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

• Lee SH
• Lee B
• Shim JH
• Lee KW
• Yun JW
• Kim SY
• Kim TY
• Kim YH
• Ko YH
• Chung HC
• Yu CS
• Lee J
• Rha SY
• Kim TW
• Jung KH
• Im SA
• Moon HG
• Cho S
• Kang JH
• Kim J
• Kim SK
• Ryu HS
• Ha SY
• Kim JI
• Chung YJ
• Kim C
• Kim HL
• Park WY
• Noh DY
• Park K

• KMID: 2437614
• DOI: http://doi.org/10.4143/crt.2018.132

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

MeSH Terms

Academies and Institutes
Asian Continental Ancestry Group
DNA
Humans
Korea
Methods
Paraffin
Point Mutation
Precision Medicine
Prevalence
DNA
Paraffin

Figure

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  Fig. 1. Diagram of central lab model. Samples are collected to a central lab and processed using the same platform so the resulting data can be easily integrated. At a central laboratory, sample preparation procedures, including quality control, sequencing, and data analysis, were performed. In this project, five tertiary hospitals were participating. FF, fresh frozen; FFPE, formalin-fixed, paraffin embedded.

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  Fig. 2. The effect of sample condition on extracted DNA size. (A) In formalin-fixed, paraffin embedded (FFPE) samples, the size of DNA was shorter with degradation. This phenomenon was more prominent in resected tissues than in biopsied tissues. The horizontal line at 350 bp represented the minimum required size of extracted DNA to be included in the sequencing step. (B) The size of DNA tended to be shorter as storage duration prolonged. The horizontal line at 350 bp represented the minimum required size of extracted DNA to be included in the sequencing step. FF, fresh frozen; NSCLC, non-small cell lung cancer; SCLC, small cell lung cancer.

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  Fig. 3. Multivariate analysis of the effect of sample condition on QC pass. QC fails were more frequently observed particularly in biopsied specimens or specimens with long storage time. In the forest plot, odds ratios (ORs) were described in log scale. When the confidence interval does not contain 1.00, the p-value is less than 0.05. FF, fresh frozen; FFPE, formalin-fixed, paraffin embedded.

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  Fig. 4. Proportion of patients having actionable variants of certain genes in this cohort. Most frequently observed mutations in each cancer types were EGFR mutation in non-small cell lung cancer (NSCLC), RICTOR amplification in small cell lung cancer (SCLC), KRAS mutation in colorectal cancer (CRC), and PIK3CA mutation in breast cancer and stomach cancer. Significant proportion of actionable mutations were found in low frequency, showing long tail.

Reference

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