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WG-CGP - 1) Genomics educational section


a. Seminal papers - review articles

Genomics 

  • Brown NA, Elenitoba-Johnson KSJ. Enabling Precision Oncology Through Precision Diagnostics. Annu Rev Pathol. 2020;15:97-121
  • Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016;17(6):333-351.
  • Berger MF, Mardis ER. The emerging clinical relevance of genomics in cancer medicine. Nat Rev Clin Oncol. 2018;15(6):353-365.
  • Paolillo C, Londin E, Fortina P. Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine. Scand J Clin Lab Invest Suppl. 2016;245:S84-S91.
  • Karczewski KJ, Francioli LC, Tiao G, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581
  • Zehir A, Benayed R, Shah RH, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients [published correction appears in Nat Med. 2017 Aug 4;23 (8):1004]. Nat Med. 2017;23(6):703-713.
  • Zaidi SH, Harrison TA, Phipps AI, et al. Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival. Nat Commun. 2020;11(1):3644.

Circulating Tumor DNA

  • Cescon et al Circulating tumor DNA and liquid biopsy in oncology. 2020. Nature Cancer 1: 276-290
  • Zill OA, Banks KC, Fairclough SR, et al. The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients. Clin Cancer Res. 2018;24(15):3528-3538.
  • Razavi P, Li BT, Brown DN, et al. High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants. Nat Med. 2019;25(12):1928-1937.
  • Wang Z, Duan J, Cai S, et al. Assessment of Blood Tumor Mutational Burden as a Potential Biomarker for Immunotherapy in Patients With Non-Small Cell Lung Cancer With Use of a Next-Generation Sequencing Cancer Gene Panel. JAMA Oncol. 2019;5(5):696-702.

Tumor heterogeneity

  • McGranahan N, Swanton C. Biological and therapeutic impact of intratumor heterogeneity in cancer evolution [published correction appears in Cancer Cell. 2015 Jul 13;28(1):141]. Cancer Cell. 2015;27(1):15-26.
  • McGranahan N, Swanton C. Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future. Cell. 2017;168(4):613-628.
  • Dagogo-Jack I, Shaw AT. Tumour heterogeneity and resistance to cancer therapies. Nat Rev Clin Oncol. 2018;15(2):81-94.

Fusion detection

  • Sussman RT, Oran AR, Paolillo C, Lieberman D, Morrissette JJD, Rosenbaum JN. Validation of a Next-Generation Sequencing Assay Targeting RNA for the Multiplexed Detection of Fusion Transcripts and Oncogenic Isoforms. Arch Pathol Lab Med. 2020;144(1):90-98.
  • Hsiao SJ, Zehir A, Sireci AN, Aisner DL. Detection of Tumor NTRK Gene Fusions to Identify Patients Who May Benefit from Tyrosine Kinase (TRK) Inhibitor Therapy. J Mol Diagn. 2019;21(4):553-571.
  • Collins RL, Brand H, Karczewski KJ, et al. A structural variation reference for medical and population genetics. Nature. 2020;581(7809):444-451.

Minimal residual disease

  • Ritterhouse LL, Parilla M, Zhen CJ, et al. Clinical Validation and Implementation of a Measurable Residual Disease Assay for NPM1 in Acute Myeloid Leukemia by Error-Corrected Next-Generation Sequencing. Mol Diagn Ther. 2019;23(6):791-802.
  • Rambow F, Rogiers A, Marin-Bejar O, et al. Toward Minimal Residual Disease-Directed Therapy in Melanoma. Cell. 2018;174(4):843-855.

Tumor mutational burden

  • Samstein RM, Lee CH, Shoushtari AN, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019;51(2):202-206.
  • Buchhalter I, Rempel E, Endris V, et al. Size matters: Dissecting key parameters for panel-based tumor mutational burden analysis. Int J Cancer. 2019;144(4):848-858.

Immunotherapy

  • Binnewies M, Roberts EW, Kersten K, et al. Understanding the tumor immune microenvironment (TIME) for effective therapy. Nat Med. 2018;24(5):541-550.
  • Waldman, A.D., Fritz, J.M. & Lenardo, M.J. A guide to cancer immunotherapy: from T cell basic science to clinical practice. Nat Rev Immunol (2020).
  • Finck, A., Gill, S.I. & June, C.H. Cancer immunotherapy comes of age and looks for maturity. Nat Commun 11, 3325 (2020).
  • Rizvi H, Sanchez-Vega F, La K, et al. Molecular Determinants of Response to Anti-Programmed Cell Death (PD)-1 and Anti-Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non-Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing [published correction appears in J Clin Oncol. 2018 Jun 1;36(16):1645]. J Clin Oncol. 2018;36(7):633-641.

Clonal hematopoiesis of indeterminate potential

  • Ptashkin RN, Mandelker DL, Coombs CC, et al. Prevalence of Clonal Hematopoiesis Mutations in Tumor-Only Clinical Genomic Profiling of Solid Tumors [published correction appears in JAMA Oncol. 2019 Jan 1;5(1):122]. JAMA Oncol. 2018;4(11):1589-1593.
  • Coombs CC, Gillis NK, Tan X, et al. Identification of Clonal Hematopoiesis Mutations in Solid Tumor Patients Undergoing Unpaired Next-Generation Sequencing Assays. Clin Cancer Res. 2018;24(23):5918-5924.
  • Pollyea DA. Next-Generation Sequencing and Eating of the Tree of Knowledge. Clin Cancer Res. 2018;24(23):5790-5791.
  • Calvillo-Argüelles O, Jaiswal S, Shlush LI, et al. Connections Between Clonal Hematopoiesis, Cardiovascular Disease, and Cancer: A Review. JAMA Cardiol. 2019;4(4):380-387.
  • Jaiswal S, Ebert BL. Clonal hematopoiesis in human aging and disease. Science. 2019;366


b. Educational resources

Podcasts

Training residents in genomics (TRIG)

Genomics education websites


c. Guidelines

  • https://www.ashg.org/tag/guidance/
  • Jenning et al. Guidelines for Validation of Next-Generation Sequencing–Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. 2017.  J Molec Diagn 19: 341-365
  • Roy S, Coldren C, Karunamurthy A, et al. Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and the College of American Pathologists. J Molec Diagn. 2018;20(1):4-27.
  • Li et al Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. 2017. J Molec Diagn. 19: 4-23
  • Lindeman NI, Cagle PT, Aisner DL, et al. Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology. Arch Pathol Lab Med. 2018;142(3):321-346.
 
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