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Investigating diagnostic sequencing techniques for CADASIL diagnosis.
Human Genomics ( IF 4.5 ) Pub Date : 2020-01-08 , DOI: 10.1186/s40246-019-0255-x P J Dunn 1 , N Maksemous 1 , R A Smith 1 , H G Sutherland 1 , L M Haupt 1 , L R Griffiths 1
Human Genomics ( IF 4.5 ) Pub Date : 2020-01-08 , DOI: 10.1186/s40246-019-0255-x P J Dunn 1 , N Maksemous 1 , R A Smith 1 , H G Sutherland 1 , L M Haupt 1 , L R Griffiths 1
Affiliation
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease caused by mutations in the NOTCH3 gene. Our laboratory has been undertaking genetic diagnostic testing for CADASIL since 1997. Work originally utilised Sanger sequencing methods targeting specific NOTCH3 exons. More recently, next-generation sequencing (NGS)-based technologies such as a targeted gene panel and whole exome sequencing (WES) have been used for improved genetic diagnostic testing. In this study, data from 680 patient samples was analysed for 764 tests utilising 3 different sequencing technologies. Sanger sequencing was performed for 407 tests, a targeted NGS gene panel which includes NOTCH3 exonic regions accounted for 354 tests, and WES with targeted analysis was performed for 3 tests. In total, 14.7% of patient samples (n = 100/680) were determined to have a mutation. Testing efficacy varied by method, with 10.8% (n = 44/407) of tests using Sanger sequencing able to identify mutations, with 15.8% (n = 56/354) of tests performed using the NGS custom panel successfully identifying mutations and a likely non-NOTCH3 pathogenic variant (n = 1/3) identified through WES. Further analysis was then performed through stratification of the number of mutations detected at our facility based on the number of exons, level of pathogenicity and the classification of mutations as known or novel. A systematic review of NOTCH3 mutation testing data from 1997 to 2017 determined the diagnostic rate of pathogenic findings and found the NGS-customised panel increases our ability to identify disease-causing mutations in NOTCH3.
中文翻译:
研究用于CADASIL诊断的诊断测序技术。
大脑皮层下梗死和白质脑病(CADASIL)是常染色体显性遗传性动脉病,是由NOTCH3基因突变引起的脑小血管疾病。自1997年以来,我们的实验室一直在进行CADASIL的基因诊断测试。研究最初使用针对特定NOTCH3外显子的Sanger测序方法。最近,基于下一代测序(NGS)的技术(例如靶向基因组和全外显子组测序(WES))已用于改进的基因诊断测试。在这项研究中,使用3种不同的测序技术对680例患者的数据进行了764项分析。Sanger测序进行了407次测试,靶向的NGS基因组(包括NOTCH3外显子区域)进行了354次测试,并进行了有针对性分析的WES进行了3次测试。总共14。确定有7%的患者样本(n = 100/680)具有突变。测试功效因方法而异,使用Sanger测序的10.8%(n = 44/407)的测试能够识别突变,使用NGS自定义面板进行的15.8%(n = 56/354)的测试成功地识别了突变,并且可能通过WES鉴定的非NOTCH3致病变体(n = 1/3)。然后根据外显子的数量,致病性水平和已知或新颖的突变分类,对在我们设施中检测到的突变数量进行分层,从而进行进一步的分析。对1997年至2017年NOTCH3突变测试数据的系统回顾确定了病原学发现的诊断率,发现NGS定制小组提高了我们识别NOTCH3致病突变的能力。
更新日期:2020-04-22
中文翻译:
研究用于CADASIL诊断的诊断测序技术。
大脑皮层下梗死和白质脑病(CADASIL)是常染色体显性遗传性动脉病,是由NOTCH3基因突变引起的脑小血管疾病。自1997年以来,我们的实验室一直在进行CADASIL的基因诊断测试。研究最初使用针对特定NOTCH3外显子的Sanger测序方法。最近,基于下一代测序(NGS)的技术(例如靶向基因组和全外显子组测序(WES))已用于改进的基因诊断测试。在这项研究中,使用3种不同的测序技术对680例患者的数据进行了764项分析。Sanger测序进行了407次测试,靶向的NGS基因组(包括NOTCH3外显子区域)进行了354次测试,并进行了有针对性分析的WES进行了3次测试。总共14。确定有7%的患者样本(n = 100/680)具有突变。测试功效因方法而异,使用Sanger测序的10.8%(n = 44/407)的测试能够识别突变,使用NGS自定义面板进行的15.8%(n = 56/354)的测试成功地识别了突变,并且可能通过WES鉴定的非NOTCH3致病变体(n = 1/3)。然后根据外显子的数量,致病性水平和已知或新颖的突变分类,对在我们设施中检测到的突变数量进行分层,从而进行进一步的分析。对1997年至2017年NOTCH3突变测试数据的系统回顾确定了病原学发现的诊断率,发现NGS定制小组提高了我们识别NOTCH3致病突变的能力。