Abstract

The extent of heterogeneity among driver gene mutations present in naturally occurring metastases—that is, treatment-naive metastatic disease—is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.

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Acknowledgements

We thank the Memorial Sloan Kettering Cancer Center Molecular Cytology core facility for immunohistochemistry staining. This work was supported by Office of Naval Research grant N00014-16-1-2914, the Bill and Melinda Gates Foundation (OPP1148627), and a gift from B. Wu and E. Larson (M.A.N.), National Institutes of Health grants CA179991 (C.A.I.-D. and I.B.), F31 CA180682 (A.P.M.-M.), CA43460 (B.V.), and P50 CA62924, the Monastra Foundation, the Virginia and D.K. Ludwig Fund for Cancer Research, the Lustgarten Foundation for Pancreatic Cancer Research, the Sol Goldman Center for Pancreatic Cancer Research, the Sol Goldman Sequencing Center, ERC Start grant 279307: Graph Games (J.G.R., D.K., and C.K.), Austrian Science Fund (FWF) grant P23499-N23 (J.G.R., D.K., and C.K.), and FWF NFN grant S11407-N23 RiSE/SHiNE (J.G.R., D.K., and C.K.).

Author information

Author notes

    • Alvin P Makohon-Moore

    Present address: David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Alvin P Makohon-Moore
    • , Ming Zhang
    •  & Johannes G Reiter

    These authors contributed equally to this work.

Affiliations

  1. Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Alvin P Makohon-Moore
    • , Laura D Wood
    • , Ralph H Hruban
    •  & Bert Vogelstein
  2. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Alvin P Makohon-Moore
    • , Laura D Wood
    •  & Ralph H Hruban
  3. Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Ming Zhang
    • , Fay Wong
    • , Yuchen Jiao
    • , Nickolas Papadopoulos
    • , Kenneth W Kinzler
    •  & Bert Vogelstein
  4. IST Austria (Institute of Science and Technology Austria), Klosterneuburg, Austria.

    • Johannes G Reiter
    • , Deepanjan Kundu
    •  & Krishnendu Chatterjee
  5. Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts, USA.

    • Johannes G Reiter
    • , Ivana Bozic
    • , Benjamin Allen
    •  & Martin A Nowak
  6. Department of Mathematics, Harvard University, Cambridge, Massachusetts, USA.

    • Ivana Bozic
    •  & Martin A Nowak
  7. Center for Mathematical Sciences and Applications, Harvard University, Cambridge, Massachusetts, USA.

    • Benjamin Allen
  8. Department of Mathematics, Emmanuel College, Boston, Massachusetts, USA.

    • Benjamin Allen
  9. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Zachary A Kohutek
  10. David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Jungeui Hong
    • , Marc Attiyeh
    • , Breanna Javier
    •  & Christine A Iacobuzio-Donahue
  11. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.

    • Ralph H Hruban
  12. Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.

    • Martin A Nowak
  13. Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA.

    • Bert Vogelstein
  14. Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.

    • Christine A Iacobuzio-Donahue

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Contributions

C.I.D. and A.M.M. performed the autopsies. C.I.D., A.P.M.-M., R.H.H., L.D.W., B.V., K.W.K., N.P., M.Z., F.W., and Y.J. designed experiments. A.M.M., J.R., I.B., F.W., J.H., and M.A. performed biostatistical analyses. A.M.M., M.Z., B.J., and Z.A.K. performed the experiments. J.G.R., I.B., J.H., D.K., and K.C. performed computational analysis. J.R., I.B., B.A., and M.A.N. performed modeling. All authors interpreted the data. C.A.I.-D., A.M.M., and B.V. wrote the manuscript, J.R., I.B., and M.A.N. provided input to the manuscript, and all authors read and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christine A Iacobuzio-Donahue.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–14, Supplementary Tables 1 and 2, and Supplementary Note

Excel files

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    Supplementary Table 3

    Samples analyzed.

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    Supplementary Table 4

    Average coverage per base.

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    Supplementary Table 5

    Summary of somatic copy number alterations identified in whole-genome sequencing samples.

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    Supplementary Table 6

    Major driver gene mutations identified in each patient.

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    Supplementary Table 7

    SCNAs identified in known PDAC driver genes.

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    Supplementary Table 8

    Candidate structural variants identified in Pam01.

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    Supplementary Table 9

    Candidate structural variants identified in Pam02.

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    Supplementary Table 10

    Candidate structural variants identified in Pam03.

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    Supplementary Table 11

    Candidate structural variants identified in Pam04.

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    Supplementary Table 12

    Variants validated by targeted sequencing.

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    Supplementary Table 13

    Jaccard similarity coefficients of metastases based on stringently filtered whole-genome sequencing and whole-exome sequencing.

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    Supplementary Table 14

    Similarity coefficients of normal organs from Blokzjil et al.

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    Supplementary Table 15

    Genetic distances among metastases based on targeted sequencing.

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    Supplementary Table 16

    Jaccard similarity coefficients of metastases based on targeted sequencing (founder mutations excluded).

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    Supplementary Table 17

    Genetic distances among metastases based on whole-genome sequencing.

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    Supplementary Table 18

    Variants identified by whole-exome sequencing in the validation set.

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    Supplementary Table 19

    Primers.

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DOI

https://doi.org/10.1038/ng.3764

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