Critical review of NGS analyses for de novo genotyping multigene families

The authors use MHC genes as an example, but these analyses may also be relevant for following alleles across homeologs.


They suggest “ultra-deep” sequencing:

“An alternative approach that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. “


Critical review of NGS analyses for de novo genotyping multigene families

Jackie Lighten, Cock van Oosterhout, and Paul Bentzen

DOI: 10.1111/mec.12843