Guidelines for Splicing Analysis in Molecular Diagnosis Derived from a Set of 327 Combined In Silico/In Vitro Studies on BRCA1 and BRCA2 Variants
Guidelines for Splicing Analysis in Molecular Diagnosis Derived from a Set of 327 Combined In Silico/In Vitro Studies on BRCA1 and BRCA2 Variants
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DOI：
10.1002/humu.22101
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发表时间：
2012-08-01
期刊：
影响因子：
3.9
通讯作者：
Stoppa-Lyonnet, Dominique
中科院分区：
文献类型：
--
作者：
Houdayer, Claude;Caux-Moncoutier, Virginie;Stoppa-Lyonnet, Dominique
评估未知意义变异体（VUS）对剪接的影响是分子诊断中的关键问题。这种影响可以通过计算机工具预测，但缺乏适当的评估和用户指南。为了填补这一空白，我们开始了迄今为止最大的BRCA 1和BRCA 2剪接研究，在Unicancer的BRCA剪接网络中测试了272个VUS（327次分析）。所有这些VUSs进行了分析，通过使用六个工具（剪接位点预测神经网络，剪接位点查找器（SSF），MaxEntScan（MES），ESE查找器，相对增强子和沉默子分类一致富集，和人类剪接查找器），并获得的预测结果与转录分析结果进行了比较。MES和SSF的组合对于在共有剪接位点附近发生的VUS给出了96%的灵敏度和83%的特异性，所述共有剪接位点即5'和3'位点分别围绕11和14个碱基。这项研究也是一个机会，可以沿着定义转录本分析指南以及剪接变体的初步分类。从这个大系列中得出的指导方针应该对整个社区有用，特别是在测序能力不断增长的背景下，需要强大的变体解释管道。Mutat 33：1228-1238，2012. (c)2012 Wiley Periodicals，Inc.
Assessing the impact of variants of unknown significance (VUS) on splicing is a key issue in molecular diagnosis. This impact can be predicted by in silico tools, but proper evaluation and user guidelines are lacking. To fill this gap, we embarked upon the largest BRCA1 and BRCA2 splice study to date by testing 272 VUSs (327 analyses) within the BRCA splice network of Unicancer. All these VUSs were analyzed by using six tools (splice site prediction by neural network, splice site finder (SSF), MaxEntScan (MES), ESE finder, relative enhancer and silencer classification by unanimous enrichment, and human splicing finder) and the predictions obtained were compared with transcript analysis results. Combining MES and SSF gave 96% sensitivity and 83% specificity for VUSs occurring in the vicinity of consensus splice sites, that is, the surrounding 11 and 14 bases for the 5' and 3' sites, respectively. This study was also an opportunity to define guidelines for transcript analysis along with a tentative classification of splice variants. The guidelines drawn from this large series should be useful for the whole community, particularly in the context of growing sequencing capacities that require robust pipelines for variant interpretation. Hum Mutat 33:1228-1238, 2012. (c) 2012 Wiley Periodicals, Inc.