Dataset Information

Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study.

ABSTRACT: Next-generation sequencing (NGS)-based cancer panel tests are actively being applied in the clinic for precision oncology. Given the importance of NGS panel tests in the palliative clinical setting, it is critical to understand success rates, factors responsible for test failures, and the incidence of clinically meaningful genetic alterations. We performed NGS cancer panel test with tumors from the stomach (n?=?234), colorectum (n?=?196), and rare tumors (n?=?105) from 535 recurrent or metastatic cancer patients for 1 year. Sequencing was successful in 483 (95.3%) archival tumor samples to find single nucleotide variant (SNV), copy number alteration (CNA), and fusion. NGS testing was unsuccessful in 52 (9.7%) specimens due to inadequate tissue (n?=?28), low tumor volume (n?=?19), and poor quality of nucleic acid (n?=?5). According to the Tier system, variants were classified as Tier IA, 0.8%; IIC, 10.3%; IID, 2.0%; III, 66.7% for gastric: Tier IA, 3.6%; IIC, 11.6% for colorectal: Tier IA, 1.6%; IIC, 13.5%; IID, 0.5%; III, 70.8% for melanoma, and Tier IA, 9.1%; IIC, 1.8%; IID, 1.0%; III, 66.4% for GIST. In total, 30.8% of 483 sequenced cases harbored clinically meaningful variants. In Tier IA, KRAS and ERBB2 were the most commonly altered genes. Interestingly, we identified CD274 (PD-L1) amplification, PTPN11 (SHP2) SNV, TPM3-NTRK1 fusion, and FGFR3-TACC3 fusion as a rare (<2%) alteration having therapeutic targets. In conclusion, although small biopsy samples constitute half of cases, informative NGS results were successfully reported in >90% of archival tissue samples, and 30.8% of them harbored clinically meaningful variants.

SUBMITTER: Kwon D

PROVIDER: S-EPMC6710823 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study.

Kwon Dohee D Kim Binnari B Shin Hyeong Chan HC Kim Eun Ji EJ Ha Sang Yun SY Jang Kee-Taek KT Kim Seung Tae ST Lee Jeeyun J Kang Won Ki WK Park Joon Oh JO Kim Kyoung-Mee KM

Translational oncology 20190820 11

Next-generation sequencing (NGS)-based cancer panel tests are actively being applied in the clinic for precision oncology. Given the importance of NGS panel tests in the palliative clinical setting, it is critical to understand success rates, factors responsible for test failures, and the incidence of clinically meaningful genetic alterations. We performed NGS cancer panel test with tumors from the stomach (n = 234), colorectum (n = 196), and rare tumors (n = 105) from 535 recurrent or metastati ...[more]

PMID: 31442744

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Project description:IntroductionCompared with breast cancer (BC) in women, BC in men is a rare disease with genetic and molecular peculiarities. Therapeutic approaches for male BC (MBC) are currently extrapolated from the clinical management of female BC, although the disease does not exactly overlap in males and females. Data on specific molecular biomarkers in MBC are lacking, cutting out male patients from more appropriate therapeutic strategies. Growing evidence indicates that Next Generation Sequencing (NGS) multigene panel testing can be used for the detection of predictive molecular biomarkers, including Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI).MethodsIn this study, NGS multigene gene panel sequencing, targeting 1.94 Mb of the genome at 523 cancer-relevant genes (TruSight Oncology 500, Illumina), was used to identify and characterize somatic variants, Copy Number Variations (CNVs), TMB and MSI, in 15 Formalin-Fixed Paraffin-Embedded (FFPE) male breast cancer samples.Results and discussionA total of 40 pathogenic variants were detected in 24 genes. All MBC cases harbored at least one pathogenic variant. PIK3CA was the most frequently mutated gene, with six (40.0%) MBCs harboring targetable PIK3CA alterations. CNVs analysis showed copy number gains in 22 genes. No copy number losses were found. Specifically, 13 (86.7%) MBCs showed gene copy number gains. MYC was the most frequently amplified gene with eight (53.3%) MBCs showing a median fold-changes value of 1.9 (range 1.8-3.8). A median TMB value of 4.3 (range 0.8-12.3) mut/Mb was observed, with two (13%) MBCs showing high-TMB. The median percentage of MSI was 2.4% (range 0-17.6%), with two (13%) MBCs showing high-MSI. Overall, these results indicate that NGS multigene panel sequencing can provide a comprehensive molecular tumor profiling in MBC. The identification of targetable molecular alterations in more than 70% of MBCs suggests that the NGS approach may allow for the selection of MBC patients eligible for precision/targeted therapy.

Dataset Information

Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study.

Publications

Cancer Panel Assay for Precision Oncology Clinic: Results from a 1-Year Study.

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