BeadChip genotyping is an efficient and scalable way of genotype resolution, with two inherent limitations: a necessity to decompose binary alleles and confinement to a predefined list of genotyped variants. These two limitations, however, do not prevent its usefulness for a variety of clinical and non-clinical applications [3]. Predefined nature of the variants to be tested makes BeadChip genotyping amenable to validation by either PCR (polymerase chain reaction), or Sanger sequencing which has been recently shown to have limited utility and erroneous behaviour in the validation of NGS variants [4]. A comparison of genotyping calls made by BeadChip and WGS/WES techniques may provide an insight into the possible nature of the discordant calls observed during genotyping quality control stage. Here we attempted to identify analytical issues leading to the discordance in genotyping calls made independently by WGS and BeadChip techniques.
