HAPCAD: An open-source tool to detect PCR crossovers in next-generation sequencing generated HLA data

Human Immunology
Shana L McDevittJanelle A Noble

Abstract

Next-generation sequencing (NGS) based HLA genotyping can generate PCR artifacts corresponding to IMGT/HLA Database alleles, for which multiple examples have been observed, including sequence corresponding to the HLA-DRB1(∗)03:42 allele. Repeat genotyping of 131 samples, previously genotyped as DRB1(∗)03:01 homozygotes using probe-based methods, resulted in the heterozygous call DRB1(∗)03:01+DRB1(∗)03:42. The apparent rare DRB1(∗)03:42 allele is hypothesized to be a "hybrid amplicon" generated by PCR crossover, a process in which a partial PCR product denatures from its template, anneals to a different allele template, and extends to completion. Unlike most PCR crossover products, "hybrid amplicons" always corresponds to an IMGT/HLA Database allele, necessitating a case-by-case analysis of whether its occurrence reflects the actual allele or is simply the result of PCR crossover. The Hybrid Amplicon/PCR Crossover Artifact Detector (HAPCAD) program mimics jumping PCR in silico and flags allele sequences that may also be generated as hybrid amplicon.

References

Jul 24, 1998·Frontiers in Bioscience : a Journal and Virtual Library·G Andersson
Feb 9, 2012·Cold Spring Harbor Perspectives in Medicine·Janelle A Noble, Henry A Erlich
May 17, 2012·Proceedings of the National Academy of Sciences of the United States of America·Chunlin WangMichael Mindrinos
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Nov 22, 2014·Nucleic Acids Research·James RobinsonSteven G E Marsh

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Citations

Apr 12, 2016·Human Immunology·James RobinsonWolfgang Helmberg
Oct 13, 2017·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Liyuan LiZhao Wang
Feb 29, 2020·Transfusion Medicine and Hemotherapy : Offizielles Organ Der Deutschen Gesellschaft Fur̈ Transfusionsmedizin Und Immunham̈atologie·Daniel FürstChristof Weinstock

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