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Bayesian method to predict individual SNP genotypes from gene expression data

Nature Genetics volume 44, pages 603–608 (2012)Cite this article

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Abstract

RNA profiling can be used to capture the expression patterns of many genes that are associated with expression quantitative trait loci (eQTLs). Employing published putative cis eQTLs, we developed a Bayesian approach to predict SNP genotypes that is based only on RNA expression data. We show that predicted genotypes can accurately and uniquely identify individuals in large populations. When inferring genotypes from an expression data set using eQTLs of the same tissue type (but from an independent cohort), we were able to resolve 99% of the identities of individuals in the cohort at Padjusted ≤ 1 × 10−5. When eQTLs derived from one tissue were used to predict genotypes using expression data from a different tissue, the identities of 90% of the study subjects could be resolved at Padjusted ≤ 1 × 10−5. We discuss the implications of deriving genotypic information from RNA data deposited in the public domain.

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Figure 1: Accuracy of RNA-derived genotypes.

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Author information

Author notes

  1. Sangsoon Woo

    Present address: Present addresses: Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA, and Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,

  2. Eric E Schadt, Sangsoon Woo and Ke Hao: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, USA

    Eric E Schadt & Ke Hao

  2. Department of Biostatistics, University of Washington, Seattle, Washington, USA

    Sangsoon Woo

  3. Research Genetics, Rosetta Inpharmatics, Seattle, Washington, USA

    Ke Hao

Authors
  1. Eric E Schadt
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  2. Sangsoon Woo
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  3. Ke Hao
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Contributions

E.E.S., S.W. and K.H. designed the methods and experiments, and jointly analyzed the data sets. E.E.S. and K.H. wrote the manuscript.

Corresponding authors

Correspondence to Eric E Schadt or Ke Hao.

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Competing interests

The authors declare no competing financial interests.

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Supplementary Tables 1 and 2, Supplementary Figures 1–3 and Supplementary Note (PDF 274 kb)

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Schadt, E., Woo, S. & Hao, K. Bayesian method to predict individual SNP genotypes from gene expression data. Nat Genet 44, 603–608 (2012). https://doi.org/10.1038/ng.2248

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