Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement.
Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement.
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DOI：
10.1186/gm471
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发表时间：
2013
期刊：
影响因子：
12.3
通讯作者：
Hakonarson H
中科院分区：
文献类型：
--
作者：
Wang K;Kim C;Bradfield J;Guo Y;Toskala E;Otieno FG;Hou C;Thomas K;Cardinale C;Lyon GJ;Golhar R;Hakonarson H
全外显子组测序已经通过分析多个无关病例确定了几种孟德尔疾病的病因，但更具挑战性的是解决个别家庭中极其罕见和疑似孟德尔疾病的病因。我们确认了一个有两个孩子的家庭四人组，两个孩子都患有以前没有报道的疾病，特征是进行性肌肉无力和心肌病，智力正常。在研究过程中，我们确定了另外一名具有相似表型的无关患者。我们对转化的淋巴母细胞系进行了全基因组测序(Complete Genome Platform)、全外显子测序(Agilent SureSelect Exon Capture和Illumina Genome Analyzer II Platform)、SNP基因分型(Illumina HumanHap550 SNP阵列)和Sanger测序以及RNA-Seq(Illumina HiSeq Platform)。从全基因组序列数据中，我们确定编码E3泛素蛋白连接酶的基因RBCK1是最有可能的候选基因，在第一个家族的先证者中有两个蛋白质截断突变。然而，由于区域覆盖率较低，外显子组数据未能提名RBCK1作为候选基因。Sanger测序在第二个家系的先证者中发现了RBCK1中的一个私人纯合子剪接变体，但SNP基因分型显示了覆盖RBCK1的1.2mb拷贝中性纯合区。RNA-Seq证实了RBCK1转录本的异常剪接，导致蛋白质产物被截断。虽然这些突变导致疾病的确切机制尚不清楚，但我们的研究提供了一个例子，说明结合使用全基因组DNA和RNA测序如何为一种新型和极其罕见的孟德尔疾病识别致病基因。
Whole-exome sequencing has identified the causes of several Mendelian diseases by analyzing multiple unrelated cases, but it is more challenging to resolve the cause of extremely rare and suspected Mendelian diseases from individual families. We identified a family quartet with two children, both affected with a previously unreported disease, characterized by progressive muscular weakness and cardiomyopathy, with normal intelligence. During the course of the study, we identified one additional unrelated patient with a comparable phenotype. We performed whole-genome sequencing (Complete Genomics platform), whole-exome sequencing (Agilent SureSelect exon capture and Illumina Genome Analyzer II platform), SNP genotyping (Illumina HumanHap550 SNP array) and Sanger sequencing on blood samples, as well as RNA-Seq (Illumina HiSeq platform) on transformed lymphoblastoid cell lines. From whole-genome sequence data, we identified RBCK1, a gene encoding an E3 ubiquitin-protein ligase, as the most likely candidate gene, with two protein-truncating mutations in probands in the first family. However, exome data failed to nominate RBCK1 as a candidate gene, due to poor regional coverage. Sanger sequencing identified a private homozygous splice variant in RBCK1 in the proband in the second family, yet SNP genotyping revealed a 1.2Mb copy-neutral region of homozygosity covering RBCK1. RNA-Seq confirmed aberrant splicing of RBCK1 transcripts, resulting in truncated protein products. While the exact mechanism by which these mutations cause disease is unknown, our study represents an example of how the combined use of whole-genome DNA and RNA sequencing can identify a disease-predisposing gene for a novel and extremely rare Mendelian disease.
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DOI：
10.1126/science.1215040
发表时间：
2012-02-17
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
MacArthur DG;Balasubramanian S;Frankish A;Huang N;Morris J;Walter K;Jostins L;Habegger L;Pickrell JK;Montgomery SB;Albers CA;Zhang ZD;Conrad DF;Lunter G;Zheng H;Ayub Q;DePristo MA;Banks E;Hu M;Handsaker RE;Rosenfeld JA;Fromer M;Jin M;Mu XJ;Khurana E;Ye K;Kay M;Saunders GI;Suner MM;Hunt T;Barnes IH;Amid C;Carvalho-Silva DR;Bignell AH;Snow C;Yngvadottir B;Bumpstead S;Cooper DN;Xue Y;Romero IG;1000 Genomes Project Consortium;Wang J;Li Y;Gibbs RA;McCarroll SA;Dermitzakis ET;Pritchard JK;Barrett JC;Harrow J;Hurles ME;Gerstein MB;Tyler-Smith C
通讯作者：
Tyler-Smith C
影响因子：
30.8
作者：
通讯作者：
--
影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
Diskin SJ;Li M;Hou C;Yang S;Glessner J;Hakonarson H;Bucan M;Maris JM;Wang K
通讯作者：
Wang K