Using exome and amplicon-based sequencing data for high-resolution HLA typing with ATHLATES

Chang Liu, Xiao Yang

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

2 Scopus citations

Abstract

ATHLATES (accurate typing of human leukocyte antigen through exome sequencing) was originally developed to analyze whole-exome sequencing (exome-seq) data from the Illumina platform and to predict the HLA genotype at 2-field or higher resolution. HLA locus-specific reads are first collected by stringent read mapping to the IMGT/HLA database. ATHLATES then performs read assembly, candidate allele identification, and genotype inference. Here, we describe the protocol of using ATHLATES for the above purpose and expand the application to analyze targeted sequencing data using amplicons of full HLA genes.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages203-213
Number of pages11
DOIs
StatePublished - 2018

Publication series

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

Keywords

  • Amplicons
  • HLA typing
  • Human leukocyte antigen (HLA)
  • Polymerase chain reaction (PCR)
  • Targeted sequencing
  • Whole-exome sequencing (exome-seq)

Fingerprint

Dive into the research topics of 'Using exome and amplicon-based sequencing data for high-resolution HLA typing with ATHLATES'. Together they form a unique fingerprint.

Cite this