{"id":10724,"date":"2021-08-11T03:06:40","date_gmt":"2021-08-11T03:06:40","guid":{"rendered":"https:\/\/www.rhesusnegative.net\/staynegative\/?p=10724"},"modified":"2021-08-11T03:06:47","modified_gmt":"2021-08-11T03:06:47","slug":"neanderthal-abo-genotype-calls","status":"publish","type":"post","link":"https:\/\/www.rhesusnegative.net\/staynegative\/neanderthal-abo-genotype-calls\/","title":{"rendered":"Neanderthal ABO genotype calls"},"content":{"rendered":"<div style=\"padding-bottom:20px; padding-top:10px;\" class=\"hupso-share-buttons\"><!-- Hupso Share Buttons - https:\/\/www.hupso.com\/share\/ --><a class=\"hupso_toolbar\" href=\"https:\/\/www.hupso.com\/share\/\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/static.hupso.com\/share\/buttons\/share-medium.png?w=640&#038;ssl=1\" style=\"border:0px; padding-top:5px; float:left;\" alt=\"Share Button\"\/><\/a><script type=\"text\/javascript\">var hupso_services_t=new Array(\"Twitter\",\"Facebook\",\"Pinterest\",\"Linkedin\");var hupso_background_t=\"#EAF4FF\";var hupso_border_t=\"#66CCFF\";var hupso_toolbar_size_t=\"medium\";var hupso_twitter_via = \"datebytype\";var hupso_image_folder_url = \"\";var hupso_twitter_via=\"datebytype\";var hupso_url_t=\"\";var hupso_title_t=\"Neanderthal ABO genotype calls\";<\/script><script type=\"text\/javascript\" src=\"https:\/\/static.hupso.com\/share\/js\/share_toolbar.js\"><\/script><!-- Hupso Share Buttons --><\/div>\n<figure class=\"wp-block-image\"><img data-recalc-dims=\"1\" loading=\"lazy\" decoding=\"async\" width=\"640\" height=\"494\" src=\"https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/journal.pone_.0254175.g003-1-1.png?resize=640%2C494&#038;ssl=1\" alt=\"\" class=\"wp-image-10722\" srcset=\"https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/journal.pone_.0254175.g003-1-1.png?resize=1024%2C791&amp;ssl=1 1024w, https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/journal.pone_.0254175.g003-1-1.png?resize=300%2C232&amp;ssl=1 300w, https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/journal.pone_.0254175.g003-1-1.png?resize=768%2C593&amp;ssl=1 768w, https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/journal.pone_.0254175.g003-1-1.png?w=1060&amp;ssl=1 1060w\" sizes=\"auto, (max-width: 640px) 100vw, 640px\" \/><\/figure>\n\n\n\n<p>We inferred the\u00a0<em>ABO<\/em>\u00a0alleles according to the functional approach developed by [<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.ref018\">18<\/a>,\u00a0<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.ref019\">19<\/a>] for pure and chimeric A-B transferase cDNAs. In conformity with this approach, we identified the\u00a0<em>ABO<\/em>\u00a0alleles by 4 letters corresponding to the 4 main amino acid changes in the catalytic site of the glycosyltransferase of pure A or B allele positions, preceded by the presence or not of the G in position c.261 (rs8176719) (i.e. G-AAAA meaning 4 SNPs of\u00a0<em>A<\/em>\u00a0allele generating A phenotype) and the deletion or not of the C at position c.1061 (rs56392308) to differentiate the\u00a0<em>A1<\/em>\u00a0and\u00a0<em>A2<\/em>\u00a0alleles. We achieved the\u00a0<em>ABO<\/em>\u00a0allele identification with the screening of all exons and collected the genotypes at 39 additional loci previously identified as responsible for various\u00a0<em>ABO<\/em>\u00a0alleles [<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.ref020\">20<\/a>] (<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.s005\">S2 Table<\/a>; Fig A in\u00a0<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.s002\">S1 File<\/a>). Special attention has been taken to\u00a0<em>FUT2<\/em>\u00a0whose amino acid numbering in NBCI and hg19 should be rectified to get the correct amino-acid changes as mentioned by the ISBT. This is due to the fact that the initiation codon is the third ATG at the beginning of exon 2 (19: 49,206,247) [<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0254175#pone.0254175.ref021\">21<\/a>].<\/p>\n\n\n\n<figure class=\"wp-block-embed-wordpress aligncenter wp-block-embed is-type-wp-embed is-provider-rh-negative-blood-and-people\"><div class=\"wp-block-embed__wrapper\">\n<blockquote class=\"wp-embedded-content\" data-secret=\"7Nk462L9E8\"><a href=\"https:\/\/www.rhesusnegative.net\/staynegative\/identifying-and-interpreting-apparent-neanderthal-ancestry-in-african-individuals\/\">Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals<\/a><\/blockquote><iframe loading=\"lazy\" class=\"wp-embedded-content\" sandbox=\"allow-scripts\" security=\"restricted\" style=\"position: absolute; clip: rect(1px, 1px, 1px, 1px);\" title=\"&#8220;Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals&#8221; &#8212; The Rh Negative Blog\" src=\"https:\/\/www.rhesusnegative.net\/staynegative\/identifying-and-interpreting-apparent-neanderthal-ancestry-in-african-individuals\/embed\/#?secret=KQfg2RjZQe#?secret=7Nk462L9E8\" data-secret=\"7Nk462L9E8\" width=\"600\" height=\"338\" frameborder=\"0\" marginwidth=\"0\" marginheight=\"0\" scrolling=\"no\"><\/iframe>\n<\/div><\/figure>\n\n\n\n<p><br><\/p>\n<div style=\"padding-bottom:20px; padding-top:10px;\" class=\"hupso-share-buttons\"><!-- Hupso Share Buttons - https:\/\/www.hupso.com\/share\/ --><a class=\"hupso_toolbar\" href=\"https:\/\/www.hupso.com\/share\/\"><img data-recalc-dims=\"1\" decoding=\"async\" src=\"https:\/\/i0.wp.com\/static.hupso.com\/share\/buttons\/share-medium.png?w=640&#038;ssl=1\" style=\"border:0px; padding-top:5px; float:left;\" alt=\"Share Button\"\/><\/a><script type=\"text\/javascript\">var hupso_services_t=new Array(\"Twitter\",\"Facebook\",\"Pinterest\",\"Linkedin\");var hupso_background_t=\"#EAF4FF\";var hupso_border_t=\"#66CCFF\";var hupso_toolbar_size_t=\"medium\";var hupso_twitter_via = \"datebytype\";var hupso_image_folder_url = \"\";var hupso_twitter_via=\"datebytype\";var hupso_url_t=\"\";var hupso_title_t=\"Neanderthal ABO genotype calls\";<\/script><script type=\"text\/javascript\" src=\"https:\/\/static.hupso.com\/share\/js\/share_toolbar.js\"><\/script><!-- Hupso Share Buttons --><\/div>","protected":false},"excerpt":{"rendered":"<div style=\"padding-bottom:20px; padding-top:10px;\" class=\"hupso-share-buttons\"><!-- Hupso Share Buttons - https:\/\/www.hupso.com\/share\/ --><a class=\"hupso_toolbar\" href=\"https:\/\/www.hupso.com\/share\/\"><img src=\"https:\/\/static.hupso.com\/share\/buttons\/share-medium.png\" style=\"border:0px; padding-top:5px; float:left;\" alt=\"Share Button\"\/><\/a><script type=\"text\/javascript\">var hupso_services_t=new Array(\"Twitter\",\"Facebook\",\"Pinterest\",\"Linkedin\");var hupso_background_t=\"#EAF4FF\";var hupso_border_t=\"#66CCFF\";var hupso_toolbar_size_t=\"medium\";var hupso_twitter_via = \"datebytype\";var hupso_image_folder_url = \"\";var hupso_twitter_via=\"datebytype\";var hupso_url_t=\"\";var hupso_title_t=\"Neanderthal ABO genotype calls\";<\/script><script type=\"text\/javascript\" src=\"https:\/\/static.hupso.com\/share\/js\/share_toolbar.js\"><\/script><!-- Hupso Share Buttons --><\/div>We inferred the\u00a0ABO\u00a0alleles according to the functional approach developed by  for pure and chimeric A-B transferase cDNAs. In conformity with this approach, we identified the\u00a0ABO\u00a0alleles by 4 letters corresponding to the 4 main amino acid changes in the catalytic site of the glycosyltransferase of pure A or B allele positions, preceded by the presence or not of the G in position c.261 (rs8176719) (i.e. G-AAAA meaning 4 SNPs of\u00a0A\u00a0allele generating A phenotype) and the deletion or not of the C at position c.1061 (rs56392308) to differentiate the\u00a0A1\u00a0and\u00a0A2\u00a0alleles. We achieved the\u00a0ABO\u00a0allele identification with the screening of all exons and collected the genotypes at 39 additional loci previously identified as responsible for various\u00a0ABO\u00a0alleles  (S2 Table; Fig A in\u00a0S1 File). Special <div style=\"padding-bottom:20px; padding-top:10px;\" class=\"hupso-share-buttons\"><!-- Hupso Share Buttons - https:\/\/www.hupso.com\/share\/ --><a class=\"hupso_toolbar\" href=\"https:\/\/www.hupso.com\/share\/\"><img src=\"https:\/\/static.hupso.com\/share\/buttons\/share-medium.png\" style=\"border:0px; padding-top:5px; float:left;\" alt=\"Share Button\"\/><\/a><script type=\"text\/javascript\">var hupso_services_t=new Array(\"Twitter\",\"Facebook\",\"Pinterest\",\"Linkedin\");var hupso_background_t=\"#EAF4FF\";var hupso_border_t=\"#66CCFF\";var hupso_toolbar_size_t=\"medium\";var hupso_twitter_via = \"datebytype\";var hupso_image_folder_url = \"\";var hupso_twitter_via=\"datebytype\";var hupso_url_t=\"\";var hupso_title_t=\"Neanderthal ABO genotype calls\";<\/script><script type=\"text\/javascript\" src=\"https:\/\/static.hupso.com\/share\/js\/share_toolbar.js\"><\/script><!-- Hupso Share Buttons --><\/div>","protected":false},"author":1,"featured_media":10713,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"amp_status":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","enabled":false},"version":2}},"categories":[1],"tags":[],"class_list":["post-10724","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-facts"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"https:\/\/i0.wp.com\/www.rhesusnegative.net\/staynegative\/wp-content\/uploads\/2021\/08\/preview.jpg?fit=2000%2C770&ssl=1","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p5DV68-2MY","_links":{"self":[{"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/posts\/10724","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/comments?post=10724"}],"version-history":[{"count":4,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/posts\/10724\/revisions"}],"predecessor-version":[{"id":10731,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/posts\/10724\/revisions\/10731"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/media\/10713"}],"wp:attachment":[{"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/media?parent=10724"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/categories?post=10724"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rhesusnegative.net\/staynegative\/wp-json\/wp\/v2\/tags?post=10724"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}