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

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.

Hybridization with mountain hares increases the functional allelic repertoire in brown hares

“…PCR products were then purified, and after estimation of amplicon concentrations, all samples were normalized, pooled and sent to the Microsynth (AG) for sequencing on an Illumina Miseq as 250 bp paired-end. Initial amplicon data processing was achieved as outlined in Biedrzycka et al 70 and Sebastian et al 71 using the different amplicon sequencing analysis tools available at: http://evobiolab.biol.amu.edu.pl/amplisat/ . Allele calls for the low polymorphism loci ( TLR2 and SDHa ) were validated via Sanger sequencing in both directions, using the same primers as for their amplification.…”

The best of both worlds: Shortcutting evolution through adaptive hybridization in hares

“…PCR products were then puri ed, and after estimation of amplicon concentrations, all samples were normalized, pooled and sent to the Microsynth (AG) for sequencing on an Illumina Miseq as 250 bp paired-end. Initial amplicon data processing was achieved as outlined in Biedrzycka et al 61 and Sebastian et al 62 using the different amplicon sequencing analysis tools available at: http://evobiolab.biol.amu.edu.pl/amplisat/. Allele calls for the low polymorphism loci (TLR2 and SDHa) were validated via Sanger sequencing in both directions, using the same primers as for their ampli cation.…”