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. 2023 Jul 6:13:1208244.
doi: 10.3389/fonc.2023.1208244. eCollection 2023.

Molecular profiling of solid tumors by next-generation sequencing: an experience from a clinical laboratory

Pratibha Bhai  1   2 , Jacob Turowec  1   2 , Stephanie Santos  1   3 , Jennifer Kerkhof  1   2 , LeeAnne Pickard  4 , Aidin Foroutan  2 , Daniel Breadner  4 , Matthew Cecchini  1   3 , Michael A Levy  1   2 , Alan Stuart  1   2 , Stephen Welch  4 , Christopher Howlett  3 , Hanxin Lin  5 , Bekim Sadikovic  1   2   3
Affiliations

Molecular profiling of solid tumors by next-generation sequencing: an experience from a clinical laboratory

Pratibha Bhai et al. Front Oncol. .

Abstract

Background: Personalized targeted therapies have transformed management of several solid tumors. Timely and accurate detection of clinically relevant genetic variants in tumor is central to the implementation of molecular targeted therapies. To facilitate precise molecular testing in solid tumors, targeted next-generation sequencing (NGS) assays have emerged as a valuable tool. In this study, we provide an overview of the technical validation, diagnostic yields, and spectrum of variants observed in 3,164 solid tumor samples that were tested as part of the standard clinical diagnostic assessment in an academic healthcare institution over a period of 2 years.

Methods: The Ion Ampliseq™ Cancer Hotspot Panel v2 assay (ThermoFisher) that targets ~2,800 COSMIC mutations from 50 oncogenes and tumor suppressor genes was validated, and a total of 3,164 tumor DNA samples were tested in 2 years. A total of 500 tumor samples were tested by the comprehensive panel containing all the 50 genes. Other samples, including 1,375 lung cancer, 692 colon cancer, 462 melanoma, and 135 brain cancer, were tested by tumor-specific targeted subpanels including a few clinically actionable genes.

Results: Of 3,164 patient samples, 2,016 (63.7%) tested positive for at least one clinically relevant variant. Of 500 samples tested by a comprehensive panel, 290 had a clinically relevant variant with TP53, KRAS, and PIK3CA being the most frequently mutated genes. The diagnostic yields in major tumor types were as follows: breast (58.4%), colorectal (77.6%), lung (60.4%), pancreatic (84.6%), endometrial (72.4%), ovary (57.1%), and thyroid (73.9%). Tumor-specific targeted subpanels also demonstrated high diagnostic yields: lung (69%), colon (61.2%), melanoma (69.7%), and brain (20.7%). Co-occurrence of mutations in more than one gene was frequently observed.

Conclusions: The findings of our study demonstrate the feasibility of integrating an NGS-based gene panel screen as part of a standard diagnostic protocol for solid tumor assessment. High diagnostic rates enable significant clinical impact including improved diagnosis, prognosis, and clinical management in patients with solid tumors.

Keywords: NGS; colon cancer; lung cancer; melanoma; solid tumor.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Details of variants identified by the targeted lung subpanel (N = 1,375). (A) Frequency of variants in genes identified in NSCLC tumors tested by the lung subpanel; (B) co-occurring mutations in NSCLC samples; (C) frequency of EGFR gene variants.
Figure 2
Figure 2
(A) Frequency of variants identified in tumor samples tested by the colorectal subpanel; (B) frequency of variants identified in tumor samples tested by the melanoma subpanel.
Figure 3
Figure 3
Frequency of variants in genes included in the comprehensive panel (n = 500).
Figure 4
Figure 4
OncoPrint diagram of mutation frequencies of the genes included in the comprehensive panel in common tumor types tested in our study. All samples (with in each tumor type) are included and genes with ≥1 Tier I/II variant are shown. Each row is one gene (mutation frequencies are shown as % of total samples tested) and each column is one tumor sample. (A) Breast (n = 77); (B) colorectal (n = 67); (C) endometrial (n = 29); (D) non-small cell lung cancer (n = 48); (E) ovary (n = 28); (F) pancreas (n = 39); (G) thyroid (n = 23).
See this image and copyright information in PMC

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