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 KimSang 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

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3 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)211-222
Number of pages12
JournalCancer Research and Treatment
Volume51
Issue number1
DOIs
Publication statusPublished - 2019 Jan 1

All Science Journal Classification (ASJC) codes

  • Oncology
  • Cancer Research

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    Lee, S. H., Lee, B., Shim, J. H., Lee, K. W., Yun, J. W., Kim, S. Y., Kim, T. Y., Kim, Y. H., Ko, Y. H., Chung, H. C., Yu, C. S., Lee, J., Rha, S. Y., Kim, T. W., Jung, K. H., Im, S. A., Moon, H. G., Cho, S., Kang, J. H., ... Park, K. (2019). Landscape of actionable genetic alterations profiled from 1,071 tumor samples in Korean cancer patients. Cancer Research and Treatment, 51(1), 211-222. https://doi.org/10.4143/crt.2018.132