a marker linked to the eye color gene in several generations, it is possible to determine from which grandparents a child has inherited its eye color alleles. More importantly, \ufb01nding a marker linked to a disease can lead to location of the faulty gene causing the disease. Finding the gene is very valuable in the search for the cure. The distance between two loci can be expressed either as physical or genetic distance.", + "Genetic variation For decades researchers used single markers to elucidate clinal differentiation and spatial variation in allele frequencies.This approach revealed multiple markers with variation that tracked the clines, including some with the same allele at higher frequency at the same latitude in the Northern and Southern hemispheres.Examples include alcohol dehydrogenase (Adh), a-glycerol-3-phosphate dehydrogenase (Gpdh), glucose-6-phosphate dehydrogenase (G6pd), esterase-6 (Est-6), octanol dehydrogenase (Odh), and 6-phosphogluconate dehydrogenase (Pgd) [30][31][32][33] (Table 1).Perhaps the most heavily explored locus in D. melanogaster has been Adh, the first step in the ethanol detoxification pathway.The Adh-F allele encodes high catalytic activity of ADH, but this increase in activity trades off with enzyme stability at higher temperatures [34,35].Unsurprisingly, the Adh-F allele is found at a higher frequency in cooler high-latitude populations, and differentiation has occurred in parallel along clines in", + "In the case of genetic markers, this easily runs in the several hundreds to thousands. Moreover, the optimal subset of markers is heavily dependent on how these markers are combined, i.e. dependent on the optimal Boolean function . Altogether, one frequently has to rely on greedy search strategies that easily get stuck in local optima or near exhaustive searches that are computationally too expensive, especially when employed in permutation procedures required to assess statistical significance. Our solution to this problem hinges upon two observations.", + "GENE MAPPING The opportunity to merge advances in molecular genetic technology with advances in statistical techniques expanded in earnest with the development of DNA markers such as restriction fragment length polymorphisms (Lander and Botstein, 1989).Research exploded in the past decade with the continued refinement of molecular technology yielding a variety of DNA markers-e.g., short tandem repeats (STRs) or microsatellites; variable number of tandem repeats (VNTRs); single nucleotide polymorpohisms (SNPs), and gene expression microarrays or gene chips.A genetic marker is a measurable polymorphic sequence of DNA whose chromosomal location is known.Markers often have no known functional significance but are used as pointers to a particular chromosomal location.The logic of gene mapping technology is simple: Determine if there is a relationship between variability in a phenotype and variability in an anonymous DNA marker of known chromosomal location.If there is a relationship, it is taken as evidence that there is a gene that influences the trait at or near the marker.", + "Genetic drift. Genetic changes in populations caused by random phenomena rather than by selection.Genetic marker.A segment of DNA with an identifiable physical location on a chromosome whose inheritance can be followed.A marker can be a gene, or it can be some section of DNA with no known function.", + " Biological characteristics indicating initial resiliency or susceptibility of an organism include genetic profiles.As noted above, genetic markers need to have a high prevalence in the population and have a reasonably strong effect on common population health outcomes, or have an interaction effect with other health-affecting mechanisms, to be candidates for inclusion in population studies.At the moment, the only known genetic marker of clear value in a population survey is the apolipoprotein E gene (APOE), although this is likely to change in the very near future.APOE allele status is clearly related to a number of major health outcomes in older populations which are reasonably well measured in population surveys: mortality, heart disease, and cognitive functioning (Albert et al., 1995b;Corder et al., 1993;Evans et al., 1997;Ewbank, 1997;Hofman et al., 1997;Hyman et al., 1996;Luc et al., 1994;Saunders et al., 1993).Both the prevalence of alleles indicating higher risk and the size of the effect are large enough to be of importance in explaining variability in currently studied health outcomes.APOE allele status has been shown to have independent effects on health outcomes and to interact with other life circumstances such as sex and race in its effect on health outcomes (Jarvik et al., 1995;Maestre et al., 1995;Payami et al., 1992).Incorporation of information on this genetic indicator could lead to increased knowledge of the interactive mechanisms of this genetic marker and other social and behavioral variables and thus clarify some of the mechanisms leading to population differentials in cognition, heart disease, and mortality.", + " As described by Hermalin (1999), if genetic markers are modeled as part of an individual's physiological structure, they can provide controls for predisposing factors that affect more proximate mid-level markers of function as well as downstream health outcomes.This potential benefit of genetic information-i.e., its power in explicating the black box of Figure 11-1-may outweigh, or at least precede, its near-term potential for discovering genetic links to chronic disease.As discussed by Weiss (1998b), the situation with chronic disease differs from single locus disorders that are inherited following well-identified Mendelian rules.In general, we cannot expect to find relationships that are even as straightforward as the APOE links to cardiovascular and Alzheimer's disease.Variation across populations, difficulty in identifying a small enough area on the chromosome to search for disease-associated genes, and the problems inherent in identifying continuous outcomes with particular genes may limit finding the connections.", + "This capacity allows samples to be placed into meaningful genetic groups that reflect evolutionary relationships (more stable, lower diversity markers), while simultaneously permitting high levels of strain resolution (high diversity markers). From a clinical perspective, markers that accurately reflect broad evolutionary relationships are valuable for comparing the genetic similarity of an isolate to isolates on a regional or global scale, whereas high-resolution markers are valuable for detailed epidemiological tracking in an outbreak. Variable-number tandem repeats (VNTRs) are genetic markers that can span a range of variability and, therefore, can capture genetic relationships on multiple scales (18\u201319).", + "These variations provide a species the ability of adapting to the environment change (Liu and Cordes, 2004). DNA markers are among the most powerful tools for revealing genetic variations in organisms. Historically, many different types of markers have been used for aquaculture studies Functional Genomics in Aquaculture, First Edition. Edited by Marco Saroglia and Zhanjiang (John) Liu. \u2402 C 2012 John Wiley & Sons, Inc. Published 2012 by John Wiley & Sons, Inc. 41 42 Functional Genomics in Aquaculture Table 2.1 A summary of characteristics of various molecular markers used in aquaculture species.", + "For instance, mapping of a trait or a phenotype would require polymorphic DNA markers such as microsatellites (SSRs) or single nucleotide polymorphisms (SNPs); expression pro\ufb01ling would require genome annotation information; microarray design would require sequence information of genes, etc. The objective of this chapter is to provide a general review of genomic resources needed, and currently present for aquaculture species, for functional genomics studies. Polymorphic DNA Markers The key factor behind the signi\ufb01cant differences at the level of individuals, species, and higher order of taxonomic groups is genetic variation (polymorphism).", + "Functional genomics: The study of genes, their resulting proteins, and the role played by the proteins in the biochemical processes of the body.Gene: A unit of inheritance; a working subunit of DNA.Each of the 20 000 to 25 000 genes in the body contains the code for a specific product, typically a protein such as an enzyme.Gene expression: The process by which the coded information of a gene is translated into the structures present and operating in the cell (either proteins or ribonucleic acids).Gene markers: Landmarks for a target gene, either detectable traits that are inherited along with the gene or distinctive segments of DNA.Gene map: A description of the relative positions of genes on a chromosome and the distance between them.Genetic counseling: A short-term educational counseling process for individuals and families who have a genetic disease or who are at risk for such a disease.Genetic counseling provides patients with information about their condition and helps them make informed decisions.Genetic linkage maps: DNA maps that assign relative chromosomal locations to genetic landmarks-either genes for known traits or distinctive sequences of DNA (ie, genetic markers)-on the basis of how frequently they are inherited together.Genetic testing: Examining a sample of blood or other body fluid or tissue for biochemical, chromosomal, or genetic markers that indicate the presence or absence of genetic disease.Genetics: The scientific study of heredity, how particular qualities or traits are transmitted from parents to offspring.Genome: All the genetic material in the chromosomes of a particular organism.Genome-wide: Descriptor that indicates that the entire breadth of the genome has been examined in a study (eg, a linkage or association study).Genome-wide studies do not resequence the entire genome but type (an increasingly large set of) markers distributed throughout the genome.Genomics: A \"scaled-up\" version of the science of genetics that investigates the structure and function of large sections of the genome simultaneously.Genotype: The actual genes carried by an individual (as distinct from phenotype-ie, the physical, bodily characteristics into which genes are translated).Haplotype: A way of denoting the collective genotype of a number of closely linked loci on a chromosome.Heritability (h 2 ): For any trait, the proportion of the phenotypic variability resulting from genetic variance.Note that heritability does not indicate the degree to which a trait is \"genetic. \"Nor does a high h 2 mean that the trait cannot be influenced by environment.A heritability significantly \u03fe0, however, can provide a rationale for further genetic and genomic study of a trait of interest.Heterozygous: Possessing 2 different sequences (ie, genotypes) of a particular gene, 1 inherited from each parent.High-throughput genotyping: In contrast to the older labor-and time-intensive genotyping methods, high-throughput genotyping makes use of robots, computers, and other evolving technologies, thus enabling laboratories to type up to hundreds of thousands of polymorphisms in many samples in a relatively short period of time.Homozygous: Possessing 2 identical sequences of a particular gene, 1 inherited from each parent.Interaction: The differing effect of 1 independent variable on the dependent variable, depending on the particular level of another independent variable.For example, there would be an interaction between the factors sex and treatment if the effect of treatment was not the same for male and female subjects in a drug trial.Linkage analysis: A gene-hunting technique that traces patterns of heredity in large, high-risk families in an attempt to locate a disease-causing gene mutation by identifying traits that are coinherited with it.Linkage disequilibrium: Two alleles at different loci that occur together on the same chromosome more often than would be predicted by chance alone.It is a measure of cosegregation of alleles in a population.", + "Source: Kearsey and Pooni (1996). Genetic maps consist of a series of markers or identifiable features at known, or perhaps best described as estimated, locations on the genome (see Figure 9). For some discrete traits, simple Mendelian inheritance is followed and the phenotype has a one to one correspondence with the genes controlling it. These are so called morphological markers, which were then related to continuous or quantitative traits of interest. Examples are shape, colour, size or height in particular varieties of peas, as studied by Mendel. For another example, see Appendix A.2.", + "Genomic markers used in linkage mapping have evolved from restriction fragment length polymorphisms (RFLPs) to microsatellites (simple sequence repeat polymorphisms; SSRPs), to single-nucleotide polymorphisms (SNPs), with the more modern markers exhibiting higher frequencies in the genome (thus ensuring fuller coverage). Linkage mapping of a trait is in fact the demonstration of linkage between the phenotype and a genomic marker, followed by an inference of linkage between the genomic marker and the responsible DNA variant. Transitive logic ties the phenotype with the DNA variant, which is of course the point of the exercise. See Fig.", + "However, because of time constraints it is often more practicable to choose an appropriate mapping population that is already available through the current stock centers. Plant species chosen for study will depend largely on the availability of suitable plant resources. Obtain appropriate mapping population information to include information on markers/genotypes (see Note 4). A marker is an identifying factor; a gene or other DNA of known location that is used to track the inheritance and so on of other genes whose exact location is not yet known.", + "The closer two genes are together on a chromosome, the less likely it is for a recombination event to occur between the two, causing a non-random association. This is the basis for genetic linkage. The development of genetic markers allowed the theory of linkage disequilibrium (LD) to be used in mapping genes. Genetic markers are speci c genetic di\u241berences between species or cultivars, and genetic linkage of these markers to particular morphological traits can allow genetic markers to be used to represent the gene of interest (Collard et al. , 2005)." + ], + [ + "This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1. Introduction The association between a complex phenotypic trait and genetic markers on the chromosomes can be detected through statistical analysis, leading to the identification of quantitative trait loci (QTL)\u2014regions of the chromosomes that appear to be associated with the phenotype. Quantitative trait loci (QTL) are expected to be associated with the genes controlling some aspects of the phenotype.", + "Nowadays many different cost-efficient genotyping solutions (including sequencing and Single Nucleotide Polymorphisms arrays) have opened the way to systematic genome-wide fine mapping of quantitative traits (Quantitative Trait Locus or QTL mapping). The process of QTL mapping (Figure 1) consists in searching for genome regions that influence the value of a given trait. For example, identifying a QTL for plant height means finding a DNA region at which the plants that carry a certain allele tend to be significantly higher or lower than those carrying another allele.", + "QTLs are regions within the genome whose genetic variation modulates quantitatively a phenotype characteristic of the particular trait under study (Lynch and Walsh, 1998). Determining the association between variations in specific disease phenotypes or a trait, with variations in genotypes of a reference population can be used to locate a QTL. One of the methods used for mapping QTLs associated with complex traits is genetic markers-trait association. Genetic markers associated with certain loci can be inherited in linkage disequilibrium. Generating populations with linked loci in disequilibrium is achieved though either crosses between inbred lines, or use of the out-bred populations.", + "Often, the first step in analysis of new trait data is single-marker regression across all chromosomes. A hypothetical QTL is evaluated at the location of each marker locus, and the significance of that QTL is estimated from a likelihood ratio statistic (LRS) (Haley and Knott, 1992). For this analysis, WebQTL automatically does a permutation test to establish genomewide significance criteria for the trait (Churchill and Doerge, 1994).", + "One possible approach to facilitate this endeavor is to identify quantitative trait loci (QTL) that contribute to the phenotype and consequently unravel the candidate genes within these loci. Each proposed candidate locus contains multiple genes and, therefore, further analysis is required to choose plausible candidate genes. One of such methods is to use comparative genomics in order to narrow down the QTL to a region containing only a few genes. We illustrate this strategy by applying it to genetic findings regarding physical activity (PA) in mice and human.", + "Elucidation of the molecular basis of these traits has proven difficult as they are under the control of multiple genes and genetic loci. The standard approach to gene identification involves mapping by linkage analysis in experimental crosses, and this has led to the localization in the rat genome of hundreds of quantitative trait loci (QTLs) underlying trait variation (68). We refer to these loci as physiological quantitative trait loci (pQTLs).", + " Often, the first step in analysis of new trait data is single-marker regression across all chromosomes.A hypothetical QTL is evaluated at the location of each marker locus, and the significance of that QTL is estimated from a likelihood ratio statistic (LRS) (Haley and Knott, 1992).For this analysis, WebQTL automatically does a permutation test to establish genomewide significance criteria for the trait (Churchill and Doerge, 1994).By default, it returns a list of marker loci that show greater than sugges-tive association with the trait according to standard criteria (Lander and Kruglyak, 1995), but it will also accept user-defined criteria.Local maxima in the LRS in this list identify loci that are most likely to be near QTLs.WebQTL provides this list within a few seconds.", + "QTLs can be identified through their genetic linkage to visible marker loci with genotypes that can be readily classified [94, 97]. As such, markers that are genetically linked quantitative trait will segregate more often with trait values, whereas unlinked markers will lack an association with the phenotype [94, 98]. The principal goal of a QTL analysis is to identify all QTLs linked to a trait and discern whether phenotypic differences are mainly due to a few loci with large effects, or many loci with small effects [98].", + "This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 1. Introduction The association between a complex phenotypic trait and genetic markers on the chromosomes can be detected through statistical analysis, leading to the identification of quantitative trait loci (QTL)\u2014regions of the chromosomes that appear to be associated with the phenotype. Quantitative trait loci (QTL) are expected to be associated with the genes controlling some aspects of the phenotype.", + "The basic principle of classic QTL is trait segregation along with the markers and necessitated the availability of two or more genetically different lines corresponding with the phenotypic trait. Markers like single nucleotide polymorphisms (SNPs) and microsatellites are used for genotypic distinctions (Vignal et al. , 2002). QTL mapping is achieved in four basic steps; the first one is the measurement of variation for a trait in the individuals. It is a prerequisite to have the traits that show phenotypic variability among the individuals (inbred strains).", + " Often, the first step in analysis of new trait data is single-marker regression across all chromosomes.A hypothetical QTL is evaluated at the location of each marker locus, and the significance of that QTL is estimated from a likelihood ratio statistic (LRS) (Haley and Knott, 1992).For this analysis, WebQTL automatically does a permutation test to establish genomewide significance criteria for the trait (Churchill and Doerge, 1994).By default, it returns a list of marker loci that show greater than sugges-tive association with the trait according to standard criteria (Lander and Kruglyak, 1995), but it will also accept user-defined criteria.Local maxima in the LRS in this list identify loci that are most likely to be near QTLs.WebQTL provides this list within a few seconds.", + "Often, the first step in analysis of new trait data is single-marker regression across all chromosomes. A hypothetical QTL is evaluated at the location of each marker locus, and the significance of that QTL is estimated from a likelihood ratio statistic (LRS) (Haley and Knott, 1992). For this analysis, WebQTL automatically does a permutation test to establish genomewide significance criteria for the trait (Churchill and Doerge, 1994).", + "Quantitative Trait Locus (QTL) mapping To map QTL, we used 934 AXB/BXA genetic informative markers obtained from http://www. genenetwork.org. For all the in vitro measurements and gene expression linkage analysis, a genome-wide scan was performed using R/qtl [57]. Significance of QTL logarithm-of-odds (LOD) scores was assessed using 1000 permutations of the phenotype data [114] and the corresponding p-values reported. For the cellular phenotypes, QTL significance was reported at a genome-wide threshold corresponding to p < 0.05.", + "Typically one may obtain a location known to derive from only one of the two parent strains that contains a chromosomal region that correlates with a trait of interest. Since the actual gene and gene product will frequently remain unknown, the region is referred to as quantitative trait locus (QTL), and is simply named for the trait itself (Alberts & Schughart, 2010). Growing sets of strain-dependent marker locations in established RI strains are continually updated in online repositories.", + "By definition, a quantitative trait locus is a chromosomal region that contains a gene, or genes, that regulate a portion of the genetic variation for a particular phenotype (Wehner et al. 2001). The goal of QTL mapping is to identify regions of the genome that harbour genes relevant to a specified trait. QTL map locations are commonly determined by initial screening of mice with specific genetic characteristics, such as recombinant inbred strains, the F2 of two inbred strains, or recombinant congenic strains (Flint 2003).", + "Often, the first step in analysis of new trait data is single-marker regression across all chromosomes. A hypothetical QTL is evaluated at the location of each marker locus, and the significance of that QTL is estimated from a likelihood ratio statistic (LRS) (Haley and Knott, 1992). For this analysis, WebQTL automatically does a permutation test to establish genomewide significance criteria for the trait (Churchill and Doerge, 1994).", + "QTL linkage studies are conducted in order to map a region or regions of the genome which affect a continuous or quantitative trait. In agriculture, as soon as markers linked to QTL are found for economically important traits, these markers can be used for selecting individuals in breeding programmes. In human studies, the aim is often to identify markers indicating disease susceptibility. Current techniques for measuring markers are usually relatively slow and laborious. Newer DNA technology, such as SNP or single nucleotide polymorphisms (Kwok, 2001b; Patil et al.", + "Genomic regions linked to complex traits can be identified by genetic mapping and quantitative trait locus (QTL) analysis (Shehzad and Okuno 2014). 7 QTL mapping QTL mapping with molecular markers is the first strategy in genetic studies. In plant breeding, QTL mapping is an essential step required for marker-assisted selection (Mohan et al. 1997; Shehzad and Okuno 2014). The fundamental idea underlying QTL analysis is to associate genotype and phenotype in a population exhibiting a genetic variation (Broman and Sen 2009).", + "Four steps of QTL mapping are (1) development a W population, (2) genotyping the population using molecular markers, (3) phenotyping the population for an interested trait, and (4) QTL analysis using statistical procedures to find IE markers linked to the QTL (Bernardo 2002). PR EV Populations used for genetic mapping can be a segregating population (F2 and backcross) or a permanent population (double haploids or recombinant inbred lines). Recombinant inbred lines (RILs) are developed by selfing of individual progenies of the F2 plants until homozygosity is achieved (F7-F8).", + "This tool allows systems genetic analysis of single genes or small sets of genes using a bottom-up approach. relations define quantitative trait loci (QTLs). Because the marker is not typically the actual site of the polymorphism, interpolative methods have been developed to estimate the distance of the QTL from the marker and the strength of the association. Using multiple-regression and model-fitting methods, the true complexity of the phenotypic variation can be modeled through the consideration of multiple loci and environmental factors as predictors [13]." + ], + [ + " To overcome the lack of phenotypic information in the 1000 Genomes Project, The ClinSeq Project was developed to pilot large-scale genome sequencing for research in genomic medicine at the National Institutes of Health Clinical Research Center in Bethesda, MD. 40 The study seeks to enroll 1000 individuals who will be evaluated for personal health status and family history.The project aims to:", + "We (Hein, Schierup and Wiuf) have published a 300 page book on molecular population genetics titled \u201cGene Genealogies, Sequence Variation and Evolution\u201d Oxford University Press, and are presently developing a tutorial in association mapping that we hope to publish as a booklet in 2006 and are also involved in a very large EU collaboration (Holland, Denmark, Iceland and UK) to find susceptibility genes for breast and prostate cancer. In comparative genomics, the most fundamental investigation is to find genes in a pair of aligned genomes.", + "Key bioinformatic steps to take a genetic study from an initial linkage or association to laboratory genotyping are illustrated. The reader should note the role of genomic sequence as a common thread through every stage regions in man (see Chapter 5). Similar issues also exist in the establishment of true orthology between genes in different species, where one is identified to play a role in a disease model. If two genes are truly orthologous, their evolution closely follows patterns of speciation (Fitch, 2000).", + "In general terms, the approaches we describe can be applied to sequence data from any collection of organisms, but our emphasis here is primarily on Bioinformatics for Geneticists, Second Edition. Edited by Michael R. Barnes 2007 John Wiley & Sons, Ltd ISBN 978-0-470-02619-9 (HB) ISBN 978-0-470-02620-5 (PB) \u2402 C 106 CH 6 COMPARATIVE GENOMICS questions of relevance to human genetics. We begin, in Section 6.2 by presenting an overview of genome structure and content, providing a context for the subsequent discussions.", + "4 Assembling a View of the Human Genome Colin A. M. Semple Bioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK 4.1 Introduction The miraculous birth of the draft human genome sequence took place against the odds. It was only made possible by parallel revolutions in the technologies used to produce, store and analyse the sequence data, and by the development of new, large-scale consortia to organize and obtain funding for the work (Watson, 1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond.", + "This fully indexed but semi-intelligible Bioinformatics for Geneticists, Second Edition. Edited by Michael R. Barnes 2007 John Wiley & Sons, Ltd ISBN 978-0-470-02619-9 (HB) ISBN 978-0-470-02620-5 (PB) \u2402 C 4 CH 1 BIOINFORMATICS CHALLENGES FOR THE GENETICIST \u2018book of life\u2019 immediately began to serve as a valuable framework for integration of genetic and biological data. However, knowledge of the genome sequence did not immediately clarify the nature and structure of human genetic variation.", + " Methods for DNA sequencing are constantly being improved, with the ultimate goal of sequencing a human genome in a single day for a cost of about US $1,000, an end that appears to be in sight (Hayden, 2014).In the very near future, whole-genome sequencing will be routinely available for clinical purposes, perhaps even beginning at birth.The major challenge ahead is the interpretation of this information.How do our genes interact with each other, and how does the environment contribute to the development of health and disease?What are the individual and societal implications of knowing our genome sequence?The answers to these and other important questions will unfold in the years ahead.Thus, we are truly in an era where precision medicine may soon become a reality.", + " Characteristics of genotyping and sequencing technologies", + "Key bioinformatic steps to take a genetic study from an initial linkage or association to laboratory genotyping are illustrated. The reader should note the role of genomic sequence as a common thread through every stage regions in man (see Chapter 5). Similar issues also exist in the establishment of true orthology between genes in different species, where one is identified to play a role in a disease model. If two genes are truly orthologous, their evolution closely follows patterns of speciation (Fitch, 2000).", + "In general terms, the approaches we describe can be applied to sequence data from any collection of organisms, but our emphasis here is primarily on Bioinformatics for Geneticists, Second Edition. Edited by Michael R. Barnes 2007 John Wiley & Sons, Ltd ISBN 978-0-470-02619-9 (HB) ISBN 978-0-470-02620-5 (PB) \u2402 C 106 CH 6 COMPARATIVE GENOMICS questions of relevance to human genetics. We begin, in Section 6.2 by presenting an overview of genome structure and content, providing a context for the subsequent discussions.", + "4 Assembling a View of the Human Genome Colin A. M. Semple Bioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK 4.1 Introduction The miraculous birth of the draft human genome sequence took place against the odds. It was only made possible by parallel revolutions in the technologies used to produce, store and analyse the sequence data, and by the development of new, large-scale consortia to organize and obtain funding for the work (Watson, 1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond.", + "Introduction Since the first human genome was sequenced at an estimated cost of $150 million, several advanced high-throughput techniques \u2013 some with lower costs - have come up. At the same time, this resulted in a data deluge and a critical need to connect the heterogeneous sequencing data and associated annotations \u2013 structural and functional with the basic tenets of biology or molecular basis of development and disease.", + "Key bioinformatic steps to take a genetic study from an initial linkage or association to laboratory genotyping are illustrated. The reader should note the role of genomic sequence as a common thread through every stage regions in man (see Chapter 5). Similar issues also exist in the establishment of true orthology between genes in different species, where one is identified to play a role in a disease model. If two genes are truly orthologous, their evolution closely follows patterns of speciation (Fitch, 2000).", + "In general terms, the approaches we describe can be applied to sequence data from any collection of organisms, but our emphasis here is primarily on Bioinformatics for Geneticists, Second Edition. Edited by Michael R. Barnes 2007 John Wiley & Sons, Ltd ISBN 978-0-470-02619-9 (HB) ISBN 978-0-470-02620-5 (PB) \u2402 C 106 CH 6 COMPARATIVE GENOMICS questions of relevance to human genetics. We begin, in Section 6.2 by presenting an overview of genome structure and content, providing a context for the subsequent discussions.", + "4 Assembling a View of the Human Genome Colin A. M. Semple Bioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK 4.1 Introduction The miraculous birth of the draft human genome sequence took place against the odds. It was only made possible by parallel revolutions in the technologies used to produce, store and analyse the sequence data, and by the development of new, large-scale consortia to organize and obtain funding for the work (Watson, 1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond.", + " Ample time was allotted to answer questions and a copy of \"A Guide to Your Genome\" (National Human Genome Research Institute 2007) was provided to further assist participants' understanding and ability to communicate results with family members or others.", + " Whether within 10 or 12 (or 8) years, such inexpensive sequencing will change both research and clinical care, and progress does not need to wait even that long.The National Human Genome Research Institute (NHGRI) plans to focus a significant portion of the sequencing capacity that it supports on medical sequencing.For instance, the NHGRI and the National Cancer Institute are actively considering a Human Cancer Genome Project, 22 which would use DNA sequencing and a host of other genome technologies to gather information about the mutations and functional abnormalities found in multiple samples from many major types of cancer.Medical sequencing should also provide important insight into many other diseases.For example, sequencing all exons in X-linked mental retardation syndromes may reveal much about their etiology.Sequencing candidate genes in the extremes of the distribution of quantitative traits should also reveal much of importance about common diseases, such as coronary atherosclerosis. 23With further technological advances, other previously unimaginable research approaches will become real.", + "Key bioinformatic steps to take a genetic study from an initial linkage or association to laboratory genotyping are illustrated. The reader should note the role of genomic sequence as a common thread through every stage regions in man (see Chapter 5). Similar issues also exist in the establishment of true orthology between genes in different species, where one is identified to play a role in a disease model. If two genes are truly orthologous, their evolution closely follows patterns of speciation (Fitch, 2000).", + "In general terms, the approaches we describe can be applied to sequence data from any collection of organisms, but our emphasis here is primarily on Bioinformatics for Geneticists, Second Edition. Edited by Michael R. Barnes 2007 John Wiley & Sons, Ltd ISBN 978-0-470-02619-9 (HB) ISBN 978-0-470-02620-5 (PB) \u2402 C 106 CH 6 COMPARATIVE GENOMICS questions of relevance to human genetics. We begin, in Section 6.2 by presenting an overview of genome structure and content, providing a context for the subsequent discussions.", + "4 Assembling a View of the Human Genome Colin A. M. Semple Bioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK 4.1 Introduction The miraculous birth of the draft human genome sequence took place against the odds. It was only made possible by parallel revolutions in the technologies used to produce, store and analyse the sequence data, and by the development of new, large-scale consortia to organize and obtain funding for the work (Watson, 1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + ], + [ + " In birds, where erythrocyte telomere length (ETL) is measured, the majority of species sampled have shown no sex difference (36).Nonetheless, bird telomere dynamics are complex and, as with humans, may be affected by environment and stress.For example, a longitudinal study of black-tailed gulls (Larus crassitostris) over 2-5 years found no correlation between ETL and age or sex.Rather, ETL attrition was correlated with reduced food availability and environmental stressors (55).In a captive zebra finch (Taeniopygia guttata) population, male and female mean telomere length decreased with increasing age of the animals, but did differ between sexes (56).As these examples illustrate, the relationship between telomere length, lifespan, and sex is likely to be complex in other vertebrates.", + " Comparative studies of age-related telomere attrition in other species also reveal a variety of patterns.Barrett and Richardson (36) recently summarized the comparative data available on sex differences in telomere length.They found a strong correlation between male-biased mortality and either shorter telomeres or greater telomere attrition in males across bird and mammal taxa.However, telomere length did not differ between males and females in species where females are shorter-lived than males (36), suggesting that telomere shortening is not associated with species-specific longevity in a simple linear fashion.These studies generally suffer from relatively small sample sizes and are largely cross-sectional.Further, the use of diverse assays, different tissues (eg, leukocytes in mammals vs erythrocytes in birds), and lack of standardized benchmarks for accuracy makes comparisons between studies difficult.", + " In some organisms, there is no clear relationship between telomere length and lifespan.Age-related telomere attrition could not be detected in Daphnia pulex (57) or sea urchin species (Strongylocentrotus franciscanus and Lytechinus variegatus) (58).Studies in C. elegans examining natural variation in telomere length and experimentally manipulated telomere length detect no correlation with lifespan (59,60), and in Drosophila, which uses a telomerase-independent mechanism for telomere maintenance, there is a similar lack of correlation between longevity and telomere length (61).Similarly, data on sex differences in age-related telomere shortening are mixed.For example, in the ant species Lasius niger, the rate of telomere shortening is more rapid in short-lived males compared to longer-lived females.But, mean telomere length does not differ between the two types of females, queens and workers, despite the fact that queens live much longer than workers (up to 28 years vs 2-3 months) (62).These findings suggest that the question of how telomere shortening affects aging across species and how sex affects telomere attrition rates are complex.", + " With new methodologies to assess relative telomere length by Q-PCR, studies were designed to address the impact of telomere length on aging, aging associated pathologies, and mortality.One such study has correlated shorter leukocyte telomere lengths at age 60 with a three times higher risk of heart disease and an eightfold increase in risk of infection-related death (36), thereby associating measured relative cellular aging with disease and life expectancy.In a similar way, chronic stress was shown to correlate with short leukocyte telomere length, a phenomenon attributed to higher levels of oxidative stress at the cellular level (70).More recent studies have linked telomere length in smooth muscle cells with senescence and disease severity in patients with atherosclerosis (141,150).Leukocyte telomere length was also short in a cohort of similar patients and associated with a higher risk of developing occult cardiovascular disease (71).More data are needed to understand and validate the use of leukocyte telomere length as a biomarker for cardiovascular and other diseases.", + " Shortening of the telomeres at the ends of chromosomes has been associated with age-related disease and mortality [16][17][18].A recent study identified a common haplotype of four SNPs in the human telomerase reverse transcriptase gene (hTERT) that is enriched in centenarians and associated with longer telomere length [19].It was also shown that centenarians and their offspring maintain longer telomeres compared with controls and that longer telomeres are associated with protection from age-related diseases, better cognitive function and lipid profiles of healthy ageing [19].", + " New research has indicated how social factors, such as subordination, may translate into biological effects (epel et al. 2004;Chae et al. 2014).In a now classic study, epel et al. ( 2004) examined the telomere lengths of fifty-eight healthy premenopausal women who either had a healthy child (n = 19) or were giving care to a chronically ill child (n = 39. )They measured perceived stress, years of caregiving, telomere length, and oxidative stress.They found highly statistically significant differences in telomere length between women taking care of chronically ill children and those who had healthy children.They found highly statistically significant negative correlations between telomere length and perceived stress and years of caregiving.Telomerase activity had highly statistically significant negative correlations with perceived stress and years of caregiving.Oxidative stress was highly positively correlated with perceived stress and years of caregiving.They concluded that the telomere length shortening was equivalent to 9 to 17 years of aging in the high stress group.Telomere length is considered a biomarker of aging (Finch and Kirkwood 2000).Thus, this study showed that caregiver stress had essentially aged these women 9 to 17 years compared to women who had healthy children.", + " The single, consistent predictor of the rate of telomere attrition shown in multiple adult and the few child longitudinal studies is the baseline measurement of telomere length at the start of each study.This suggests the importance of understanding predictors of telomere length prior to adulthood, as it determines in part the rate of change (Revesz et al. 2014a, b;Nordfjall et al. 2009).Moreover, longitudinal studies in adults have had found that telomere attrition rate is dependent on baseline telomere length independent of any phenotypic predictors of shortening, such as disease or demographic variables (Nordfjall et al. 2009), attesting to the importance of studies to evaluate risk factors for shortening prior to adulthood.", + " Rates of decline in childhood may be particularly relevant for later chronic disease risk as shorter telomere length has been implicated in disease progression through exposure to cellular senescence, inflammatory cytokines and adipocyte hypertrophy (Raschenberger et al. 2015;Willeit et al. 2014;Monickaraj et al. 2012;Fyhrquist et al. 2013).", + " Adult studies have also found a negative correlation with baseline telomere length, suggesting a negative feedback regulation of leukocyte telomere length (Farzaneh-Far et al. 2010;Aviv et al. 2009;Epel et al. 2008;Nordfjall et al. 2009).It is possible that while our follow-up period was shorter than Shalev et al. 2013 and adult studies, which had a minimum of 5 year intervals with the exception of Puterman et al. (2015) who followed for a one-year time period, there may be biological regulation of telomere length at 4 and 5 years of age such that shorter telomeres are more robustly maintained, whereas longer telomeres have greater rates of decline, over a short period of one year.It is unlikely that this relationship is due to assay error or regression to the mean given the consistency of our findings across studies.We have had similar findings of longer telomeres having greater rates of decline and shorter telomeres being maintained in our different studies (Farzaneh-Far et al. 2010;Epel et al. 2008;Puterman et al. 2015).", + " We found primarily maintenance and lengthening from 4 to 5 years of age in children, with minimal telomere attrition, indicating that most of the telomere loss happens in the first 4 years, plateauing by age 4. Lastly, we found close to 10 % of the variance in rate of change in children shared by mothers.While some of this shared variance is genetic, there are likely environmental factors that need to be further identified that impact rate of telomere length change.", + " Abstract Telomeres are the protective complexes at the end of chromosomes, required for genomic stability.Little is known about predictors of attrition in young children or the relationship between parental and child patterns of telomere change.Telomere length was assessed twice over one year, at 4 and at 5 years of age, in Latino preschool children (n = 77) and their mothers (n = 70) in whole blood leukocytes.Maternal and child rates of attrition during the same time period were compared in 70 mother-child pairs.More children showed lengthened telomeres over one year compared to their mothers and very few children showed attrition (2.6 %).Approximately 31 % of children and 16 % of mothers displayed lengthening over one year while 66 % of children showed maintenance in contrast with 74 % of mothers.The strongest predictor for child telomere length change was child's baseline telomere length (r = \u22120.61,p < 0.01).Maternal rate of change was associated with child rate of change (r = 0.33, p < 0.01).After controlling for child baseline telomere length, the relationship between child and maternal rate of change trended towards significance (Coeff = 0.20, 95 % CI \u22120.03 to 0.43; p = 0.08).", + " Blackburn and Epel, a health psychologist who did original research on how specific lifestyle and psychological habits can protect telomeres, published The Telomere Effect (Blackburn & Epel, 2017), in which they suggested that individuals with shorter telomeres developed diseases earlier in life (a shorter \"disease span\").What follows is the evidence from these authors, their colleagues, and other researchers describing how length of telomeres contributes to mind-body connection and healthy longevity.", + " As early as at the time of birth, each of the 92 telomeres of the human genome has its own characteristic length.Additionally, each telomere shortens by its individual attrition rate.In general, longer telomeres at birth are associated with higher age-dependent attrition rates and vice versa.Overall, telomere shortening appears more dynamic in males.", + " In conclusion, a combination of overall and chromosomespecifi c shorter telomeres and more pronounced age-dependent telomere erosion could be observed in males.There is a prospective clinical study strongly suggesting that longer telomeres decrease the risk of dying (Cawthon et al., 2003).With this in mind, the telomere length discrepancies between the sexes may indeed be a factor infl uencing the differences in their life expectancy.", + " In every chromosome a linear decline of telomere length with age was observed, being more pronounced in men independent of the examined chromosome arm.This might suggest that telomere length on single chromosome arms may be infl uenced by the same factors which determine overall telomere length.", + " S. Mayer a S. Br\u00fcderlein a S. Perner a I. Waibel a A. Holdenried a N. Ciloglu a C. Hasel a T. Mattfeldt a K.V. Nielsen b P. M\u00f6ller a a Institute of Pathology, University of Ulm, Ulm (Germany); b DakoCytomation A/S, Glostrup (Denmark) follow uniformity.In previous studies, sex-specifi c differences in telomere length and attrition rate of men and women were found (Benetos et al., 2001;Cawthon et al., 2003;Nawrot et al., 2004), suggesting gender differences in behavior of telomeres.In individual chromosome arms, telomere length was also shown not to be homogeneous (Lansdorp et al., 1996;Benn, 1997;Martens et al., 1998;Surralles et al., 1999;Hao and Tan, 2001;Londono-Vallejo et al., 2001;Graakjaer et al., 2003), some telomeres being signifi cantly shorter, others longer than the average length.", + " To date, these characteristics in telomere lengths could not be set in a biological context, as only a few groups have provided detailed information about chromosome-specifi c patterns of telomere distribution (Lansdorp et al., 1996;Graakjaer et al., 2003).Whether accumulation of short telomeres (Martens et al., 2000;Londono-Vallejo et al., 2001) or rather the shortest telomere of one specifi c chromosome arm (Hemann et al., 2001) elicits senescence, remains an open question so far.", + " In recent literature, there are hints that the average telomere length may be higher in women and that their annual shortening rate may be somewhat lower (Vaziri et al., 1993;Rufer et al., 1998;Jeanclos et al., 2000), but these reported differences failed to reach statistical signifi cance except for one study (Jeanclos et al., 2000).Here, we provide compelling evidence that this is indeed the case.", + " It is generally accepted that telomeres shorten during DNA replication both in vitro and in vivo.In individuals, short telomeres are considered to be a sign of advanced age.Cawthon and coworkers (2003) showed that telomere shortening in humans likely contributes to mortality, supporting the hypothesis that they might act as a mitotic clock (Allsopp et al., 1992).Telomere length dynamics, however, does not seem to Abstract.During aging, telomeres are gradually shortened, eventually leading to cellular senescence.By T/C-FISH (telomere/centromere-FISH), we investigated human telomere length differences on single chromosome arms of 205 individuals in different age groups and sexes.For all chromosome arms, we found a linear correlation between telomere length and donor age.Generally, males had shorter telomeres and higher attrition rates.Every chromosome arm had its individual age-specifi c telomere length and erosion pattern, resulting in an unexpected heterogeneity in chromosomespecifi c regression lines.This differential erosion pattern, however, does not seem to be accidental, since we found a correlation between average telomere length of single chromosome arms in newborns and their annual attrition rate.Apart from the above-mentioned sex-specifi c discrepancies, chromosome arm-specifi c telomere lengths were strikingly similar in men and women.This implies a mechanism that arm specifi cally regulates the telomere length independent of gender, thus leading to interchromosomal telomere variations.", + " Shortening of the telomeres at the ends of chromosomes has been associated with age-related disease and mortality [16][17][18].A recent study identified a common haplotype of four SNPs in the human telomerase reverse transcriptase gene (hTERT) that is enriched in centenarians and associated with longer telomere length [19].It was also shown that centenarians and their offspring maintain longer telomeres compared with controls and that longer telomeres are associated with protection from age-related diseases, better cognitive function and lipid profiles of healthy ageing [19]." + ], + [ + " Selection could occur at multiple levels, from germ cell generation and propagation to fertilization and early embryonic growth.Chromosomal abnormalities, including aneuploidy, were found in 10-20% of spermatozoa and oocytes (20) and in the cleaved embryo, with a 21% rate of abnormalities in preimplantation embryos (21).These findings led to a model for natural selection against chromosome abnormalities (21).Selection extends to the end of gestation: Only approximately 30% of all conceptions result in a live birth, with more than half of aborted fetuses containing chromosomal abnormalities (22), a number likely to be an underestimate because of technological limitations in measuring all possible mutations.But even in the very small fraction of germ cell duos that survive this withering genome attack and result in a live birth, a number of severe de novo mutations will still be found (23).The data on gross chromosomal alterations suggest that overall, mutation frequency early in life is very high.The functional consequence, however, is limited because of selection.Somewhat surprisingly, this picture points toward an initial decline in genomic alterations, allowing the adult individual to acquire a somatic genome optimally equipped to provide function.", + "The phenotype of the F1 hybrids is compared to those of the parental inbred strains to reveal dominance or semi-dominance relationships between the alleles that a\u00a1ect the phenotype. Phenotypic di\u00a1erences between reciprocal F1 hybrids indicate that one or more of the following factors may a\u00a1ect the trait: (1) sex linkage (X- or Ylinked traits), (2) genomic imprinting of QTLs that a\u00a1ect the phenotype, (3) prenatal maternal e\u00a1ects (e\u00a1ects of intrauterine environment), and/or (4) postnatal maternal or paternal e\u00a1ects (e\u00a1ects of maternal and/or paternal parenting behaviour on o\u00a1spring).", + "Sex brings harmful alleles together into the same genetic background, allowing selection to more efficiently purge them from the population and potentially producing some offspring that are fitter than either parent. However, the benefit of recombining deleterious mutations may depend on the nature of the epistatic interactions between them. The mutational deterministic hypothesis (Kondrashov 1988) depends partly on this epistasis.", + "In most plants and animals, sex is a necessary component of reproduction, and the question for evolutionary biologists is why reproductive mechanisms have evolved that way. In one of the experiments described next, evolutionary geneticists have nevertheless devised a way to compare evolution with and without recombination in the obligately sexual fruit fly.", + "This disparity in investment is the basis for the twofold cost: asexual females hypothetically could transmit twice as many alleles at the same cost. In most plants and animals, mates tend to be unrelated, leading to outcrossing. But sex usually also involves the basic process of physical recombination: the breakage and reunion of two different DNA or RNA molecules. Of these two processes, recombination is clearly the more widespread feature of sexual reproduction. A variety of reproductive systems, such as selfing and automixis, involve recombination but not outcrossing. In contrast, relatively few reproductive systems have outcrossing without recombination.", + " Crossing over-The swapping of genetic material that occurs in the germline.During the formation of egg and sperm cells, also known as meiosis, paired chromosomes from each parent align so that similar DNA sequences from the paired chromosomes cross over one another.Crossing over results in a shuffling of genetic material and is an important cause of the genetic variation seen among offspring.This process is also known as meiotic recombination.", + " The reason for the rarity of these mutations is natural selection: If the mutations result in disorders that decrease health and reproductive fitness, they will eventually be eliminated from a population.In exceptional cases, mutations may cause both beneficial and detrimental consequences, resulting in opposing forces of positive selection and negative selection that may cause the mutations to be preserved at nonrare frequencies in a population.For example, the HbS mutation in the HBB gene (which produces the \u03b2 subunit of hemoglobin) causes sickle cell disease when present in both alleles, a detrimental consequence, but protects against malaria when present in 1 allele, a beneficial consequence, ensuring that the mutation persists in populations in areas of the world where malaria is endemic.Genes are passed from parents to offspring via the process of meiosis by which gametes, the egg cells in the mother and the sperm cells in the father, are generated.Ordinarily, each cell has 23 pairs of chromosomes; the gametes have 23 unpaired chromosomes.In meiosis, the 23 pairs are split so that each gamete receives 1 chromosome from each pair (Figures 8 and 9).Two gametes (egg and sperm) ultimately join into a single cell, the zygote, which has the full complement of 23 chromosome pairs restored.If all goes well, the zygote gives rise to a live offspring.", + " Recombination (meiotic recombination)-The swapping of genetic material that occurs in the germline.During the formation of egg and sperm cells, also known as meiosis, paired chromosomes from each parent align so that similar DNA sequences from the paired chromosomes recombine with one another.Recombination results in a shuffling of genetic material and is an important cause of the genetic variation seen among offspring.Also known as crossing over.", + " In the generation of gametes, crossing over regularly occurs, and genetic information is swapped between members of a chromosome pair.That doesn't matter within inbred animals, because the swapped parts are identical.In an F 1 animal, however, the chromosomes of a particular pair are genetically different, one each having come from each parent.Each gamete produced will be unique, as will be each F 2 zygote formed by uniting of the gametes from two F 1 parents.An F 2 group thus provides for expression of some genetic variability.This variability is limited to the allelic differences existing between the parent strains of the F 1 s, so that another F 2 , derived from different inbred strains, will express different genetic differences.", + "Sex brings harmful alleles together into the same genetic background, allowing selection to more efficiently purge them from the population and potentially producing some offspring that are fitter than either parent. However, the benefit of recombining deleterious mutations may depend on the nature of the epistatic interactions between them. The mutational deterministic hypothesis (Kondrashov 1988) depends partly on this epistasis.", + "In most plants and animals, sex is a necessary component of reproduction, and the question for evolutionary biologists is why reproductive mechanisms have evolved that way. In one of the experiments described next, evolutionary geneticists have nevertheless devised a way to compare evolution with and without recombination in the obligately sexual fruit fly.", + "This disparity in investment is the basis for the twofold cost: asexual females hypothetically could transmit twice as many alleles at the same cost. In most plants and animals, mates tend to be unrelated, leading to outcrossing. But sex usually also involves the basic process of physical recombination: the breakage and reunion of two different DNA or RNA molecules. Of these two processes, recombination is clearly the more widespread feature of sexual reproduction. A variety of reproductive systems, such as selfing and automixis, involve recombination but not outcrossing. In contrast, relatively few reproductive systems have outcrossing without recombination.", + " Aberrant recombination patterns on chromosomes that have missegregated have also been identified as an important factor, in both male and female gametes (Table I).This is because recombination together with cohesion of sister chromatids establish the unique 'bivalent' chromosome structure where homologous partner chromosomes are tethered together, a configuration that is critical for their accurate segregation in meiosis I (Fig. 2A).The remarkable feature is that recombination occurs in foetal oocytes whereas chromosome segregation takes place decades later (Fig. 2A).Since mammalian oocytes are arrested at the G2/M transition (or dictyate stage), this raises the intriguing question of how the bivalent is maintained until the meiotic divisions.", + "Traditionally, it has been agreed that the \ufb01nal sex of an individual (phenotypic sex) depends on two sequential processes: the sex determination system of the species and the gonad differentiation process (Valenzuela, 2008). However, recently, these two seemingly distinct processes are viewed as part of a general process leading to gonad formation and sex ratios (Sarre et al. , 2004; Quinn et al. , 2011; Uller and Helantera\u0308, 2011).", + "However, we expect that only at this level, the most signi\ufb01cant contributions brought by integrating epigenetics will be made. Concluding Remarks and Future Prospects Fish sex ratios are the result of a complex interaction between genetic, biochemical, and environmental interactions. The ultimate result of these interactions at the individual level is gender: male or female. However, at the population level, the combination of sex determination and differentiation sets the sex ratio. In turn, sex ratios de\ufb01ne the reproductive capacity of populations and, if sex growth dimorphism exists, also the growth characteristics, something very important in an aquaculture context.", + "Obehav is, in turn, influenced by offspring genes and environment (Ogene and Oenvir respectively). Hence, indirect genetic effects (blue arrows) and direct genetic effects (red arrow) are important influencers of behaviour. B) Parentoffspring conflict theory predicts that parental resource investment and offspring solicitation behaviours are influenced by the fitness benefit to a focal individual (O), cost to a social partner such as a sibling (S1 and S2) or parent (P), and by their coefficient of relatedness (black arrows). 42 Figure 2: Genomic imprinting can result in divergent phenotypes from the same genotype. A) A paternally imprinted gene, i.e. maternally expressed.", + "Because of the small contribution, through the sperm, of the paternal transcriptome to the fertilized zygote, and because of the stronger maternal contribution to child rearing in most model organisms, parental effects are typically thought of as synonymous with maternal effects, although true paternal effects are known to exist (Rando, 2012). Maternal effects have been shown to be important during embryonic development, leading to differences in the birth weight of mice depending on the genotype of the mother (Cowley et al. , 1989; Wolf et al. , 2011).", + "Therefore, the resulting phenotypic patterns lag a generation behind the genetic transmission of the causal variants. The most well-studied parental genetic effects are caused by deposition of maternal transcripts into the egg prior to fertilization, resulting in differences in early embryonic development depending on the genotype of the mother. Certain genes have also been shown to respond to maternal influence after birth through genetically defined maternal behaviors (Weaver et al. , 2004).", + "The phenotype of the F1 hybrids is compared to those of the parental inbred strains to reveal dominance or semi-dominance relationships between the alleles that a\u00a1ect the phenotype. Phenotypic di\u00a1erences between reciprocal F1 hybrids indicate that one or more of the following factors may a\u00a1ect the trait: (1) sex linkage (X- or Ylinked traits), (2) genomic imprinting of QTLs that a\u00a1ect the phenotype, (3) prenatal maternal e\u00a1ects (e\u00a1ects of intrauterine environment), and/or (4) postnatal maternal or paternal e\u00a1ects (e\u00a1ects of maternal and/or paternal parenting behaviour on o\u00a1spring).", + "It was believed by many that for each trait variant we should expect to find a corresponding genetic change, or \u201egene for\u201f that trait. Through historical happenstance the relationship between genes and traits was set up and treated as if it were one-to-one. But the production of a trait involves not only genes, but also their interactions with each other and the environment, and chance." + ], + [ + "distinguishing prenatal from postnatal maternal effects, see below). Maternal effects can account for a large proportion of phenotypic variance, especially during early life, and for some traits explain more variation than direct genetic effects [33, 97, 99, 100, 102\u2013115]. However, maternal and offspring genotype are correlated (i.e. half their genes are shared), and in inbred lines they are fully confounded, thus separating the effects of their respective genotypes is difficult. To remove this confounding effect cross-fostering has been used, both in the laboratory and in the field [119, 131].", + "Using genetic markers, the pattern of inheritance can be tracked through families. For example, by analyzing a marker linked to the eye color gene in several generations, it is possible to determine from which grandparents a child has inherited its eye color alleles. More importantly, \ufb01nding a marker linked to a disease can lead to location of the faulty gene causing the disease. Finding the gene is very valuable in the search for the cure. The distance between two loci can be expressed either as physical or genetic distance.", + " Although autosomal SNPs are commonly used as genetic markers to infer ancestry or race/ethnicity membership, haploid such as mitochondria, Y-DNA, and X-lined markers are also important to provide separate stories of ancestry of individuals from paternal and maternal sides [42,43].Therefore, genetic structure created due to autosomal markers could be different from those of lineage markers (often influenced by political, social, and migration history of individuals/populations).mitochondrial DNA or mtDNA haploid is the maternally inherited mitochondrial genome (mtDNA) [44].All children inherit mtDNA from their mother, with no admixture from the father.Like Y-line DNA, mtDNA is passed intact from one generation to the next but through maternal line.", + " a) Autosomal DNA (testing both sexes) markers: autosomal DNA tests utilize DNA from the 22 pairs of autosomal chromosomes.Autosomal DNA is inherited from both parents.Autosomal testing provides percentages of ethnicity using autosomal DNA SNP test (i.e., ancestry informative markers), and it is the most commonly used test to infer ancestry across diploid genome.b) Y-DNA or Y-SNPs (paternal line testing) markers: a haploid Y-DNA is the paternally inherited non-recombining portion of the Y chromosome, and it tests only for males.The Y-DNA testing tests the Y chromosome which is passed intact from father to son with no DNA from the mother.Y-DNA testing can then be used to trace direct paternal line.Y-DNA remains the same in each generation, allowing us to compare surname from different regions to see if we are from the same family.Y-line testing does not indicate anything about the contributions of the other ancestors in a family tree.In other words, you could be 3/4th Native American, with only the direct paternal line being European, and this test would tell you nothing at all about those other three Native lines.When testing the Y-chromosome, there are two types of tests, short tandem repeat (STR) and SNP markers.STR tests are best for recent ancestry while SNP tests tell about more ancient ancestry.c) Mitochondrial DNA (maternal line testing) markers:", + " Additional information about past breeding practices can be gleaned by quantifying the number of reproductive males and females in a population.This can be achieved by comparing levels of genetic diversity between sex chromosomes, autosomes and mtDNA 99 .In cattle, for example, gene flow from aurochs is evident in the autosomes but is absent in mtDNA 41 .This has been interpreted as a management strategy that may have involved allowing insemination of domesticated females by wild bulls 41,100 .In horses, a comparison of the levels of diversity of the Y chromosome and the autosomal chromosomes demonstrated that some cultures allowed fewer males to breed and instead selected specific stallion bloodlines 55 .This male-oriented breeding strategy was not practised by the Romans and only became increasingly prominent in the past 1,000 years as a result of the growing influence of Oriental stallions (Arabian, Persian and Turkmen) 101 .", + " Dr Ring: What makes the maternal gene so peculiar compared to the paternal?Dr Cookson: If you look in the epidemiologic sense, many studies show that there is increased risk of allergic disease if the mother is affected.However, very few studies have actually set out to test that formally and most of them might suffer from some sort of selection bias because the mother is more likely to be aware of her symptoms and feel guilty, and so on.It is very difficult to explain.Is it genomic imprinting, where the gene is only active when transmitted through the mother?I do not think all of these genes would be imprinted, though it is possible.It also seems that there are effects of the maternal phenotype.The maternal phenotype, if the mother is affected or unaffected, determines the strength of the maternal effect.Again, if a gene was imprinted, you would not expect maternal phenotype to be important.So, I think that this has something to do with maternal/fetal interaction, either through the placenta or shortly after birth.There is the issue of immune conflict between mother and child.At the same time, the mother is trying to prime the infant's immune system.", + "Genetic and Genomic Discovery Using Family Studies Ingrid B. Borecki, PhD; Michael A. Province, PhD G enetic studies traditionally have been performed on sets of related individuals, that is, families.Mendel's early studies in sweet peas (Pisum sativum) on the inheritance patterns of discrete traits from parents with specific mating types to offspring has shed light on the basic mechanisms of inheritance, including the fundamental laws of segregation of discrete factors (genes) from parents to offspring and the cosegregation of genes that are closely located on a chromosome (linkage).The distribution of traits within families exhibited mathematical segregation ratios in offspring from known mating types.These expected segregation ratios have been used as an important discovery tool in the study of human diseases in pedigrees, providing evidence for a multitude of single-gene disorders.Furthermore, in some cases, trait cosegregation with genetic markers with known positions provides mapping information that enables localization and, ultimately, identification of the relevant causative gene.", + "In fact, this idea has been pursued before in the context of signatures of reproductive isolation and shown to reveal patterns consistent with epistatic gene interactions that arise in the shape of Dobzhansky-Muller incompatibilities [10,11]. In contrast to the mouse data, the available human genotypes were derived from outbred, ethnically distinct populations. In this case pairs of functionally interacting genes can be detected following a slightly different approach.", + "Family Structure The first re-identification method (FAMILY) employs genealogical data accompanying genomic data.Genealogies, rich in depth and structure, permit the construction of complex familial relationships.Consider a simple family structure of two parents and one child.Since the parental genders are guaranteed, there exist 2 variants of this structure, since the child's gender is either male or female.When disease status is taken into account, it is represented as a Boolean variable; either an individual afflicted or not afflicted.In this aspect, all three family members can be represented as three attributes {Father, Mother, Child}, and there exist (father's disease status)*(mother's disease status)*(child's disease status)*(child's gender) = 2*2*2*2 = 16 possible family-disease combinations.In reality, pedigrees are much more robust than a simple nuclear family.For example, a three-generation family of two children per family permits on the order of 10 5 distinct variants of the family-disease structure and 10 6 individuals that could be uniquely characterized.The number of combinationsk is larger when supplementary information, such as living status or medical/genetic features, is considered. 16e ability to determine unique family structures is only one part of the re-identification process.These structures must be linked to identifiable information, which, in many instances, is publicly available in the form of various genealogical databases.These databases are accessible both offline and via the World Wide Web.For example, genealogical records are available in many public databases, including ,Ancestry.com>,,Infospace.com>,,RootsWeb.com>,,GeneaNet.com>,,FamilySearch.org>, and ,Genealogy.com>. {From such data, it is not difficult to construct family structures and, with such information in hand, an adversary can link disease-labeled family structures to named individuals.", + " Fig. 3. Illustrations of the three CEU pedigrees (black) showing how genetic information from distant patrilineal relatives (arrow; red, patrilineal lines) can identify individuals.Filled squares represent sequenced individuals.To respect the privacy of these families, only abbreviated versions are presented.The sex of the CEU grandchildren was randomized.The numbers of grandchildren are not given.", + " When I was in high school, I remember often trying to match my friends to their parents at various school functions and being surprised at how easy this was.As human geneticists, in spite of the enormous advances being made in our field, we still cannot answer many of the everyday questions that we are asked, such as: \"Why does he look just like his mother? \"Max Perutz [1], in a recent editorial comment in the New Scientist entitled \"The Molecular Biology of the Future,\" suggested some questions, for, as he put it, \"an examination in some future century. \"Here are two of them: (1) \"The time has come\" the Walrus said, \"To talk of many things ...And why the sea is boiling hot And whether pigs have wings. \"Calculate the amount of genetic information this would require in megacricks.", + "Using genetic markers, the pattern of inheritance can be tracked through families. For example, by analyzing a marker linked to the eye color gene in several generations, it is possible to determine from which grandparents a child has inherited its eye color alleles. More importantly, \ufb01nding a marker linked to a disease can lead to location of the faulty gene causing the disease. Finding the gene is very valuable in the search for the cure. The distance between two loci can be expressed either as physical or genetic distance.", + "In contrast, genomic imprinting is due to epigenetic changes within the individual causing differential gene expression characterized by either complete or partial silencing of one parental allele (Barlow, 2011; Abramowitz and Bartolomei, 2012; Ashbrook and Hager, 2013). As both mothers and fathers had contact with the pups in our study, our observed PGEs could come from either parent. Among quantitative USV traits only peak amplitude of call displayed a possible parent-of-origin effect. For call number, call duration, mean peak frequency, and all morphological traits, there were no significant parent-of-origin effect in reciprocal F1 females. In contrast, Thornton et al.", + " Another way of avoiding stratification is to use family-based samples.This approach has several theoretical advantages: as well as being immune to stratification 114 , these samples can be used to determine whether an allele has different effects on disease when it is inherited maternally or paternally 115 , and DISCORDANT SIB designs [116][117][118] can control for the effects of shared environment.Furthermore, more complex family-based designs are possible 119 that might allow combined association and linkage analysis 120 , and family-based association tests have also been developed for quantitative traits [94][95][96][97][98] .However, pure sibship-based association studies are underpowered relative to case-control studies 107,116,117 , and the requirement for living parents might introduce an age-of-onset bias towards younger patients for diseases that usually arise late in life.Furthermore, family-based samples are often much more difficult to collect, particularly if larger pedigrees are sought.Finally, the most commonly used family-based design, the TRANSMISSION DISEQUILIBIRIUM TEST (TDT; see REF. 114) is susceptible to technical artefacts (see below).", + " Because mtDNA is not subjected (as far as we know) to sexual recombination and crossover at the time of nuclear meiosis, nature must call on other means to ensure that inevitable germ plasm mtDNA mutations (Medvedev, 1981) are not transmitted.These mutations among primary oocytes, on the face of it, can be expected to increase with time, that is with maternal age.Empirical data on this question are incomplete and conflicting, being mostly confined so far to searches for deletions rather than point mutations (Chen et al., 1995;Keefe et al., 1995).It is inevitable, however, that there will be such mutations and that there must therefore be a reliable physiological mechanism (a) for giving an opportunity for back-mutations to occur, (b) for selecting in favor of those back-mutations (thus preserving the genome) and in favor of rare advantageous mutations, and (c) for preventing the spread of persistent harmful mutations through the population -mutations that are too slight (or too late in origin) to have escaped intraovarian culling.The sheer conservation of the mitochondrial genome over 0.5 billion years or more, despite a mutation rate estimated at 10 -20 times that of nuclear DNA, is ample reason to conclude that such a physiological purification process must exist.", + "To scrutinize the polygenic networks underlying complex diseases, however, mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background will be insufficient on their own. For example, predisposition to the metabolic syndrome is inherited in a non-Mendelian fashion stressing genetic heterogeneity and multigenetic pathogenesis (Nandi et al. , 2004). With the reawakening as to the extraordinary genetic resources and phenotypic diversity archived in extant inbred strains, however, a foundation is in place for tracking down these complex traits and quantitative trait loci (QTL).", + "Otherwise, tens of thousands or markers will appear significant in the genome-wise association studies using up to one million genetic markers. Approaches to control for stratification include using of self report of ancestry or genetically derived principle components in the analysis. For studies using inbred mouse lines, a cladogram which is a hierarchical grouping based on phylogenetic analysis of strain relatedness can be created to subdivide inbred strains into more genetically homogenous subgroups.", + " Although bilateral descent is the norm in Western societies, it is not universal and there is variation with cultural practices around lineage.In certain societies, individuals place greater importance on (and have greater knowledge about) one side of the family than another (unilineal descent).Thus, individuals in patrilineal groups trace relationships through males only so that your father's brother's children are members of your family, but not your father's sisters (Kottak, 2007).They are members of their husband's group or family.Efforts to create a family pedigree may be hampered if the participant is not familiar with her mother's relatives, but her mother's brother's children (her cousins) may be able to supplement her overall family history.Knowledge about the cultural system of unilineal descent avoids assuming the universality of bilateral descent.Cultural beliefs such as these also have implications in the conduct of genetic research in terms of confidentiality and autonomy (Benkendorf et al., 1997;Wertz, 1997).One cannot assume that the named proband is in a position to speak for the extended family in agreeing to participate in any genetic research (DudokdeWit et al., 1997).", + "In particular in polygynous species, a female\u2019s offspring may have different fathers and are thus more closely related through the maternal than the paternal line. Therefore, any fitness cost to mothers, such as increased provisioning and care, affect maternally derived genes more strongly than paternally derived genes, leading to the silencing of the maternal copy (i.e. paternal expression) of genes that increase resource transfer. 5. Coadaptation between offspring and maternal traits The genetics of the co-evolution of parental and offspring traits has been investigated using quantitative genetics models and in several empirical studies (Agrawal et al.", + "In this scenario, genes expressed in parents will be selected for their effects on parental behaviour while genes expressed in offspring will be selected for their effects on influencing parental behaviour. At the genetic level the predicted conflict between paternal and maternal genomes is thought to have led to the evolution of genomic imprinting (monoallelic gene expression). Genomic imprinting effects are good examples of offspring genetic effects on maternal care because of the impact on the quality of maternal care and level of resource provisioning (e.g. Li et al. , 1999)." + ], + [ + "Genetic mapping in mouse strains enhances the power of detecting modifier genes and identifying complex genetic interactions. Genomewide quantitative trait locus (QTL) analysis, as described in more detail below, represents a promising approach to detect genetic variants that are associated with specific phenotypes and interact with each other. 16 ACCEPTED MANUSCRIPT In experimental crosses of two (inbred) strains the first generation (F1) of offsprings is genetically heterozygous but equal. Then in the next generation (F2) the PT strain-specific genetic information is distributed across the genomes of their progeny and RI each offspring is genetically unique.", + "Second, and perhaps more important, is the difference in the size and types of the genetic reference populations. In our previous study, we mapped the QTL with 36 F2 mice that were genotyped at 82 markers. In the current study, by comparison, we were able to map QTLs after examining 342 mice from 55 strains that were genotyped at approximately 4000 markers.", + "This contrast can be exploited to identify subregions that underlie the trans-QTLs [67]. SNPs were counted for all four pairs of parental haplotypes\u2014B vs D, B vs H, B vs C, and L vs S\u2014and SNP profiles for the four crosses were compared (figure 6). Qrr1 is a highly polymorphic PLoS Genetics | www.plosgenetics.org 8 November 2008 | Volume 4 | Issue 11 | e1000260 QTL Hotspot on Mouse Distal Chromosome 1 Figure 5. QTL for aminoacyl-tRNA synthetases in distal Qrr1.", + "The traditional approach to QTL mapping is to use two strains that differ maximally in the phenotype as parental strains for genetic crosses, with the following caveats. QTL analysis based on a single cross will most likely reflect only a small portion of the net genetic variation, and QTL detection will be limited to regions where the two progenitor strains have functional polymorphisms. Data from multiple crosses, or from an HS, will overcome this limitation and can also be used to reduce QTL intervals [5,30].", + "These candidate genes are then sequenced in the two parental inbred strains looking for sequence di\u00a1erences in coding or regulatory regions. After \u00a2ne mapping the QTL interval and shortening the list of plausible candidate polymorphisms, the major challenge remains \u2401 proving de\u00a2nitively which nucleotide polymorphism underlies the QTL. The most direct proof would be replacing one strain\u2019s allele with another strain\u2019s allele (creating a FIG. 1. Intercross breeding strategy for mapping quantitative trait loci (QTLs). On the right, the parental, F1 hybrid, and intercross (F2) mouse generations are depicted.", + "Furthermore, splicing QTLs (sQTLs) rather than eQTLs could comprise the molecular mechanism linking DNA variants with YFP53; thus, sQTL analysis could uncover genes that would not normally be detected at the level of differential gene expression (DGE),53 and thus, a differentially 181 182 Molecular-Genetic and Statistical Techniques for Behavioral and Neural Research Figure 8.5 Schematic for immediate, rapid \ufb01ne mapping in select F2 recombinants of the RCC-F2 cross. Top panel: Genome-wide signi\ufb01cant QTL (green trace; red dashed line \u00bc signi\ufb01cance threshold; blue vertical lines \u00bc Bayes credible interval).", + "Interval-specific haplotype analysis Approximately 97% of the genetic variation between inbred mouse strains is ancestral [22], so regions of identity by descent (IBD) between two strains used to detect a QTL are highly unlikely to contain the causal genetic polymorphism underlying the QTL [28]. For example, a cross between C57BL/6J and A/J mice detected www.sciencedirect.com a blood pressure QTL on Chr 1 [7].", + "Interval-specific haplotype analysis Approximately 97% of the genetic variation between inbred mouse strains is ancestral [22], so regions of identity by descent (IBD) between two strains used to detect a QTL are highly unlikely to contain the causal genetic polymorphism underlying the QTL [28]. For example, a cross between C57BL/6J and A/J mice detected www.sciencedirect.com a blood pressure QTL on Chr 1 [7].", + "At present, the BXD panel is composed of 80 different strains that all have been fully genotyped.26 Variation in any quantifiable trait can be associated with the segregation of parental alleles, and linkage genetics can map this variation to quantitative trait loci (QTLs), thereby identifying the genomic region(s) affecting that trait. An overview of the QTL mapping approach is depicted in Figure 2. Classical QTL analysis has permitted the identification of loci that are associated with variation in HSC traits.", + "In general, linking genetic variation with trait variation identifies QTL and a significant linkage of phenotype and genotype suggest that the DNA status helps to determine trait expression. As stated above, mouse QTL studies provide distinct advantages over human studies in the examination of genetic causes of a quantitative trait (e.g. alcoholism), even in the absence of specific hypotheses regarding its aetiology or candidate genes.", + "The progenitor mouse strains should have sufficient variation for the traits of interest and they should be genetically diverse enough to enable genetic mapping (BENNETT et al. 2006; FLINT 2003; GRISEL 2000). The sample size required for the identification of QTL depends largely on the effect size that a QTL contributes to phenotypes on interest. Inference about QTL can be made if one or more genetic markers are over- or underrepresented in the analysed individuals. Genotyping is often done by means of microsatellite markers, which contains mono, di-, tri-, or tetranucleotide tandem repeats flanked by specific sequences (Figure 4a).", + "This comparison gives information about the reliability of the observed genotype information: The more the marker locations differ between the two maps (which signifies variation in marker positions), the higher the possibility of genotyping errors. QTL mapping was done in several stages to identify loci acting individually and QTL that interacted, either additively or epistatically. To determine individually-acting QTL, a singleQTL genome scan was conducted with the function scanone.", + "Importantly, whereas these studies required substantial labor, time, and resources, X-QTL is a quick and easy approach to achieve a comparable level of genetic dissection. The levels of complexity observed here (e.g. 14 loci explaining 70% of the genetic variance for 4-NQO resistance) are still dramatically lower than those seen in for some human traits in GWAS (e.g. 40 loci explaining 5% of the variance for height 2,5). One obvious explanation is the difference in experimental designs (line crosses vs. population association studies), but differences in genetic architectures among species and traits may also contribute.", + "The method uses two pieces of information: mapping data from crosses that involve more than two inbred strains and sequence variants in the progenitor strains within the interval containing a quantitative trait locus (QTL). By testing whether the strain distribution pattern in the progenitor strains is consistent with the observed genetic effect of the QTL we can assign a probability that any sequence variant is a quantitative trait nucleotide (QTN). It is not necessary to genotype the animals except at a skeleton of markers; the genotypes at all other polymorphisms are estimated by a multipoint analysis.", + "The method uses two pieces of information: mapping data from crosses that involve more than two inbred strains and sequence variants in the progenitor strains within the interval containing a quantitative trait locus (QTL). By testing whether the strain distribution pattern in the progenitor strains is consistent with the observed genetic effect of the QTL we can assign a probability that any sequence variant is a quantitative trait nucleotide (QTN). It is not necessary to genotype the animals except at a skeleton of markers; the genotypes at all other polymorphisms are estimated by a multipoint analysis.", + "Genotyping all the individual progeny for markers that show allelic variation between the parental strains (either single nucleotide polymorphisms or simple sequence repeats) will allow the detection of associations between trait values and marker genotype, and in this way demonstrate to which set of markers a QTL is linked. To reduce the genotyping effort, selective genotyping of the individuals at the extremes of the phenotypic spectrum can be performed (20,23). Although these three approaches are in general considered to be the best to detect and map QTL, they have several disadvantages for quantitative traits involving HSC.", + "So, how do you go about planning and performing a QTL study, and how do you identify the responsible gene within a QTL that you have identified? Generally, one starts by performing a strain survey to find two parental inbred strains that have a markedly different trait. One can now look up many different traits of inbred mice online at the Mouse Phenome Database (http://phenome. jax.org/pub-cgi/phenome/mpdcgi?rtn=docs/home). However, the trait you may want to study may not be present in wild type mice, so you may want to cross a mutant (or genetically engineered) strain onto several inbred strains.", + "QTL Theory and Planning The theory behind the most basic form of QTL mapping is based upon intercrossing two inbred strains. The mouse genome consists of 19 pairs of autosomes (non sex-determining chromosome) and the X and Y chromosomes. In the example shown in Fig. 18.1, we are intercrossing stain A (shown with a black chromosome pair) with strain B (shown with a white chromosome pair). The initial F1 (filial generation 1) mice are true hybrids, with each individual From: Molecular Biomethods Handbook, 2nd Edition.", + "These candidate genes are then sequenced in the two parental inbred strains looking for sequence di\u00a1erences in coding or regulatory regions. After \u00a2ne mapping the QTL interval and shortening the list of plausible candidate polymorphisms, the major challenge remains \u2401 proving de\u00a2nitively which nucleotide polymorphism underlies the QTL. The most direct proof would be replacing one strain\u2019s allele with another strain\u2019s allele (creating a FIG. 1. Intercross breeding strategy for mapping quantitative trait loci (QTLs). On the right, the parental, F1 hybrid, and intercross (F2) mouse generations are depicted.", + "QTL mapping studies then seek to detect the polymorphisms underlying the complex traits of interest by scanning for alleles that co-vary with the traits. Similar experiments also can be conducted with special derivatives of inbred strains known as recombinant inbred (RI) mice. These animals are derived by cross-breeding two or more distinct parental strains (which often diverge widely for the trait of interest), followed by inbreeding of the offspring for several generations (Bailey 1971). Given the correct breeding strategy, this method 1 This is an issue faced by GWASs researchers when classifying samples as cases or controls." + ] + ] +} -- cgit v1.2.3