Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors

Hovelson, Daniel H.; McDaniel, Andrew S.; Cani, Andi K.; Johnson, Bryan; Rhodes, Kate; Williams, Paul D.; Bandla, Santhoshi; Bien, Geoffrey; Choppa, Paul; Hyland, Fiona; Gottimukkala, Rajesh; Liu, Guoying; Manivannan, Manimozhi; Schageman, Jeoffrey; Ballesteros-Villagrana, Efren; Grasso, Catherine S.; Quist, Michael J.; Yadati, Venkata; Amin, Anmol; Siddiqui, Javed; Betz, Bryan L.; Knudsen, Karen E.; Cooney, Kathleen A.; Feng, Felix Y.; Roh, Michael H.; Nelson, Peter S.; Liu, Chia-Jen; Beer, David G.; Wyngaard, Peter; Chinnaiyan, Arul M.; Sadis, Seth; Rhodes, Daniel R.; Tomlins, Scott A.

doi:10.1016/j.neo.2015.03.004

Cited by 224Cancer Genomics and DiagnosticsGenomics and Rare DiseasesBRCA gene mutations in cancer

Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors

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Hovelson, Daniel H., McDaniel, Andrew S., Cani, Andi K., Johnson, Bryan, Rhodes, Kate, Williams, Paul D., Bandla, Santhoshi, Bien, Geoffrey +25 more·2015·Neoplasia

DOI 10.1016/j.neo.2015.03.004PMC PMC4415141

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Abstract

Next-generation sequencing (NGS) has enabled genome-wide personalized oncology efforts at centers and companies with the specialty expertise and infrastructure required to identify and prioritize actionable variants. Such approaches are not scalable, preventing widespread adoption. Likewise, most targeted NGS approaches fail to assess key relevant genomic alteration classes. To address these challenges, we predefined the catalog of relevant solid tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics analysis of >700,000 samples. To detect these variants, we developed the Oncomine Comprehensive Panel (OCP), an integrative NGS-based assay [compatible with <20 ng of DNA/RNA from formalin-fixed paraffin-embedded (FFPE) tissues], coupled with an informatics pipeline to specifically identify relevant predefined variants and created a knowledge base of related potential treatments, current practice guidelines, and open clinical trials. We validated OCP using molecular standards and more than 300 FFPE tumor samples, achieving >95% accuracy for KRAS, epidermal growth factor receptor, and BRAF mutation detection as well as for ALK and TMPRSS2:ERG gene fusions. Associating positive variants with potential targeted treatments demonstrated that 6% to 42% of profiled samples (depending on cancer type) harbored alterations beyond routine molecular testing that were associated with approved or guideline-referenced therapies. As a translational research tool, OCP identified adaptive CTNNB1 amplifications/mutations in treated prostate cancers. Through predefining somatic variants in solid tumors and compiling associated potential treatment strategies, OCP represents a simplified, broadly applicable targeted NGS system with the potential to advance precision oncology efforts.

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Targeted multiplexed hotspot panels are already developed and available in CAP-accredited academic and commercial laboratories.
“Targeted multiplexed hotspot panels (e.g., Agena Oncocarta [Agena Bioscience, San Diego, CA], 47 SNaPshot [Applied Biosystems, Foster City, CA], 48 and next-generation sequencing [NGS] panels 49,50 ) have already been developed and are available in College of American Pathologists (CAP)-accredited academic and commercial laboratories.”
From The International Association for the Study of Lung Cancer Consensus Statement on Optimizing Management of EGFR Mutation–Positive Non–Small Cell Lung Cancer: Status in 2016 (2016) · cites this paper as [50]

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A genomic survey of sarcomas on sun-exposed skin reveals distinctive candidate drivers and potentially targetable mutations
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Authors: Hovelson, D. H., McDaniel, A. S., Cani, A. K., Johnson, B., Rhodes, K., Williams, P. D., Bandla, S., Bien, G., Choppa, P., Hyland, F., Gottimukkala, R., Liu, G., Manivannan, M., Schageman, J., Ballesteros-Villagrana, E., Grasso, C. S., Quist, M. J., Yadati, V., Amin, A., Siddiqui, J., Betz, B. L., Knudsen, K. E., Cooney, K. A., Feng, F. Y., Roh, M. H., Nelson, P. S., Liu, C.-J., Beer, D. G., Wyngaard, P., Chinnaiyan, A. M., Sadis, S., Rhodes, D. R., & Tomlins, S. A.
Affiliations: University of Michigan (US)
Thermo Fisher Scientific (United States) (US)
Oregon Health & Science University (US)
Thomas Jefferson University (US)
Fred Hutch Cancer Center (US)
Howard Hughes Medical Institute (US)
Corresponding author: Tomlins, Scott A.
ORCID: Hovelson, Daniel H.
Cani, Andi K.
Johnson, Bryan
Grasso, Catherine S.
Siddiqui, Javed
Knudsen, Karen E.
Cooney, Kathleen A.
Feng, Felix Y.
Nelson, Peter S.
Liu, Chia-Jen
Beer, David G.
Chinnaiyan, Arul M.
Rhodes, Daniel R.
Tomlins, Scott A.
Venue: Neoplasia
Publisher: Elsevier BV
Published: 2015-04
Volume: 17
Issue: 4
Pages: 385-399
ISSN: 1476-5586 (ISSN-L)
DOI: 10.1016/j.neo.2015.03.004
PMC: PMC4415141
OpenAlex: W2141420424
Cited by: 224
References: 56
Citations by year: 2026: 1 · 2025: 7 · 2024: 13 · 2023: 17 · 2022: 14 · 2021: 21 · 2020: 23 · 2019: 29 · 2018: 28 · 2017: 28 · 2016: 28 · 2015: 14 · 2014: 1
FWCI: 10.80
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
creativecommons.org/licenses/by-nc-nd/4.0/ (vor, 5 d)
Locations: Neoplasia (publishedVersion, cc-by-nc-nd)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by-nc-nd)
PubMed (publishedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: National Human Genome Research Institute (UM1HG006508)
National Cancer Institute (R01CA159945, R01CA183857, R01CA181605, R01CA154365, P50CA186786)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › BRCA gene mutations in cancer
Keywords: targeted next-generation sequencing, solid tumors, somatic mutations, actionable mutations, gene fusion, copy number alterations, formalin-fixed paraffin-embedded tissue, precision oncology, KRAS, EGFR, BRAF, anaplastic lymphoma kinase, TMPRSS2-ERG fusion, CTNNB1, prostate cancer, targeted therapy
MeSH terms: Transcriptional Regulator ERG, Anaplastic Lymphoma Kinase, Aged, DNA Mutational Analysis, DNA, Neoplasm, Female, Humans, Male, Middle Aged, Mutation, Neoplasms, Proto-Oncogene Proteins, Retrospective Studies, Serine Endopeptidases, Trans-Activators, Proto-Oncogene Proteins p21(ras), ras Proteins, Computational Biology, Receptor Protein-Tyrosine Kinases, Proto-Oncogene Proteins B-raf, beta Catenin, High-Throughput Nucleotide Sequencing, ErbB Receptors

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