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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, Amalio Telenti, Rhonda K. Roby, Franz J. Och, and J. Craig Venter
PNAS September 19, 2017 114 (38) 10166-10171; published ahead of print 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.orgclippert@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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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.orgclippert@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)

This article has a correction. Please see:

  • Correction for Lippert et al., Identification of individuals by trait prediction using whole-genome sequencing data
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Online Impact

 

Article Information

vol. 114 no. 38 10166-10171
DOI: 
https://doi.org/10.1073/pnas.1711125114
PubMed: 
28874526

Published By: 
National Academy of Sciences
Print ISSN: 
0027-8424
Online ISSN: 
1091-6490
History: 
  • Published in issue September 19, 2017.
  • Published first September 5, 2017.

Copyright & Usage: 
Freely available online through the PNAS open access option.

Author Information

  1. Christoph Lipperta,1,
  2. Riccardo Sabatinia,
  3. M. Cyrus Mahera,
  4. Eun Yong Kanga,
  5. Seunghak Leea,
  6. Okan Arikana,
  7. Alena Harleya,
  8. Axel Bernala,
  9. Peter Garsta,
  10. Victor Lavrenkoa,
  11. Ken Yocuma,
  12. Theodore Wonga,
  13. Mingfu Zhua,
  14. Wen-Yun Yanga,
  15. Chris Changa,
  16. Tim Lub,
  17. Charlie W. H. Leeb,
  18. Barry Hicksa,
  19. Smriti Ramakrishnana,
  20. Haibao Tanga,
  21. Chao Xiec,
  22. Jason Piperc,
  23. Suzanne Brewertonc,
  24. Yaron Turpazb,c,
  25. Amalio Telentib,
  26. Rhonda K. Robyb,d,2,
  27. Franz J. Ocha, and
  28. J. Craig Venterb,d,1
  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
  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)

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.

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Article usage

Article usage: August 2017 to February 2019

AbstractFullPdf
Aug 2017743
Sep 2017194351273910808
Oct 2017694434992394
Nov 2017366820061398
Dec 201715961288981
Total 2017316501953615584
Jan 201813521204736
Feb 201815821439387
Mar 201811791352406
Apr 201810751201344
May 201815441825325
Jun 2018870980220
Jul 20187431128227
Aug 2018709811191
Sep 2018680791221
Oct 20181751261222
Nov 201850820273
Dec 2018231089157
Total 20189982139013709
Jan 2019281241212
Feb 20192225852
Total 2019501499264
Total416823493619557
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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, 114 (38) 10166-10171; 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, 114 (38) 10166-10171; DOI: 10.1073/pnas.1711125114
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