Cancer Res Treat.  2019 Jan;51(1):211-222. 10.4143/crt.2018.132.

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

Affiliations
  • 1Division of Hematology and Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea. kpark@skku.edu
  • 2Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
  • 3Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
  • 4Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
  • 5Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, Korea.
  • 6Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
  • 7Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea.
  • 8Department of Colon & Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
  • 9Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
  • 10Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea. dynoh@snu.ac.kr
  • 11Department of Thoracic and Cardiovascular Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea.
  • 12Department of Internal Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea.
  • 13Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
  • 14Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea.
  • 15Department of Pathology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea.
  • 16Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Korea.
  • 17Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.
  • 18Department of Medical Informatics, Pusan National University School of Medicine, Yangsan, Korea.
  • 19Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea.
  • 20Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Kor.

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.

Keyword

Actionable genetic alteration; Precision medicine; Next generation sequencing; Targeted panel sequencing; Cancer genomics
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