Genotype fingerprints enable fast and private comparison of genetic testing results for research and direct-to-consumer applications

As genetic testing expands out of the research laboratory into medical practice as well as the direct-to-consumer market, the efficiency with which the resulting genotype data can be compared between individuals is of increasing importance.\n\nWe present a method for summarizing personal genotypes, yielding genotype fingerprints that can be derived from any single nucleotide polymorphism (SNP)-based assay and readily compared to estimate relatedness. The resulting fingerprints remain comparable as chip designs evolve to higher marker densities. We demonstrate that they support applications including distinguishing genotypes of closely related individuals by relationship type, distinguishing closely related individuals from individuals from the same background population, identification of individuals in known background populations, and de novo identification of subpopulations within a large cohort in a high-throughput manner.\n\nAn important feature of genotype fingerprints is that, while fingerprints do not preserve anonymity, they summarize individual marker data in a way that prevents phenotype prediction. Genotype fingerprints are therefore well-suited to public sharing for ancestry determination purposes, without revealing personal health risk status.