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IGHV allele similar...
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
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- Peres, Ayelet (author)
- Bar-Ilan University
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Lees, William D. (author)
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- Rodriguez, Oscar L. (author)
- University of Louisville
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- Lee, Noah Y. (author)
- Yale University
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- Polak, Pazit (author)
- Bar-Ilan University
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- Hope, Ronen (author)
- Bar-Ilan University
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- Kedmi, Meirav (author)
- Yale University,Sheba Medical Center
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- Collins, Andrew M. (author)
- University of New South Wales
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- Ohlin, Mats (author)
- Lund University,Lunds universitet,Institutionen för immunteknologi,Institutioner vid LTH,Lunds Tekniska Högskola,LUCC: Lunds universitets cancercentrum,Övriga starka forskningsmiljöer,LTH profilområde: Teknik för hälsa,LTH profilområden,Department of Immunotechnology,Departments at LTH,Faculty of Engineering, LTH,LUCC: Lund University Cancer Centre,Other Strong Research Environments,LTH Profile Area: Engineering Health,LTH Profile areas,Faculty of Engineering, LTH
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- Kleinstein, Steven H. (author)
- Yale University
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- Watson, Corey T. (author)
- Bar-Ilan University
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- Yaari, Gur (author)
- Bar-Ilan University
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(creator_code:org_t)
- 2023
- 2023
- English.
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In: Nucleic Acids Research. - 0305-1048. ; 51:16, s. 86-86
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Abstract
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- In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV-reference-book).
Subject headings
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Publication and Content Type
- art (subject category)
- ref (subject category)
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- By the author/editor
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Peres, Ayelet
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Lees, William D.
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Rodriguez, Oscar ...
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Lee, Noah Y.
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Polak, Pazit
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Hope, Ronen
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show more...
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Kedmi, Meirav
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Collins, Andrew ...
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Ohlin, Mats
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Kleinstein, Stev ...
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Watson, Corey T.
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Yaari, Gur
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Computer and Inf ...
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and Bioinformatics
- Articles in the publication
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Nucleic Acids Re ...
- By the university
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Lund University