Identity inference of genomic data using long-range familial searches

Erlich, Yaniv; Shor, Tal; Pe’er, Itsik; Carmi, Shai

doi:10.1126/science.aau4832

Cited by 267 publications

(241 citation statements)

References 22 publications

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“…This material was originally posted on the Coop lab site on May 7th, 2018, soon after the reporting of the arrest of Joseph DeAngelo in the Golden State Killer case, one of the first high-profile uses of long-range familial search. Subsequently, Erlich et al (2018) published a detailed analysis in a large empirical dataset along with a theoretical analysis of a model similar to the one we use here, obtaining results broadly consistent with the ones presented here. Because Erlich and colleagues kindly cited this work when describing their model, we thought it would be appropriate to post this material in a venue where it is more easily cited.…”

Section: Notesupporting

confidence: 79%

How lucky was the genetic investigation in the Golden State Killer case?

Edge

Coop²

2019

Preprint

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Long-range forensic familial searching is a new method in forensic genetics. In long-range search, a sample of interest is genotyped at single-nucleotide polymorphism (SNP) markers, and the genotype is compared with a large database in order to find relatives. Here, we perform some simple calculations that explore the basic phenomena that govern long-range searching. Two opposing phenomenaone genealogical and one genetic-govern the success of the search in a database of a given size. As one considers more distant genealogical relationships, any target sample is likely to have more relatives-on average, one has more second cousins than first cousins, and so on. But more distant relatives are also harder to detect genetically. Starting with third cousins, there is an appreciable chance that a given genealogical relationship will not be detectable genetically. Given the balance of these genealogical and genetic phenomena and the size of databases currently queryable by law enforcement, it is likely that most people with substantial recent ancestry in the United States are accessible via long-range search.

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Section: Notesupporting

confidence: 79%

How lucky was the genetic investigation in the Golden State Killer case?

Edge

Coop²

2019

Preprint

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“…These entities generally offer some subset of their services at no charge to uploaders, which helps to grow their databases. Upload services have also been used by law enforcement, with the goal of identifying relatives of the source of a crime-scene sample (Erlich et al, 2018; Edge and Coop, 2019), prompting discussion about genetic privacy (Court, 2018; Ram et al, 2018; Kennett, 2019; Scudder et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Attacks on genetic privacy via uploads to genealogical databases

Edge

Coop

2019

Preprint

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7Direct-to-consumer (DTC) genetics services are increasingly popular for genetic genealogy, with 8 tens of millions of customers as of 2019. Several DTC genealogy services allow users to upload 9 their own genetic datasets in order to search for genetic relatives. A user and a target person in 10 the database are identified as genetic relatives if the user's uploaded genome shares one or more 11 sufficiently long segments in common with that of the target person-that is, if the two genomes 12 share one or more long regions identical by state (IBS). IBS matches reveal some information 13 about the genotypes of the target person, particularly if the chromosomal locations of IBS matches 14 are shared with the uploader. Here, we describe several methods by which an adversary who 15 wants to learn the genotypes of people in the database can do so by uploading multiple datasets. 16Depending on the methods used for IBS matching and the information about IBS segments 17 returned to the user, substantial information about users' genotypes can be revealed with a few 18 hundred uploaded datasets. For example, using a method we call IBS tiling, we estimate that an 19 adversary who uploads approximately 900 publicly available genomes could recover at least one 20 allele at SNP sites across up to 82% of the genome of a median person of European ancestries. 21In databases that detect IBS segments using unphased genotypes, approximately 100 uploads of 22 falsified datasets can reveal enough genetic information to allow accurate genome-wide imputation 23 of every person in the database. We provide simple-to-implement suggestions that will prevent the 24 exploits we describe and discuss our results in light of recent trends in genetic privacy, including 25 the recent use of uploads to DTC genetic genealogy services by law enforcement. 26(Regalado, 2019). One of the major applications of DTC genetics has been genetic genealogy. 31Customers of companies such as 23andMe and Ancestry, once they are genotyped, can view a list 32 of other customers who are likely to be genetic relatives. These putative relatives' full names are 33 often given, and sometimes contact details are given as well. Such genealogical matching services 34 are of interest to people who want to find distant genetic relatives to extend their family tree, and 35 can be particularly useful to people who otherwise may not have information about their genetic 36 relatives, such as adoptees or the biological children of sperm donors. Several genetic genealogy 37 services-including GEDmatch, MyHeritage, FamilyTreeDNA, and LivingDNA (Table 1)-allow 38 users to upload their own genetic data if they have been genotyped by another company. These 39 entities generally offer some subset of their services at no charge to uploaders, which helps to 40 grow their databases. Upload services have also been used by law enforcement, with the goal of 41 identifying relatives of the source of a crime-scene sample (Erlich et al., 2018; Edge and Coop, 42 2019), prompting discussion abo...

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“…Previously the concerns have been focused on the potential discrimination by employers and health insurance companies against carriers of certain mutations 13,14 . Recently, a new concern 15 has been raised regarding law enforcement's access to biobank scale genomic databases for solving criminal cases by connecting remote relatives genetically. Our study demonstrated that those two concerns are indeed two faces of the same coin as one's genome can be largely reconstructed by the genomes of his/her genetic cousins traditionally thought as "unrelated".…”

Section: Discussionmentioning

confidence: 99%

Personalized genealogical history inferred from biobank-scale IBD segments

Naseri

Tang

Geng

et al. 2019

Preprint

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When modern biobanks collect genotype information for a significant fraction of a population, dense genetic connections of a person can be traced using identity by descent (IBD) segments. These connections offer opportunities to characterize individuals in the context of the underlying populations. Here, we conducted an individual-centric analysis of IBDs among the UK Biobank participants that represent 0.7% of the UK population. On average, one UK individual shares IBDs over 5 cM with 14,000 UK Biobank participants, which we refer to as "cousins". Using these segments, approximately 80% of a person's genome can be reconstructed. Also, using changes of cousin counts sharing IBDs at different lengths, we identified a group, potentially British Jews, who has a distinct pattern of familial expansion history. Finally, using the enrichment of cousins in one's neighborhood, we identified regional variations of personal preference favoring living closer to one's extended families. In summary, our analysis revealed genetic makeup, personal genealogical history, and social behaviors at population scale, opening possibilities for further studies of individual's genetic connections in biobank data.

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Identity inference of genomic data using long-range familial searches

Cited by 267 publications

References 22 publications

How lucky was the genetic investigation in the Golden State Killer case?

How lucky was the genetic investigation in the Golden State Killer case?

Attacks on genetic privacy via uploads to genealogical databases

Personalized genealogical history inferred from biobank-scale IBD segments

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