Cited by 1,221Forensic and Genetic ResearchGenetic diversity and population structureGenetic Associations and Epidemiology

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

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Homer, Nils, Szelinger, Szabolcs, Redman, Margot, Duggan, David, Tembe, Waibhav, Muehling, Jill, Pearson, John V., Stephan, Dietrich A. +2 more·2008·PLoS Genetics

Abstract

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixture, then show, through simulations, the limits associated with our method, and finally demonstrate experimentally the identification of the presence of genomic DNA of specific individuals within a series of highly complex genomic mixtures, including mixtures where an individual contributes less than 0.1% of the total genomic DNA. These findings shift the perceived utility of SNPs for identifying individual trace contributors within a forensics mixture, and suggest future research efforts into assessing the viability of previously sub-optimal DNA sources due to sample contamination. These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed.

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  • Genomic data can never be truly anonymized, and a steady stream of provocative studies has demonstrated that it is possible to discover the identities of individuals whose genomic data had otherwise been considered deidentified.

    “However, this rapidly evolving research arena has been accompanied by equally rapid confirmation that genomic data can never be truly anonymized. A steady stream of provocative studies (51, 62, 68, 122) has demonstrated that it is possible to discover the identities of individuals whose genomic data had otherwise been considered deidentified.”

    From Lessons from HeLa Cells: The Ethics and Policy of Biospecimens (2016) · cites this paper as [62]

    The Discussion shows that summary-level statistics, used in part to mask individual-level data, can reveal whether a specific person is in a study. That supports a privacy risk, but the method tests for the presence of a person whose genotype is already known; it does not demonstrate discovering an unknown person's identity or establish that genomic data can never be anonymized. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

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Research works printed but not linked: 1

  1. [10]Goodwin W Linacre A Vanezis P 1999 The use of mitochondrial DNA and short tandem repeat typing in the identification of air crash victims. Electrophoresis 20 1707 1711 10435435

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Authors
Homer, N., Szelinger, S., Redman, M., Duggan, D., Tembe, W., Muehling, J., Pearson, J. V., Stephan, D. A., Nelson, S. F., & Craig, D. W.
Affiliations
  • Translational Genomics Research Institute (US)
  • University of California, Los Angeles (US)
Corresponding author
Craig, David W.
Venue
PLoS Genetics
Published
2008-08-29
Volume
4
Issue
8
Pages
e1000167
ISSN
  • 1553-7390 (ISSN-L)
  • 1553-7404
OpenAlex
W2040228409
Cited by
1,221
References
21
Citations by year
2026: 24 · 2025: 42 · 2024: 54 · 2023: 71 · 2022: 81 · 2021: 76 · 2020: 89 · 2019: 103 · 2018: 87 · 2017: 81 · 2016: 65 · 2015: 59 · 2014: 79 · 2013: 62 · 2012: 63
FWCI
34.85
Type
journal article
Language
en
Open access
Locations
  • PLoS Genetics (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Wellcome Trust (076113)
  • Translational Genomics Research Institute
  • National Institutes of Health
  • National Heart, Lung, and Blood Institute (U01HL086528)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Keywords
DNA mixture analysis, single nucleotide polymorphisms, forensic DNA identification, sample contamination, genome-wide association study
MeSH terms
Computer Simulation, Genetics, Medical, Genotype, Humans, Genome, Human, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide

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