Broad, hybrid capture-based next generation sequencing in metastatic colorectal
PUBLISHED: 2015-11-27  591 total views, 1 today

Helei Hou1, Xiaofei Wang2, Chengquan Wen2, Xiaomei Xu2, Lihua Deng2, Chuantao Zhang2, Wenjun Yu2, Dong Liu2, Xiaonan Yang3, Xiaoping Zhang4Zhuokun Li5, Yingxin Han4, Rongjiao Wang4, Yanfang Guan4, Xin Yi4Shiying Xuan2, Xiaochun Zhang2

1Cancer Center, Qingdao Municipal Hospital, Qingdao University, 2Qingdao University, Qingdao Municipal Hospital, 3BGI, Beijing Genomics Institute (BGI)-Shenzhen; Innovation College of Qingdao University (QDU)-BGI; Beijing Genomics Institute (BGI)-Qingdao, 4BGI, Beijing Genomics Institute (BGI)-Shenzhen, 5Beijing Genomics Institute (BGI)-Qingdao, Beijing Genomics Institute (BGI)-Shenzhen


Objective:Patients with metastatic colorectal cancer are now recommended to profile for RAS and BRAF mutations before receiving cetuximab or panitumumab. However, lots of patients with both RAS and BRAF wild-type tumors determined by non-NGS testing might still notrespond due to the presence of additional gene mutation such as PIK3CA or PTEN. Therefore, it's necessary to screen mutations in genes other than RAS and BRAF on the efficacy of anti-EGFR therapy. Besides, new available agents could potentially be used based on the other targetable alterations discovered. In this study, abroad, hybrid capture-based next generation sequencing (NGS) assay was used to identify RAS, BRAF and additionally targetable genetic alterations from colorectal cancer tissue. Method: 64 cases of colorectal cancers were enrolled and all the patients signed the informed consent before assay. 7708 exons of 508 tumor related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, indels, copy numberalterations, and gene fusions. The average median sequencing depth was 460×. Result: 50.0% (32/64) of the tumors harbored a KRAS mutation, 4.7% (3/64) harbored a NRAS mutation and 4.7% (3/64) harbored a BRAF mutation. More specifically, 80.0% (28/35) of RAS mutation was located in exon2. Except for RAS and RAF, 6.3% (4/64) anti-EGFR therapy response genetic mutations were found in PTEN (n=3) and PIK3CA (n=1). It's also worth noting that actionable alterations were found in HER2 (n=5), FBXW7 (n=4), NF1 (n=2), SMAD4 (n=2), and others (n=6). assay was used to identify RAS, BRAF and additionally targetable genetic alterations from colorectal cancer tissue. Conclusion: Our results implied that 65.6% (42/64) metastatic colorectal cancers with genetic mutations including RAS, BRAF, PIK3CA and PTEN might not benefit from anti-EGFR therapy. Significantly, 40.6% (26/64) of samples harbored at least one actionable genetic alteration rather than RAS identified by NGS testing. These findings suggest that high throughput NGS testing in colorectal cancer tissue was a comprehensive and efficient genomic profiling assay to guide personalized therapy.


Key Words: colorectal cancer  genetic alteration  next generation

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