Genomics Inform.  2014 Jun;12(2):50-57. 10.5808/GI.2014.12.2.50.

New Lung Cancer Panel for High-Throughput Targeted Resequencing

• Kim EH
• Lee S
• Park J
• Lee K
• Bhak J
• Kim BC

• KMID: 2026459
• DOI: http://doi.org/10.5808/GI.2014.12.2.50

Abstract

We present a new next-generation sequencing-based method to identify somatic mutations of lung cancer. It is a comprehensive mutation profiling protocol to detect somatic mutations in 30 genes found frequently in lung adenocarcinoma. The total length of the target regions is 107 kb, and a capture assay was designed to cover 99% of it. This method exhibited about 97% mean coverage at 30x sequencing depth and 42% average specificity when sequencing of more than 3.25 Gb was carried out for the normal sample. We discovered 513 variations from targeted exome sequencing of lung cancer cells, which is 3.9-fold higher than in the normal sample. The variations in cancer cells included previously reported somatic mutations in the COSMIC database, such as variations in TP53, KRAS, and STK11 of sample H-23 and in EGFR of sample H-1650, especially with more than 1,000x coverage. Among the somatic mutations, up to 91% of single nucleotide polymorphisms from the two cancer samples were validated by DNA microarray-based genotyping. Our results demonstrated the feasibility of high-throughput mutation profiling with lung adenocarcinoma samples, and the profiling method can be used as a robust and effective protocol for somatic variant screening.

Keyword

high-throughput nucleotide sequencing; lung neoplasms; next-generation sequencing; selector technology; somatic mutation screening; target enrichment

MeSH Terms

Adenocarcinoma
DNA
Exome
High-Throughput Nucleotide Sequencing
Lung
Lung Neoplasms*
Mass Screening
Polymorphism, Single Nucleotide
Sensitivity and Specificity
DNA