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diff --git a/web/dbdoc/BXSGeno.html b/web/dbdoc/BXSGeno.html deleted file mode 100755 index dd9ea76f..00000000 --- a/web/dbdoc/BXSGeno.html +++ /dev/null @@ -1,173 +0,0 @@ -<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> -<HTML><HEAD><TITLE>BXD Genotype / WebQTL</TITLE> -<META http-equiv=Content-Type content="text/html; charset=iso-8859-1"> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'> -<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'> - -</HEAD> -<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff> -<TABLE cellSpacing=5 cellPadding=4 width="100%" border=0> -<TBODY> -<TR> -<script language="JavaScript" src="/javascript/header.js"></script> -</TR> -<TR> -<TD bgColor=#eeeeee class="solidBorder"> -<Table width= "100%" cellSpacing=0 cellPadding=5><TR> -<!-- Body Start from Here --> -<TD valign="top" height="200" width="100%" bgcolor="#eeeeee"> - -<P class="title">BXD Genotypes Database (August 2003) - - <A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A></P> - - -<P class="subtitle"> Summary:</P> - -<Blockquote><P> -This BXD genotype data set is currently used to map all BXD phenotypes, including over 600 phenotypes in the Published Phenotypes database and all BXD array data sets. This genotype file is a superset of that described by Williams and colleagues (2001) and includes some new SNPs from Tim Wiltshire and Mathew Pletcher, new microsatellite markers generated by Grant Morahan and Jing Gu (Msw), and a few CTC markers by Jing Gu. -</P> -</Blockquote> - - - -<P class="subtitle"> About the genotypes used in these studies:</P> - -<Blockquote> WebQTL mapping algorithms rely on genotypes for the BXD strains that include both microsatellite markers (labeled <I>Mit</I> and <I>Msw</I>) and single nucleotide polymorphisms (labeled <I>Gnf</I>). The current set of markers (n = 779) have been carefully error-checked. Closely linked genetic markers often have the same strain distribution pattern (SDP) across the BXD strains. For computational efficiency, we only use a single marker associated with each SDP. -</Blockquote> - -<Blockquote>We have genotyped all available BXD strains from The Jackson Laboratory. BXD1 through BXD32 were produced by Benjamin Taylor starting in the late 1970s. BXD33 through BXD42 were produced by Taylor in the 1990s (Taylor et al., 1999). All BXD strains with numbers higher than BXD42 were generated by Lu Lu and Robert Williams at UTHSC and by Jeremy Peirce and Lee Silver at Princeton University. We thanks Guomin Zhou for generating the advanced intercross stock used to produce most of these advanced RI strains. <!--As of August 2003, these lines are an average of 15 generations inbred.--> There are approximately 48 of these advanced BXD strains, each of which archives approximately twice the recombinations present in typical F2-derived RI strains (Peirce et al. <A HREF="http://www.webqtl.org/reference.html" target="_blank" class="fs14">2003</a>). -</Blockquote> - -<Blockquote>Marker-strain pairs for which we were missing genotypes were often inferred from flanking markers. In marker sets lacking genotypes for a particular strain, a note is included to that effect in the marker set description below. -</Blockquote> - - -<P class="subtitle"> About the marker sets:</P> - -<Blockquote> <U><B>Mit</B></U><br> - -<I>Mit</I> markers, described by William Dietrich and colleagues (<a href="http://www.broad.mit.edu/cgi-bin/mouse/sts_info?database=mouserelease" target="_blank" class="fs14">1992</a>), are the most widely used of the three marker sets. These markers typically consist of regions of repeated dinucleotides (so-called CA repeat microsatellites) that vary in length among strains. The CA repeat polymorphisms are flanked by unique sequence that can be used to design polymerase chain reaction (PCR) primers that will selectively amplify the intervening variable region. While many of the <i>Mit</i> markers have been typed in the BXD strain set by a number of investigators, the genotypes used here are those reported in the consensus map created by Williams and colleagues (<a href="http://www.genomebiology.com/2001/2/11/research/0046" target="_blank" class="fs14">2001</a>). - -<br> -<br><i>Mit</i> marker names: D + (Chr of Marker) + Mit + (Order Found) <UL> -<LI>D indicates that the marker is a DNA segment. -<LI><i>Mit</i> indicates that the marker was identified at the Massachusetts Institute of Technology. -<LI>Order Found indicates the order in which the markers were identified. </UL> -</Blockquote> - -<Blockquote><B><U>Gnf</U></B> -<br><i>Gnf</i> markers are single nucleotide polymorphisms (SNPs) identified between B6 and D2 by genomic sequence sampling. Polymorphisms were typed by Mathew Pletcher and Tim Wiltshire using the Sequenom MassEXTEND system (Wiltshire et al., <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12612341&dopt=Abstract" target="_blank" class="fs14">2003</A>) For BXD8 as well as BXD67 and BXD68, genotypes were ofteninferred from flanking markers. Each of the genotyping reactions was set up in duplicate. Physical positions were determined for each marker and integrated with previous BXD RI mapping data based on a combination of physical and genetic positions. Unsupported double crossovers were verified by manual inspection to ensure accuracy of calls. A full list of SNPs identified in the sequence sampling can be found at <a href="http://www.gnf.org/SNP/" class = "normalsize">http://www.gnf.org/SNP</a>. -<br> -<br><i>Gnf</i> marker names: S + (Chr of Marker) + Gnf + (Mb position) <UL> -<LI>S indicates the marker is a SNP -<LI><i>Gnf</i> indicates that the marker originated at the Genomics Institute of the Novartis Research Foundation. -<LI>Mb position may include decimal values. </UL> -</Blockquote> - -<Blockquote><B><U>Msw</U></B> - -<br><i>Msw</i> markers are variable length tracts of nucleotide repeats designed and tested by Grant Morahan, Keith Satterley, Robert W. Williams, and Jing Gu. In contrast to the variable CA repeats of Mit markers, the <i>Msw</i> markers exploit polymorphisms in tri- tetra-, penta-, and hexa-nucleotide repeats. <i>Msw</i> markers were typed by Shuhua Qi and Jing Gu at UTHSC using previously described methods (Williams et al. <a href="http://www.genomebiology.com/2001/2/11/research/0046" target="_blank" class="fs14">2001</a>). Genotypes for BXD67 and BXD68 were often inferred from flanking markers. Physical positions were determined for each marker by BLAT analysis of the microsatellite sequence against the most recent assembly of the mouse genome (currently mm5 of May 2004) and integrated with previous BXD RI mapping data based on a combination of physical and genetic positions. -<br> - -<br><i>Msw</i> marker names: D + (Chr of Marker) + <i>Msw</i> + (Mb Position)<UL> -<LI>D indicates that the marker is a DNA segment <i>Msw</i> indicates the marker source. -<LI>Mb Position is marker position to the nearest megabase. -<LI>Mb position may include decimal values and, in rare cases, a letter suffix (a or b) if alternative primers were used to amplify the same repeat. -</UL></Blockquote> - - -<P class="subtitle"> Acknowledgments:</P> -<Blockquote> -Genotypes for the Mit and Msw marker sets were determined by Jing Gu and - -Lu Lu. Markers for the <i>Msw</i> set were designed by Grant Morahan, Keith - -Satterley. <i>Gnf</i> SNP genotypes were generated by Tim - -Wiltshire and Mathew Pletcher. The selection of markers to included in the final file was carried out - -by Jing Gu. - -This text file was originally written by Jeremy Peirce (August 21, - -2003). Updated August 22, 2003 by RW/JP/LL. Updated October 19, 2004 by RW. - - -</Blockquote> - -<P class="subtitle"> Reference:</P> -<Blockquote><P>Dietrich WF, Katz H, Lincoln SE (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=1353738&dopt=Abstract" class="fs14">1992</a>) A genetic map of the mouse suitable for typing in intraspecific crosses. Genetics 131:423-447. -</P></Blockquote> - - -<Blockquote><P> - - -Taylor BA, Wnek C, Kotlus BS, Roemer N, MacTaggart T, Phillips SJ (<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10087289&dopt=Abstract" class="fs14">1999</A>) Genotyping new BXD recombinant inbred mouse strains and comparison of BXD and consensus maps. -Mamm Genome 10:335-348. -</P></Blockquote> - -<Blockquote><P> -Williams RW, Gu J, Qi S, Lu L (<a href="http://www.genomebiology.com/2001/2/11/research/0046" class=normal>2001</a>) The genetic structure of recombinant inbred mice: High-resolution consensus maps for complex trait analysis. Genome Biology 2:RESEARCH0046 -</P></Blockquote> - -<Blockquote><P> - -Wiltshire T, Pletcher MT, Batalov S, Barnes SW, Tarantino LM, Cooke MP, Wu H, Smylie K, Santrosyan A, Copeland NG, Jenkins NA, Kalush F, Mural RJ, Glynne RJ, Kay SA, Adams MD, Fletcher CF (<A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12612341&dopt=Abstract" class="fs14">2003</A>) Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. 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