MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples.
MotorPlex provides accurate variant detection across large muscle genes both in single myopathic patients and in pools of DNA samples.
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DOI：
10.1186/s40478-014-0100-3
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发表时间：
2014-09-11
影响因子：
7.1
通讯作者：
Nigro V
中科院分区：
文献类型：
--
作者：
Savarese M;Di Fruscio G;Mutarelli M;Torella A;Magri F;Santorelli FM;Comi GP;Bruno C;Nigro V
~100个基因的突变导致肌肉疾病，具有复杂且往往无法解释的基因型/表型相关性。下一代测序研究发现，人类基因组中的遗传变异数量比预期的要多。这表明现有的临床单基因检测系统性地遗漏了非常相关的信息。我们已经创建了一个核心的基因小组，这些基因导致了所有已知的非综合征性肌肉疾病(Motorplex)。它由93个基因座组成，其中包括TTN、RYR1、NEB和DMD等人类最大、最复杂的基因。Motorplex以非常准确和统一的覆盖范围捕获了2544个外显子中的至少99.2%。与整个外显子组测序相比，发现了20%-30%的变异，这突显了这一特点。覆盖面的同质性也使得在保持最佳灵敏度和特异度的同时应用具有成本效益的集合测序策略成为可能。我们研究了177个尚未解决的肌病病例，其中最佳候选基因之前被排除在外。我们已经在52名患者中确定了已知的致病变异，并在另外56名患者中确定了潜在的致病变异。我们还发现23名患者表现出多个真实的疾病相关变异，表明复杂的遗传。此外，我们经常在最大的肌肉基因中检测到其他意义未知的非同义变体。经济实惠的DNA样本组合池也同样准确(97-99%)。Motorplex是一个非常强大的平台，它克服了逐个基因策略的功率、成本、速度、敏感性和特异性。池的适用性使该工具在更大的人群中也适用于肌肉基因的遗传变异性的筛选。我们认为，我们的策略可以有更广泛的应用。本文的在线版本(doi：10.1186/s40478-0140100-3)包含补充材料，授权用户可以使用。
Mutations in ~100 genes cause muscle diseases with complex and often unexplained genotype/phenotype correlations. Next-generation sequencing studies identify a greater-than-expected number of genetic variations in the human genome. This suggests that existing clinical monogenic testing systematically miss very relevant information. We have created a core panel of genes that cause all known forms of nonsyndromic muscle disorders (MotorPlex). It comprises 93 loci, among which are the largest and most complex human genes, such as TTN, RYR1, NEB and DMD. MotorPlex captures at least 99.2% of 2,544 exons with a very accurate and uniform coverage. This quality is highlighted by the discovery of 20-30% more variations in comparison with whole exome sequencing. The coverage homogeneity has also made feasible to apply a cost-effective pooled sequencing strategy while maintaining optimal sensitivity and specificity. We studied 177 unresolved cases of myopathies for which the best candidate genes were previously excluded. We have identified known pathogenic variants in 52 patients and potential causative ones in further 56 patients. We have also discovered 23 patients showing multiple true disease-associated variants suggesting complex inheritance. Moreover, we frequently detected other nonsynonymous variants of unknown significance in the largest muscle genes. Cost-effective combinatorial pools of DNA samples were similarly accurate (97-99%). MotorPlex is a very robust platform that overcomes for power, costs, speed, sensitivity and specificity the gene-by-gene strategy. The applicability of pooling makes this tool affordable for the screening of genetic variability of muscle genes also in a larger population. We consider that our strategy can have much broader applications. The online version of this article (doi:10.1186/s40478-014-0100-3) contains supplementary material, which is available to authorized users.
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影响因子：
14.8
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
通讯作者：
Ng, Pauline C.
影响因子：
7
作者：
Pollard, Katherine S.;Hubisz, Melissa J.;Siepel, Adam
通讯作者：
Siepel, Adam
使用下一代 DNA 测序数据进行变异发现和基因分型的框架。
影响因子：
30.8
作者：
通讯作者：
--
DOI：
10.1038/nrg3463
发表时间：
2013-04
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
一种基于社区的资源，用于Mendelian疾病中的自动外显子变体呼叫和注释。
影响因子：
4.4
作者：
Mutarelli M;Marwah V;Rispoli R;Carrella D;Dharmalingam G;Oliva G;di Bernardo D
通讯作者：
di Bernardo D