ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.

Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks.

BACKGROUND: Advances in large-scale tumor sequencing have led to an understanding that there are combinations of genomic and transcriptomic alterations specific to tumor types, shared across many patients. Unfortunately, computational identification of functionally meaningful and recurrent alteration patterns within gene/protein interaction networks has proven to be challenging. FINDINGS: We introduce a novel combinatorial method, cd-CAP (combinatorial detection of conserved alteration patterns), for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not) and simultaneously detects multiple alteration profile conserved subnetworks. CONCLUSIONS: In a number of The Cancer Genome Atlas datasets, cd-CAP identified large biologically significant subnetworks with conserved alteration patterns, shared across many tumor samples.