MRSD: a novel quantitative approach for assessing suitability of RNA-seq in the clinical investigation of mis-splicing in Mendelian disease
MRSD: a novel quantitative approach for assessing suitability of RNA-seq in the clinical investigation of mis-splicing in Mendelian disease
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MRSD：一种新的定量方法，用于评估 RNA-seq 在孟德尔病错误剪接临床研究中的适用性
DOI：
10.1101/2021.03.19.21253973
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发表时间：
2021
影响因子：
0.7
通讯作者：
J. Ellingford
中科院分区：
文献类型：
--
作者：
Charlie F. Rowlands;Algy Taylor;G. Rice;N. Whiffin;H. N. Hall;W. Newman;G. Black;R. O’Keefe;S. Hubbard;A. Douglas;D. Baralle;T. Briggs;J. Ellingford
背景资料：患者生物样品的RNA测序是描绘基因组变体对剪接的影响的有前景的方法，但是组织之间的可变基因表达使适当组织的选择复杂化。相对表达水平通常用作预测RNA测序效用的度量。在这里，我们描述了一个基因和组织特异性指标，以告知RNA测序的可行性，克服了一些问题，单独使用表达值。结果如下：我们推导出一个新的度量，最小所需测序深度（MRSD），所有基因在三个人类生物样本（全血，淋巴母细胞系（LCL）和骨骼肌）。MRSD估计RNA测序所需的测序深度，以实现用户指定的目标基因、转录物或基因组的测序覆盖率。MRSD以高精度（90.1 - 98.2%）预测剪接点覆盖水平，并克服转录本区域特异性测序偏差。将MRSD评分应用于已建立的疾病基因组显示，在三种研究的生物样品中，对于69.3%的基因组，LCL是RNA的最佳来源。我们的方法表明，在ClinVar中预测影响剪接的不确定意义的变体中，高达59.4%可以通过RNA测序在至少一个研究的生物样品中进行功能测定。结论：我们证明了MRSD作为衡量标准的能力，以告知选择合适的生物样本进行剪接畸变的功能评估。我们将MRSD应用于孟德尔遗传性疾病的背景下，并说明其优势，基于表达的方法。我们预计，MRSD整合到临床管道将提高变异的解释，并最终提高诊断率。
Background: RNA-sequencing of patient biosamples is a promising approach to delineate the impact of genomic variants on splicing, but variable gene expression between tissues complicates selection of appropriate tissues. Relative expression level is often used as a metric to predict RNA-sequencing utility. Here, we describe a gene- and tissue-specific metric to inform the feasibility of RNA-sequencing, overcoming some issues with using expression values alone. Results: We derive a novel metric, Minimum Required Sequencing Depth (MRSD), for all genes across three human biosamples (whole blood, lymphoblastoid cell lines (LCLs) and skeletal muscle). MRSD estimates the depth of sequencing required from RNA-sequencing to achieve user-specified sequencing coverage of a gene, transcript or group of genes of interest. MRSD predicts levels of splice junction coverage with high precision (90.1-98.2%) and overcomes transcript region-specific sequencing biases. Applying MRSD scoring to established disease gene panels shows that LCLs are the optimum source of RNA, of the three investigated biosamples, for 69.3% of gene panels. Our approach demonstrates that up to 59.4% of variants of uncertain significance in ClinVar predicted to impact splicing could be functionally assayed by RNA-sequencing in at least one of the investigated biosamples. Conclusions: We demonstrate the power of MRSD as a metric to inform choice of appropriate biosamples for the functional assessment of splicing aberrations. We apply MRSD in the context of Mendelian genetic disorders and illustrate its benefits over expression-based approaches. We anticipate that the integration of MRSD into clinical pipelines will improve variant interpretation and, ultimately, diagnostic yield.
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影响因子：
3.7
作者：
Katherine A. Wood;Charlie F. Rowlands;Huw B. Thomas;Steven Woods;Julieta O’Flaherty;S. Douzgou;S. Kimber;W. Newman;R. O’Keefe
通讯作者：
Katherine A. Wood;Charlie F. Rowlands;Huw B. Thomas;Steven Woods;Julieta O’Flaherty;S. Douzgou;S. Kimber;W. Newman;R. O’Keefe
影响因子：
29.7
作者：
Schneider WM;Chevillotte MD;Rice CM
通讯作者：
Rice CM
影响因子：
16.6
作者：
Kremer LS;Bader DM;Mertes C;Kopajtich R;Pichler G;Iuso A;Haack TB;Graf E;Schwarzmayr T;Terrile C;Koňaříková E;Repp B;Kastenmüller G;Adamski J;Lichtner P;Leonhardt C;Funalot B;Donati A;Tiranti V;Lombes A;Jardel C;Gläser D;Taylor RW;Ghezzi D;Mayr JA;Rötig A;Freisinger P;Distelmaier F;Strom TM;Meitinger T;Gagneur J;Prokisch H
通讯作者：
Prokisch H
影响因子：
15.9
作者：
Murdock, David R.;Dai, Hongzheng;Lee, Brendan
通讯作者：
Lee, Brendan