• Molecules and Cells
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• 제42권1호
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• pp.8-16
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• 2019

Mutations in the ${\beta}-catenin$ gene (CTNNB1) have been implicated in the pathogenesis of some cancers. The recent development of cancer genome databases has facilitated comprehensive and focused analyses on the mutation status of cancer-related genes. We have used these databases to analyze the CTNNB1 mutations assembled from different tumor types. High incidences of CTNNB1 mutations were detected in endometrial, liver, and colorectal cancers. This finding agrees with the oncogenic role of aberrantly activated ${\beta}-catenin$ in epithelial cells. Elevated frequencies of missense mutations were found in the exon 3 of CTNNB1, which is responsible for encoding the regulatory amino acids at the N-terminal region of the protein. In the case of metastatic colorectal cancers, in-frame deletions were revealed in the region spanning exon 3. Thus, exon 3 of CTNNB1 can be considered to be a mutation hotspot in these cancers. Since the N-terminal region of the ${\beta}-catenin$ protein forms a flexible structure, many questions arise regarding the structural and functional impacts of hotspot mutations. Clinical identification of hotspot mutations could provide the mechanistic basis for an oncogenic role of mutant ${\beta}-catenin$ proteins in cancer cells. Furthermore, a systematic understanding of tumor-driving hotspot mutations could open new avenues for precision oncology.

• Genomics & Informatics
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• 제15권4호
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• pp.136-141
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• 2017

Accurate detection of genomic alterations, especially druggable hotspot mutations in tumors, has become an essential part of precision medicine. With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. In this study, we aimed to validate its performance. The cancer panel targets 95 cancer-related genes. In terms of the limit of detection, more than 86% of target mutations with a mutant allele frequency (MAF) <1% can be identified, and any mutation with >3% MAF can be detected. When we applied this system for the analysis of Acrometrix Oncology Hotspot Control DNA, which contains more than 500 COSMIC mutations across 53 genes, 99% of the expected mutations were robustly detected. We also confirmed the high reproducibility of the detection of mutations in multiple independent analyses. When we explored copy number alterations (CNAs), the expected CNAs were successfully detected, and this result was confirmed by target-specific genomic quantitative polymerase chain reaction. Taken together, these results support the reliability and accuracy of our cancer panel in detecting mutations. This panel could be useful for key mutation profiling research in solid tumors and clinical translation.

• BMB Reports
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• 제44권5호
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• pp.317-322
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• 2011

Hereditary non-polyposis Colorectal Cancer (HNPCC) is an autosomal dominant inheritance syndrome. HNPCC is the most common hereditary variant of colorectal cancer (CRC), which accounts for 2-5% CRCs, mainly due to hMLH1 and hMSH2 mutations that impair DNA repair functions. Our study aimed to identify the patterns of hMSH2 and hMLH1 mutations in Chinese HNPCC patients. Ninety-eight unrelated families from China meeting Amsterdam or Bethesda criteria were included in our study. Germline mutations in MLH1 and MSH2 genes, located in the exons and the splice-site junctions, were screened in the 98 probands by direct sequencing. Eleven mutations were found in ten patients (11%), with six in MLH1 (54.5%) and five in MSH2 (45.5%) genes. One patient had mutations in both MLH1 and MSH2 genes. Three novel mutations in MLH1 gene (c.157_160delGAGG, c.2157dupT and c.-64G>T) were found for the first time, and one suspected hotspot in MSH2 (c.1168C>T) was revealed.

• Journal of Gastric Cancer
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• 제20권1호
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• pp.29-40
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• 2020

Purpose: Gastrointestinal stromal tumors (GISTs) frequently harbor activating gene mutations in either KIT or platelet-derived growth factor receptor A (PDGFRA) and are highly responsive to several selective tyrosine kinase inhibitors. In this study, a targeted next-generation sequencing (NGS) assay with an Oncomine Focus Assay (OFA) panel was used for the genetic characterization of molecular targets in 30 Korean patients with GIST. Materials and Methods: Using the OFA that enables rapid and simultaneous detection of hotspots, single nucleotide variants (SNVs), insertion and deletions (Indels), copy number variants (CNVs), and gene fusions across 52 genes relevant to solid tumors, targeted NGS was performed using genomic DNA extracted from formalin-fixed and paraffin-embedded samples of 30 GISTs. Results: Forty-three hotspot/other likely pathogenic variants (33 SNVs, 8 Indels, and 2 amplifications) in 16 genes were identified in 26 of the 30 GISTs. KIT variants were most frequent (44%, 19/43), followed by 6 variants in PIK3CA, 3 in PDGFRA, 2 each in JAK1 and EGFR, and 1 each in AKT1, ALK, CCND1, CTNNB1, FGFR3, FGFR4, GNA11, GNAQ, JAK3, MET, and SMO. Based on the mutation types, majority of the variants carried missense mutations (60%, 26/43), followed by 8 frameshifts, 6 nonsense, 1 stop-loss, and 2 amplifications. Conclusions: Our study confirmed the advantage of using targeted NGS with a cancer gene panel to efficiently identify mutations associated with GISTs. These findings may provide a molecular genetic basis for developing new drugs targeting these gene mutations for GIST therapy.

• Journal of Genetic Medicine
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• 제14권2호
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• pp.56-61
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• 2017

Purpose: Neurofibromatosis type 2 (NF2) is characterized by multiple tumors, including vestibular schwannoma (VS) and others affecting cranial and peripheral nerves. NF2 is caused by mutation of the NF2 gene. The mutation spectrum of NF2 has not been characterized in Korean patients. In the current study, the clinical and genetic characteristics of Korean NF2 patients were analyzed. Materials and Methods: Twenty-five unrelated Korean families were enrolled according to the Manchester criteria. Genetic analysis was performed by direct sequencing and multiplex ligation-dependent probe amplification methods using genomic DNA from peripheral lymphocytes or tumor tissues. Results: All patients had bilateral/unilateral VS and/or other cranial and peripheral nerve tumors. Two patients were familial cases and the other 24 patients were sporadic. Germline NF2 mutations were detected in peripheral lymphocytes from both familial cases, but only in 26.1% of the 23 sporadic families. Somatic mutations were also found in tumor tissues from two of the sporadic families. These somatic mutations were not found in peripheral lymphocytes. A total of 10 different mutations including 2 novel mutations were found in 40.0% of studied families. Five mutations (50.0%) were located in exon 6 of NF2, the FERM domain coding region. Conclusion: Family history was an important factor in identifying germline NF2 mutations. Further study is required to investigate whether exon 6 is a mutation hotspot in Korean NF2 patients and its correlation to phenotypic severity.

• Asian Pacific Journal of Cancer Prevention
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• 제17권12호
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• pp.5195-5201
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• 2016

Background: Brain tumors, constituting one of the most deadly forms of cancer worldwide, result from the accumulation of multiple genetic and epigenetic alterations in genes and signaling pathways. Isocitrate dehydrogenase enzyme isoform 1 (IDH1) mutations are frequently identified in primary brain tumors and acute myeloid leukemia. Studies on IDH1 gene mutations have been extensively performed in various populations worldwide but not in Malaysia. This work was conducted to study the prevalence of IDH1 c.395G>A (R132H) hotspot mutations in a group of Malaysian patients with brain tumors in order to gain local data for the IDH1 mutation profile in our population. Methods: Mutation analysis of c.395G>A (R132H) of IDH1 was performed in 40 brain tumor specimens by the polymerase chain reaction-restriction fragment length polymorphism method (PCR-RFLP) and then verified by direct sequencing. Associations between the IDH1 c.395G>A (R132H) mutation and clinicopathologic characteristics were also analyzed. Results: The IDH1 c.395G>A (R132H) mutation was detected in 14/40 patients (35%). A significant association was found with histological tumor types, but not with age, gender and race. Conclusions: IDH1 is frequently mutated and associated with histological subtypes in Malay brain tumors.

• 대한임상검사과학회지
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• 제55권2호
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• pp.93-104
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• 2023

이전 연구에서 83명의 한국인 폐선암 환자의 차세대 염기서열 분석법(next generation sequencing, NGS) 분석 결과 돌연변이 빈도가 높은 상위 5개 유전자 TP53 (60%), EGFR (48%), KRAS (14%), PIK3CA (8%), CDKN2A (6%)를 확인했다. 본연구는 NGS 분석을 이용하여 최근 한국인의 폐선암에서 돌연변이 발생 빈도가 높은 상위 5개 유전자에 대한 돌연변이 핫스팟을 분석하여 폐선암을 유발하는 새로운 표지자를 확인하고자 했으며 가장 많은 돌연변이가 발생한 TP53 유전자의 돌연변이 유형과 패턴을 폐암의 주요 원인인 흡연과의 연관성을 분석했으며 TP53 P72R SNP가 발생한 폐선암 환자의 임상병리학적 특성을 분석하고자 했다. TP53, EGFR, KRAS, PIK3CA, CDKN2A의 돌연변이 핫스팟을 분석한 결과 이전에 보고된 결과와 일치했으나 TP53의 경우 약간의 차이를 나타냈다. TP53 돌연변이 핫스팟은 DBD에 집중하여 발생하는 점은 기존 연구 결과와 같았으나 코돈 72에서 발생하는 높은 돌연변이 빈도는 이전에 보고된 연구 결과와 다르게 나타났다. TP53 돌연변이가 발생한 폐선암 환자의 임상 특성을 분석한 결과 남성보다 여성, 흡연자보다 비흡연자에게 더 많이 발생했다. 또한, TP53 돌연변이 유형은 흡연 여부와 상관없이 전환의 비율이 가장 높았으며 전환 또는 결실 그리고 전환과 결실이 동시에 발생하는 비율이 전이의 발생 비율보다 높게 나타났다. 한국인의 폐선암 증례에서 흡연 여부와 상관없이 가장 발생 빈도가 높은 돌연변이 핫스팟은 TP53 코돈 72 뉴클레오타이드 염기가 C에서 G로의 전환되어 아미노산이 proline에서 arginine으로 치환되는 TP53 P72R SNP 발생 비율이 가장 높게 나타났다. TP53 P72R SNP가 발생한 폐선암 증례들의 임상병리학적 특성을 분석한 결과 환자의 연령, 성별, 흡연 유무 그리고 종양의 분화도와 유의한 상관관계를 보이지 않았지만 낮은 병기와 유의한 상관관계를 나타냈다(P-value=0.026). 본연구는 NGS를 통해 한국인의 폐선암에서 돌연변이 발생 빈도가 가장 많이 보고되었던 EGFR이 아닌 TP53의 증가를 확인했고 그중에서도 흡연 여부와 관계없이 TP53 P72R SNP의 발생 빈도가 가장 높음을 보고하는 바이다.

• Asian Pacific Journal of Cancer Prevention
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• 제14권4호
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• pp.2393-2399
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• 2013

Objective: Mitochondrial DNA (mtDNA) is considered a hotspot of mutations in various tumors. However, the relationship between microsatellite instability (MSI) and mtDNA copy number alterations in lung cancer has yet to be fully clarifieds. In the current study, we investigated the copy number and MSI of mitochondrial genome in lung carcinomas, as well as their significance for cancer development. Methods: The copy number and MSI of mtDNA in 37 matched lung carcinoma/adjacent histological normal lung tissue samples were examined by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) assays for sequence variation, followed by sequence analysis and fluorogenic 5'-nuclease real-time PCR. Student's t test and linear regression analyses were employed to analyze the association between mtDNA copy number alterations and mitochondrial MSI (mtMSI). Results: The mean copy number of mtDNA in lung carcinoma tissue samples was significantly lower than that of the adjacent histologically normal lung tissue samples (p<0.001). mtMSI was detected in 32.4% (12/37) of lung carcinoma samples. The average copy number of mtDNA in lung carcinoma samples containing mtMSI was significantly lower than that in the other lung carcinoma samples (P<0.05). Conclusions: Results suggest that mtMSI may be an early and important event in the progression of lung carcinogenesis, particularly in association with variation in mtDNA copy number.

• Tuberculosis and Respiratory Diseases
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• 제58권1호
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• pp.11-17
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• 2005

연구배경 : 결핵의 발병에 유전적인 소인이 존재하며 숙주 면역 반응에 $IFN-{\gamma}$가 중요한 역할을 한다고 알려져 있다. 파종성 NTM 또는 BCG 감염증 환자에서 $IFN-{\gamma}$ 수용체 유전자 돌연변이가 밝혀져 있는데, 결핵 환자에서 $IFN-{\gamma}$ 수용체의 부분결핍 유무는 잘 알려져 있지 않았다. 방 법 : 2개 이상의 장기를 침범한 파종성 결핵 환자 6명을 대상으로 염기순서분석을 통해 $IFN-{\gamma}$ 수용체 1과 $IFN-{\gamma}$ 수용체 2의 부분결핍을 초래하는 유전자 이상이 있는지를 살펴보았다. 결 과 : $IFN-{\gamma}R1$의 부분결핍을 초래하는 I87T와 818delT 818del4, 818insA 그리고 $IFN-{\gamma}R2$의 부분결핍을 초래하는 R114C 돌연변이 등 기존에 보고된 유전자 이상은 발견되지 않았다. 결 론 : 본 연구의 대상인 6명의 파종성 결핵 환자에서 $IFN-{\gamma}$ 수용체의 부분결핍을 초래하는 유전자 이상은 발견되지 않았다.