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HLA Typing pp 235-247 | Cite as

Accurate Assembly and Typing of HLA using a Graph-Guided Assembler Kourami

  • Heewook LeeEmail author
  • Carl Kingsford
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

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.

Keywords

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

Notes

Funding

This research was funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554 to C.K., by the US National Science Foundation (CCF-1256087, CCF-1319998) and by the US National Institute of Health (R01HG007104, R01GM122935).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Computational Biology Department, School of Computer ScienceCarnegie Mellon UniversityPittsburghUSA

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