HLA Typing pp 203-213 | Cite as

Using Exome and Amplicon-Based Sequencing Data for High-Resolution HLA Typing with ATHLATES

  • Chang LiuEmail author
  • Xiao Yang
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)


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.


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


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

Authors and Affiliations

  1. 1.Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUSA
  2. 2.Grail, Inc.Menlo ParkUSA

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