Supplementary Materials

Supplementary Material for:

Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA

Florian Scherer, David M. Kurtz, Aaron M. Newman, Henning Stehr, Alexander F. M. Craig, Mohammad Shahrokh Esfahani, Alexander F. Lovejoy, Jacob J. Chabon, Daniel M. Klass, Chih Long Liu, Li Zhou, Cynthia Glover, Brendan C. Visser, George A. Poultsides, Ranjana H. Advani, Lauren S. Maeda, Neel K. Gupta, Ronald Levy, Robert S. Ohgami, Christian A. Kunder, Maximilian Diehn,* Ash A. Alizadeh*

*Corresponding author. Email: diehn{at}stanford.edu (M.D.); arasha{at}stanford.edu (A.A.A.)

Published 9 November 2016, Sci. Transl. Med. 8, 364ra155 (2016)
DOI: 10.1126/scitranslmed.aai8545

This PDF file includes:

  • Materials and Methods
  • Fig. S1. Overview of DLBCL tumor genotyping results.
  • Fig. S2. Sensitivity and specificity of ctDNA detection in DLBCL pretreatment plasma samples.
  • Fig. S3. Performance assessment of biopsy-free tumor genotyping from DLBCL plasma samples.
  • Fig. S4. Utility of biopsy-free genotyping for translocation detection and ctDNA monitoring.
  • Fig. S5. Analysis of biopsy-free ctDNA monitoring in serial plasma samples.
  • Fig. S6. Correlation of mutant AF from pretreatment tumor/plasma pairs.
  • Fig. S7. Noninvasive detection of ibrutinib resistance mutations in lymphoma patients.
  • Fig. S8. Noninvasive detection of an emergent somatic alteration after targeted therapy in a patient with tFL.
  • Fig. S9. Relationship between pretreatment ctDNA concentration and key DLBCL clinical indices.
  • Fig. S10. Performance comparison of CAPP-Seq and IgHTS for DLBCL relapse detection.
  • Fig. S11. Association between ctDNA positivity after curative therapy and overall survival.
  • Fig. S12. Genomic features incorporated into the DLBCL COO classifier.
  • Fig. S13. Analysis of mutation evolution in serial lymphoma tumor biopsies.
  • Fig. S14. Evolutionary patterns distinguishing lymphoma histologies.
  • Legends for Tables S1 to S5
  • References (6382)

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Other Supplementary Material for this manuscript includes the following:

  • Table S1 (Microsoft Excel format). DLBCL selector design with references and final coordinates.
  • Table S2 (Microsoft Excel format). Overview of patients, samples, and clinical characteristics.
  • Table S3 (Microsoft Excel format). Somatic mutations and V(D)J recombination sequences detected in tumor biopsies and a list of driver genes used in this work.
  • Table S4 (Microsoft Excel format). Univariate and multivariate outcome analysis.
  • Table S5 (Microsoft Excel format). Illustrative example of DLBCL subtype determination.

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