Accurate assembly and typing of HLA using a graph-guided assembler kourami

Heewook Lee, Carl Kingsford

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Abstract

Accurate typing of human leukocyte antigen (HLA) is essential for successful organ transplantation and HLA genes are heavily associated with various diseases. Widely used typing assays often involve a set of specially designed primers or probes requiring additional experiments. With the maturing of high-throughput sequencing (HTS) technologies, whole genome sequencing (WGS) as well as other HTS assays are becoming more accessible even in the clinical settings. We describe various computational methods capable of directly typing HLA genes using HTS data including Kourami, our HLA assembler. Kourami is the first HLA assembler capable of discovering novel alleles. Kourami assembles full-length sequences across the peptide-binding regions of HLA genes. Here, we focus on how a user would use Kourami on a new sample. We demonstrate the application by typing HLA alleles from a recently published WGS data with validated HLA types using Kourami.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages235-247
Number of pages13
DOIs
StatePublished - 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1802
ISSN (Print)1064-3745

Keywords

  • Assembly
  • Bioinformatics in silico
  • High-throughput
  • HLA
  • WGS
  • Whole genome sequencing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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