Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients

Youngwook Kim, Peter S. Hammerman, Jaegil Kim, Ji Ae Yoon, Yoomi Lee, Jong Mu Sun, Matthew D. Wilkerson, Chandra Sekhar Pedamallu, Kristian Cibulskis, Yeong Kyung Yoo, Michael S. Lawrence, Petar Stojanov, Scott L. Carter, Aaron McKenna, Chip Stewart, Andrey Y. Sivachenko, In Jae Oh, Hong Kwan Kim, Yong Soo Choi, Kwhanmien KimYoung Mog Shim, Kyu Sik Kim, Sang Yun Song, Kook Joo Na, Yoon La Choi, D. Neil Hayes, Jhingook Kim, Sukki Cho, Young Chul Kim, Jin Seok Ahn, Myung Ju Ahn, Gad Getz, Matthew Meyerson, Keunchil Park*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

166 Scopus citations


Purpose: Lung squamous cell carcinoma (SCC) is the second most prevalent type of lung cancer. Currently, no targeted therapeutics are approved for treatment of this cancer, largely because of a lack of systematic understanding of the molecular pathogenesis of the disease. To identify therapeutic targets and perform comparative analyses of lung SCC, we probed somatic genome alterations of lung SCC by using samples from Korean patients. Patients and Methods: We performed whole-exome sequencing of DNA from 104 lung SCC samples from Korean patients and matched normal DNA. In addition, copy-number analysis and transcriptome analysis were conducted for a subset of these samples. Clinical association with cancer-specific somatic alterations was investigated. Results: This cancer cohort is characterized by a high mutational burden with an average of 261 somatic exonic mutations per tumor and a mutational spectrum showing a signature of exposure to cigarette smoke. Seven genes demonstrated statistical enrichment for mutation: TP53, RB1, PTEN, NFE2L2, KEAP1, MLL2, and PIK3CA). Comparative analysis between Korean and North American lung SCC samples demonstrated a similar spectrum of alterations in these two populations in contrast to the differences seen in lung adenocarcinoma. We also uncovered recurrent occurrence of therapeutically actionable FGFR3-TACC3 fusion in lung SCC. Conclusion: These findings provide new steps toward the identification of genomic target candidates for precision medicine in lung SCC, a disease with significant unmet medical needs.

Original languageEnglish
Pages (from-to)121-128
Number of pages8
JournalJournal of Clinical Oncology
Issue number2
StatePublished - 10 Jan 2014
Externally publishedYes


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