{"id":1713,"date":"2008-09-19T13:22:38","date_gmt":"2008-09-19T11:22:38","guid":{"rendered":"http:\/\/www.wjst.de\/blog\/?p=1713"},"modified":"2008-10-14T09:46:06","modified_gmt":"2008-10-14T07:46:06","slug":"will-current-snp-chips-unintentionally-diagnose-huntington","status":"publish","type":"post","link":"https:\/\/www.wjst.de\/blog\/sciencesurf\/2008\/09\/will-current-snp-chips-unintentionally-diagnose-huntington\/","title":{"rendered":"Will current SNP chips unintentionally diagnose Huntington?"},"content":{"rendered":"<p>I wondered if <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/entrez\/dispomim.cgi?id=143100\">Chorea Huntington<\/a> may be unintentionally diagnosed by current SNP chips used in <a href=\"http:\/\/www.ncbi.nlm.nih.gov\/sites\/entrez?db=gap\">research projects of other diseases<\/a>. On a first glance, this seems to be unlikely &#8211; we are dealing with repeated CAG repeats in huntingtin <a href=\"http:\/\/genome.ucsc.edu\/cgi-bin\/hgTracks?position=chr4:3046206-3215485&#038;hgsid=112576328&#038;knownGene=pack&#038;hgFind.matches=uc010icr.1,\">located on chromosome 4p16.3<\/a> that are not easily accessible by SNP panels.<!--more--> An earlier <a href=\"http:\/\/www.nature.com\/nature\/journal\/v326\/n6109\/abs\/326194a0.html\">paper<\/a> described linkage with the microsatellite D4S10. But that&#8217;s linkage not association and the probability remains low that any (random) SNP chip can diagnose Huntington. Or &#8211; are there any disease haplotypes? When discussing this question with a  colleague, he pointed me to a follow-up article in Nature March 12, 1987 where indeed, studying the same Venezuelan pedigree from lake Maracaibo, a haplotype in the D4S10<br \/>\nregion was found. This 17 kb fragment could be characterized by 4 RFLPs, forming 7 haplotypes where only one (the C1 haplotype) was associated with HD. So there is some chance that a closer related haplotype in an outbred population may be constructed from GWA data that is associated with HD.<br \/>\n<a href=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2008\/10\/htt.png\" data-rel=\"key-image-0\" data-rl_title=\"\" data-rl_caption=\"\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/www.wjst.de\/blog\/wp-content\/uploads\/2008\/10\/htt.png\" alt=\"\" title=\"\" width=\"480\" height=\"273\" class=\"alignnone size-full wp-image-1728\" \/><\/a><br \/>\nOr will there be other gene variants like MSX1 loci that are interacting with huntingtin? I will take the opportunity next week to ask the <a href=\"http:\/\/www.hdsa.org\/research\/pipeline\/coalition\/james-gusella.html\">discoverer of the HD gene<\/a> if there are any GWA data that may allow a diagnosis of Huntington, yea, yea.<\/p>\n\n<p>&nbsp;<\/p>\n<div class=\"bottom-note\">\n  <span class=\"mod1\">CC-BY-NC Science Surf , accessed 11.04.2026<\/span>\n <\/div>","protected":false},"excerpt":{"rendered":"<p>I wondered if Chorea Huntington may be unintentionally diagnosed by current SNP chips used in research projects of other diseases. On a first glance, this seems to be unlikely &#8211; we are dealing with repeated CAG repeats in huntingtin located on chromosome 4p16.3 that are not easily accessible by SNP panels. &nbsp; CC-BY-NC Science Surf &hellip; <a href=\"https:\/\/www.wjst.de\/blog\/sciencesurf\/2008\/09\/will-current-snp-chips-unintentionally-diagnose-huntington\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Will current SNP chips unintentionally diagnose Huntington?<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[2],"tags":[2063,2061,2062,207],"class_list":["post-1713","post","type-post","status-publish","format-standard","hentry","category-genetics-biology","tag-cag","tag-chorea-huntington","tag-first-glance","tag-snp"],"_links":{"self":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1713","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/comments?post=1713"}],"version-history":[{"count":0,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/posts\/1713\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/media?parent=1713"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/categories?post=1713"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.wjst.de\/blog\/wp-json\/wp\/v2\/tags?post=1713"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}