{"id":321,"date":"2026-01-01T12:03:14","date_gmt":"2026-01-01T12:03:14","guid":{"rendered":"https:\/\/wordpress.vdjbase.org\/?p=321"},"modified":"2026-01-16T08:13:04","modified_gmt":"2026-01-16T08:13:04","slug":"human-ighc-set-released","status":"publish","type":"post","link":"https:\/\/wordpress.vdjbase.org\/index.php\/ogrdb\/human-ighc-set-released\/","title":{"rendered":"Human IGHC set released"},"content":{"rendered":"\n

We’re pleased to publish the first version of a human IGHC germline set on OGRDB. The set is based on the work of Jana et al., 2025<\/a>, and contains 105 full-length IGH constant region sequences, derived from long-read genomic sequencing. This work substantially increased the number of published sequences and revealed significant polymorphism and population diversity in constant region genes. Cell Genomics have also published a helpful commentary<\/a>.<\/p>\n\n\n\n

Formats<\/em><\/p>\n\n\n\n

The downloadable sets in FASTA format contain full-length coding sequences of both the transmembrane and secreted forms. The sequences of the secreted forms have a _SC suffix to the name. Please note that the nucleotide sequences are not in-frame, because, during splicing, the constant region picks up a G from the J-gene at its 5′ end.<\/p>\n\n\n\n

The downloadable JSON file contains full metadata. We have added extensions to the MiAIRR germline schema<\/a> for this purpose: specifically we have added c_exon coordinates for up to 9 constant region exons, and the field secretory_coding_sequence. The transmembrane coding sequence is stored in coding_seq_imgt. These extensions to the schema will be submitted to the AIRR Community’s Standards Working Group for ratification.<\/p>\n\n\n\n

Naming<\/em><\/p>\n\n\n\n

The sequences are named after the closest currently-named allele in the IUIS set, with snps added to describe the variation, for example IGHA1*01_c1068g. Where the number of snps would make the name unfeasibly long, a four-character code is used in place of the snp, for example IGHA1*06_6bc5. While the sequences will be submitted to IUIS for specific names, we elected to publish with interim names because the the review and naming process may take some time: in particular because the gene duplication and other structural variation discovered in the study raises some complex questions.<\/p>\n\n\n\n

Usage<\/em><\/p>\n\n\n\n

A growing number of methods such as 10x, PacBio and ONT technologies allow the constant region to be fully or near-fully characterized in repertoire sequencing. For other short-read methods, where only a small length of the constant region is captured, we recommend building a tailored set that is matched to the expected length captured and disambiguated so that it does not contain multiple identical sequences.<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

We’re pleased to publish the first version of a human IGHC germline set on OGRDB. The set is based on the work of Jana et al., 2025, and contains 105 full-length IGH constant region sequences, derived from long-read genomic sequencing. This work substantially increased the number of published sequences and revealed significant polymorphism and population… Continue reading Human IGHC set released<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[6,13],"tags":[],"class_list":["post-321","post","type-post","status-publish","format-standard","hentry","category-ogrdb","category-ogrdb_news","entry"],"_links":{"self":[{"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/posts\/321","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/comments?post=321"}],"version-history":[{"count":3,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/posts\/321\/revisions"}],"predecessor-version":[{"id":333,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/posts\/321\/revisions\/333"}],"wp:attachment":[{"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/media?parent=321"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/categories?post=321"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/wordpress.vdjbase.org\/index.php\/wp-json\/wp\/v2\/tags?post=321"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}