Template‐specific optimization of NGS genotyping pipelines reveals allele‐specific variation in MHC gene expression

Author:

Efstratiou Artemis12ORCID,Gaigher Arnaud123ORCID,Künzel Sven4,Teles Ana125,Lenz Tobias L.12

Affiliation:

1. Research Unit for Evolutionary Immunogenomics, Department of Biology University of Hamburg Hamburg Germany

2. Research Group for Evolutionary Immunogenomics Max Planck Institute for Evolutionary Biology Plön Germany

3. CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources University of Porto Vairão Portugal

4. Department of Evolutionary Genetics Max Planck Institute for Evolutionary Biology Plön Germany

5. Department of Evolutionary Ecology Max Planck Institute for Evolutionary Biology Plön Germany

Abstract

AbstractUsing high‐throughput sequencing for precise genotyping of multi‐locus gene families, such as the major histocompatibility complex (MHC), remains challenging, due to the complexity of the data and difficulties in distinguishing genuine from erroneous variants. Several dedicated genotyping pipelines for data from high‐throughput sequencing, such as next‐generation sequencing (NGS), have been developed to tackle the ensuing risk of artificially inflated diversity. Here, we thoroughly assess three such multi‐locus genotyping pipelines for NGS data, the DOC method, AmpliSAS and ACACIA, using MHC class IIβ data sets of three‐spined stickleback gDNA, cDNA and “artificial” plasmid samples with known allelic diversity. We show that genotyping of gDNA and plasmid samples at optimal pipeline parameters was highly accurate and reproducible across methods. However, for cDNA data, the gDNA‐optimal parameter configuration yielded decreased overall genotyping precision and consistency between pipelines. Further adjustments of key clustering parameters were required tο account for higher error rates and larger variation in sequencing depth per allele, highlighting the importance of template‐specific pipeline optimization for reliable genotyping of multi‐locus gene families. Through accurate paired gDNA‐cDNA typing and MHC‐II haplotype inference, we show that MHC‐II allele‐specific expression levels correlate negatively with allele number across haplotypes. Lastly, sibship‐assisted cDNA‐typing of MHC‐I revealed novel variants linked in haplotype blocks, and a higher‐than‐previously‐reported individual MHC‐I allelic diversity. In conclusion, we provide novel genotyping protocols for the three‐spined stickleback MHC‐I and ‐II genes, and evaluate the performance of popular NGS‐genotyping pipelines. We also show that fine‐tuned genotyping of paired gDNA‐cDNA samples facilitates amplification bias‐corrected MHC allele expression analysis.

Funder

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

Deutsche Forschungsgemeinschaft

Publisher

Wiley

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