Landscape of Actionable Genetic Alterations Profiled from 1,071 Tumor Samples in Korean Cancer Patients

• Published in: Cancer research and treatment Vol. 51; no. 1; pp. 211 - 222
• Main Authors: Lee, Se-Hoon, Lee, Boram, Shim, Joon Ho, Lee, Kwang Woo, Yun, Jae Won, Kim, Sook-Young, Kim, Tae-You, Kim, Yeul Hong, Ko, Young Hyeh, Chung, Hyun Cheol, Yu, Chang Sik, Lee, Jeeyun, Rha, Sun Young, Kim, Tae Won, Jung, Kyung Hae, Im, Seock-Ah, Moon, Hyeong-Gon, Cho, Sukki, Kang, Jin Hyoung, Kim, Jihun, Kim, Sang Kyum, Ryu, Han Suk, Ha, Sang Yun, Kim, Jong Il, Chung, Yeun-Jun, Kim, Cheolmin, Kim, Hyung-Lae, Park, Woong-Yang, Noh, Dong-Young, Park, Keunchil
• Format: Journal Article
• Language: English
• Published: Korea (South) Korean Cancer Association 01.01.2019; 대한암학회
• Subjects: DNA, Neoplasm - genetics; DNA, Neoplasm - standards; Gene Amplification; Genetic Predisposition to Disease; High-Throughput Nucleotide Sequencing - methods; Humans; Mutation; Neoplasms - genetics; Original; Precision Medicine; Republic of Korea; Sequence Analysis, DNA - methods; Tissue Fixation; 의학일반; Republic of Korea; Actionable genetic alteration; Precision medicine; Targeted panel sequencing; Next generation sequencing; Cancer genomics
• ISSN: 1598-2998; 2005-9256; 2005-9256
• DOI: 10.4143/crt.2018.132

With the emergence of next-generation sequencing (NGS) technology, profiling a wide range of genomic alterations has become a possibility resulting in improved implementation of targeted cancer therapy. In Asian populations, the prevalence and spectrum of clinically actionable genetic alterations has not yet been determined because of a lack of studies examining high-throughput cancer genomic data. To address this issue, 1,071 tumor samples were collected from five major cancer institutes in Korea and analyzed using targeted NGS at a centralized laboratory. Samples were either fresh frozen or formalin-fixed, paraffin embedded (FFPE) and the quality and yield of extracted genomic DNA was assessed. In order to estimate the effect of sample condition on the quality of sequencing results, tissue preparation method, specimen type (resected or biopsied) and tissue storage time were compared. We detected 7,360 non-synonymous point mutations, 1,164 small insertions and deletions, 3,173 copy number alterations, and 462 structural variants. Fifty-four percent of tumors had one or more clinically relevant genetic mutation. The distribution of actionable variants was variable among different genes. Fresh frozen tissues, surgically resected specimens, and recently obtained specimens generated superior sequencing results over FFPE tissues, biopsied specimens, and tissues with long storage duration. In order to overcome, challenges involved in bringing NGS testing into routine clinical use, a centralized laboratory model was designed that could improve the NGS workflows, provide appropriate turnaround times and control costs with goal of enabling precision medicine.