外显子组测序是发现单基因病致病基因的捷径

新一代测序技术的产生和发展为疾病研究带来了新的机遇.作为一种高效、快速和高性价比的研究方法,外显子组测序技术已经开始应用于单基因疾病等遗传病的研究.该技术已经得到国际学术界的广泛认可,也将越来越多地应用于单基因疾病的研究中.这将对单基因病致病基因的发现产生巨大推动作用.作者对国内外近两年应用外显子测序技术检测疾病相关基因的一些研究进行文献综述.     

全外显子组捕获测序技术在单基因遗传病研究和诊断中的意义

外显子组（exome）即一个个体的基因组DNA上所有蛋白质编码序列（外显子）的总和。人类外显子组序列仅占人类整个基因组序列的1%,约为30 Mb,包括18万个左右的外显子,估计85%的人类致病突变都位于这1%的蛋白质编码序列上。在单基因病的致病基因定位和克隆研究中,通常采用的家系连锁分析法及定位克隆技术是最有效、最准确的方法之一。但是,如果患病亲属的人数有限,或不外显、外显不全,或基因突变是自发产生的,则连锁分析多半失效。这是单基因疾病分子遗传学研究中常常难以克服的＂瓶颈＂。然而,对各种遗传病患者的外显子组进行测序分析,所针对的是与疾病最相关的＂蛋白质编码序列＂区域,捕捉的是疾病的大部分致病突变信息,具有所需样本数量少、低费用、高通量的优势和特点,故可以大大加快鉴定人类疾病基因的进程。另外,对于外显子数目庞大的致病基因（如DMD、FBN1、PKD1等）,用全外显子组测序技术进行基因诊断,则比传统的PCR＋Sanger测序法更为经济。     

Diagnosis of monogenic liver diseases in childhood by next‐generation sequencing

Next‐generation sequencing (NGS) has opened up novel diagnostic opportunities for children with unidentified, but suspected inherited diseases. We describe our single‐center experience with NGS diagnostics in standard clinical scenarios in pediatric hepatology. We investigated 135 children with suspected inherited hepatopathies, where initially no causative pathogenic variant had been identified, with an amplicon‐based NGS panel of 21 genes associated with acute and chronic hepatopathies. In 23 of these patients, we detected pathogenic or likely pathogenic variants in 10 different genes. We present 6 novel variants. A total of 14 of these patients presented with the characteristic phenotype of the related hepatopathy. Nine patients showed only few or atypical clinical symptoms or presented with additional signs. In another 13 out of 135 cases, we detected variants of unknown significance (VUS) in 9 different genes. Only 2 of these patients showed characteristic phenotypes conclusive with the detected variants, whereas 11 patients showed unspecific or atypical phenotypes. Our multi‐gene panel is a fast and comprehensive tool to diagnose inherited pediatric hepatopathies. We also illustrate the challenge of dealing with genetic variants and highlight arising clinical questions, especially in patients with atypical phenotypes.     

Novel glucokinase mutations in patients with monogenic diabetes - clinical outline of GCK-MD and potential for founder effect in Slavic population

Glucokinase (GCK) gene mutations are the causative factor of GCK-MD (monogenic diabetes) characterized by a mild clinical phenotype and potential for insulin withdrawal. This study presents the results of a nationwide genetic screening for GCK-MD performed in Poland. A group of 194 patients with clinical suspicion of GCK-MD and 17 patients with neonatal diabetes were subjected to GCK sequencing. Patients negative for GCK mutations were subjected to multiplex ligation-dependent probe amplification (MLPA) to detect deletions or insertions. A total of 44 GCK heterozygous mutations were found in 68 probands (35%). Among those, 20 mutations were novel ones: A282fs, D198V, E158X, G246V, G249R, I348N, L165V, L315Q, M115I, N254S, P284fs, Q338P, R377L, R43C, R46S, S212fs, S212P, T255N, V406A and Y214D. No abnormalities were detected in MLPA analysis. Homozygous D278E mutation was found in one patient with neonatal diabetes. The most frequently observed combinations of symptoms typical for GCK-MD were mild diabetes and/or fasting hyperglycaemia (98.3%), positive C-peptide at diagnosis (76%) and dominant mode of inheritance (59%). This study outlines numerous novel mutations of the GCK gene present in white Caucasians of Slavic origin. Thorough clinical assessment of known factors associated with GCK-MD may facilitate patient selection.     

Disease gene identification strategies for exome sequencing

Next generation sequencing can be used to search for Mendelian disease genes in an unbiased manner by sequencing the entire protein-coding sequence, known as the exome, or even the entire human genome. Identifying the pathogenic mutation amongst thousands to millions of genomic variants is a major challenge, and novel variant prioritization strategies are required. The choice of these strategies depends on the availability of well-phenotyped patients and family members, the mode of inheritance, the severity of the disease and its population frequency. In this review, we discuss the current strategies for Mendelian disease gene identification by exome resequencing. We conclude that exome strategies are successful and identify new Mendelian disease genes in approximately 60% of the projects. Improvements in bioinformatics as well as in sequencing technology will likely increase the success rate even further. Exome sequencing is likely to become the most commonly used tool for Mendelian disease gene identification for the coming years.     

Doubling the referral rate of monogenic diabetes through a nationwide information campaign - update on glucokinase gene mutations in a Polish cohort

Borowiec M, Fendler W, Antosik K, Baranowska A, Gnys P, Zmyslowska A, Malecki M, Mlynarski W. Doubling the referral rate of monogenic diabetes through a nationwide information campaign - update on glucokinase gene mutations in a Polish cohort. In order to improve recruitment efficiency of patients with monogenic diabetes in Poland, in September 2010 a nationwide advertising campaign was launched to inform multiple target groups interested or participating in pediatric diabetologic care. Promotional actions aimed at informing physicians, patients, parents and educators were carried out through nationwide newspapers, medical and patient-developed websites and educational conference presentations. Recruitment efficiency was compared between September 2010 (publication of the first report on project's results) and the following 12 months. The number of families and patients referred to genetic screening was increased by 92% and 96% respectively nearly reaching the numbers recruited throughout the initial 4 years of the project. Participation of non-academic centers was also significantly increased from 2.3% to 7.5% (p = 0.0005). DNA sequencing and Multiplex Ligation-dependant Probe Amplification of the glucokinase gene resulted in finding 50 different mutations. Among those mutations, 19 were novel variants, which included: 17 missense mutations (predicted to be pathogenic according to bioinformatic analysis), 1 nonsense mutation and 1 mutation affecting a consensus intronic splice site. Advertising actions directed at increasing recruitment efficiency are a powerful and possibly neglected tool in screening for rare genetic disorders with a clinically defined phenotype.     

Disease mechanisms of monogenic congenital anomalies of the kidney and urinary tract

Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) is a developmental disorder of the kidney and/or genito-urinary tract that results in end stage kidney disease (ESKD) in up to 50% of children. Despite the congenital nature of the disease, CAKUT accounts for almost 10% of adult onset ESKD. Multiple lines of evidence suggest that CAKUT is a Mendelian disorder, including the observation of familial clustering of CAKUT. Pathogenesis in CAKUT is embryonic in origin, with disturbances of kidney and urinary tract development resulting in a heterogeneous range of disease phenotypes. Despite polygenic and environmental factors being implicated, a significant proportion of CAKUT is monogenic in origin, with studies demonstrating single gene defects in 10%–20% of patients with CAKUT. Here, we review monogenic disease causation with emphasis on the etiological role of gene developmental pathways in CAKUT.     

Novel myosin mutations for hereditary hearing loss revealed by targeted genomic capture and massively parallel sequencing

Hereditary hearing loss is genetically heterogeneous, with a large number of genes and mutations contributing to this sensory, often monogenic, disease. This number, as well as large size, precludes comprehensive genetic diagnosis of all known deafness genes. A combination of targeted genomic capture and massively parallel sequencing (MPS), also referred to as next-generation sequencing, was applied to determine the deafness-causing genes in hearing-impaired individuals from Israeli Jewish and Palestinian Arab families. Among the mutations detected, we identified nine novel mutations in the genes encoding myosin VI, myosin VIIA and myosin XVA, doubling the number of myosin mutations in the Middle East. Myosin VI mutations were identified in this population for the first time. Modeling of the mutations provided predicted mechanisms for the damage they inflict in the molecular motors, leading to impaired function and thus deafness. The myosin mutations span all regions of these molecular motors, leading to a wide range of hearing phenotypes, reinforcing the key role of this family of proteins in auditory function. This study demonstrates that multiple mutations responsible for hearing loss can be identified in a relatively straightforward manner by targeted-gene MPS technology and concludes that this is the optimal genetic diagnostic approach for identification of mutations responsible for hearing loss.     

Evaluation of exome filtering techniques for the analysis of clinically relevant genes

A significant challenge facing clinical translation of exome sequencing is meaningful and efficient variant interpretation. Each exome contains ～500 rare coding variants; laboratories must systematically and efficiently identify which variant(s) contribute to the patient's phenotype. In silico filtering is an approach that reduces analysis time while decreasing the chances of incidental findings. We retrospectively assessed 55 solved exomes using available datasets as in silico filters: Online Mendelian Inheritance in Man (OMIM), Orphanet, Human Phenotype Ontology (HPO), and Radboudumc University Medical Center curated panels. We found that personalized panels produced using HPO terms for each patient had the highest success rate (100%), while producing considerably less variants to assess. HPO panels also captured multiple diagnoses in the same individual. We conclude that custom HPO‐derived panels are an efficient and effective way to identify clinically relevant exome variants.     

一例糖原累积病Ⅵ型患儿的PYGL基因变异分析CSCD

目的分析1例糖原累积病Ⅵ型(glycogen storage disease typeⅥ,GSD-Ⅵ)患儿的临床特征和基因变异情况,明确其致病原因。方法收集1例GSD-Ⅵ患儿的临床资料,采集患儿及其父母外周血提取基因组DNA,应用全外显子测序对患者进行基因检测,对疑似变异进行Sanger测序验证并行生物信息学分析。结果患儿表现为空腹低血糖、肝大、生长迟缓、转氨酶增高、代谢性酸中毒、高乳酸,肝穿刺病理提示糖原累积病。基因测序提示患儿PYGL基因存在c.2089A>G(p・Asn697Asp)和c.158_160delACT(p.Tyr53del)复合杂合变异。Sanger测序验证提示患儿母亲存在c.2089A>G杂合变异,患儿父亲存在c.158_160delACT杂合变异。这两种变异均为罕见的变异,既往未见报道,其位点高度保守且Provean、MutationTaster预测为有害。结论PYGL基因复合杂合变异(c.2089A>G/c.158_160delACT)为患儿的致病原因。新变异位点的检出丰富了PYGL基因的变异谱,为该家系的遗传咨询提供了依据。     

Prediction of functional regulatory SNPs in monogenic and complex disease

Next-generation sequencing (NGS) technologies are yielding ever higher volumes of human genome sequence data. Given this large amount of data, it has become both a possibility and a priority to determine how disease-causing single nucleotide polymorphisms (SNPs) detected within gene regulatory regions (rSNPs) exert their effects on gene expression. Recently, several studies have explored whether disease-causing polymorphisms have attributes that can distinguish them from those that are neutral, attaining moderate success at discriminating between functional and putatively neutral regulatory SNPs. Here, we have extended this work by assessing the utility of both SNP-based features (those associated only with the polymorphism site and the surrounding DNA) and gene-based features (those derived from the associated gene in whose regulatory region the SNP lies) in the identification of functional regulatory polymorphisms involved in either monogenic or complex disease. Gene-based features were found to be capable of both augmenting and enhancing the utility of SNP-based features in the prediction of known regulatory mutations. Adopting this approach, we achieved an AUC of 0.903 for predicting regulatory SNPs. Finally, our tool predicted 225 new regulatory SNPs with a high degree of confidence, with 105 of the 225 falling into linkage disequilibrium blocks of reported disease-associated genome-wide association studies SNPs.     

NDP基因c.361C>T错义变异致诺里病一家系

目的分析1个诺里病家系的致病基因变异,确定其遗传学病因。方法对先证者核心家系4名成员的DNA样本进行全外显子组检测,筛选变异位点,确定致病基因。通过Sanger测序对核心家系及7名其他家系成员进行验证。结果全外显子组检测及Sanger测序结果显示先证者及另外3例男性患者的NDP基因均存在c.361C>T(p.Arg121Trp)半合子错义变异,先证者母亲、外祖母和2个表妹均为c.361C>T杂合变异携带者,正常表型男性家系成员均未检测到该变异,符合X连锁隐性遗传病的特点。结论NDP基因c.361C>T错义变异是该诺里病家系的遗传学病因。     

First successful double‐factor PGD for Lynch syndrome: monogenic analysis and comprehensive aneuploidy screening

Preimplantation genetic diagnosis (PGD) has been applied worldwide for a great variety of single‐gene disorders over the last 20 years. The aim of this work was to perform a double‐factor preimplantation genetic diagnosis (DF‐PGD) protocol in a family at risk for Lynch syndrome. The family underwent a DF‐PGD approach in which two blastomeres from each cleavage‐stage embryo were biopsied and used for monogenic and comprehensive cytogenetic analysis, respectively. Fourteen embryos were biopsied for the monogenic disease and after multiple displacement amplification (MDA), 12 embryos were diagnosed; 5 being non‐affected and 7 affected by the disease. Thirteen were biopsied to perform the aneuploidy screening by short‐comparative genomic hybridization (CGH). The improved DF‐PGD approach permitted the selection of not only healthy but also euploid embryos for transfer. This has been the first time a double analysis of embryos has been performed in a family affected by Lynch syndrome, resulting in the birth of two healthy children. The protocol described in this work offers a reliable alternative for single‐gene disorder assessment together with a comprehensive aneuploidy screening of the embryos that may increase the chances of pregnancy and birth of transferred embryos.     

一个先天性小眼畸形家系的全外显子组测序分析及产前诊断

目的分析1个先天性小眼畸形家系的临床表型及遗传学病因。方法应用高通量测序技术对先证者及其父母进行全外显子组测序,筛选候选致病位点,对其家系进行Sanger测序验证,并通过羊水穿刺和Sanger测序为先证者母亲提供产前诊断。结果全外显子组测序和Sanger测序发现家系中的3例患者均携带OTX2基因c.289C>T(p.R97*)杂合变异,先证者母亲亦携带该变异,但无小眼畸形。先证者的父亲、舅母和胎儿未携带上述变异。结论OTX2基因c.289C>T(p.R97*)杂合变异很可能是该家系的发病原因。上述诊断将有助于该家系的遗传咨询和产前诊断。     

一例婴儿型多囊肾病胎儿的 HNF1B基因新发变异分析

目的:对一例婴儿型多囊肾病胎儿的 HNF1B基因变异进行分析,明确其致病原因。 方法:收集引产胎儿的新鲜组织及其父母外周静脉血样,提取基因组DNA,进行全外显子测序分析,筛查出与临床表型相关的变异位点,并通过Sanger测序进行位点验证。结果:胎儿组织样本中检测到 HNF1B基因的一...     

一例婴儿型多囊肾病胎儿的HNF1B基因新发变异分析CSCD

目的对一例婴儿型多囊肾病胎儿的HNF1B基因变异进行分析, 明确其致病原因。方法收集引产胎儿的新鲜组织及其父母外周静脉血样, 提取基因组DNA, 进行全外显子测序分析, 筛查出与临床表型相关的变异位点, 并通过Sanger测序进行位点验证。结果胎儿组织样本中检测到HNF1B基因的一个c.1370C>T(p.P457L) 杂合变异, 其父母为正常。该变异经检索相关数据库及文献均未见报道为新变异。结论 HNF1B基因的c.1370C>T新发杂合变异可能为婴儿型多囊肾的致病原因。本研究结果为该病的遗传咨询和临床产前诊断提供了依据。     

Iranome: A catalog of genomic variations in the Iranian population

Considering the application of human genome variation databases in precision medicine, population‐specific genome projects are continuously being developed. However, the Middle Eastern population is underrepresented in current databases. Accordingly, we established Iranome database ( www.iranome.com ) by performing whole exome sequencing on 800 individuals from eight major Iranian ethnic groups representing the second largest population of Middle East. We identified 1,575,702 variants of which 308,311 were novel (19.6%). Also, by presenting higher frequency for 37,384 novel or known rare variants, Iranome database can improve the power of molecular diagnosis. Moreover, attainable clinical information makes this database a good resource for classifying pathogenicity of rare variants. Principal components analysis indicated that, apart from Iranian‐Baluchs, Iranian‐Turkmen, and Iranian‐Persian Gulf Islanders, who form their own clusters, rest of the population were genetically linked, forming a super‐population. Furthermore, only 0.6% of novel variants showed counterparts in “Greater Middle East Variome Project”, emphasizing the value of Iranome at national level by releasing a comprehensive catalog of Iranian genomic variations and also filling another gap in the catalog of human genome variations at international level. We introduce Iranome as a resource which may also be applicable in other countries located in neighboring regions historically called Greater Iran (Persia).