HLA Typing pp 193-201 | Cite as

PHLAT: Inference of High-Resolution HLA Types from RNA and Whole Exome Sequencing

  • Yu BaiEmail author
  • David Wang
  • Wen Fury
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)


Inferring HLA types from genome-wide sequencing data has gained growing attention with the development of new cost-efficient sequencing technologies and the increasing need to integrate HLA types with transcriptomic or other genomic information for insights into immune-mediated diseases, vaccination, and cancer immunotherapy. PHLAT is a computational tool designed for high-resolution (4-digit) typing of the major class I and class II HLA genes using RNAseq or exome sequencing data as input. We illustrate here how PHLAT can be installed, configured, and executed. This document also provides guidance for how to read and interpret the output results. Finally, the best practices of using PHLAT are also discussed.


RNAseq Whole exome sequencing Transcriptome sequencing Human leukocyte antigen High-resolution HLA typing Hematopoietic transplant Organ transplant HLA matching Autoimmune Immuno-oncology Cancer vaccine Bayesian inference 


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

Authors and Affiliations

  1. 1.Regeneron PharmaceuticalsTarrytownUSA
  2. 2.Department of Biological Statistics and Computational BiologyCornell UniversityIthacaUSA

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