Needles in the Haystack: Identifying individuals present in pooled genomic data

Rosemary Braun, William Rowe, Carl Schaefer, Jinghui Zhang, Kenneth Buetow

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

Recent publications have described and applied a novel metric that quantifies the genetic distance of an individual with respect to two population samples, and have suggested that the metric makes it possible to infer the presence of an individual of known genotype in a sample for which only the marginal allele frequencies are known. However, the assumptions, limitations, and utility of this metric remained incompletely characterized. Here we present empirical tests of the method using publicly accessible genotypes, as well as analytical investigations of the method's strengths and limitations. The results reveal that the null distribution is sensitive to the underlying assumptions, making it difficult to accurately calibrate thresholds for classifying an individual as a member of the population samples. As a result, the falsepositive rates obtained in practice are considerably higher than previously believed. However, despite the metric's inadequacies for identifying the presence of an individual in a sample, our results suggest potential avenues for future research on tuning this method to problems of ancestry inference or disease prediction. By revealing both the strengths and limitations of the proposed method, we hope to elucidate situations in which this distance metric may be used in an appropriate manner. We also discuss the implications of our findings in forensics applications and in the protection of GWAS participant privacy.

Original languageEnglish (US)
Article numbere1000668
JournalPLoS Genetics
Volume5
Issue number10
DOIs
StatePublished - Oct 2009
Externally publishedYes

Fingerprint

Needles
genomics
genotype
Genotype
sampling
Privacy
Genome-Wide Association Study
methodology
Gene Frequency
ancestry
Population
gene frequency
genetic distance
allele
prediction
method
testing

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Needles in the Haystack : Identifying individuals present in pooled genomic data. / Braun, Rosemary; Rowe, William; Schaefer, Carl; Zhang, Jinghui; Buetow, Kenneth.

In: PLoS Genetics, Vol. 5, No. 10, e1000668, 10.2009.

Research output: Contribution to journalArticle

Braun, Rosemary ; Rowe, William ; Schaefer, Carl ; Zhang, Jinghui ; Buetow, Kenneth. / Needles in the Haystack : Identifying individuals present in pooled genomic data. In: PLoS Genetics. 2009 ; Vol. 5, No. 10.
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