Abstract 3171: Powerful target capture/NGS approach reveals extensive genetic changes including SNVs, CNVs and gross chromosomal rearrangements in colorectal cancers
Authors: Dai Hongzheng , Tian Xia , Chen Stella , Wang Yue , Yang Tzu-Wei , Lin Chun-Che , Tsai Ming-Chang , Wang Chih-Hong , Huang Chi-Chou , Shih Chin-Ying , Chiou Guang-Yuh , Jong Yuh-Jyh , Wong Lee-Jun 
Published: July 2016

Abstract
Introduction: Accurate and comprehensive molecular analyses of genetic changes in cancer tissues are critical for cancer management, treatment, and genetic counseling. Study of the complete molecular profiles in patient's blood, cacinoma tissue and surrounding pathological normal tissues will help us understand the etiology of colorectal cancers (CRC) as either hereditary or sporadic. In addition, this study will also reveal somatic changes and possible targets for therapy. Multigene target capture followed by deep next generation sequencing (NGS) provides a powerful approach to simultaneously detect both single nucleotide variants (SNVs) and exonic copy number variants (CNVs) in a time and cost effective fashion.
Method: DNA samples were prepared from blood, freshly frozen normal surrounding and carcinoma or polyp tissues from 20 patients with CRC and 10 patients with colorectal polyps. A custom probe library containing 183 cancer related genes was used to capture the target sequences followed by NGS with deep coverage (average depth per base is ∼1000X). Both SNVs and CNVs were analyzed based on in-house developed analytical algorithm and bioinformatics pipeline.
Results: This study revealed extensive genetic changes in colon carcinoma tissues. At least 40% of the colon carcinoma samples harbor loss-of-function pathogenic germline mutations in cancer related genes. However, loss of function germline mutations were not found in the polyps. Germline missense variants of unknown significance were identified in 60% of the polyps. Multiple deleterious somatic mutations are identified in all carcinoma tissues but only 1-2 somatic mutations per sample are found in the polyps. Almost every carcinoma tissue harbor gross chromosomal rearrangement, which is only found in about 50% of the polyp tissues.. NGS based CNV analysis revealed 2 germline events (FANCD2 E15-16 del; whole ALK gene dup). Somatic CNV events are more frequently observed in carcinoma tissues. Gross changes at chromosomal levels were also detected by using the NGS CNV analytical algorithm. Recurrent somatic pathogenic variants in genes associated with CRC, such as APC, TP53, and KRAS were identified while novel likely pathogenic variants in novel genes possibly linked to CRC were also discovered for further investigation. Heterogeneity of carcinoma tissues within the same individual was suggested by comparing allele frequency of different somatic mutations. Numerous loss of heterozygosity was observed in both carcinoma and polyp tissues.
Conclusion: Target capture/NGS approach allows simultaneous analyses of SNVs and CNVs with quantitative data to distinguish between germline and somatic mutations. These analyses reveal abundant and valuable molecular information for target therapy, patient management, genetic counseling, and new insights of possible pathogenic mechanism
Citation Format: Hongzheng Dai, Xia Tian, Stella Chen, Yue Wang, Tzu-Wei Yang, Chun-Che Lin, Ming-Chang Tsai, Chih-Hong Wang, Chi-Chou Huang, Chin-Ying Shih, Guang-Yuh Chiou, Yuh-Jyh Jong, Lee-Jun Wong. Powerful target capture/NGS approach reveals extensive genetic changes including SNVs, CNVs and gross chromosomal rearrangements in colorectal cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3171.