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外显子组测序探寻中国汉族人群先天性脊柱侧凸致病基因的研究
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摘要
研究背景:
     先天性脊柱侧凸(Congenital scoliosis,CS)是由胚胎期椎体发育异常导致的脊柱侧方弯曲≥10°。CS具有进展快、畸形重、并发症多等特点,严重时可致患者瘫痪,是造成青少年残疾的主要疾病之一,给家庭和社会带来极大负担。
     脊椎动物的脊柱是由体前中胚层周期性形成的体节发育而来,这一过程叫做体节形成(somitogenesis),体节形成异常即可导致先天性椎体畸形。体节形成是由WNT、NOTCH和FGF三个通路及其中的基因相互作用、共同调节来完成的。由于其确切病因不明,目前尚无有效的预测手段,治疗仍以支具或手术治疗来缓解病情发展为主,因此探寻其发病原因,对于从病因学领域控制发病率、早期诊断和早期干预这种严重致残性脊柱畸形疾病、缓解家庭和社会负担具有重要意义。CS可由基因异常或环境因素变化导致,随着越来越多的遗传学病因报道,遗传因素在CS发病中起到的作用逐渐被人们重视。CS是一种复杂、多基因、多遗传模式疾病。目前国际上对于CS的遗传学病因研究少有大样本的遗传学研究报道,难以获得临床表型一致的大样本病例、基于人数共线性模型的研究策略以及CS的遗传异质性等是限制开展大规模研究的主要因素。
     随着测序技术的不断进步,高通量测序成本逐渐下降,全外显子组测序(Whole exome sequence, WES)已成为最有效的进行疾病定位研究的手段。WES是一种高效、快速和高性价比的研究方法,该技术被《Science》杂志评为2010年十大科学突破之一。到目前为止,已有百余篇报道应用外显子组测序成功定位了大量疾病的致病突变。WES的出现给CS遗传学研究提供了方法学的革新,为从组学水平探究CS遗传致病因素提供了可能,人们能够从以往“被动”的以“人鼠共线性”为基础的候选基因研究策略,上升为“主动”的从“全外显子组水平”寻找CS的致病性突变。
     研究目的:
     本研究以中国汉族人群CS患者为研究对象,拟在全外显子组水平寻找与CS发病相关的基因突变。
     研究内容:
     选取4例散发(编号分别为CS012/CS039/CS070/CS108)及1例核心家系trio (CS051/CS052/CS053)的中国汉族人群CS患者(临床分型为Ⅲ型, ICVAS分型为M-SDV-U),完整采集数据资料。排除环境因素影响后,采集外周静脉血4-6m1,提取全基因组DNA。对上述样本进行WES,所得数据采用严格的质量控制,数据分析时考虑多种显性遗传及隐性遗传模型的可能,并在以往研究的基础上,对数据进行深入挖掘,以探索CS可能的致病突变。
     研究结果:
     1、在隐性遗传模型下,没有发现2个以上患者共有的杂合或纯合突变。
     2、在显性新发突变遗传模型下,在CS051患者中得到了1个可以导致编码氨基酸改变的新发突变(FAM179B,14_45475484_A/G),但功能上没有明确的意义。
     3、在不完全外显的显性遗传模型下,分别得到1个基因(FANCA)的两个非同义突变(CS05116_89833556_A/G和CS10816_89842161_T/A)为2个患者共有,无3个或以上患者共有的突变。
     4、经过基于先验的深入挖掘,分别得到ZIC3(CS070X_136651147_A/T、CS108X_136648948_C/T)和TBX6(CS07016_30100451_G/A)2个基因的感兴趣突变。
     研究结论:
     1、采用“核心家系结合散发病例、在多模型下探寻全外显子组水平致病突变"的策略,是CS遗传学研究较为可行的思路。
     2、FANCA基因突变(16_89833556_A/G和16_89842161-T/A)可能与CS发病密切相关,其遗传模式可能为不完全外显的显性遗传。
     3、ZIC3基因突变(X_136651147_A/T和X_136648948_C/T)可能导致CS的发生,其可能与CS患者伴有神经管发育异常及心脏发育障碍的表型有关。
     4、TBX6基因突变(16_30100451_G/A)可能是CS的致病因素之一,TBX6基因异常可能与CS患者伴有肋骨畸形的表型有关。
Background:
     Congenital Scoliosis (CS) is a spinal deformity with a spinal coronary curvature of10°or greater caused by abnormal vertebrate development during embryo. CS is charatered by rapid development, severe deformity and multiple complications. It is one of the most causes of adolescent disability and brings high burden to the family and the society.
     The spine of the vertebrate is developed from the presomitc mesoderm (PSM) from which somite is periodically developed, this process is called somitogenesis. Abnormal somitogenesis is the reason of congenital vertebrate deformity. Somitogenesis is regulated by the mutual cooperation of WNT, NOTCH and FGF signaling pathway and their taget genes. However, the definite etiology of CS is obscure and there is still no effective method for its early prediction. Clinially, the treatment of CS is mainly focused on bracement and operation in order to avoid the rapid progress of the disease. Therefore, it is important to find the etiology and to reduce the occurrence of this high pathogenic spinal deformity.
     The abnormal of genes and changes of environmental factors in embryo or during labor are the main casue of CS. With more and more genetic etiology were reported, the genetic influence of CS is gradually remarked. CS is a complicated disease with multiple genes and multi genetic models related. Little larege sample of genetics research of CS was reported because it is difficult to collect large scale of patients with the same phenotype as patients are usually infertile, furthermore, the strategy of analysis based on the mouse-human synteny restricts the profound and creative study as the real mechanism of molecular biological etiology of CS is unknow either.
     With the rapid advancement of the sequencing technique, the coast of sequencing is reducing correspondingly. Up to now, whole exome sequencing (WES) has been the most effective method to locate the genetic cause of diseases. WES is a high-performance method in detecting mutations in exome wide and according to the journal of "Science", WES was chosen as one of the top ten breakthroughs of science in2010. There are hundreds of publications reporting using WES to find the genetics etiology of certain disease. As the importance of WES is realized by more and more researchers and the further decline of the cost of WES, it will be used in more cases especially those complicated ones and more important genetic foundamental knowledge of disease wll be provided. The apperance of WES brings evolution in methodology of genetic research of CS, and it is possible for us to find the pathogenic mutation in the level of exome wide.
     Objects:
     To investigate the genetic mutation of CS in whole exome level.
     Methods:
     We collected four sporadic cases (CS012/CS039/CS070/CS108) and one trio of CS (CS051/CS052/CS053) in Chinese Han population, the classification was type III clinically and M-SDV-U according to ICVAS. Genomic DNA was draw from the whole peripheral blood. We used whole exome sequencing and construct different models in statistical analysis to identify genetic mutations in these cases.
     Results:
     1. No homozygous of compound heterozygou mutation were shared by two or more patients in recessive model.
     2. One non-synonymous mutation of FAM179B (CS05114_45475484_A/G) was identified in dominant de novo mutation model, but functionally inexplainable.
     3. Two non-synonymous mutations of FANCA (CS05116_89833556_A/G and CS1081689842161_T/A) were identified in two cases. No exome mutation was found in three or more cases.
     4. After knowledge-based data mining, two candidate mutations, ZIC3(CS070X_136651147_A/T、CS108X_136648948_C/T) and TBX6(CS01016_30100451_G/A), were identified.
     Conclusions:
     1. The strategy of "sporadic cases combined with trio in identifying exome level mutatoins of CS in mutiple models" is a feasible approcah for genetic research of CS.
     2. The mutation of FANCA (16_89833556_A/G and16_89842161_T/A) may be closely related to CS with the model of incomplete penetrance.
     3. The mutation of ZIC3(X_136651147_A/T and X_136648948_C/T) may be the cause of CS especially those associated with neural tube defects and congenital heart malformations.
     4. The mutation of TBX6(16_30100451_G/A) may be the cause of CS especially those associated with abnormal ribs.
引文
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