The mutation spectrum revealed by paired genome sequences from a lung cancer patient (original) (raw)

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Gene Expression Omnibus

Data deposits

Sequence data has been submitted to the NCBI Short Read Archive under accession number SRA012097. Microarray data has been submitted to the NCBI Gene Expression Omnibus under accession number GSE20585.

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Acknowledgements

We thank T. Wu for critical reading of manuscript, C. Santos for sample handling, M. Vasser and the DNA Synthesis Group for oligonucleotide synthesis, J. Turcotte and G. Cavet for coordination, G. Nilsen for data submission, J. Fitzgerald and A. Baucom for data storage, J. Lee for laboratory support, A. Bruce for graphical assistance, and T. Bhangale, S. Jhunhunwala and A. Halpern for discussion.

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Authors and Affiliations

1. Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California 94080, USA,
   William Lee, Zhaoshi Jiang, Jinfeng Liu, Peter M. Haverty, Peng Yue, Yan Zhang, Colin Watanabe, Robert Gentleman & Zemin Zhang
2. Department of Molecular Biology, Genentech Inc., South San Francisco, California 94080, USA,
   Yinghui Guan, Jeremy Stinson, Deepali Bhatt, Connie Ha, Frederic J. de Sauvage, Zora Modrusan & Somasekar Seshagiri
3. Complete Genomics Inc., Mountain View, California 94043, USA ,
   Krishna P. Pant, Michael I. Kennemer, Igor Nazarenko, Andrew B. Sparks, Dennis G. Ballinger & Radoje Drmanac
4. Department of Pathology, Genentech Inc., South San Francisco, California 94080, USA,
   Stephanie Johnson & Howard Stern
5. Department of Oncology Diagnostics, Genentech Inc., South San Francisco, California 94080, USA,
   Sankar Mohan, David S. Shames & Ajay Pandita

Authors

1. William Lee
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2. Zhaoshi Jiang
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3. Jinfeng Liu
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4. Peter M. Haverty
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5. Yinghui Guan
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6. Jeremy Stinson
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7. Peng Yue
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8. Yan Zhang
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9. Krishna P. Pant
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10. Deepali Bhatt
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11. Connie Ha
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12. Stephanie Johnson
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13. Michael I. Kennemer
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14. Sankar Mohan
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15. Igor Nazarenko
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16. Colin Watanabe
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17. Andrew B. Sparks
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18. David S. Shames
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19. Robert Gentleman
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20. Frederic J. de Sauvage
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21. Howard Stern
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22. Ajay Pandita
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23. Dennis G. Ballinger
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24. Radoje Drmanac
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25. Zora Modrusan
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26. Somasekar Seshagiri
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27. Zemin Zhang
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Contributions

W.L., project coordination, SNV and overall data analysis and preparation of manuscript; Z.J., structural variation analysis and preparation of manuscript; J.L., mutation pattern and trend analysis, loss of heterozygosity analysis, expression analysis and preparation of manuscript; P.M.H., copy number/loss of heterozygosity analysis, pathway analysis, expression analysis and preparation of manuscript; P.Y., mutation analysis and preparation of manuscript; Y.G. and Z.M., PCR validation of structural variations; J.S., D.B. and S.S., MassArray mutation validation; Y.Z., bioinformatic prediction of mutations and data processing; K.P.P., M.I.K., I.N. and A.B.S., DNA nanoball preparation and sequencing, base calling, quality control and structural variation mapping; C.H. and Z.M., microarray data production; S.J. and H.S., sample handling and pathology analysis; C.W., structural variation breakpoint mapping; D.S.S., pathway analysis and data interpretation; R.G., manuscript critiques and statistical analysis; F.J.d.S., project coordination and manuscript commenting; A.P. and S.M., FISH analysis; R.D. and D.G.B., project coordination, data interpretation and manuscript commenting; Z.Z., project design, data interpretation and preparation of manuscript.

Corresponding author

Correspondence toZemin Zhang.

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Competing interests

Authors are employees of either Genentech Inc. or Complete Genomics Inc. Employees of Complete Genomics have stock options in the company.

Supplementary information

Supplementary Information

This file contains Supplementary Sections S1-S10, Supplementary References, legends for Supplementary Tables 1-7 and Supplementary Figures 1-17 with legends. (PDF 4981 kb)

Supplementary Tables

This file contains Supplementary Tables 1 – 7, including column descriptions. See Supplementary Information file for legends. (XLS 11059 kb)

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Lee, W., Jiang, Z., Liu, J. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient.Nature 465, 473–477 (2010). https://doi.org/10.1038/nature09004

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• Received: 07 December 2009
• Accepted: 10 March 2010
• Issue Date: 27 May 2010
• DOI: https://doi.org/10.1038/nature09004