Cancer Research and Treatment

Original Articles

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 Res Treat. 2019;51(1):211-222. Published online April 23, 2018; DOI: https://doi.org/10.4143/crt.2018.132

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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.

Citations

Citations to this article as recorded by

Clinical implementation of next-generation sequencing testing and genomically-matched therapy: a real-world data in a tertiary hospital
Jin Won Kim, Hee Young Na, Sejoon Lee, Ji-Won Kim, Koung Jin Suh, Se Hyun Kim, Yu Jung Kim, Keun-Wook Lee, Jong Seok Lee, Jaihwan Kim, Jin-Hyeok Hwang, Kihwan Hwang, Chae-Yong Kim, Yong Beom Kim, Soomin Ahn, Kyu Sang Lee, Hyojin Kim, Hye Seung Lee, So Yeo
Scientific Reports.2025;[Epub] CrossRef
Real-World Data and Clinical Implications of Next-Generation Sequencing (NGS)-Based Analysis in Metastatic Breast Cancer Patients
Fabio Canino, Antonio Tornincasa, Stefania Bettelli, Samantha Manfredini, Monica Barbolini, Luca Moscetti, Claudia Omarini, Angela Toss, Fabio Tamburrano, Giuseppina Antonelli, Federica Baglio, Lorenzo Belluzzi, Giulio Martinelli, Salvatore Natalizio, Orn
International Journal of Molecular Sciences.2024; 25(5): 2490. CrossRef
Exploring the DNA methylome of Korean patients with colorectal cancer consolidates the clinical implications of cancer-associated methylation markers
Sejoon Lee, Kil-yong Lee, Ji-Hwan Park, Duck-Woo Kim, Heung-Kwon Oh, Seong-Taek Oh, Jongbum Jeon, Dongyoon Lee, Soobok Joe, Hoang Bao Khanh Chu, Jisun Kang, Jin-Young Lee, Sheehyun Cho, Hyeran Shim, Si-Cho Kim, Hong Seok Lee, Young-Joon Kim, Jin Ok Yang,
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Establishing molecular pathology curriculum for pathology trainees and continued medical education: a collaborative work from the Molecular Pathology Study Group of the Korean Society of Pathologists
Jiwon Koh, Ha Young Park, Jeong Mo Bae, Jun Kang, Uiju Cho, Seung Eun Lee, Haeyoun Kang, Min Eui Hong, Jae Kyung Won, Youn-La Choi, Wan-Seop Kim, Ahwon Lee
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IC Uzoma, IA Taiwo, NI Ugwu, MA Durosinmi, O Akinloye
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Effects of Polymorphisms of Innate Immunity Genes and Environmental Factors on the Risk of Noncardia Gastric Cancer: Jeongseon Kim, Young Ae Cho, Il Ju Choi, Yeon-Su Lee, Sook-Young Kim, Jung-Ah Hwang, Soo-Jeong Cho, Myeong-Cherl Kook, Chan Gyoo Kim, Young-Woo Kim; Cancer Res Treat. 2013;45(4):313-324. Published online December 31, 2013; DOI: https://doi.org/10.4143/crt.2013.45.4.313

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PURPOSE
Increasing evidence suggests that polymorphisms in innate immunity genes are associated with Helicobacter pylori-induced inflammation and may influence susceptibility in developing noncardia gastric cancer. Therefore, we investigate the effect of polymorphisms of innate immunity genes and interactions with environmental factors in the Korean population.
MATERIALS AND METHODS
We genotyped four polymorphisms of TLR2 (rs1898830), TLR4 (rs10983755 and rs10759932), and CD14 (rs2569190) in a case-control study of 487 noncardia gastric cancer patients and 487 sex- and age-matched healthy controls. Polytomous logistic regression models were used to detect the effects of genetic polymorphisms and environmental factors, which were stratified by the histological type of gastric cancer.
RESULTS
TLR4 rs10983755 A carriers were found to have higher risk of intestinal-type noncarida gastric cancer than G homozygotes (odds ratio [OR], 1.41; 95% confidence interval [CI], 1.01 to 1.97), but other genetic variants showed no association with the risk of noncardia gastric cancer. Among H. pylori-positive participants, smokers carrying TLR4 rs10983755 A had a higher risk of intestinal-type gastric cancer than nonsmoking TLR4 rs10983755 G homozygotes (OR, 4.28; 95% CI, 2.12 to 8.64). In addition, compared with tap water, other drinking water sources during childhood were found to be associated with the elevated risk of intestinal-type gastric cancer, and these associations were slightly stronger among TLR4 rs10983755 A carriers.
CONCLUSION
The genetic polymorphisms of innate immunity genes are associated with the development of intestinal-type noncardia gastric cancer and these associations may differ in accordance to an exposure to certain environmental factors.

Citations

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