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Updated: Mar 25, 2026
Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing
Published on: October 10, 2025
Chromosomal microarray provides enhanced targetable gene aberration detection when paired with next generation
S Mukherjee1, Z Ma1, S Wheeler1
1PathGroup, Nashville, TN, USA.
Abstract:
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.
Insights
Combining chromosomal microarray (CMA) and next-generation sequencing (NGS) enhances genomic assessment for lung and colorectal cancers. This integrated approach identifies more clinically actionable drug targets than NGS alone, improving cancer treatment strategies.
Area of Science:
- Oncology
- Genomics
- Cancer Research
Background:
- Targeted therapies for lung and colorectal cancers rely on identifying specific genomic alterations.
- Chromosomal microarray (CMA) and next-generation sequencing (NGS) are key technologies for genomic analysis in cancer.
Purpose of the Study:
- To evaluate the combined utility of CMA and NGS for comprehensive genomic assessment of lung and colorectal adenocarcinomas.
- To identify drug targets through integrated genomic analysis.
Main Methods:
- Comparative analysis of NGS and CMA data from 60 lung and 51 colorectal tumors.
- Assessment of copy number variations (CNVs), pathogenic variants, and loss of heterozygosity.
Main Results:
- NGS identified pathogenic variants in 81% of colorectal and 67% of lung tumors.
- CMA revealed widespread copy number alterations, including amplification, gains, losses, and loss of heterozygosity.
- 23% of tumors had targetable CNVs identified by CMA when NGS detected no pathogenic variants.
- Specific genomic alterations like KRAS mutations with TP53 loss and BRCA1/NF1 loss in male lung cancer patients were noted.
Conclusions:
- Combining CMA and NGS offers a significant benefit for comprehensive genomic assessment in clinical settings.
- The integrated approach identifies clinically actionable targets missed by NGS alone, enhancing molecularly guided cancer therapies.
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