Attacks on genetic privacy via uploads to genealogical databases

Abstract

Direct-to-consumer (DTC) genetics services are increasingly popular for genetic genealogy, with tens of millions of customers as of 2019. Several DTC genealogy services allow users to upload their own genetic datasets in order to search for genetic relatives. A user and a target person in the database are identified as genetic relatives if the users uploaded genome shares one or more sufficiently long segments in common with that of the target person--that is, if the two genomes share one or more long regions identical by state (IBS). IBS matches reveal some information about the genotypes of the target person, particularly if the chromosomal locations of IBS matches are shared with the uploader. Here, we describe several methods by which an adversary who wants to learn the genotypes of people in the database can do so by uploading multiple datasets. Depending on the methods used for IBS matching and the information about IBS segments returned to the user, substantial information about users genotypes can be revealed with a few hundred uploaded datasets. For example, using a method we call IBS tiling, we estimate that an adversary who uploads approximately 900 publicly available genomes could recover at least one allele at SNP sites across up to 82% of the genome of a median person of European ancestries. In databases that detect IBS segments using unphased genotypes, approximately 100 uploads of falsified datasets can reveal enough genetic information to allow accurate genome-wide imputation of every person in the database. Different DTC services use different methods for identifying and reporting IBS segments, leading to differences in vulnerability to the attacks we describe. We provide a proof-of-concept demonstration that the GEDmatch database in particular uses unphased genotypes to detect IBS and is vulnerable to genotypes being revealed by artificial datasets. We suggest simple-to-implement suggestions that will prevent the exploits we describe and discuss our results in light of recent trends in genetic privacy, including the recent use of uploads to DTC genetic genealogy services by law enforcement.