Future directions for high-throughput splicing assays in precision medicine.
Future directions for high-throughput splicing assays in precision medicine.
复制标题
精准医学中高通量剪接测定的未来方向。
DOI：
10.1002/humu.23866
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发表时间：
2019
期刊：
影响因子：
3.9
通讯作者：
Fairbrother,WilliamG
中科院分区：
文献类型：
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作者：
Rhine,ChristyL;Neil,Christopher;Glidden,DavidT;Cygan,KamilJ;Fredericks,AlgerM;Wang,Jing;Walton,NephiA;Fairbrother,WilliamG
未知意义变异的分类是临床遗传学中具有挑战性的技术难题。由于多达三分之一的致病突变被认为会影响前mRNA剪接，因此准确分类患者测序数据中的剪接突变非常重要。一些联盟和医疗保健系统已经进行了大规模的患者测序研究，发现新的变异比它们可以分类的速度更快。在这里，我们比较了几种旨在缓解这一瓶颈的高通量剪接检测的优势和局限性，并描述了我们使用大规模平行剪接检测（MaPSy）分析的约5，000个变体的数据集。基因组解读批判性评估小组（CAGI）组织了一项挑战，参与者提交了机器学习模型来预测该数据集中变体的剪接效应。我们讨论了获胜的挑战（MMSplice），它优于现有的软件提交。最后，我们强调了克服MaPSy和类似检测的局限性的方法，例如组织特异性剪接，周围序列背景的影响，对内含子变体进行分类，合成大外显子，以及扩增小基因物种的复杂文库。这些检测的进一步发展将极大地有利于临床遗传学领域，该领域缺乏用于变异解释的高通量方法。
Classification of variants of unknown significance is a challenging technical problem in clinical genetics. As up to one‐third of disease‐causing mutations are thought to affect pre‐mRNA splicing, it is important to accurately classify splicing mutations in patient sequencing data. Several consortia and healthcare systems have conducted large‐scale patient sequencing studies, which discover novel variants faster than they can be classified. Here, we compare the advantages and limitations of several high‐throughput splicing assays aimed at mitigating this bottleneck, and describe a data set of ~5,000 variants that we analyzed using our Massively Parallel Splicing Assay (MaPSy). The Critical Assessment of Genome Interpretation group (CAGI) organized a challenge, in which participants submitted machine learning models to predict the splicing effects of variants in this data set. We discuss the winning submission of the challenge (MMSplice) which outperformed existing software. Finally, we highlight methods to overcome the limitations of MaPSy and similar assays, such as tissue‐specific splicing, the effect of surrounding sequence context, classifying intronic variants, synthesizing large exons, and amplifying complex libraries of minigene species. Further development of these assays will greatly benefit the field of clinical genetics, which lack high‐throughput methods for variant interpretation.