Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.

@article{Biedrzycka2016TestingGS,
  title={Testing genotyping strategies for ultra-deep sequencing of a co-amplifying gene family: MHC class I in a passerine bird.},
  author={Aleksandra Biedrzycka and Alvaro San Sebasti{\'a}n and Magdalena Migalska and Helena Westerdahl and Jacek Radwan},
  journal={Molecular ecology resources},
  year={2016},
  volume={17 4},
  pages={
          642-655
        }
}
Characterization of highly duplicated genes, such as genes of the major histocompatibility complex (MHC), where multiple loci often co-amplify, has until recently been hindered by insufficient read depths per amplicon. Here, we used ultra-deep Illumina sequencing to resolve genotypes at exon 3 of MHC class I genes in the sedge warbler (Acrocephalus schoenobaenus). We sequenced 24 individuals in two replicates and used this data, as well as a simulated data set, to test the effect of amplicon… CONTINUE READING
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