OptiType: precision HLA typing from next-generation sequencing data.

ABSTRACT:

Motivation

The human leukocyte antigen (HLA) gene cluster plays a crucial role in adaptive immunity and is thus relevant in many biomedical applications. While next-generation sequencing data are often available for a patient, deducing the HLA genotype is difficult because of substantial sequence similarity within the cluster and exceptionally high variability of the loci. Established approaches, therefore, rely on specific HLA enrichment and sequencing techniques, coming at an additional cost and extra turnaround time.

Result

We present OptiType, a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate predictions from NGS data not specifically enriched for the HLA cluster. We also present a comprehensive benchmark dataset consisti

SUBMITTER: Szolek A 

PROVIDER: S-EPMC4441069 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature