{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/per-sample-immunoglobulin-germline-inference","title":"Per-sample immunoglobulin germline inference from B cell receptor deep sequencing data","arxiv_id":"1711.05843","date":"2018-04-28","proceeding":null,"authors":[],"abstract":"The collection of immunoglobulin genes in an individual's germline, which\ngives rise to B cell receptors via recombination, is known to vary\nsignificantly across individuals. In humans, for example, each individual has\nonly a fraction of the several hundred known V alleles. Furthermore, the\ncurrently-accepted set of known V alleles is both incomplete (particularly for\nnon-European samples), and contains a significant number of spurious alleles.\nThe resulting uncertainty as to which immunoglobulin alleles are present in any\ngiven sample results in inaccurate B cell receptor sequence annotations, and in\nparticular inaccurate inferred naive ancestors. In this paper we first show\nthat the currently widespread practice of aligning each sequence to its closest\nmatch in the full set of IMGT alleles results in a very large number of\nspurious alleles that are not in the sample's true set of germline V alleles.\nWe then describe a new method for inferring each individual's germline gene set\nfrom deep sequencing data, and show that it improves upon existing methods by\nmaking a detailed comparison on a variety of simulated and real data samples.\nThis new method has been integrated into the partis annotation and clonal\nfamily inference package, available at https://github.com/psathyrella/partis,\nand is run by default without affecting overall run time.","url_abs":"http://arxiv.org/abs/1711.05843v2","url_pdf":"http://arxiv.org/pdf/1711.05843v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"per-sample-immunoglobulin-germline-inference","repo_url":"https://github.com/psathyrella/partis","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}