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. 2018 Apr 17;9(29):20304-20322.
doi: 10.18632/oncotarget.24854.

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 , Aaron M Elliott  1
Affiliations

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 et al. Oncotarget. .

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.

Keywords: Lynch syndrome; colorectal cancer; microsatellite instability; mismatch repair deficiency; next generation sequencing.

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Conflict of interest statement

CONFLICTS OF INTEREST PG, PT, DC, SW, WM, BL, HV, HL, JH, NB, SW, LU, SS, CG, MU and AE are all employees of Ambry Genetics. MJ is a paid consultant for Ambry Genetics.

Figures

Figure 1
Figure 1
(A) Representation of the suggested ACMG algorithm for Lynch syndrome testing. Figure adopted from “ACMG technical standards and guidelines for genetic testing for inherited colorectal cancer (Lynch syndrome, familial adenomatous polyposis, and MYH-associated polyposis)”, Genetics in Medicine (2014) 16, 101-116 (https://doi.org/10.1038/gim.2013.166). (B) TumorNext-Lynch-MMR workflow. Paired analysis of blood and tumor is performed to detect germline and somatic SNVs, indels, SVs and somatic MSI and LOH. Tumor tissue is also analyzed for MLH1 promoter hypermethylation and CNVs.
Figure 2
Figure 2. Representative patient scenarios observed since the launch of TumorNext-Lynch-MMR
(A) Germline mutation + somatic mutation as the second hit, (B) Germline mutation + LOH as second hit, plus somatic mutation, (C) Somatic mutation + LOH, (D) Double somatic mutations, (E) Germline VUS + somatic mutation, (F) Multiple somatic mutations + LOH, (G) Somatic mutation leading to promoter hypermethylation + LOH, (H) Germline mutation + multiple somatic mutations.
See this image and copyright information in PMC

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