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

 Se-Hoon Lee  ;  Boram Lee  ;  Joon Ho Shim  ;  Kwang Woo Lee  ;  Jae Won Yun  ;  Sook-Young Kim  ;  Tae-You Kim  ;  Yeul Hong Kim  ;  Young Hyeh Ko  ;  Hyun Cheol Chung  ;  Chang Sik Yu  ;  Jeeyun Lee  ;  Sun Young Rha  ;  Tae Won Kim  ;  Kyung Hae Jung  ;  Seock-Ah Im  ;  Hyeong-Gon Moon  ;  Sukki Cho  ;  Jin Hyoung Kang  ;  Jihun Kim  ;  Sang Kyum Kim  ;  Han Suk Ryu  ;  Sang Yun Ha  ;  Jong Il Kim  ;  Yeun-Jun Chung  ;  Cheolmin Kim  ;  Hyung-Lae Kim  ;  Woong-Yang Park  ;  Dong-Young Noh  ;  Keunchil Park 
 Cancer Research and Treatment, Vol.51(1) : 211-222, 2019 
Journal Title
 Cancer Research and Treatment 
Issue Date
DNA, Neoplasm/genetics ; DNA, Neoplasm/standards ; Gene Amplification ; Genetic Predisposition to Disease ; High-Throughput Nucleotide Sequencing/methods* ; Humans ; Mutation* ; Neoplasms/genetics* ; Precision Medicine ; Republic of Korea ; Sequence Analysis, DNA/methods* ; Tissue Fixation
Actionable genetic alteration ; Cancer genomics ; Next generation sequencing ; Precision medicine ; Targeted panel sequencing
PURPOSE: 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. Materials and Methods: 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. RESULTS: 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. CONCLUSION: 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.
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1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Internal Medicine (내과학교실) > 1. Journal Papers
Yonsei Authors
Kim, Sang Kyum(김상겸) ORCID logo https://orcid.org/0000-0003-0768-9923
Rha, Sun Young(라선영) ORCID logo https://orcid.org/0000-0002-2512-4531
Chung, Hyun Cheol(정현철) ORCID logo https://orcid.org/0000-0002-0920-9471
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