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Oncomine comprehensive assay

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The Oncomine Comprehensive Assay is a targeted next-generation sequencing (NGS) panel that enables the detection of DNA and RNA alterations across a comprehensive set of genes associated with solid tumors. The assay is designed to provide comprehensive genomic profiling to support personalized cancer care.

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Lab products found in correlation

Ion torrent pgm, by Thermo Fisher Scientific (1 mentions) Ion ampliseq cancer hotspot panel, by Thermo Fisher Scientific (1 mentions) Picopure dna extraction kit, by Arcturus (1 mentions) Oncomine focus assay, by Thermo Fisher Scientific (1 mentions) Tso500 assay, by Illumina (1 mentions) Oncomine tumor mutational load assay, by Thermo Fisher Scientific (1 mentions)

4 protocols using oncomine comprehensive assay

1

Comprehensive Molecular Profiling of Lung Cancer

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As of May 2021, more than 13,000 lung cancer patients were enrolled from a total of 307 institutions across Japan. For the molecular screening, DNA and RNA were extracted from fresh and frozen tissues and/or from formalin-fixed paraffin-embedded (FFPE) samples. Between February of 2013 and March of 2015, RT-PCR and FISH analysis revealed ALK, ROS1, and RET fusions. From March 2015, a targeted next-generation sequencing (NGS) system (Oncomine Comprehensive Assay, Thermo Fisher Scientific, MA, USA) has been used for the molecular screening, and from September 2019, a multi-gene quantitative PCR (qPCR) assay (Amoy 9-in-1 kit, AmoyDx, Xiamen, China) has been also implemented. The research protocol (#2018-010) was approved by the Research Ethics Committees at National Cancer Center and all institutions participating in LC-SCRUM-Asia, and written informed consent was provided from each subject. This research protocol includes whole-transcriptome sequencing described below.
Izumi H., Matsumoto S., Liu J., Tanaka K., Mori S., Hayashi K., Kumagai S., Shibata Y., Hayashida T., Watanabe K., Fukuhara T., Ikeda T., Yoh K., Kato T., Nishino K., Nakamura A., Nakachi I., Kuyama S., Furuya N., Sakakibara-Konishi J., Okamoto I., Taima K., Ebi N., Daga H., Yamasaki A., Kodani M., Udagawa H., Kirita K., Zenke Y., Nosaki K., Sugiyama E., Sakai T., Nakai T., Ishii G., Niho S., Ohtsu A., Kobayashi S.S, & Goto K. (2021). The CLIP1-LTK fusion is an oncogenic driver in non-small cell lung cancer. Nature, 600(7888), 319-323.
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2

Comprehensive Cancer Gene Profiling via Oncomine Assay

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Oncomine™ comprehensive assay (TMO comprehensive assay, Thermo Fisher Scientific, Waltham, MA) was used to profile thousands of variants across 161 cancer-relevant genes using FFPE tissues (17 (link)). Analyses of TMO comprehensive assay included identification of genes and detection of mutation types such as frameshift, missense, synonymous, single nucleotide variation (SNV), insertion/deletion (Indel), and copy number variation (CNV) observed in individual subject.
Amplicon libraries were constructed with multiplex polymerase chain reaction (PCR) primers for preparation of DNA and RNA (for fusion genes) from FFPE samples. Sequencing was performed with the Ion Gene Studio S5 System and Ion 540 Chips. Raw data process, alignment, and variant calling were performed with Torrent Suite™ Software, with variant calling using the Torrent Variant Caller plug-in. Further management was proceeded by Ion Reporter™ Software with workflow “Oncomine Comprehensive v3 - w3.2 - DNA and Fusions - Single Sample” version 5.10 selected and filter chain “Oncomine Variants” version 5.10 applied. Reference genome was hg19.
Chao T.C., Tsai Y.F., Liu C.Y., Lien P.J., Lin Y.S., Feng C.J., Chen Y.J., Lai J.I., Hsu C.Y., Lynn J.J., Huang C.C, & Tseng L.M. (2023). Prevalence of PIK3CA mutations in Taiwanese patients with breast cancer: a retrospective next-generation sequencing database analysis. Frontiers in Oncology, 13, 1192946.
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3

DNA Extraction and NGS-based Mutation Detection

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The Pico Pure DNA Extraction Kit (Arcturus, Mountain View, CA, USA) and the Agentcourt AMPureXP Kit (Agentcourt Biosciences, Beverly, MA, USA) were employed for DNA purification from marked areas of FFPE tumor sections from each specimen (usually five unstained slides with a minimum of 20% tumor cellularity). Approximately 10 ng (50-gene panel) or 20 ng (134-gene panel) of purified DNA were applied for targeted NGS-based DNA-seq for detections of gene mutations and gene amplifications, as reported previously [10 (link),11 (link),29 (link),30 (link)]. DNA sequencing was performed using the Ion Torrent PGM, but the number of target genes was historically expanded from 50 (Ion AmpliSeq Cancer Hotspot Panel, Thermo Fisher Scientific, Waltham, MA, USA) to 134 (OncoMine Comprehensive Assay, Thermo Fisher Scientific), referred to as the “50-gene panel” and “134-gene panel”, respectively [10 (link),11 (link),29 (link),30 (link)]. However, genes such as ALK, BRAF, EGFR, KRAS, RET and many other mutations that are considered to be hotspots for lung cancer are included in both 50-gene and 134-gene panels. DNA extraction from peripheral blood of the same individual (in most patients) was used as a control for the differentiation of constitutional and somatic aberrations in tumor specimens.
Tang Z., Chen H., Hong L., Tang G., Toruner G.A., Wang W., Roy Chowdhuri S., Yin W., Jung H.S., Gu J., Routbort M.J., Zhang J., Khoury J.D, & Medeiros L.J. (2020). Inconsistent Intersample ALK FISH Results in Patients with Lung Cancer: Analysis of Potential Causes. Cancers, 12(7), 1903.
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4

Comprehensive Genomic Profiling by NGS for Precision Oncology

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Comprehensive genomic profiling (CGP) via targeted NGS was performed at the LMU Munich Institute of Pathology. Patients with externally performed CGP were registered and discussed within our MTB in select cases. Starting in 2016, in-house panel sequencing was performed with Oncomine™ Focus Assay, a 52-gene panel, which was continuously replaced by the 161-gene panel Oncomine™ Comprehensive Assay (Thermo Fisher, Darmstadt, Germany) and the TruSight Oncology (TSO) 500™ Assay (Illumina, San Diego, USA). All panels allow simultaneous RNA and DNA sequencing with detection of insertions/deletions (indels), gene fusions, single-nucleotide variants (SNV), and copy number variations (CNV). Additionally, tumor mutational burden (TMB) was evaluated in select cases (Oncomine™ Tumor Mutational Load Assay, ThermoFisher Scientific). CGP was either performed on FFPE tumor tissue or liquid biopsies (e.g., cerebrospinal fluid, blood, or ascites). Material from primary tumor, metastases, or locally recurrent tumor was used. Young patients with rare sarcomas were referred to the National Center for Tumor Diseases (NCT) and German Cancer Consortium (DKTK) Molecularly Aided Stratification for Tumor Eradication (MASTER) program for whole genome/exome and transcriptome analysis in select cases (Horak et al. 2017 (link), 2021 (link)).
Berclaz L.M., Burkhard-Meier A., Lange P., Di Gioia D., Schmidt M., Knösel T., Klauschen F., von Bergwelt-Baildon M., Heinemann V., Greif P.A., Westphalen C.B., Heinrich K, & Lindner L.H. (2023). Implementing precision oncology for sarcoma patients: the CCCLMUmolecular tumor board experience. Journal of Cancer Research and Clinical Oncology, 149(15), 13973-13983.
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