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.
Bibliographical noteFunding Information:
We thank Kirsten Curnow, Kristine Jinnett, and Mueller Amy, an employee of Illumina Inc., for providing medical writing support. This research was supported by a grant of the Korean Health Technology R&D Project through the Korea Health Industry Development Institute, funded by the Ministry of Health & Welfare, Republic of Korea (HI13C2096 to W.Y.P., HI14C0072 to H.L.K.), and grant from Ministry of Food and Drug Safety, Republic of Korea (16173-MFDS004 to W.Y.P.).
The authors declare that they have no conflicts of interests. This research was mainly funded by Illumina Inc. (San Diego, CA, USA).
Copyright © 2019 by the Korean Cancer Association
- Actionable genetic alteration
- Cancer genomics
- Next generation sequencing
- Precision medicine
- Targeted panel sequencing
ASJC Scopus subject areas
- Cancer Research