Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis

  • Authors:
    • Li Tai Fang
    • Sharon Lee
    • Helen Choi
    • Hong Kwan Kim
    • Gregory Jew
    • Hio Chung Kang
    • Lin Chen
    • David Jablons
    • Il-Jin Kim
  • View Affiliations

  • Published online on: Friday, October 25, 2013
  • Pages: 211-221
  • DOI: 10.3892/ijo.2013.2150

Abstract

We performed whole exome sequencing and gene expression analysis on a metastatic colon cancer to the lung, along with the adjacent normal tissue of the lung. Whole exome sequencing uncovered 71 high-confidence non‑synonymous mutations. We selected 16 mutation candidates, and 13 out of 16 mutations were validated by targeted deep sequencing using the Ion Torrent PGM customized AmpliSeq panel. By integrating mutation, copy number and gene expression microarray data, we identified a JAZF1 mutation with a gain-of-copy, suggesting its oncogenic potential for the lung metastasis from colon cancer. Our pathway analyses showed that the identified mutations closely reflected characteristics of the metastatic site (lung) while mRNA gene expression patterns kept genetic information of its primary tumor (colon). The most significant gene expression network was the ‘Colorectal Cancer Metastasis Signaling’, containing 6 (ADCY2, ADCY9, APC, GNB5, K-ras and LRP6) out of the 71 mutated genes. Some of these mutated genes (ADCY9, ADCY2, GNB5, K-ras, HDAC6 and ARHGEF17) also belong to the ‘Phospholipase C Signaling’ network, which suggests that this pathway and its mutated genes may contribute to a lung metastasis from colon cancer.
Journal Cover

January 2014
Volume 44 Issue 1

Print ISSN: 1019-6439
Online ISSN:1791-2423

2013 Impact Factor: 2.773
Ranked #30/202 Oncology
(total number of cites)

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APA
Fang, L., Fang, L., Lee, S., Lee, S., Choi, H., Choi, H., Kim, H., Kim, H., Jew, G., Jew, G., Kang, H., Kang, H., Chen, L., Chen, L., Jablons, D., Jablons, D., Kim, I., & Kim, I. (2014). Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis. International Journal of Oncology, 44(1), 211-221.
MLA
Fang, Fang, Lee, Lee, Choi, Choi, Kim, Kim, Jew, Jew, Kang, Kang, Chen, Chen, Jablons, Jablons, Kim, and Il-Jin Kim. "Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis." International Journal of Oncology International Journal of Oncology 44.1 (2014): 211-221.
Chicago
Fang, Fang, Lee, Lee, Choi, Choi, Kim, Kim, Jew, Jew, Kang, Kang, Chen, Chen, Jablons, Jablons, Kim, and Il-Jin Kim. "Comprehensive genomic analyses of a metastatic colon cancer to the lung by whole exome sequencing and gene expression analysis." International Journal of Oncology International Journal of Oncology 44 no. 1 (2014): 211-221.