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Research Article

Identification of individuals by trait prediction using whole-genome sequencing data

Christoph Lippert, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arikan, Alena Harley, Axel Bernal, Peter Garst, Victor Lavrenko, Ken Yocum, Theodore Wong, Mingfu Zhu, Wen-Yun Yang, Chris Chang, Tim Lu, Charlie W. H. Lee, Barry Hicks, Smriti Ramakrishnan, Haibao Tang, Chao Xie, Jason Piper, Suzanne Brewerton, Yaron Turpaz, View ORCID ProfileAmalio Telenti, Rhonda K. Roby, Franz J. Och, and J. Craig Venter
  1. aHuman Longevity, Inc., Mountain View, CA 94303;
  2. bHuman Longevity, Inc., San Diego, CA 92121;
  3. cHuman Longevity Singapore, Pte. Ltd., Singapore 138542;
  4. dJ. Craig Venter Institute, La Jolla, CA 92037

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PNAS first published September 5, 2017; https://doi.org/10.1073/pnas.1711125114
Christoph Lippert
aHuman Longevity, Inc., Mountain View, CA 94303;
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  • For correspondence: jcventer@jcvi.org clippert@humanlongevity.com
Riccardo Sabatini
aHuman Longevity, Inc., Mountain View, CA 94303;
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M. Cyrus Maher
aHuman Longevity, Inc., Mountain View, CA 94303;
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Eun Yong Kang
aHuman Longevity, Inc., Mountain View, CA 94303;
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Seunghak Lee
aHuman Longevity, Inc., Mountain View, CA 94303;
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Okan Arikan
aHuman Longevity, Inc., Mountain View, CA 94303;
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Alena Harley
aHuman Longevity, Inc., Mountain View, CA 94303;
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Axel Bernal
aHuman Longevity, Inc., Mountain View, CA 94303;
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Peter Garst
aHuman Longevity, Inc., Mountain View, CA 94303;
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Victor Lavrenko
aHuman Longevity, Inc., Mountain View, CA 94303;
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Ken Yocum
aHuman Longevity, Inc., Mountain View, CA 94303;
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Theodore Wong
aHuman Longevity, Inc., Mountain View, CA 94303;
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Mingfu Zhu
aHuman Longevity, Inc., Mountain View, CA 94303;
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Wen-Yun Yang
aHuman Longevity, Inc., Mountain View, CA 94303;
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Chris Chang
aHuman Longevity, Inc., Mountain View, CA 94303;
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Tim Lu
bHuman Longevity, Inc., San Diego, CA 92121;
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Charlie W. H. Lee
bHuman Longevity, Inc., San Diego, CA 92121;
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Barry Hicks
aHuman Longevity, Inc., Mountain View, CA 94303;
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Smriti Ramakrishnan
aHuman Longevity, Inc., Mountain View, CA 94303;
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Haibao Tang
aHuman Longevity, Inc., Mountain View, CA 94303;
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Chao Xie
cHuman Longevity Singapore, Pte. Ltd., Singapore 138542;
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Jason Piper
cHuman Longevity Singapore, Pte. Ltd., Singapore 138542;
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Suzanne Brewerton
cHuman Longevity Singapore, Pte. Ltd., Singapore 138542;
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Yaron Turpaz
bHuman Longevity, Inc., San Diego, CA 92121;
cHuman Longevity Singapore, Pte. Ltd., Singapore 138542;
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Amalio Telenti
bHuman Longevity, Inc., San Diego, CA 92121;
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  • ORCID record for Amalio Telenti
Rhonda K. Roby
bHuman Longevity, Inc., San Diego, CA 92121;
dJ. Craig Venter Institute, La Jolla, CA 92037
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Franz J. Och
aHuman Longevity, Inc., Mountain View, CA 94303;
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J. Craig Venter
bHuman Longevity, Inc., San Diego, CA 92121;
dJ. Craig Venter Institute, La Jolla, CA 92037
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  • For correspondence: jcventer@jcvi.org clippert@humanlongevity.com
  1. Contributed by J. Craig Venter, June 28, 2017 (sent for review February 7, 2017; reviewed by Jean-Pierre Hubaux, Bradley Adam Malin, and Effy Vayena)

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Significance

By associating deidentified genomic data with phenotypic measurements of the contributor, this work challenges current conceptions of genomic privacy. It has significant ethical and legal implications on personal privacy, the adequacy of informed consent, the viability and value of deidentification of data, the potential for police profiling, and more. We invite commentary and deliberation on the implications of these findings for research in genomics, investigatory practices, and the broader legal and ethical implications for society. Although some scholars and commentators have addressed the implications of DNA phenotyping, this work suggests that a deeper analysis is warranted.

Abstract

Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.

  • genomic privacy
  • genome sequencing
  • DNA phenotyping
  • phenotype prediction
  • reidentification

Footnotes

  • ↵1To whom correspondence may be addressed. Email: jcventer{at}jcvi.org or clippert{at}humanlongevity.com.
  • ↵2Present address: Forensic Biology Unit, Alameda County Sheriff's Office, Oakland, CA 94605.

  • Author contributions: C.L., M.C.M., F.J.O., and J.C.V. designed research; C.L., M.C.M., V.L., and F.J.O. devised the method for reidentification; C.L., M.C.M., and C.X. performed research; C.L., R.S., M.C.M., E.Y.K., O.A., A.H., A.B., P.G., V.L., K.Y., T.W., M.Z., W.-Y.Y., C.C., T.L., C.W.H.L., B.H., C.X., J.P., S.B., and Y.T. contributed new reagents/analytic tools; C.L., R.S., M.C.M., E.Y.K., O.A., A.H., A.B., P.G., K.Y., T.W., M.Z., W.-Y.Y., T.L., C.W.H.L., and J.P. contributed phenotype prediction models; C.L., R.S., M.C.M., E.Y.K., S.L., O.A., A.H., A.B., P.G., V.L., K.Y., T.W., C.C., S.R., H.T., C.X., R.K.R., and F.J.O. analyzed data; C.L., F.J.O., and J.C.V. supervised the data analysis; A.T., R.K.R., and J.C.V. supervised the study cohort; C.L., M.C.M., A.T., and R.K.R. wrote the paper; and C.L., M.C.M., E.Y.K., S.L., O.A., A.H., A.B., P.G., K.Y., T.W., M.Z., W.-Y.Y., and R.K.R. wrote the supporting information.

  • Reviewers: J.-P.H., Ecole Polytechnique Fédérale de Lausanne; B.A.M., Vanderbilt University; and E.V., University of Zurich.

  • Conflict of interest statement: The authors are employees of and own equity in Human Longevity Inc.

  • Data deposition: Access to genome data is possible through a managed access agreement (www.hli-opendata.com/docs/HLIDataAccessAgreement061617.docx).

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1711125114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Genomics of physical traits
Christoph Lippert, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arikan, Alena Harley, Axel Bernal, Peter Garst, Victor Lavrenko, Ken Yocum, Theodore Wong, Mingfu Zhu, Wen-Yun Yang, Chris Chang, Tim Lu, Charlie W. H. Lee, Barry Hicks, Smriti Ramakrishnan, Haibao Tang, Chao Xie, Jason Piper, Suzanne Brewerton, Yaron Turpaz, Amalio Telenti, Rhonda K. Roby, Franz J. Och, J. Craig Venter
Proceedings of the National Academy of Sciences Sep 2017, 201711125; DOI: 10.1073/pnas.1711125114

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Genomics of physical traits
Christoph Lippert, Riccardo Sabatini, M. Cyrus Maher, Eun Yong Kang, Seunghak Lee, Okan Arikan, Alena Harley, Axel Bernal, Peter Garst, Victor Lavrenko, Ken Yocum, Theodore Wong, Mingfu Zhu, Wen-Yun Yang, Chris Chang, Tim Lu, Charlie W. H. Lee, Barry Hicks, Smriti Ramakrishnan, Haibao Tang, Chao Xie, Jason Piper, Suzanne Brewerton, Yaron Turpaz, Amalio Telenti, Rhonda K. Roby, Franz J. Och, J. Craig Venter
Proceedings of the National Academy of Sciences Sep 2017, 201711125; DOI: 10.1073/pnas.1711125114
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