Chromosomal microarray provides enhanced targetable gene aberration detection when paired with next generation sequencing panel in profiling lung and colorectal tumors

• Published in: Cancer genetics Vol. 209; no. 4; pp. 119 - 129
• Main Authors: Mukherjee, S, Ma, Z, Wheeler, S, Sathanoori, M, Coldren, C, Prescott, J.L, Kozyr, N, Bouzyk, M, Correll, M, Ho, H, Chandra, P.K, Lennon, P.A
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.04.2016
• Subjects: Chromosome Aberrations; CMA; Cohort Studies; colon; Colorectal Neoplasms - genetics; Hematology, Oncology and Palliative Medicine; High-Throughput Nucleotide Sequencing - methods; Humans; Loss of Heterozygosity; lung; Lung Neoplasms - genetics; Male; Medical Education; NGS; profiling; Tissue Array Analysis - methods; Transcriptional Activation - genetics; lung; colon; NGS; profiling; CMA
• ISSN: 2210-7762; 2210-7770
• DOI: 10.1016/j.cancergen.2015.12.011

The development of targeted therapies based on specific genomic alterations has altered the treatment and management of lung and colorectal cancers. Chromosomal microarray (CMA) has allowed identification of copy number variations (CNVs) in lung and colorectal cancers in great detail, and next-generation sequencing (NGS) is used extensively to analyze the genome of cancers for molecular subtyping and use of molecularly guided therapies. The main objective of this study was to evaluate the utility of combining CMA and NGS for a comprehensive genomic assessment of lung and colorectal adenocarcinomas, especially for detecting drug targets. We compared the results from NGS and CMA data from 60 lung and 51 colorectal tumors. From CMA analysis, 33% were amplified, 89% showed gains, 75% showed losses and 41% demonstrated loss of heterozygosity; pathogenic variants were identified in 81% of colon and 67% lung specimens through NGS. KRAS mutations commonly occurred with loss in TP53 and there was significant loss of BRCA1 and NF1 among male patients with lung cancer. For clinically actionable targets, 23% had targetable CNVs when no pathogenic variants were detected by NGS. The data thus indicate that combining the two approaches provides significant benefit in a routine clinical setting not available by NGS alone.