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Pharmacogenomics J. 2014 Dec;14(6):503-8. doi: 10.1038/tpj.2014.17. Epub 2014 Apr 8.

Whole-genome analysis of a patient with early-stage small-cell lung cancer.

Author information

1
Lung Cancer Branch, National Cancer Center, Goyang, Republic of Korea.
2
Cancer Genomics Branch, National Cancer Center, Goyang, Republic of Korea.
3
Clinomics Inc, Suwon, Republic of Korea.
4
1] Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea [2] Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea.
5
Theragen Bio Institute, TheragenEtex, Suwon, Republic of Korea.
6
Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea.

Abstract

We performed whole-genome sequencing (WGS) of a case of early-stage small-cell lung cancer (SCLC) to analyze the genomic features. WGS revealed a lot of single-nucleotide variations (SNVs), small insertion/deletions and chromosomal abnormality. Chromosomes 4p, 5q, 13q, 15q, 17p and 22q contained many block deletions. Especially, copy loss was observed in tumor suppressor genes RB1 and TP53, and copy gain in oncogene hTERT. Somatic mutations were found in TP53 and CREBBP. Novel nonsynonymous (ns) SNVs in C6ORF103 and SLC5A4 genes were also found. Sanger sequencing of the SLC5A4 gene in 23 independent SCLC samples showed another nsSNV in the SLC5A4 gene, indicating that nsSNVs in the SLC5A4 gene are recurrent in SCLC. WGS of an early-stage SCLC identified novel recurrent mutations and validated known variations, including copy number variations. These findings provide insight into the genomic landscape contributing to SCLC development.

PMID:
24709692
DOI:
10.1038/tpj.2014.17
[Indexed for MEDLINE]
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