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
Part of the Methods in Molecular Biology book series (MIMB, volume 1802)


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.


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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