Statistical Detection of Relatives Typed with Disjoint Forensic and Biomedical Loci

Kim, Jaehee; Edge, Michael D.; Algee‐Hewitt, Bridget F. B.; Li, Jun Z.; Rosenberg, Noah A.

doi:10.1016/j.cell.2018.09.008

Cited by 40 publications

(64 citation statements)

References 36 publications

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“…The IBS-based privacy attacks we describe here add to a growing set of threats to genetic privacy (Homer et al, 2008; Nyholt et al, 2009; Im et al, 2012; Gymrek et al, 2013; Humbert et al, 2015; Shringarpure and Bustamante, 2015; Edge et al, 2017; Ayday and Humbert, 2017; Kim et al, 2018; Erlich et al, 2018). A person’s genotype includes sensitive health information that might be used for discrimination, particularly as our ability to genetically predict traits and disease predispositions will likely improve over the coming years.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

confidence: 99%

Attacks on genetic privacy via uploads to genealogical databases

Edge

Coop

2019

Preprint

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“…However, with improved technology and time, this obstacle was overcome. Scientists developed informatic tools to interpret STR repeat lengths from genome-wide SNP haplotype data (6,44) and eventually were able to reconstitute STR profiles of an individual from biomedical data, at least with some degree of probability (64). Now it is conceivable that if crime scene evidence samples are too minute for SNP genotyping or have been consumed, destroyed, or lost, an investigator could hypothesize SNP haplotypes based on the existing STR DNA data (27).…”

Section: Likelihood Of Predicting Short Tandem Repeat Genotypes From Single-nucleotide Polymorphism Haplotypesmentioning

confidence: 99%

Pedigrees and Perpetrators: Uses of DNA and Genealogy in Forensic Investigations

Katsanis

2020

Annu. Rev. Genom. Hum. Genet.

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In the past few years, cases with DNA evidence that could not be solved with direct matches in DNA databases have benefited from comparing single-nucleotide polymorphism data with private and public genomic databases. Using a combination of genome comparisons and traditional genealogical research, investigators can triangulate distant relatives to the contributor of DNA data from a crime scene, ultimately identifying perpetrators of violent crimes. This approach has also been successful in identifying unknown deceased persons and perpetrators of lesser crimes. Such advances are bringing into focus ethical questions on how much access to DNA databases should be granted to law enforcement and how best to empower public genome contributors with control over their data. The necessary policies will take time to develop but can be informed by reflection on the familial searching policies developed for searches of the federal DNA database and considerations of the anonymity and privacy interests of civilians. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 21 is August 31, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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“…Previously findings of autosomal chromosomes indicate that some forensically useful marker sets might bear substantial ancestry information (3), indicating a significant connection between genes and geography (4). Besides, potential matches for two kinds of distinct genetic markers were reported, such as Combined DNA Index System (CODIS) profile and single nucleotide polymorphism (SNP) data, making it possible to link a CODIS profile to a whole-genome SNP profile (5)(6)(7). For Y chromosomes, the correlation of surnames and male-specific region markers in Y chromosome is vital (8,9).…”

Section: Introductionmentioning

confidence: 99%

YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

Song

Zhao

et al. 2021

Preprint

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Human Y chromosome reflects the evolutionary process of males. Male lineage tracing by Y chromosome is of great use in evolutionary, forensic, and anthropological studies when male samples exist or especially when the biological sample is a mixture of male and female individuals. Identifying the male lineage based on the specific distribution of Y haplogroups narrows down the investigation scope. Integrating previously published datasets with genotypes of Y chromosome short tandem repeats (Y-STRs) and high-resolution haplogroups (122 haplogroups in total), we developed YHP (Y Haplogroup Predictor), an open-access and userfriendly software package to predict haplogroups, compare the similarity, and conduct mismatch analysis of samples with Y-STR profiles. The software is available at Github (https://github.com/cissy123/YHP-Y-Haplogroup-Predictor-).Author SummaryFamilial searching has been used in forensic, anthropologic, and personalized scenarios. Software packages have been developed to assist in male familial searching, such as predicting Y-SNP haplogroups by Y-STRs. However, these software packages, in general, achieve this goal with a rough resolution. In this study, we developed a software package to conduct high-resolution haplogroup inference to help familial searching and at the same time reduce the cost, since it does not require tiresome Y-SNP sequencing.

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Statistical Detection of Relatives Typed with Disjoint Forensic and Biomedical Loci

Cited by 40 publications

References 36 publications

Attacks on genetic privacy via uploads to genealogical databases

Attacks on genetic privacy via uploads to genealogical databases

Pedigrees and Perpetrators: Uses of DNA and Genealogy in Forensic Investigations

YHP: Y-chromosome Haplogroup Predictor for predicting male lineages based on Y-STRs

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