Evaluation of Matrix-assisted laser desorption/ionization Time-of flight Mass spectrometry (MALDI TOF MS) and VITEK 2 in routine microbial identification

BacgroundMicrobial Identification was done by phenotypic methods. VITEK-2 and Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) are now being increasingly used in laboratories.ObjectivesTo compare and evaluate the usefulness of MALDI-TOF MS and VITEK-2 in routine microbial identification.MethodsThe performances of MALDI-TOF MS and VITEK 2 were compared for identifying microorganisms.ResultsMALDI- TOF MS and VITEK-2 correctly identified 96 % (96/100) and 97% (97/100) of the isolates upto the genus level.ConclusionMALDI TOF MS and VITEK -2 gave comparable identification and error rates. The rapid reduction in turnaround time with MALDI TOF is a significant game-changer in the field of clinical microbiology.FundingState Board of Medical Research (SBMR).     

Harmonization and Standardization of Panel-Based Tumor Mutational Burden Measurement: Real-World Results and Recommendations of the Quality in Pathology Study

IntroductionTumor mutational burden (TMB) is a quantitative assessment of the number of somatic mutations within a tumor genome. Immunotherapy benefit has been associated with TMB assessed by whole-exome sequencing (wesTMB) and gene panel sequencing (psTMB). The initiatives of Quality in Pathology (QuIP) and Friends of Cancer Research have jointly addressed the need for harmonization among TMB testing options in tissues. This QuIP study identifies critical sources of variation in psTMB assessment.MethodsA total of 20 samples from three tumor types (lung adenocarcinoma, head and neck squamous cell carcinoma, and colon adenocarcinoma) with available WES data were analyzed for psTMB using six panels across 15 testing centers. Interlaboratory and interplatform variation, including agreement on variant calling and TMB classification, were investigated. Bridging factors to transform psTMB to wesTMB values were empirically derived. The impact of germline filtering was evaluated.ResultsSixteen samples had low interlaboratory and interpanel psTMB variation, with 87.7% of pairwise comparisons revealing a Spearman’s ρ greater than 0.6. A wesTMB cut point of 199 missense mutations projected to psTMB cut points between 7.8 and 12.6 mutations per megabase pair; the corresponding psTMB and wesTMB classifications agreed in 74.9% of cases. For three-tier classification with cut points of 100 and 300 mutations, agreement was observed in 76.7%, weak misclassification in 21.8%, and strong misclassification in 1.5% of cases. Confounders of psTMB estimation included fixation artifacts, DNA input, sequencing depth, genome coverage, and variant allele frequency cut points.ConclusionsThis study provides real-world evidence that all evaluated panels can be used to estimate TMB in a routine diagnostic setting and identifies important parameters for reliable tissue TMB assessment that require careful control. As complex or composite biomarkers beyond TMB are likely playing an increasing role in therapy prediction, the efforts by QuIP and Friends of Cancer Research also delineate a general framework and blueprint for the evaluation of such assays.     

眼皮肤白化病Ⅰ型产前基因诊断二例

目的对生育过眼皮肤白化病（oculocutaneous albinism,OCA）患儿的2个家系进行基因诊断分型,并在此基础上提供产前基因诊断。方法采用PCR扩增先证者OCA 1型疾病相关基因TYR的所有5个编码外显子,PCR产物直接测序,在确定致病突变的基础上对及家系成员进行综合分析。结果 2个OCA先证者均携带TYR基因复合杂合突变,确定2例先证者均为OCA1型患者。TYR基因共检测到3种突变：c.71G〉A,c.896G〉A和c.929ins C。产前诊断：第1个家系提示胎儿基因型与先证者一致,家属选择终止妊娠;第2个家系中胎儿为TYR基因野生型携带者,继续妊娠至足月分娩,新生儿随访正常。结论利用基因检测可为眼皮肤白化病患者提供确切的临床分型,并在此基础上提供有效的产前基因诊断。     

无创DNA产前检测在诊断胎儿染色体非整倍体疾病中的应用

目的探讨新一代测序技术的无创DNA产前检测在诊断胎儿染色体非整倍体疾病中的应用价值。方法 2012年8月1日至2013年12月31日在辽宁省大连市妇幼保健院接受孕妇外周血中游离胎儿DNA检测者2548例,均为单胎,妊娠12周-26周,按照孕妇年龄、血清学筛查结果及超声检测结果分为唐氏综合征筛查（唐筛）高危组、高龄组（孕产期年龄超过35周岁）、B超检测异常组和其他原因组,共计4组,由北京贝瑞和康生物技术有限公司和湖南家辉遗传专科医院合作开展的＂大规模基于新一代测序技术的新型无创DNA产前检测＂对孕妇外周血中游离胎儿DNA进行序列分析,对检测结果阳性者进行羊水穿刺或脐血穿刺及胎儿染色体核型分析;对检测结果阴性者行电话随访其胎儿出生后情况。结果 ①4组孕妇共计2548例均成功完成游离胎儿DNA检测,检测结果为阳性者共39例,包括21三体18例、18三体7例、13三体2例、性染色体异常12例。其中唐筛高危组检出21三体5例、18三体1例、13三体0例、性染色体异常3例;高龄组检出21三体3例、18三体3例、13三体0例、性染色体异常5例;B超检测异常组检出21三体9例、18三体2例、13三体0例、性染色体异常2例;其他原因组检出21三体1例、18三体1例、13三体2例、性染色体异常2例;②孕妇游离胎儿DNA检测结果异常的39例孕妇中,32例进行了羊水穿刺或脐血穿刺及染色体核型分析。18例21三体检测阳性者中,13例进行了羊水穿刺或脐血穿刺,其中12例结果与无创DNA吻合,1例不吻合,5例拒绝羊水穿刺或脐血穿刺而直接引产,经随访胎儿均有异常。结果检出率100%,准确率92.3%。7例18三体检测阳性者中,有6例进行了羊水穿刺或脐血穿刺,其中5例结果与无创DNA吻合,1例不吻合,1例拒绝羊水穿刺或脐血穿刺而直接引产,经随访胎儿存在多处异常。结果检出率100%,准确率83.3%。2例13三体检?     

东莞市2011年手足口病肠道病毒型别分析

目的了解引起东莞市2011年手足口病疫情的肠道病毒型别。方法采用荧光RT-PCR方法对标本中总肠道病毒、肠道病毒71型(EV71)和柯萨奇病毒A组16型(CVA16)进行特异性核酸检测。对非EV71非CVA16的其它肠道病毒采用VP4基因测序进行型别鉴定。结果 2011年共检测608份手足口病病例标本,537份为阳性,其中198份为EV71阳性(占36.87%),128份为CVA16阳性(占23.84%),211份为非EV71、非CVA16的其它肠道病毒阳性(占39.29%)。对其它肠道病毒进行VP4基因测序分型,共获得50个可用序列,通过BLAST在线比对确定型别,1例CVA1,43例CVA6,4例CVA10,1例CVA12,1例CVB1。结论 2011年引起手足口病的非EV71非CVA16肠道病毒构成比已超过EV71和CVA16,成为东莞引起手足口病主要病原体之一,其中CVA6构成比较大,值得进一步研究。     

PCR-DGGE结合测序在检测混合细菌感染中的价值

目的探讨变性梯度凝胶电泳（Denaturinggradientgelelectrophoresis,DGGE）结合测序在检测混合细菌感染中的作用,为细菌多重感染的诊断提供新的思路。方法以3份临床培养鉴定为混合感染的胆囊穿刺引流液为对象,提取细菌总DNA并扩增16SrDNA-V3区,后进行DGGE分析,将所得条带切胶纯化再扩增,扩增产物进行测序及BLAST比对,比较比对结果与临床培养结果的一致性。结果DGGE可以很好地分离16SrDNA-V3区混合PCR产物,每一个扩增子的测序比对结果与临床培养结果一致。结论PCR-DGGE结合测序的方法可以很好地鉴定临床混合感染标本中的病原茵,可作为快速检测方法在临床应用。     

乳腺癌BRCA1基因突变的研究

目的　乳腺癌易感基因 (BRCA1基因 )是一种抑癌基因。本研究检测BRCA1基因在乳腺癌中的突变情况 ,探讨BRCA1基因突变与乳腺癌的关系。方法　选取 89例乳腺癌患者标本作实验组 ,另取非癌乳腺组织标本 30例作对照组。每一例标本分别捣碎 ,分别用酚 -氯仿抽提法提取DNA ,每例DNA用PCR扩增BRCA1基因的 2、5、1 7、2 0等 4个外显子。分别将每例病人每个外显子的PCR扩增产物进行SSCP分析 ,对出现异常区带的PCR扩增产物进行DNA测序 ,与基因库序列比对分析其突变情况。结果　 30例非癌乳腺组织未检测出BRCA1基因突变 ,89例乳腺癌共检测出 4例突变 ,其中 2例为 5外显子的错义突变 (2 73C >G ,2 87A >T) ,2例为 1 7外显子的错义突变 (5 1 1 5T >C ,5 1 1 6A >G)。乳腺癌BRCA1的基因突变率为 4 5 %(4 / 89)。结论　BRCA1突变与乳腺癌有关系 ,检测BRCA1基因突变对于乳腺癌患病风险评估及早期诊断具有重要意义     

原发性肝癌发生与ras基因突变的关系

目的 探讨H-ras、K-ras、N-ras基因突变与原发性肝癌发生发展的关系.方法 采用HotStarTaq聚合酶链反应(PCR)检测32例原发性肝癌组织中H-ras、K-ras、N-ras基因的表达并采用PCR直接测序分析H-ras、K-ras、N-ras基因突变x2检验检测H-ras突变与临床病理的关系.结果 在32例原发性肝癌组织中均可检测到H-ras、K-ras、N-ras基因的表达,32例原发性肝癌标本PCR结果经测序后,17例标本发现H-ras基因发生突变(17/32,53.1％),14例40密码子中A突变成G,3例62密码子中G突变成A.K-ras、N-ras基因未发生突变,H-ras突变与肿瘤转移有关.结论 H-ras基因异常表达与肝癌相关,可能导致了原发性肝癌的发生.     

胃肠道间质瘤c-kit基因全部外显子的突变研究

目的 c-kit基因全部外显子在胃肠道间质瘤疾病中的突变情况,并探讨其意义.方法 收集2010年9月至2012年12月胃肠道间质瘤手术切除标本62例,其中胃间质瘤41例,小肠14例,直肠4例,结肠1例,腹膜2例,年龄20～82岁,男性40例,女性22例,中位年龄54岁,术前筛查均无GIST家族史,患者术前均未接受过放疗或化疗,都是经术中病理报告和最终石蜡切片病理报告确诊的GIST标本.设计特异性PCR引物,用肿瘤组织提取的DNA为模板进行PCR扩增后测序,研究c-kit基因突变在胃肠道间质瘤组织中的突变规律.结果 在62例胃肠道间质瘤组织标本中有53例c-kit基因发生突变,突变率85.5%（53例/62例）,PCR产物突变率为3.8%（62例/1612例）,外显子2突变6例（9.7%）,外显子8突变7例（11.3%）,外显子10突变14例（22.6%）,外显子11突变8例（12.9%）,外显子21突变27例（43.5%）.此外第21号外显子有8例位于c-kit基因第80778位点的C突变成T,有19例位于c-kit基因第80846位点的G突变成A.结论 胃肠道间质瘤中c-kit基因突变率高达85.5%,表明c-kit基因突变可能对胃肠道间质瘤的发生发展起重要作用.