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diff --git a/gnqa/paper1_eval/src/data/responses/general/experts/07.json b/gnqa/paper1_eval/src/data/responses/general/experts/07.json new file mode 100644 index 0000000..007dd4d --- /dev/null +++ b/gnqa/paper1_eval/src/data/responses/general/experts/07.json @@ -0,0 +1,394 @@ +{ + "created_at": "2024-06-01T14:29:54.405039Z", + "data": { + "amplify": false, + "answer": "The text mentions the application of site-specific recombinase technology, which allows investigators to engineer genes in the mouse that will allow for the deletion, insertion, inversion, or exchange of chromosomal DNA with high fidelity. However, it does not provide specific details about recombination in the human genome.", + "context": { + "081924f4-cdcc-4fce-9223-744c6ecffe4e": [ + { + "document_id": "081924f4-cdcc-4fce-9223-744c6ecffe4e", + "text": "Genome Res, 2011, 21: 1769–1776\nMattick JS, Dinger ME. The extent of functionality in the human\ngenome. HUGO J, 2013, 7, doi:10.1186/1877-6566-1187-1182\nENCODE Project Consortium, Bernstein BE, Birney E, Dunham I,\nGreen ED, Gunter C, Snyder M. An integrated encyclopedia of DNA\nelements in the human genome. Nature, 2012, 489: 57–74\nPheasant M, Mattick JS. Raising the estimate of functional human\nsequences. Genome Res, 2007, 17: 1245–1253\nHu T, Long M, Yuan D, Zhu Z, Huang Y, Huang S. The genetic\nequidistance result, misreading by the molecular clock and neutral\ntheory and reinterpretation nearly half of a century later." + } + ], + "33814fad-d831-46f5-b41f-ff31626a82ca": [ + { + "document_id": "33814fad-d831-46f5-b41f-ff31626a82ca", + "text": "This approach enables, on the one hand, studying the process of\nmammalian evolution and, on the other hand, translational studies using model\norganisms of complex human phenotypes. Detection of regions conserved between\ndistant species points to high functional importance of these fragments of the DNA\nsequence. Human and mouse developmental lines diverged about 75 million years ago, and\never since evolutionary forces shaped the two genotypes in a different manner\n(Waterston et al. , 2002). Nevertheless, the extent of the changes is, however, small\nenough for conservation of local gene order (Waterston et al. , 2002)." + } + ], + "3cafb9e7-b3d9-4e8e-a727-da79282d2b14": [ + { + "document_id": "3cafb9e7-b3d9-4e8e-a727-da79282d2b14", + "text": "First, the human and mouse genome projects\nelucidated the sequences of over 20,000 genes [Lander et al. ,\n2001; Venter et al. , 2001], and most are expressed in the CNS. The availability of gene sequences has allowed rapid analysis of\ncandidate human disease and disorder genes and the isolation of\nthe mouse homologues. Second, the application of site-specific\nrecombinase technology provides investigators with the opportunity to engineer genes in the mouse that will allow for the\ndeletion, insertion, inversion, or exchange of chromosomal\nDNA with high fidelity (for review see Branda and Dymechi,\n2004]." + } + ], + "5edf84d0-c2d9-45eb-91b9-c35743b6a463": [ + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG). The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + } + ], + "74f148ef-696c-4e25-80e5-1d44ae70540e": [ + { + "document_id": "74f148ef-696c-4e25-80e5-1d44ae70540e", + "text": "\nTHE HUMAN GENOME PROJECT IS generating vast amounts of new information at breakneck speed and causing a fundamental shift in disease research.Now with the availability of a nearly complete, high-accuracy sequence of the mouse genome (7), a new and powerful paradigm for biomedical research is established.The remarkable similarity of mouse and human genomes, in both synteny and sequence, unconditionally validates the mouse as an exceptional model organism for understanding human biology.The discovery among inbred mouse strains of defined regions of high and low genomic variation inherited primarily from two ancestral Mus subspecies (6) holds great promise to make mapping and positional cloning more rapid and feasible.Haplotype maps of inbred mouse strains combined with sophisticated delineation of their phenotypic variation and gene expression patterns will enable complex trait analysis on an unprecedented scale.This issue of Journal of Applied Physiology highlights inbred strain surveys exploring phenotypic variation in drug responses [see Crabbe et al. (1) and Watters et al. (8) in this issue].These mouse initiatives demonstrate a viable, cost-effective alternative to human research requiring family studies, population linkage analysis, or genome-wide genotyping on a multitude of individuals for association mapping." + } + ], + "81c3edc4-f625-45f2-bf78-e49faf118c88": [ + { + "document_id": "81c3edc4-f625-45f2-bf78-e49faf118c88", + "text": "\n\nHow Many Genes are There in the Human Genome?" + } + ], + "b1656249-5f62-428f-8b71-7549cc2886ff": [ + { + "document_id": "b1656249-5f62-428f-8b71-7549cc2886ff", + "text": "\n\nThe Landscape of Human Genome Variation" + } + ], + "c12e853e-4f0d-48f9-93af-15db9ad2dfae": [ + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG). The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + } + ], + "da485354-fcdc-49b8-9a41-0f673610156a": [ + { + "document_id": "da485354-fcdc-49b8-9a41-0f673610156a", + "text": "Science 291:1304–\n1351\n3. Lander ES et al (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921\n4. Engle LJ, Simpson CL, Landers JE (2006) Using high-throughput SNP technologies to study cancer. Oncogene 25:1594–1601\n5. Elston RC, Anne Spence M (2006) Advances in statistical human genetics over the\nlast 25 years. Stat Med 25:3049–3080\n6. Larson GP et al (2005) Genetic linkage of prostate cancer risk to the chromosome\n3 region bearing FHIT. Cancer Res 65:805–814\n7. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes:\npast successes for mendelian disease, future approaches for complex disease." + }, + { + "document_id": "da485354-fcdc-49b8-9a41-0f673610156a", + "text": "McPherson JD, Marra M, Hillier L et al (2001) A physical map of the human\ngenome. Nature 409:934–941\n13. Burke DT, Carle GF, Olson MV. (1987) Cloning of large segments of exogenous\nDNA into yeast by means of artificial chromosome vectors. Science 236:806–812\n14. Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random\nsequencing and assembly of Haemophilus influenzae Rd Science 269:496–512\n15. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the\nflowering plant Arabidopsis thaliana. Nature 408:796–815\n16." + } + ], + "e17ef791-e77a-486b-a3c1-c7f037fa530c": [ + { + "document_id": "e17ef791-e77a-486b-a3c1-c7f037fa530c", + "text": "\n\nT he human genome has been cracked wide open in recent years and is spilling many of its secrets.More than 100 genome wide association studies have been conducted for scores of hu man diseases, identifying hun dreds of polymorphisms that are widely seen to influence disease risk.After many years in which the study of complex human traits was mired in false claims and methodologic inconsistencies, ge nomics has brought not only com prehensive representation of com mon variation but also welcome rigor in the interpretation of sta tistical evidence.Researchers now know how to properly account for most of the multiple hypothesis testing involved in mining the ge nome for associations, and most reported associations reflect real biologic causation.But do they matter?" + } + ], + "f35e02a1-3314-4663-913f-38a3fc072aa8": [ + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG). The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + } + ], + "fca531d0-d45b-495f-a02c-fbd437617b20": [ + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG). The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + } + ] + }, + "data_source": [ + { + "document_id": "81c3edc4-f625-45f2-bf78-e49faf118c88", + "section_type": "main", + "text": "\n\nHow Many Genes are There in the Human Genome?" + }, + { + "document_id": "3cafb9e7-b3d9-4e8e-a727-da79282d2b14", + "section_type": "main", + "text": "First, the human and mouse genome projects\nelucidated the sequences of over 20,000 genes [Lander et al. ,\n2001; Venter et al. , 2001], and most are expressed in the CNS.\n The availability of gene sequences has allowed rapid analysis of\ncandidate human disease and disorder genes and the isolation of\nthe mouse homologues. Second, the application of site-specific\nrecombinase technology provides investigators with the opportunity to engineer genes in the mouse that will allow for the\ndeletion, insertion, inversion, or exchange of chromosomal\nDNA with high fidelity (for review see Branda and Dymechi,\n2004]." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "In some cases, structural variations, such as copy number polymorphisms,\nexist (Feuk et al. , 2006); however, because of the nature of the genome assembly\nprocess, these will invariably be collapsed into a single contig that does not reflect\nthe natural sequence. To address the technical challenges of whole-genome assembly,\nthe human genome is released as defined ‘builds’ on a quarterly basis (Lander et al. ,\n2001; reviewed in Chapter 4). The increasing complexity of processes that map\ndata to the genome implicitly involves some lag in availability of the most current\nsequence assembly." + }, + { + "document_id": "e17ef791-e77a-486b-a3c1-c7f037fa530c", + "section_type": "main", + "text": "\n\nT he human genome has been cracked wide open in recent years and is spilling many of its secrets.More than 100 genome wide association studies have been conducted for scores of hu man diseases, identifying hun dreds of polymorphisms that are widely seen to influence disease risk.After many years in which the study of complex human traits was mired in false claims and methodologic inconsistencies, ge nomics has brought not only com prehensive representation of com mon variation but also welcome rigor in the interpretation of sta tistical evidence.Researchers now know how to properly account for most of the multiple hypothesis testing involved in mining the ge nome for associations, and most reported associations reflect real biologic causation.But do they matter?" + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG).\n The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG).\n The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG).\n The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "In\npractical terms, this has meant that we acquire many fragments, from a few hundred\nbases to a few hundred kilobases in length, of a genome that must then be assembled computationally to produce a continuous sequence. In the case of the human\ngenome, two unfinished ‘draft’ sequences were produced by different methods, one\nby the International Human Genome Sequencing Consortium (IHGSC) and one by\nCelera Genomics (CG).\n The IHGSC began with a BAC (bacterial artificial chromosome) clone-based physical map of the genome (IHGSC, 2001)." + }, + { + "document_id": "da485354-fcdc-49b8-9a41-0f673610156a", + "section_type": "main", + "text": "Science 291:1304–\n1351\n3. Lander ES et al (2001) Initial sequencing and analysis of the human genome.\n Nature 409:860–921\n4. Engle LJ, Simpson CL, Landers JE (2006) Using high-throughput SNP technologies to study cancer. Oncogene 25:1594–1601\n5. Elston RC, Anne Spence M (2006) Advances in statistical human genetics over the\nlast 25 years. Stat Med 25:3049–3080\n6. Larson GP et al (2005) Genetic linkage of prostate cancer risk to the chromosome\n3 region bearing FHIT. Cancer Res 65:805–814\n7. Botstein D, Risch N (2003) Discovering genotypes underlying human phenotypes:\npast successes for mendelian disease, future approaches for complex disease." + }, + { + "document_id": "081924f4-cdcc-4fce-9223-744c6ecffe4e", + "section_type": "main", + "text": "Genome Res, 2011, 21: 1769–1776\nMattick JS, Dinger ME. The extent of functionality in the human\ngenome. HUGO J, 2013, 7, doi:10.1186/1877-6566-1187-1182\nENCODE Project Consortium, Bernstein BE, Birney E, Dunham I,\nGreen ED, Gunter C, Snyder M. An integrated encyclopedia of DNA\nelements in the human genome. Nature, 2012, 489: 57–74\nPheasant M, Mattick JS. Raising the estimate of functional human\nsequences. Genome Res, 2007, 17: 1245–1253\nHu T, Long M, Yuan D, Zhu Z, Huang Y, Huang S. The genetic\nequidistance result, misreading by the molecular clock and neutral\ntheory and reinterpretation nearly half of a century later." + }, + { + "document_id": "b1656249-5f62-428f-8b71-7549cc2886ff", + "section_type": "main", + "text": "\n\nThe Landscape of Human Genome Variation" + }, + { + "document_id": "33814fad-d831-46f5-b41f-ff31626a82ca", + "section_type": "main", + "text": "This approach enables, on the one hand, studying the process of\nmammalian evolution and, on the other hand, translational studies using model\norganisms of complex human phenotypes. Detection of regions conserved between\ndistant species points to high functional importance of these fragments of the DNA\nsequence.\n Human and mouse developmental lines diverged about 75 million years ago, and\never since evolutionary forces shaped the two genotypes in a different manner\n(Waterston et al. , 2002). Nevertheless, the extent of the changes is, however, small\nenough for conservation of local gene order (Waterston et al. , 2002)." + }, + { + "document_id": "da485354-fcdc-49b8-9a41-0f673610156a", + "section_type": "main", + "text": "McPherson JD, Marra M, Hillier L et al (2001) A physical map of the human\ngenome. Nature 409:934–941\n13. Burke DT, Carle GF, Olson MV. (1987) Cloning of large segments of exogenous\nDNA into yeast by means of artificial chromosome vectors. Science 236:806–812\n14. Fleischmann RD, Adams MD, White O et al (1995) Whole-genome random\nsequencing and assembly of Haemophilus influenzae Rd Science 269:496–512\n15. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the\nflowering plant Arabidopsis thaliana. Nature 408:796–815\n16." + }, + { + "document_id": "74f148ef-696c-4e25-80e5-1d44ae70540e", + "section_type": "abstract", + "text": "\nTHE HUMAN GENOME PROJECT IS generating vast amounts of new information at breakneck speed and causing a fundamental shift in disease research.Now with the availability of a nearly complete, high-accuracy sequence of the mouse genome (7), a new and powerful paradigm for biomedical research is established.The remarkable similarity of mouse and human genomes, in both synteny and sequence, unconditionally validates the mouse as an exceptional model organism for understanding human biology.The discovery among inbred mouse strains of defined regions of high and low genomic variation inherited primarily from two ancestral Mus subspecies (6) holds great promise to make mapping and positional cloning more rapid and feasible.Haplotype maps of inbred mouse strains combined with sophisticated delineation of their phenotypic variation and gene expression patterns will enable complex trait analysis on an unprecedented scale.This issue of Journal of Applied Physiology highlights inbred strain surveys exploring phenotypic variation in drug responses [see Crabbe et al. (1) and Watters et al. (8) in this issue].These mouse initiatives demonstrate a viable, cost-effective alternative to human research requiring family studies, population linkage analysis, or genome-wide genotyping on a multitude of individuals for association mapping." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "4\nAssembling a View of the\nHuman Genome\nColin A. M. Semple\nBioinformatics, MRC Human Genetics Unit, Edinburgh EH4 2XU, UK\n\n4.1 Introduction\nThe miraculous birth of the draft human genome sequence took place against\nthe odds. It was only made possible by parallel revolutions in the technologies\nused to produce, store and analyse the sequence data, and by the development of\nnew, large-scale consortia to organize and obtain funding for the work (Watson,\n1990). The initial flood of human sequence has subsided as the sequencing centres have sequenced genomes from other mammalian orders and beyond." + }, + { + "document_id": "937fe28b-dbaf-422b-a2de-9ffeafd94172", + "section_type": "main", + "text": "High copy number repeat sequences\n\nThe HGP revealed that repeat sequences account for at least 50 per cent of the human genome sequence.These repeats may be classified as (i) transposon-derived repeats, (ii) partially retroposed copies of genes (referred to as processed pseudogenes), (iii) simple sequence repeats, (iv) blocks of tandemly repeated sequences at centromeres, telomeres and the short arms of acrocentric chromosomes and (v) segmental duplications (SDs) or low copy number repeats." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "6.7 Challenges and future directions\nThere has been great progress in understanding the biology and functions encoded\nby the human genome since the first draft of a reference sequence was produced in\n2001 (Lander et al. , 2001; (Venter et al. , 2001), and much of this insight has been\ngained by comparison both within and between genomes. However, as with many scientific endeavours, more questions arise with each increment in understanding." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "6.7 Challenges and future directions\nThere has been great progress in understanding the biology and functions encoded\nby the human genome since the first draft of a reference sequence was produced in\n2001 (Lander et al. , 2001; (Venter et al. , 2001), and much of this insight has been\ngained by comparison both within and between genomes. However, as with many scientific endeavours, more questions arise with each increment in understanding." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "6.7 Challenges and future directions\nThere has been great progress in understanding the biology and functions encoded\nby the human genome since the first draft of a reference sequence was produced in\n2001 (Lander et al. , 2001; (Venter et al. , 2001), and much of this insight has been\ngained by comparison both within and between genomes. However, as with many scientific endeavours, more questions arise with each increment in understanding." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "6.7 Challenges and future directions\nThere has been great progress in understanding the biology and functions encoded\nby the human genome since the first draft of a reference sequence was produced in\n2001 (Lander et al. , 2001; (Venter et al. , 2001), and much of this insight has been\ngained by comparison both within and between genomes. However, as with many scientific endeavours, more questions arise with each increment in understanding." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "After the publication of the publicly available human genome draft in 2001, the\nIHGSC undertook the arduous task of ‘finishing’: producing a genome sequence\ncovering 99 per cent of the euchromatic regions sequenced to an accuracy of 99.99\nper cent. On 14 April 2003, the IHGSC announced that this target had been reached;\nleaving less than 400 persistent gaps where highly repetitive sequences evaded current sequencing technology. A steady trickle of papers in the journal Nature has\nmarked the emergence of each finished human chromosome sequence, along with\nthe annotation describing its notable features." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "After the publication of the publicly available human genome draft in 2001, the\nIHGSC undertook the arduous task of ‘finishing’: producing a genome sequence\ncovering 99 per cent of the euchromatic regions sequenced to an accuracy of 99.99\nper cent. On 14 April 2003, the IHGSC announced that this target had been reached;\nleaving less than 400 persistent gaps where highly repetitive sequences evaded current sequencing technology. A steady trickle of papers in the journal Nature has\nmarked the emergence of each finished human chromosome sequence, along with\nthe annotation describing its notable features." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "After the publication of the publicly available human genome draft in 2001, the\nIHGSC undertook the arduous task of ‘finishing’: producing a genome sequence\ncovering 99 per cent of the euchromatic regions sequenced to an accuracy of 99.99\nper cent. On 14 April 2003, the IHGSC announced that this target had been reached;\nleaving less than 400 persistent gaps where highly repetitive sequences evaded current sequencing technology. A steady trickle of papers in the journal Nature has\nmarked the emergence of each finished human chromosome sequence, along with\nthe annotation describing its notable features." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "After the publication of the publicly available human genome draft in 2001, the\nIHGSC undertook the arduous task of ‘finishing’: producing a genome sequence\ncovering 99 per cent of the euchromatic regions sequenced to an accuracy of 99.99\nper cent. On 14 April 2003, the IHGSC announced that this target had been reached;\nleaving less than 400 persistent gaps where highly repetitive sequences evaded current sequencing technology. A steady trickle of papers in the journal Nature has\nmarked the emergence of each finished human chromosome sequence, along with\nthe annotation describing its notable features." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "6.2.3 A varied landscape\nIn probably every measure that has been made of the human genome sequence, it has\nbeen found to be far from homogeneous. We have already touched on the distinction\nbetween heterochromatic regions that perform roles in the packaging and segregation\nof chromosomes, from the remaining (euchromatic) regions. Throughout the rest of\nthe euchromatic genome, there is considerable variation in gene density (the number\nof genes per unit sequence), IRE content, nucleotide and dinucleotide frequency, and\nthe observed rates of genetic recombination, nucleotide substitution, insertions and\ndeletions." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "6.2.3 A varied landscape\nIn probably every measure that has been made of the human genome sequence, it has\nbeen found to be far from homogeneous. We have already touched on the distinction\nbetween heterochromatic regions that perform roles in the packaging and segregation\nof chromosomes, from the remaining (euchromatic) regions. Throughout the rest of\nthe euchromatic genome, there is considerable variation in gene density (the number\nof genes per unit sequence), IRE content, nucleotide and dinucleotide frequency, and\nthe observed rates of genetic recombination, nucleotide substitution, insertions and\ndeletions." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "6.2.3 A varied landscape\nIn probably every measure that has been made of the human genome sequence, it has\nbeen found to be far from homogeneous. We have already touched on the distinction\nbetween heterochromatic regions that perform roles in the packaging and segregation\nof chromosomes, from the remaining (euchromatic) regions. Throughout the rest of\nthe euchromatic genome, there is considerable variation in gene density (the number\nof genes per unit sequence), IRE content, nucleotide and dinucleotide frequency, and\nthe observed rates of genetic recombination, nucleotide substitution, insertions and\ndeletions." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "6.2.3 A varied landscape\nIn probably every measure that has been made of the human genome sequence, it has\nbeen found to be far from homogeneous. We have already touched on the distinction\nbetween heterochromatic regions that perform roles in the packaging and segregation\nof chromosomes, from the remaining (euchromatic) regions. Throughout the rest of\nthe euchromatic genome, there is considerable variation in gene density (the number\nof genes per unit sequence), IRE content, nucleotide and dinucleotide frequency, and\nthe observed rates of genetic recombination, nucleotide substitution, insertions and\ndeletions." + }, + { + "document_id": "0ecf5586-f80d-4b5e-8687-5a0d92423597", + "section_type": "main", + "text": "The precision and the power in human genetics will improve greatly over the\nnext several decades as full genome sequences, better human disease phenotyping, and\nelectronic health records are merged at the scale of millions of subjects and whole\nnations. Therefore, we need to revamp experimental genetic resources in an era flooded\nin GWAS hits. How are new and old mouse resources best repositioned to help deliver on\nthe still unmet and much more integrative promises of predictive genetics and\npersonalized precision health care?\n\n 25\nbioRxiv preprint doi: https://doi.org/10.1101/672097; this version posted July 8, 2019." + }, + { + "document_id": "da485354-fcdc-49b8-9a41-0f673610156a", + "section_type": "main", + "text": "Resequencing\nCompletion of a single version of the human genome (2,3) has now provided\nthe substrates for direct comparison of individuals in both health and disease.\n Ideally, to better understand the genetic contributions to severe diseases, one\nwould obtain the entire human genome sequence for all disease-carrying individuals for comparison to unaffected control groups. While these complete\ndata sets are not readily obtainable today, a strategy that is currently approachable is the re-sequencing of a large set of appropriate candidate genes in\nindividuals with a given disease to screen for potential causative/susceptibility\nalleles." + }, + { + "document_id": "c12e853e-4f0d-48f9-93af-15db9ad2dfae", + "section_type": "main", + "text": "The interplay between the adaptive benefits introduced by mutations and natural selection shapes the genome into\nunique patterns of genetic variations in different regions. Therefore, investigating\nthe functional roles of these genetic variations provides a great opportunity for understanding complex common diseases, such as cancer. The compilation of human\n\nBioinformatics for Geneticists, Second Edition." + }, + { + "document_id": "5edf84d0-c2d9-45eb-91b9-c35743b6a463", + "section_type": "main", + "text": "The interplay between the adaptive benefits introduced by mutations and natural selection shapes the genome into\nunique patterns of genetic variations in different regions. Therefore, investigating\nthe functional roles of these genetic variations provides a great opportunity for understanding complex common diseases, such as cancer. The compilation of human\n\nBioinformatics for Geneticists, Second Edition." + }, + { + "document_id": "fca531d0-d45b-495f-a02c-fbd437617b20", + "section_type": "main", + "text": "The interplay between the adaptive benefits introduced by mutations and natural selection shapes the genome into\nunique patterns of genetic variations in different regions. Therefore, investigating\nthe functional roles of these genetic variations provides a great opportunity for understanding complex common diseases, such as cancer. The compilation of human\n\nBioinformatics for Geneticists, Second Edition." + }, + { + "document_id": "f35e02a1-3314-4663-913f-38a3fc072aa8", + "section_type": "main", + "text": "The interplay between the adaptive benefits introduced by mutations and natural selection shapes the genome into\nunique patterns of genetic variations in different regions. Therefore, investigating\nthe functional roles of these genetic variations provides a great opportunity for understanding complex common diseases, such as cancer. The compilation of human\n\nBioinformatics for Geneticists, Second Edition." + } + ], + "document_id": "1A879F7DD77C0462CC12FB20F7D14486", + "engine": "gpt-4", + "first_load": false, + "focus": "api", + "keywords": [ + "human&genome", + "recombination", + "genes", + "CNS", + "site-specific&recombinase", + "structural&variations", + "copy&number&polymorphisms", + "genome&assembly", + "genome&wide&association&studies", + "polymorphisms" + ], + "metadata": [ + { + "object": "Transient overexpression of WRKY79 in protoplasts results in up-regulation of Gene:542165, Gene:541974, Gene:100274033, Gene:542688, Gene:542150, Gene:542151, Gene:100273457, Gene:100285509, Gene:103626248, Gene:103646045, Gene:100217270, Gene:100279981, Gene:100281950, Gene:542476, Gene:542369, Gene:100281950, and Gene:542260.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab969966" + }, + { + "object": "CAT 419 C/T gene polymorphism was not informative, -89 A/T was associated with risk, and 389 C/T conferred protection against vitiligo along with AT haplotype. VDR BsmI, ApaI, and TaqI gene polymorphisms were not associated with vitiligo in Northwestern Mexicans suggesting a role for CAT gene polymorphisms in vitiligo susceptibility in the Mexican population and a lack of association with VDR gene polymorphisms.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab122773" + }, + { + "object": "P2Y1 and P2Y12 genes were polymorphic in a Korean population; 3 intronic P2Y12 polymorphisms i-139C>T, i-744T>C, i-801insA were in complete linkage disequilibrium but not with the c.52C>T polymorphism; platelet aggregation in response to ADP associated with c.52C>T polymorphism but not with the 3 intronic polymorphisms or the P2Y1 c.1622A>T polymorphism", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab576406" + }, + { + "object": "Uniform Mu insertion results in up-regulation of cytokinin synthesis genes and down-regulation of cytokinin degradation genes. The protein binds to Gene:103632693, Gene:100502174, Gene:100283866, Gene:542044, and Gene:100037786.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab983367" + }, + { + "object": "No relationship was found between the studied polymorphisms 14094 ACE gene, rs1800469 gene TGFbeta1, GNB3 gene rs5443, rs5186 AGTR1 gene and the occurrence of primary vesicoureteral reflux. TT genotype polymorphism rs5443 of the GNB3 gene may be a protective factor for improved renal function in patients with primary vesicoureteral reflux.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab530514" + }, + { + "object": "There was no association between the extended psychosis phenotype and BDNF rs6265/COMT rs4680 polymorphisms. The lack of an association between different expression levels of the extended psychosis phenotype and the BDNF rs6265/ COMT rs4680 polymorphism might be related to sample characteristics, underlying gene-gene, gene-environment and gene-environment-gene interactions.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab888369" + }, + { + "object": "In general, the meta-analysis found no marked association between the IL-10-1082G/A gene polymorphism and HIV-1 susceptibility, IL-10-529C/A gene polymorphism might lead to a decreased risk of HIV-1 infection, and IL-10-819C/T gene polymorphism might lead to an increased risk of HIV-1 infection.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab393616" + }, + { + "object": "When rs13154178 gene polymorphism was compared with AA homozygous individuals, fasting blood glucose levels were significantly higher in carriers of either polymorphism than in those with no polymorphism. We suggest rs13154178 gene polymorphism may lead to gestational diabetes mellitus in the Turkish society.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab1015662" + }, + { + "object": "Study confirmed the presence of a gene-environment interaction between the rs1801516 polymorphism and radiation exposure in carcinogenesis, whereas no association was found between the rs1801516 polymorphism and cancer risk for individuals without radiation exposure. The heterogeneity observed in the meta-analysis of individuals with radiation exposure might be due to gene-ethnicity or gene-gene interactions.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab737660" + }, + { + "object": "Genome-wide associations P < 5 x 10-8 were found at the PCSK9 gene, the APOB gene, theLPL gene, the APOA1-APOA5 locus, the LIPC gene, the CETP gene, the LDLR gene, and the APOE locus.", + "predicate": "http://www.w3.org/2000/01/rdf-schema#comment", + "subject": "ndd791caee50643ad90a986f563d2a0dab320109" + } + ], + "question": "What about recombination in the human genome?", + "subquestions": null, + "task_id": "1A879F7DD77C0462CC12FB20F7D14486", + "usage": { + "chatgpt": 4864, + "gpt-4": 3728, + "gpt-4-turbo-preview": 2745 + }, + "user_id": 2 + }, + "document_id": "1A879F7DD77C0462CC12FB20F7D14486", + "task_id": "1A879F7DD77C0462CC12FB20F7D14486" +} |