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HLA Typing pp 249-273 | Cite as

AmpliSAS and AmpliHLA: Web Server Tools for MHC Typing of Non-Model Species and Human Using NGS Data

  • Alvaro Sebastian
  • Magdalena Migalska
  • Aleksandra Biedrzycka
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)

Abstract

AmpliSAS and AmpliHLA are web server tools for automatic genotyping of MHC genes from high-throughput sequencing data. AmpliSAS is designed specifically to analyze amplicon sequencing data from non-model species and it is able to perform de-novo genotyping without any previous knowledge of the reference alleles. AmpliHLA is a human-specific version, it performs HLA typing by comparing sequenced variants against human reference alleles from the IMGT/HLA database. Here we describe four genotyping protocols: the first two use amplicon sequencing data to genotype the MHC genes of a passerine bird and human respectively; the third and fourth present the HLA typing of a human cell line starting from RNA and exome sequencing data respectively.

Keywords

Bioinformatics Next-generation sequencing NGS Amplicon sequencing RNA-Seq WES WXS MHC HLA Genotyping Alleles Haplotypes IMGT AmpliSAS AmpliHLA 

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Copyright information

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

Authors and Affiliations

  • Alvaro Sebastian
    • 1
    • 2
    • 3
  • Magdalena Migalska
    • 3
  • Aleksandra Biedrzycka
    • 4
  1. 1.Sixth ResearcherPoznanPoland
  2. 2.Instituto Aragonés de Empleo (INAEM)ZaragozaSpain
  3. 3.Evolutionary Biology Group, Faculty of BiologyAdam Mickiewicz UniversityPoznanPoland
  4. 4.Institute of Nature ConservationPolish Academy of SciencesKrakówPoland

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