Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel

Purpose: To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing. Experimental Design: Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated. Results: cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit. Conclusions: cfDNA-based MSI detection using Guardant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate. See related commentary by Wang and Ajani, p. 6887

[1]  V. Papadimitrakopoulou,et al.  Clinical Utility of Comprehensive Cell-free DNA Analysis to Identify Genomic Biomarkers in Patients with Newly Diagnosed Metastatic Non–small Cell Lung Cancer , 2019, Clinical Cancer Research.

[2]  A. Duval,et al.  Association of Primary Resistance to Immune Checkpoint Inhibitors in Metastatic Colorectal Cancer With Misdiagnosis of Microsatellite Instability or Mismatch Repair Deficiency Status , 2019, JAMA oncology.

[3]  P. Keegan,et al.  FDA Approval Summary: Pembrolizumab for the Treatment of Microsatellite Instability-High Solid Tumors , 2019, Clinical Cancer Research.

[4]  Ahmet Zehir,et al.  Microsatellite Instability Is Associated With the Presence of Lynch Syndrome Pan-Cancer. , 2019, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[5]  Sharyn I. Katz,et al.  Clinical Implications of Plasma-Based Genotyping With the Delivery of Personalized Therapy in Metastatic Non–Small Cell Lung Cancer , 2019, JAMA oncology.

[6]  Kathleen R. Cho,et al.  Cervical Cancer, Version 3.2019, NCCN Clinical Practice Guidelines in Oncology. , 2019, Journal of the National Comprehensive Cancer Network : JNCCN.

[7]  Joon-Oh Park,et al.  Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer , 2018, Nature Medicine.

[8]  A. Bardelli,et al.  Radiologic and Genomic Evolution of Individual Metastases during HER2 Blockade in Colorectal Cancer. , 2018, Cancer cell.

[9]  David R. Riley,et al.  Abstract 1286: Analytical validation of an integrated next-generation sequencing pan-cancer liquid biopsy approach for detection of microsatellite instability , 2018, Bioinformatics and Systems Biology.

[10]  J. Lindberg,et al.  Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis , 2018, bioRxiv.

[11]  C. Paweletz,et al.  Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies , 2018, Clinical Cancer Research.

[12]  J. Marshall,et al.  Microsatellite instability status determined by next‐generation sequencing and compared with PD‐L1 and tumor mutational burden in 11,348 patients , 2018, Cancer medicine.

[13]  Kathleen R. Cho,et al.  Uterine Neoplasms, Version 1.2018, NCCN Clinical Practice Guidelines in Oncology. , 2018, Journal of the National Comprehensive Cancer Network : JNCCN.

[14]  S. Mortimer,et al.  The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients , 2017, Clinical Cancer Research.

[15]  M. Hall,et al.  Mismatch Repair Deficiency Testing in Patients With Colorectal Cancer and Nonadherence to Testing Guidelines in Young Adults , 2017, JAMA oncology.

[16]  Russell Bonneville,et al.  Landscape of Microsatellite Instability Across 39 Cancer Types. , 2017, JCO precision oncology.

[17]  G. Oxnard,et al.  Application of Plasma Genotyping Technologies in Non–Small Cell Lung Cancer: A Practical Review , 2017, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[18]  E. Nakakura,et al.  Pancreatic Adenocarcinoma, Version 2.2017, NCCN Clinical Practice Guidelines in Oncology. , 2017, Journal of the National Comprehensive Cancer Network : JNCCN.

[19]  Ludmila V. Danilova,et al.  Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade , 2017, Science.

[20]  R. Lothe,et al.  Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies , 2017, Molecular Cancer.

[21]  Zachary J. Heins,et al.  Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making. , 2017, JCO precision oncology.

[22]  Gad Getz,et al.  Polyclonal Secondary FGFR2 Mutations Drive Acquired Resistance to FGFR Inhibition in Patients with FGFR2 Fusion-Positive Cholangiocarcinoma. , 2017, Cancer discovery.

[23]  Mingming Jia,et al.  COSMIC: somatic cancer genetics at high-resolution , 2016, Nucleic Acids Res..

[24]  Jay Shendure,et al.  Classification and characterization of microsatellite instability across 18 cancer types , 2016, Nature Medicine.

[25]  Anil Vachani,et al.  Detection of Therapeutically Targetable Driver and Resistance Mutations in Lung Cancer Patients by Next-Generation Sequencing of Cell-Free Circulating Tumor DNA , 2016, Clinical Cancer Research.

[26]  James Ziai,et al.  Mismatch repair deficiency testing in clinical practice , 2016, Expert review of molecular diagnostics.

[27]  James R. Eshleman,et al.  Microsatellite Instability as a Biomarker for PD-1 Blockade , 2016, Clinical Cancer Research.

[28]  B. Kermani,et al.  Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA , 2015, PloS one.

[29]  Bert Vogelstein,et al.  PD-1 Blockade in Tumors with Mismatch-Repair Deficiency. , 2015, The New England journal of medicine.

[30]  B. Vogelstein,et al.  PD-1 blockade in tumors with mismatch repair deficiency. , 2015, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[31]  Quan P. Ly,et al.  Esophageal and Esophagogastric Junction Cancers, Version 2.2019, NCCN Clinical Practice Guidelines in Oncology. , 2019, Journal of the National Comprehensive Cancer Network : JNCCN.

[32]  Colin C Pritchard,et al.  Microsatellite instability detection by next generation sequencing. , 2014, Clinical chemistry.

[33]  James D. Murphy,et al.  Colon cancer, version 3.2014. , 2014, Journal of the National Comprehensive Cancer Network : JNCCN.

[34]  O. Griffith,et al.  COSMIC (Catalogue of Somatic Mutations in Cancer) , 2014 .

[35]  Yuheng Lu,et al.  A Novel Approach for Characterizing Microsatellite Instability in Cancer Cells , 2013, PloS one.

[36]  Quan P. Ly,et al.  Esophageal and esophagogastric junction cancers. , 2011, Journal of the National Comprehensive Cancer Network : JNCCN.

[37]  W. Frankel,et al.  Screening for the Lynch syndrome (hereditary nonpolyposis colorectal cancer). , 2005, The New England journal of medicine.

[38]  Sudhir Srivastava,et al.  Revised Bethesda Guidelines for hereditary nonpolyposis colorectal cancer (Lynch syndrome) and microsatellite instability. , 2004, Journal of the National Cancer Institute.

[39]  Daniel J Sargent,et al.  Immunohistochemistry versus microsatellite instability testing in phenotyping colorectal tumors. , 2002, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[40]  S Srivastava,et al.  A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. , 1998, Cancer research.

[41]  Matthew P. Goetz,et al.  NCCN CLINICAL PRACTICE GUIDELINES IN ONCOLOGY , 2019 .

[42]  Andrew Dunford,et al.  Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma. , 2018, Cancer discovery.

[43]  M. Millenson,et al.  Cancer-Associated Venous Thromboembolic Disease , Version 2 . 2018 Featured Updates to the NCCN Guidelines , 2018 .

[44]  A. Bronkhorst,et al.  Characterization of the cell-free DNA released by cultured cancer cells. , 2016, Biochimica et biophysica acta.

[45]  Quan P. Ly,et al.  Gastric Cancer, Version 3.2016, NCCN Clinical Practice Guidelines in Oncology. , 2016, Journal of the National Comprehensive Cancer Network : JNCCN.

[46]  H. Akaike,et al.  Information Theory and an Extension of the Maximum Likelihood Principle , 1973 .

[47]  E CARBONETTO,et al.  [Colon Cancer]. , 1958, El Dia medico.