MRSD: A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease.
MRSD: A quantitative approach for assessing suitability of RNA-seq in the investigation of mis-splicing in Mendelian disease.
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DOI：
10.1016/j.ajhg.2021.12.014
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发表时间：
2022-02-03
影响因子：
9.8
通讯作者：
Ellingford JM
中科院分区：
文献类型：
--
作者：
Rowlands CF;Taylor A;Rice G;Whiffin N;Hall HN;Newman WG;Black GCM;kConFab Investigators;O'Keefe RT;Hubbard S;Douglas AGL;Baralle D;Briggs TA;Ellingford JM
组织间基因表达水平的不同使得使用患者生物样本的RNA测序来描述基因组变异的影响变得复杂。在这里，我们描述了一种基因和组织特异性的衡量标准，以告知RNA测序的可行性。这克服了仅使用表达式值作为预测RNA测序效用的度量的局限性。我们已经得出了一个度量，即最小所需测序深度(MRSD)，它估计了RNA测序所需的测序深度，以实现用户指定的基因、转录本或基因组的测序覆盖。我们将MRSD应用于四个人类生物样本：全血、淋巴母细胞系(LCLS)、骨骼肌和培养的成纤维细胞。MRSD具有较高的准确率(90.1%-98.2%)，并克服了转录区特异性测序偏差。对已建立的疾病基因板应用MRSD评分表明，在这四个生物样本中，成纤维细胞是63.1%基因板的最佳RNA来源。使用这种方法，在ClinVar中预测会影响剪接的不确定意义的变异中，高达67.8%可以通过至少一个生物样本的RNA测序进行分析。我们展示了MRSD作为剪接异常功能评估的指标的实用性和益处，特别是在孟德尔遗传疾病的背景下，以提高诊断效率。
Variable levels of gene expression between tissues complicates the use of RNA sequencing of patient biosamples to delineate the impact of genomic variants. Here, we describe a gene- and tissue-specific metric to inform the feasibility of RNA sequencing. This overcomes limitations of using expression values alone as a metric to predict RNA-sequencing utility. We have derived a metric, minimum required sequencing depth (MRSD), that estimates the depth of sequencing required from RNA sequencing to achieve user-specified sequencing coverage of a gene, transcript, or group of genes. We applied MRSD across four human biosamples: whole blood, lymphoblastoid cell lines (LCLs), skeletal muscle, and cultured fibroblasts. MRSD has high precision (90.1%–98.2%) and overcomes transcript region-specific sequencing biases. Applying MRSD scoring to established disease gene panels shows that fibroblasts, of these four biosamples, are the optimum source of RNA for 63.1% of gene panels. Using this approach, up to 67.8% of the variants of uncertain significance in ClinVar that are predicted to impact splicing could be assayed by RNA sequencing in at least one of the biosamples. We demonstrate the utility and benefits of MRSD as a metric to inform functional assessment of splicing aberrations, in particular in the context of Mendelian genetic disorders to improve diagnostic yield.
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影响因子：
17.1
作者：
Cummings BB;Marshall JL;Tukiainen T;Lek M;Donkervoort S;Foley AR;Bolduc V;Waddell LB;Sandaradura SA;O'Grady GL;Estrella E;Reddy HM;Zhao F;Weisburd B;Karczewski KJ;O'Donnell-Luria AH;Birnbaum D;Sarkozy A;Hu Y;Gonorazky H;Claeys K;Joshi H;Bournazos A;Oates EC;Ghaoui R;Davis MR;Laing NG;Topf A;Genotype-Tissue Expression Consortium;Kang PB;Beggs AH;North KN;Straub V;Dowling JJ;Muntoni F;Clarke NF;Cooper ST;Bönnemann CG;MacArthur DG
通讯作者：
MacArthur DG
影响因子：
8.8
作者：
Aicher, Joseph K.;Jewell, Paul;Bhoj, Elizabeth J.
通讯作者：
Bhoj, Elizabeth J.
影响因子：
82.9
作者：
Fresard, Laure;Smail, Craig;Dyment, David
通讯作者：
Dyment, David
影响因子：
4
作者：
Johnston, Jennifer J.;Williamson, Kathleen A.;Biesecker, Leslie G.
通讯作者：
Biesecker, Leslie G.
影响因子：
16.6
作者：
Buskin A;Zhu L;Chichagova V;Basu B;Mozaffari-Jovin S;Dolan D;Droop A;Collin J;Bronstein R;Mehrotra S;Farkas M;Hilgen G;White K;Pan KT;Treumann A;Hallam D;Bialas K;Chung G;Mellough C;Ding Y;Krasnogor N;Przyborski S;Zwolinski S;Al-Aama J;Alharthi S;Xu Y;Wheway G;Szymanska K;McKibbin M;Inglehearn CF;Elliott DJ;Lindsay S;Ali RR;Steel DH;Armstrong L;Sernagor E;Urlaub H;Pierce E;Lührmann R;Grellscheid SN;Johnson CA;Lako M
通讯作者：
Lako M