A Computational Framework for Comprehensive Genomic Profiling in Solid Cancers: The Analytical Performance of a High-Throughput Assay for Small and Copy Number Variants.
Simple Summary: Comprehensive genomic profiling (CGP) is key to characterizing solid tumors at the molecular level and enabling personalized therapy. To this end, Fondazione Policlinico Universitario Agostino Gemelli IRCCS launched a CGP program enrolling cancer patients who were screened for nine d...
| Publicado en: | Cancers Vol. 14; no. 24; pp. 6152 - 6166 |
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| Autores principales: | , , , , , , , , , , , , , , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
MDPI
12/15/2022
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=160958733&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 160958733 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 20726694 B74B jtl: Cancers issn: 20726694 maglogo: N pubinfo: dt: 12/15/2022 vid: 14 iid: 24 pid: 97109 pub: MDPI artinfo: ui: 160958733 160958733 160958733 10.3390/cancers14246152 160958733 ppf: 6152 ppct: 14 formats: tig: atl: A Computational Framework for Comprehensive Genomic Profiling in Solid Cancers: The Analytical Performance of a High-Throughput Assay for Small and Copy Number Variants. aug: au: Giacò, Luciano Palluzzi, Fernando Guido, Davide Nero, Camilla Giacomini, Flavia Duranti, Simona Bria, Emilio Tortora, Giampaolo Cenci, Tonia Martini, Maurizio De Paolis, Elisa Onori, Maria Elisabetta De Bonis, Maria Normanno, Nicola Scambia, Giovanni Minucci, Angelo affil: Bioinformatics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy sug: subj: Conceptual Framework Gene Expression Profiling Neoplasms Bioinformatics Sequence Analysis Genomics Nucleotides Reproducibility of Results DNA Analysis RNA Analysis Data Analysis Software Descriptive Statistics ab: Simple Summary: Comprehensive genomic profiling (CGP) is key to characterizing solid tumors at the molecular level and enabling personalized therapy. To this end, Fondazione Policlinico Universitario Agostino Gemelli IRCCS launched a CGP program enrolling cancer patients who were screened for nine different solid tumors (breast, colon, GIST, lung, melanoma, ovary, pancreas, prostate and thyroid). In this context, we evaluated the performance of the Illumina® TSO500 high-throughput assay. In January 2022, our institution launched a comprehensive cancer genome profiling program on 10 cancer types using a non-IVD solution named the TruSight Oncology 500 Assay provided by Illumina®. The assay analyzes both DNA and RNA, identifying Single-Nucleotide Variants (SNV)s and Insertion–Deletion (InDel) in 523 genes, as well as known and unknown fusions and splicing variants in 55 genes and Copy Number Alterations (CNVs), Mutational Tumor Burden (MTB) and Microsatellite Instability (MSI). According to the current European IVD Directive 98/79/EC, an internal validation was performed before running the test. A dedicated open-source bioinformatics pipeline was developed for data postprocessing, panel assessment and embedding in high-performance computing framework using the container technology to ensure scalability and reproducibility. Our protocols, applied to 71 DNA and 64 RNA samples, showed full agreement between the TruSight Oncology 500 assay and standard approaches, with only minor limitations, allowing to routinely perform our protocol in patient screening. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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