Adaptive immune receptor genotyping using the corecount program

Abstract

We present a new Rep-Seq analysis tool called <i>corecount</i>, for analyzing genotypic variation in immunoglobulin (IG) and T cell receptor (TCR) genes. <i>corecount</i> is highly efficient at identifying V alleles, including those that are infrequently used in expressed repertoires and those that contain 3' end variation that are otherwise refractory to reliable identification during germline inference from expressed libraries. Furthermore, <i>corecount</i> facilitates accurate D and J gene genotyping. The output is highly reproducible and facilitates the comparison of genotypes from multiple individuals, such as those from clinical cohorts. Here, we applied <i>corecount</i> to the genotypic analysis of IgM libraries from 16 individuals. To demonstrate the accuracy of <i>corecount</i>, we Sanger sequenced all the heavy chain IG alleles (65 IGHV, 27 IGHD and 7 IGHJ) from one individual from whom we also produced two independent IgM Rep-seq datasets. Genomic analysis revealed that 5 known IGHV and 2 IGHJ sequences are truncated in current reference databases. This dataset of genomically validated alleles and IgM libraries from the same individual provides a useful resource for benchmarking other bioinformatic programs that involve V, D and J assignments and germline inference, and may facilitate the development of AIRR-Seq analysis tools that can take benefit from the availability of more comprehensive reference databases.