Re-identification of genomic data using long range familial searches

Abstract

Consumer genomics databases reached the scale of millions of individuals. Recently, law enforcement investigators have started to exploit some of these databases to find distant familial relatives, which can lead to a complete re-identification. Here, we leveraged genomic data of 600,000 individuals tested with consumer genomics to investigate the power of such long-range familial searches. We project that half of the searches with European-descent individuals will result with a third cousin or closer match and will provide a search space small enough to permit re-identification using common demographic identifiers. Moreover, in the near future, virtually any European-descent US person could be implicated by this technique. We propose a potential mitigation strategy based on cryptographic signature that can resolve the issue and discuss policy implications to human subject research.. CC-BY-NC-ND 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/350231 doi: bioRxiv preprint first posted online Jun. 18, 2018; 2 Main TextConsumer genomics has gained tremendous popularity in the last few years 1 . As of today, more than 15 million people have taken direct-to-consumer (DTC) autosomal genetic tests for self-curiosity, with about 7 million kits sold in 2017 alone 2 . Nearly all major DTC providers use dense genotyping arrays that probe ~700,000 SNPs in the genome of each participant and most DTC providers allow participants to download their raw genotype files in a textual format. This option has led to the advent of third-party services, such as DNA.Land and GEDmatch that allow participants to upload their raw genetic data in order to get further analysis (Table 1) 3 .DNA matching is one of the most popular features in consumer genomics. This feature harnesses the dense autosomal genotypes to find identity-by-descent (IBD) segments, which are indicative of a shared ancestor. Previous studies have shown that this technique has virtually perfect accuracy to find close relatives and good accuracy to find distant relatives, such as 2 nd or 3 rd cousins 4-6 , providing the option for long range familial searches. This feature has led to many "success stories" by the genetic genealogy community, including the reunions of Holocaust survivors with relatives when they thought they had no living family left, reunions of adoptees with their biological families, and investigations of potential abductions of babies 7 .From a technical and regulatory perspective, the consumer genomics tools are far more powerful for familial searches than traditional forensic techniques. Forensic familial searches use a small set of ~20 autosomal STR regions that were standardized for traditional fingerprinting 8,9 . This set is not sufficient to detect IBD matches and instead forensic techniques have to rely on partial allelic matches as a mean...

Researcher Knowledge, Attitudes, and Communication Practices for Genomic Data Sharing

“…In one study, participants ranked reidentification as a top risk of data sharing (Oliver et al, 2012). In the present study, most PIs also reported concerns about the identifiability of certain data, reflecting literature showing this possibility (Erlich et al, 2018; Erlich & Narayanan, 2014; Shringarpure & Bustamante, 2015). However, most RCs did not believe that re-identification was a risk for participants or believed that the risk was similar to the risks of sharing other types of digital data.…”

“…However, most RCs did not believe that re-identification was a risk for participants or believed that the risk was similar to the risks of sharing other types of digital data. This finding suggests a discordance between RC perceptions of risks associated with data sharing and those risks that have been published in the literature, particularly regarding the potential for participant re-identification (Erlich et al, 2018;Erlich & Narayanan, 2014;Shringarpure & Bustamante, 2015). This difference between the attitudes of PIs and RCs, and between RC attitudes and identified potential risks, could have a major effect on the consent process, as RCs are often directly involved in explaining and answering questions about risks and benefits of data sharing with study participants, while PIs are ultimately responsible for compliance with funder requirements.…”

“…Even among individuals who are willing to participate in research studies and clinical trials, most express privacy concerns specifically related to the sharing of genetic data (Burstein et al, 2014; Mello et al, 2018; Trinidad et al, 2010). Participants have also cited the possibility of reidentification as a major concern (Mello et al, 2018; Milne et al, 2019), which has been shown to be possible by combining data (Erlich et al, 2018). Other studies have reported on specific methods through which individuals can be identified using genomic data (Shringarpure & Bustamante, 2015).…”

Big Data in Medicine, the Present and Hopefully the Future

“…In fact, within the frame of this interpretation of the GDPR, the individual may not have even the option to “opt-out” (24). In fact, the exploitation of genealogy databases, or more broadly consumer genomics databases, allows to identify up to 60%, and soon nearly any US-individual of European- descent in the near future, using demographic identifiers, including research participants of public sequencing projects (25). These approaches have been recently successfully used by law enforcement agencies to identify criminals, posing significant ethical and legal challenges (26).…”

Forensic inference of biogeographical ancestry from genotype: The Genetic Ancestry Lab

“…Because of recombination and mutation events, inherited, identical sequences of DNA (haplotypes) become shorter with increasing numbers of generations. These identical‐by‐decent segments can be used to infer BGA and this is the method used by most commercial genealogy service providers (Erlich, Shor, Carmi, & Pe'er, ; Erlich, Shor, Pe'er, & Carmi, ). The forensic community has instead focused on shorter genetic sequences, most often preferring the shortest possible markers of all: SNPs.…”