Lessons learned from additional research analyses of unsolved clinical exome cases.
Lessons learned from additional research analyses of unsolved clinical exome cases.
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DOI：
10.1186/s13073-017-0412-6
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发表时间：
2017-03-21
期刊：
影响因子：
12.3
通讯作者：
Lupski JR
中科院分区：
文献类型：
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作者：
Eldomery MK;Coban-Akdemir Z;Harel T;Rosenfeld JA;Gambin T;Stray-Pedersen A;Küry S;Mercier S;Lessel D;Denecke J;Wiszniewski W;Penney S;Liu P;Bi W;Lalani SR;Schaaf CP;Wangler MF;Bacino CA;Lewis RA;Potocki L;Graham BH;Belmont JW;Scaglia F;Orange JS;Jhangiani SN;Chiang T;Doddapaneni H;Hu J;Muzny DM;Xia F;Beaudet AL;Boerwinkle E;Eng CM;Plon SE;Sutton VR;Gibbs RA;Posey JE;Yang Y;Lupski JR
鉴于大多数单基因孟德尔疾病的罕见性，临床和科学界之间的数据交换的协同努力对于优化分子诊断和新疾病基因的发现至关重要。我们设计并实施了用于研究在临床基因组学诊断实验室中未实现合理分子诊断的病例（即未解决的临床外显子组）的方案。这些病例被招募到研究实验室进行进一步分析，以便潜在地：（1）加速新疾病基因的发现;（2）增加全外显子组测序（WES）的分子诊断产率;和（3）深入了解疾病的遗传机制。试点项目的数据包括74个家庭，主要由父母子女三人组。在研究基础上进行的分析采用了来自其他家族成员的WES和互补的生物信息学方法和方案。分析孟德尔遗传的所有可能模式，重点是单核苷酸变异（SNV）和拷贝数变异（CNV）等位基因，在36%（27/74）的病例中产生了可能的贡献变异。如果包括在单个家族中鉴定出的具有变体的候选基因，则在本初步研究中入组的总共约51%（38/74）的病例中鉴定出潜在的贡献变体。30/63例（47.6%）三组病例获得了分子诊断。除此之外，分析工作流程还在4/6例单胎病例（66.6%）、1/1个涉及三个受影响兄弟姐妹的多重家族和3/4（75%）个四联体家族中获得了疾病相关基因致病性变异的证据。诊断和研究实验室之间的分析管道和合作努力提供了见解，允许最近的疾病基因发现（PURA，TANGO 2，EMC 1，GNB 5，ATAD 3A和MIPEP），并增加了新基因的数量，在本研究中定义为在一个以上的家族（DHX 30和EBF 3）中鉴定的基因。 一个有效的基因组学管道，其中在诊断实验室的临床测序之后，在研究环境中对未解决的病例进行详细的再分析，补充来自其他家族成员的WES数据，并进行辅助生物信息学分析，包括信息学管道中的宽松变体过滤参数，可以提高分子诊断产率并提供对孟德尔疾病的机制见解。实施这些方法需要合作的临床分子诊断和研究工作。本文的在线版本（doi：10.1186/s13073-017-0412-6）包含补充材料，可供授权用户使用。
Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent–offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts. The online version of this article (doi:10.1186/s13073-017-0412-6) contains supplementary material, which is available to authorized users.