Supplementary Materials

Supplementary Material for:

Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study

Sameek Roychowdhury, Matthew K. Iyer, Dan R. Robinson, Robert J. Lonigro, Yi-Mi Wu, Xuhong Cao, Shanker Kalyana-Sundaram, Lee Sam, O. Alejandro Balbin, Michael J. Quist, Terrence Barrette, Jessica Everett, Javed Siddiqui, Lakshmi P. Kunju, Nora Navone, John C. Araujo, Patricia Troncoso, Christopher J. Logothetis, Jeffrey W. Innis, David C. Smith, Christopher D. Lao, Scott Y. Kim, J. Scott Roberts, Stephen B. Gruber, Kenneth J. Pienta, Moshe Talpaz, Arul M. Chinnaiyan*

*To whom correspondence should be addressed. E-mail: arul{at}

Published 30 November 2011, Sci. Transl. Med. 3, 111ra121 (2011)
DOI: 10.1126/scitranslmed.3003161

This PDF file includes:

  • Methods
  • Results
  • Discussion
  • References
  • Fig. S1. Integrative sequencing of a patient’s prostate cancer xenograft.
  • Fig. S2. Additional aberrations reported in patient 1 (prostate cancer xenograft).
  • Fig. S3. Aberrations reported in patient 2 (prostate cancer xenograft).
  • Fig. S4. Additional aberrations reported in patient 3 (colorectal cancer).
  • Fig. S5. Bioinformatics workflow diagram.
  • Fig. S6. Tumor content estimation by pathology and in silico methods.
  • Fig. S7. Integrative sequencing coverage of COSMIC mutations.
  • Table S1. Breakdown of costs associated with integrative sequencing.
  • Table S2. Sequencing tumor board expertise.
  • Table S3. Informative gene list.
  • Table S4. Patient information.
  • Table S5. Alignment statistics.
  • Table S6. Somatic variants: Patient 1.
  • Table S7. Somatic variants: Patient 2.
  • Table S8. Somatic variants: Patient 3.
  • Table S9. Somatic variants: Patient 4.
  • Table S10. Germline variants: Patient 3.
  • Table S11. Germline variants: Patient 4.
  • Table S12. Copy number alterations by patient.
  • Table S13. Structural variants by patient.
  • Table S14. Gene fusions: Patient 1.
  • Table S15. Gene fusions: Patient 2.
  • Table S16. Gene fusions: Patient 3.
  • Table S17. Gene fusions: Patient 4.

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