皮肤黑色素瘤中IDH1基因突变分析

目的:应用癌症基因组图谱(TCGA)数据库分析皮肤黑色素瘤中IDH1基因突变情况.方法:从癌症基因组图谱(TCGA)数据库收集皮肤黑色素瘤数据集,统计患者临床信息、应用cBioPortal网站对数据集进行突变、离散基因、基因共表达、生存期等分析.结果:287个病例中,IDH1基因突变15例,其中,R132C突变10例,R132L突变2例,P33S/E361K突变各1例,X174缺失1例.结论:IDH1基因突变在皮肤黑色素瘤中有一定发生率,占比5.2%,且以R132突变为主,此位点有可能成为靶向药物作用的靶点.     

各基因亚型乳腺癌间基因组拷贝数变异的比较

目的 比较各基因亚型乳腺癌间全基因组拷贝数变异(CNV)差异,分析各亚型中特异的基因CNV.方法 在肿瘤基因组图谱(TCGA)的乳腺癌数据库中,利用AIMS软件进行基因分型(BasL型、Her2型、LumA型和LumB型),GISTIC2.0软件分析肿瘤组织中全基因组拷贝数变异情况.收集整理江门市中心医院(JMCH)3...     

中国黑色素瘤患者ＢＲＡＦ基因突变分析

目的：探讨ＢＲＡＦ基因在中国人黏膜、肢端和非肢端皮肤黑色素瘤中的突变率和类型。方法：用ＰＣＲ扩增和直接测序方法检测９０例中国恶性黑色素瘤（ＭＭ）患者肿瘤组织中ＢＲＡＦ外显子１１和１５的突变情况。结果：黏膜、肢端和非肢端皮肤黑色素瘤患者肿瘤组织中ＢＲＡＦ基因的突变率分别为２３.３％（７／３０）、１６.７％（５／３０）和４３.３％（１３／３０）;２５例ＢＲＡＦ基因突变中,１例为串联突变,其它均为点突变;仅有１例ＢＲＡＦ基因突变位于第１１外显子,其余２４例均位于ＢＲＡＦ第１５外显子。Ｖ６００Ｅ突变占所有ＢＲＡＦ基因第１５外显子突变的８３.３％（２０／２４）。结论：ＢＲＡＦ基因在中国人非肢端皮肤黑色素瘤中突变率较高,且以该基因第１５外显子Ｖ６００Ｅ点突变为主,有可能成为靶向药物作用的靶点。     

骨髓增生异常综合征患者基因突变情况分析

目的 分析骨髓增生异常综合征(MDS)患者的基因突变情况.方法 选择2016年1月至2017年7月中国中医科学院西苑医院初诊的47例MDS患者,采用NGS 127-gene panel检测基因突变,分析基因突变与临床特征的关系.结果47例MDS患者中,31例(66.0％)检测到基因突变,涉及有临床意义的突变基因23个,检出率>5％的基因共7个,由高到低依次为U2AF1(23.4％)、SF3B1(12.8％)、ASXL1(10.6％)、TET2(8.5％)、BCOR(8.5％)、TP53(8.5％)、DNMT3A(6.4％).31例基因突变患者中,16例(51.6％)存在2个以上基因协同突变,其中12例患者的协同基因突变存在于不同基因功能组内,高于单一基因功能组内的基因协同突变(4例).IDH2-KRAS、IDH2-SRSF2、IDH2-STAG2、KRAS-SRSF2、KRAS-STAG2、RUNX1-PHF6、EZH2-ASXL1、EZH2-ZRSR2、NPM1-NRAS基因之间有共存关系(均P<0.05).JAK2、KRAS、NRAS、SH2B3四个信号通路相关的变异等位基因频率(VAF)较低,处于亚克隆地位.1例JAK2突变见于MDS-U患者;1例SH2B3基因突变见于核型预后极高危患者;2例SETBP1以及2例EZH2突变均见于修订的国际预后评分系统(IPSS-R)预后高危患者.结论 MDS患者常见突变基因为U2AF1、SF3B1、ASXL1、TET2.不同基因功能组内的基因倾向于协同突变.基因突变可用于判断MDS患者预后,作为其治疗的靶点.     

肝癌组织中MPDZ基因拷贝数和表达变化及其诊断预后价值分析

目的：探讨MPDZ基因在肝癌组织中的拷贝数和表达变化情况,并评价其与临床病理指标之间的关系以及对肝癌诊断和预后判断的价值。方法：利用TCGA数据库分析MPDZ基因在299例肝癌组织中的拷贝数改变情况及其与表达的关系;同时分析TCGA数据中MPDZ基因在282例肝癌组织和50例癌旁组织中的表达及其与临床病理指标和生存预后的关系。结果：MPDZ基因在肝癌组织中存在明显的拷贝数变异,且拷贝数变异的主要类型为拷贝数缺失（31.44%）;同时MPDZ基因拷贝数缺失后MPDZ mRNA表达下调。MPDZ基因在肝癌组织中的表达显著低于癌旁组织,差异具有统计学意义（P < 0.05）。Kaplan-Meier分析显示,MPDZ基因低表达患者的生存时间短于高表达患者,差异具有统计学意义（Log-rank=12.48,P < 0.05）。受试者工作特征曲线（ROC）分析结果表明,MPDZ基因表达是一个灵敏度和特异度较好的肝癌诊断指标（AUC=0.86）。结论：MPDZ基因拷贝数缺失可能与肝癌的发生有关,MPDZ基因的表达对肝癌的诊断及生存预后判断具有参考价值。     

乳腺浸润性导管癌17号染色体拷贝数变异与临床病理特征相关性分析

目的 乳腺癌是影响妇女健康的主要癌症之一,且发病率呈现明显上升趋势.DNA拷贝数变化(copy number variation,CNV) 能够影响基因表达,从而引起肿瘤发生,研究CNV对探索肿瘤的发病机制有很大帮助.本研究探讨乳腺癌17号染色体拷贝数变异和临床病理特征关系.方法 应用荧光原位杂交(fluorescence in situ hybridization,FISH) 法检测2010-01-01-2011-01-01新疆医科大学附属肿瘤医院乳腺润性导管癌标本283例,观察17号染色体拷贝数情况及人表皮生长因子受体2(human epidermal growth factor receptor 2,HER2) 基因扩增情况,并用免疫组织化学法检测HER2受体蛋白的表达水平.结果 283例乳腺癌中17号染色体拷贝数多倍体为43例(15.19%),双倍体为226例(79.86%),单倍体为 14例(4.95%),乳腺癌17号染色体多倍体HER2基因阳性率为53.49%(23/43).283例乳腺癌中HER2基因表达阳性为84例,阳性率为29.68%(84/283);17号染色体拷贝数不同在HER2基因是否扩增方面差异有统计学意义,χ2=9.564,P=0.007;乳腺癌17号染色体拷贝数变异在p53基因表达(χ2=8.181,P=0.017)、病理组织学分级(χ2=11.203,P=0.019)方面差异有统计学意义,与年龄、肿瘤大小和淋巴结转移等指标差异无统计学意义.17号染色体拷贝数不同组中预后存在差异,差异有统计学意义,χ2=241.363,P=0.001.结论 17号染色体拷贝数变异和乳腺癌病理特征及预后相关,检测乳腺癌中17号染色体拷贝数变异可作为指导临床治疗和判断预后的参考指标.     

云南地区晚期非小细胞肺癌患者的基因突变及其临床意义

目的:探讨云南地区晚期非小细胞肺癌(non-small cell lung cancer,NSCLC)患者外周血中肺癌相关驱动基因突变及其与临床病理特征的关系.方法:收集2019年1月至2019年12月云南省肿瘤医院分子诊断中心检测的304例Ⅳ期NSCLC患者外周血,用二代测序(next generation sequ...     

新疆地区不同民族激素受体阳性乳腺癌患者CYP2D6基因多态性及拷贝数变异研究

目的:探讨新疆地区不同民族激素受体阳性乳腺癌患者CYP2D6基因多态性及拷贝数变异情况以指导临床合理用药。方法:选取2008年1月1日至2012年12月31日新疆医科大学附属肿瘤医院激素受体阳性乳腺癌患者253例,其中汉族126例、维吾尔族78例和哈萨克族49例,采用TaqMan实时荧光定量PCR技术和AccuCopyTM多重基因拷贝数检测技术进行CYP2D6基因多态性及拷贝数变异检测。结果:97.6%（247/253）的患者都检测到了CYP2D6等位基因多态性或拷贝数变异情况,最常见多态分布CYP2D6等位基因是*1、*2、*10,分布频率分别为0.577、0.320、0.462。CYP2D6的*2、*4、*10等位基因在汉族、维吾尔族及哈萨克族乳腺癌患者中分布频率分别为（0.023 8、0.038 4、0.042 9）、（0.031、0.038、0.163）、（0.635、0.372、0.184）,差异有统计学意义。汉族、维吾尔族、哈萨克族乳腺癌患者CYP2D6代谢表型及拷贝数情况分布差异无统计学意义。结论:在新疆地区汉族、维吾尔族、哈萨克族激素受体阳性乳腺癌患者CYP2D6基因在代谢表型多态性及拷贝数变异情况方面未发现明显的民族差异性,但*2、*4、*10等位基因在不同民族间分布有差异,为他莫昔芬个体化治疗的进一步研究提供了一定依据。     

恶性黑色素瘤基因改变及治疗靶点研究进展

<正>恶性黑色素瘤(malignant melanoma,MM)是一种常见肿瘤,最常见的发病部位是皮肤,其次为黏膜(约占1.2%)。皮肤恶性黑色素瘤占皮肤恶性肿瘤的5%,但死亡人数占皮肤恶性肿瘤死亡人数的75%。未发生转移的MM患者5年生存率为98%,局部淋巴结转移的患者5年生存率为62%,远处器官发生转移的患者5年生存率为15%~([1])。2014年,美国约76 100例被确诊为恶性黑色素瘤,约9 710例死亡~([2])。近年来,由于国内外学者对恶性黑色素瘤基因突变靶点的研     

肺腺癌中表皮生长因子受体基因突变与拷贝数的检测分析

目的检测肺腺癌组织中表皮生长因子受体（EGFR）19、21外显子基因突变和拷贝数,分析EGFR基因突变和拷贝数变化的相关性。方法应用荧光定量PCR技术和荧光原位杂交（FISH）技术分别检测58例肺腺癌患者肿瘤组织中的EGFR基因突变和基因扩增,用X^2检验进行数据分析。结果58例肺腺癌患者组织中,EGFR19、21外显子突变率为43．1％（25／58）,其中2例存在两种类型的突变。EGFR基因拷贝数增加阳性率为51．7％（30／58）,包括8例扩增,22例高多体扩增。不同分化程度的肺腺癌组织间,扩增阳性率差异无统计学意义（P〉0．05）,低分化癌的突变率低于高、中分化癌（P〈O．05）。EGFR基因突变与EGFR基因拷贝数之间显著相关（P〈0．01）。结论肺腺癌组织具有较高的EGFR基因突变率和扩增阳性率;联合检测EGFR基因拷贝数和基因突变,更有利于靶向药物的筛选。     

Double mutation and gene copy number of EGFR in gefitinib refractory non-small-cell lung cancer

Mutations of the epidermal growth factor receptor (EGFR) gene have been reported in non-small-cell lung cancer (NSCLC), especially in patients with adenocarcinoma and never smokers. Some common somatic mutations in EGFR, including deletion mutations in exon 19 and leucine-to-arginine substitution at amino acid position 858 (L858R) in exon 21, have been examined for their ability to predict sensitivity to gefitinib or erlotinib, which are selective EGFR tyrosine kinase inhibitors (EGFR-TKIs). On the other hand, reports have shown that the threonine-to-methionine substitution at amino acid position 790 (T790M) in exon 20 is related to gefitinib resistance. Some studies have indicated that high copy numbers of the EGFR gene may be a more effective molecular predictor to responsiveness and prolonged survival in patients treated with EGFR-TKIs. Here, we describe two NSCLC patients with the L858R mutation who did not respond to gefitinib. Case 1 harbored both the T790M and L858R mutations, and fluorescence in situ hybridization showed EGFR gene amplification. Case 2 harbored both the L858R and aspartic acid-to-tyrosine substitution at amino acid position 761 in exon 19 of EGFR mutations and had a high polysomy status for EGFR. In these two cases, tumors showed resistance to gefitinib treatment despite the presence of EGFR L858R mutation and increased copy number. Our findings encourage further molecular analysis to elucidate the relationship between the EGFR status, including mutations and amplifications, and the responsiveness of NSCLC to gefitinib.     

恶性黑素瘤患者KIT基因突变分析

背景与目的：KIT基因突变在恶性黑素瘤的发生、发展中发挥了重要作用。该研究旨在探讨KIT基因在各种组织学类型恶性黑素瘤患者中的突变率和类型。方法：用聚合酶链反应(polymerase chain reaction,PCR)扩增和直接测序方法检测144例恶性黑素瘤患者肿瘤组织中KIT外显子9、11、13和17的突变情况。结果：KIT基因在恶性黑素瘤患者中的总体突变率为9.0%(13/144)。在肢端型、黏膜型、慢性日光损伤型(chronic sun-induced damage,CSD)和非慢性日光损伤型(non-chronic sun-induced damage,non-CSD)恶性黑素瘤组织中,KIT基因的突变率分别为7.7%(4/52)、20.0%(7/35)、14.3%(1/7)和2.8%(1/36);13例KIT基因突变中,有1例位于第9外显子,9例位于第11外显子,3例位于第13外显子。第11外显子L576P为最常见的突变类型。结论：KIT基因突变在恶性黑素瘤患者中最常见于第11外显子,它可能是恶性黑素瘤治疗药物作用的潜在靶点。     

EGFR gene copy number alterations in primary cutaneous malignant melanomas are associated with poor prognosis

Copy number alterations of the epidermal growth factor receptor (EGFR) gene have been extensively analyzed in different cancers, but no data are available for primary malignant melanoma. The aim of the present study was to simultaneously investigate the EGFR gene and chromosome 7 copy number alterations in 81 cutaneous malignant melanomas by interphase FISH and correlate the data with clinicopathological parameters of patients. EGFR mRNA levels were detected by Affymetrix GeneChip Human Genome U133 Plus 2.0 expression arrays for 16 lesions. Both increased gene dosage and chromosome 7 alterations were found in 70% of tumors. Extra EGFR copies were detected in an additional 10% of samples. Polysomy 7 was associated with EGFR gene amplification. Significant correlation was found between EGFR alterations and histological subtypes, tumor thickness, ulceration and metastases formation. Amplification was significantly higher in lesions that developed metastases within 2 years after surgical excision of the primary tumor. Gene copy alterations were associated with elevated mRNA expression in 77% of lesions when compared to tumors with disomic EGFR status, the correlation was not directly proportional to gene copy number. Associations between protein expression and mRNA levels were even less prominent. In conclusion, our study indicates that amplification of the EGFR gene and polysomy 7 are frequent alterations in primary melanomas and are associated with bad prognosis. Further studies are required to clarify whether melanoma patients with EGFR alterations can benefit from anti-EGFR therapy.     

Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma

Background

Multidimensional genotyping of formalin-fixed paraffin-embedded (FFPE) samples has the potential to improve diagnostics and clinical trials for brain tumors, but prospective use in the clinical setting is not yet routine. We report our experience with implementing a multiplexed copy number and mutation-testing program in a diagnostic laboratory certified by the Clinical Laboratory Improvement Amendments.

Methods

We collected and analyzed clinical testing results from whole-genome array comparative genomic hybridization (OncoCopy) of 420 brain tumors, including 148 glioblastomas. Mass spectrometry–based mutation genotyping (OncoMap, 471 mutations) was performed on 86 glioblastomas.

Results

OncoCopy was successful in 99% of samples for which sufficient DNA was obtained (n = 415). All clinically relevant loci for glioblastomas were detected, including amplifications (EGFR, PDGFRA, MET) and deletions (EGFRvIII, PTEN, 1p/19q). Glioblastoma patients ≤40 years old had distinct profiles compared with patients >40 years. OncoMap testing reliably identified mutations in IDH1, TP53, and PTEN. Seventy-seven glioblastoma patients enrolled on trials, of whom 51% participated in targeted therapeutic trials where multiplex data informed eligibility or outcomes. Data integration identified patients with complete tumor suppressor inactivation, albeit rarely (5% of patients) due to lack of whole-gene coverage in OncoMap.

Conclusions

Combined use of multiplexed copy number and mutation detection from FFPE samples in the clinical setting can efficiently replace singleton tests for clinical diagnosis and prognosis in most settings. Our results support incorporation of these assays into clinical trials as integral biomarkers and their potential to impact interpretation of results. Limited tumor suppressor variant capture by targeted genotyping highlights the need for whole-gene sequencing in glioblastoma.     

Relationship between EGFR expression,copy number and mutation in lung adenocarcinomas

Background  

This study was designed to investigate EGFR protein expression, EGFR copy number and EGFR mutations in lung adenocarcinomas, to explore the relationship of the three markers.