IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data.

ABSTRACT: 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 pipel

SUBMITTER: Peres A 

PROVIDER: S-EPMC10484671 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature