Genotype Concordance and Polygenic Risk Score Estimation across Consumer Genetic Testing Data

The consumer genomics industry is steadily growing and delivering genetic information to over 10 million individuals. Yet, the implications of using data from different services remain unclear. We investigated the genotyped sites, concordance, and genetic risk estimation using data from three major consumer services. We found low overlap among reported genotyped sites (2.7% across all three). While there was a high concordance between overlapping sites of the two SNP-array services (99.6%), there was a lower concordance between them and a low-pass whole-genome service (73.0%). Finally, we demonstrated that the discrepancy resulted in distinct APOE genotypes and genetic risk scores of Alzheimers disease determined using these data. Our results demonstrate genotype results across consumer genomics platforms may lead to different genetic risk estimates, highlighting the need for careful quality control and interpretation.