TumorNext-Lynch-MMR: a comprehensive next generation sequencing assay for the detection of germline and somatic mutations in genes associated with mismatch repair deficiency and Lynch syndrome.

// Phillip N. Gray 1 , Pei Tsai 1 , Daniel Chen 2 , Sitao Wu 3 , Jayne Hoo 3 , Wenbo Mu 3 , Bing Li 3 , Huy Vuong 3 , Hsiao-Mei Lu 3 , Navanjot Batth 2 , Sara Willett 1 , Lisa Uyeda 2 , Swati Shah 2 , Chia-Ling Gau 2 , Monalyn Umali 2 , Carin Espenschied 2 , Mike Janicek 4 , Sandra Brown 5 , David Margileth 5 , Lavinia Dobrea 6 , Lawrence Wagman 7 , Huma Rana 8 , Michael J. Hall 9 , Theodora Ross 10 , Jonathan Terdiman 11 , Carey Cullinane 12 , Savita Ries 12 , Ellen Totten 13 and Aaron M. Elliott 1 1 Advanced Genomic Services, Ambry Genetics, Aliso Viejo, CA 92656, USA 2 Clinical Diagnostics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA 3 Bioinformatics Department, Ambry Genetics, Aliso Viejo, CA 92656, USA 4 Cancer Genetic Risk Assessment Program, Arizona Oncology, Scottsdale, AZ 85258, USA 5 Cancer Genetics Program, Saint Joseph of Orange, Orange, CA 92868, USA 6 Oncology Research and Biospecimen Program, Saint Joseph of Orange, Orange, CA 92868, USA 7 The Center for Cancer Prevention and Treatment, Saint Joseph of Orange, Orange, CA 92868, USA 8 Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02461, USA 9 Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia PA 19111, USA 10 Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA 11 Department of Medicine – Gastroenterology, University of California San Francisco, San Francisco, CA 94115, USA 12 Department of Pathology, Long Beach Memorial Medical Center, Long Beach, CA 90801, USA 13 Advocate Medical Group, Park Ridge, Illinois 60068, USA Correspondence to: Phillip N. Gray, email: pgray@ambrygen.com Keywords: Lynch syndrome; colorectal cancer; microsatellite instability; mismatch repair deficiency; next generation sequencing Received: December 15, 2017      Accepted: March 06, 2018      Published: April 17, 2018 ABSTRACT The current algorithm for Lynch syndrome diagnosis is highly complex with multiple steps which can result in an extended time to diagnosis while depleting precious tumor specimens. Here we describe the analytical validation of a custom probe-based NGS tumor panel, TumorNext-Lynch-MMR, which generates a comprehensive genetic profile of both germline and somatic mutations that can accelerate and streamline the time to diagnosis and preserve specimen. TumorNext-Lynch-MMR can detect single nucleotide variants, small insertions and deletions in 39 genes that are frequently mutated in Lynch syndrome and colorectal cancer. Moreover, the panel provides microsatellite instability status and detects loss of heterozygosity in the five Lynch genes; MSH2 , MSH6 , MLH1 , PMS2 and EPCAM . Clinical cases are described that highlight the assays ability to differentiate between somatic and germline mutations, precisely classify variants and resolve discordant cases.