Analysis of Copy Number Variations in Solid Tumors Using a Next Generation Sequencing Custom Panel

• Main Authors: Marta Vives-Usano (Author), Beatriz García Pelaez (Author), Ruth Román Lladó (Author), Mónica Garzón Ibañez (Author), Erika Aldeguer (Author), Sonia Rodriguez (Author), Andrés Aguilar (Author), Francesc Pons (Author), Santiago Viteri (Author), Carlos Cabrera (Author), Maria José Catalán (Author), Irene Moya (Author), María Gonzalez Cao (Author), Juan José García-Mosquera (Author), Alejandro Martinez-Bueno (Author), Ekaterina Meshoulam (Author), Nuria Jordana (Author), Laura Berrocal (Author), Rafael Rosell (Author), Miguel Angel Molina (Author), Clara Mayo de las Casas (Author)
• Format: Book
• Published: MDPI AG, 2021-05-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.
• Notes: 10.3390/jmp2020013; 2673-5261
• Keywords: tumor; mutations; next generation sequencing; copy number alterations; Pathology; RB1-214
• Source: Journal of Molecular Pathology, Vol 2, Iss 2, Pp 123-134 (2021)

Somatic copy number variations (CNV; i.e., amplifications and deletions) have been implicated in the origin and development of multiple cancers and some of these aberrations are designated targets for therapies. Although FISH is still considered the gold standard for CNV detection, the increasing number of potentially druggable amplifications to be assessed makes a gene-by-gene approach time- and tissue-consuming. Here we investigated the potential of next generation sequencing (NGS) custom panels to simultaneously determine CNVs across FFPE solid tumor samples. DNA was purified from cell lines and FFPE samples and analyzed by NGS sequencing using a 20-gene custom panel in the GeneReader Platform^®. CNVs were identified using an in-house algorithm based on the UMI read coverage. Retrospective validation of in-house algorithm to identify CNVs showed 97.1% concordance rate with the NGS custom panel. The prospective analysis was performed in a cohort of 243 FFPE samples from patients arriving at our hospital, which included 74 NSCLC tumors, 148 CRC tumors, and 21 other tumors. Of them, 33% presented CNVs by NGS and in 14 cases (5.9%) the CNV was the only alteration detected. We have identified CNV alterations in about one-third of our cohort, including <i>FGFR1</i>, <i>CDK6</i>, <i>CDK4</i>, <i>EGFR</i>, <i>MET</i>, <i>ERBB2</i>, <i>BRAF</i>, or <i>KRAS</i>. Our work highlights the need to include CNV testing as a part of routine NGS analysis in order to uncover clinically relevant gene amplifications that can guide the selection of therapies.