目的 采用基于全外显子组测序的单核苷酸变异(SNV) /小插入缺失(InDel)和拷贝数变异(CNV)家系分析(Trios-WES)提高发育迟缓/智力障碍(DD/ID)诊断能力。方法 纳入2017年3月1日—2019年3月31日期间,就诊于上海市儿童医院高危儿整合门诊及康复科门诊,经Gesell、WPPSI-Ⅳ或WISC-Ⅳ评估非外在因素引起、常规遗传检测为阴性、原因不明的58例DD/ID患儿,采用Trios-WES技术分析,对所发现基因变异进一步进行表型与Sanger测序验证,统计与分析结果。结果 58例原因不明的DD/ID患儿,经Trios-WES分析,发现41个DD/ID相关的基因变异,其中13个首次报道。33个基因变异(33/58, 56.9%)经验证为致病性单基因或多基因变异,包括3例CNV变异和1例父源单亲二倍体;含10个错义突变,7个剪切突变,7个移码突变,5个无义突变;新发变异占所有致病变异的79%;其中MECP2、TCF4、SYNGAP1、UBE3A、SHANK3基因变异高频出现。结论 采用Trios-WES临床遗传检测策略,可提高不明原因DD/ID患儿的诊断率,为其进一步治疗及遗传咨询提供依据。
Abstract
Objective To improve diagnostic accuracy of developmental delay/intellectual disability (DD/ID) using genetic variation analysis of single nucleotide variant (SNV)/small insertion-deletion (InDel) and copy number variant (CNV) based on Trios-whole-exome sequencing (Trios-WES). Methods From March 1st, 2017 to March 31st, 2019, 58 children with DD/ID were enrolled and analyzed by Trios-WES technique, who were treated in the High-Risk Infants Multi-Disciplinary Treatment Outpatient and Rehabilitation Department Outpatient of Shanghai Children's Hospital, and were assessed by Gesell, WPPIS-Ⅳ or WISC-Ⅳ as non-external factors, negative by conventional genetic tests, and with unexplained reasons. Further phenotypic confirmation and Sanger sequencing verification were performed to analyze the results. Results Among 58 unknown-cause children with DD/ID, 41 DD/ID related gene variants were identified by Trios-WES analysis and 13 genes variants were reported for the first time. Thirty-threegenes variants (33/58, 56.9%) were found to be pathogenic single genes or multiple gene variants, including three CNV variants and one paternal uniparental disomy (UPD). There were 10 missense variants, 7 splicing variants, 7 frameshift variants and 5 nonsense variants. The de novo variants accounted for 79% of all pathogenic variants. Among them, MECP2, TCF4, SYNGAP1, UBE3A and SHANK3 gene variants appeared frequently. Conclusions The clinical genetic testing strategy of Trios-WES analysis can improve the diagnosis rate of children with unexplained DD/ID, help to identify the cause, and provide a basis for further treatment and genetic counseling.
关键词
发育迟缓/智力障碍 /
核心家系全外显子组检测 /
遗传检测 /
基因变异
Key words
developmental delay/intellectual disability /
Trios-Whole-Exome Sequencing /
genetic testing /
genetic variation
{{custom_sec.title}}
{{custom_sec.title}}
{{custom_sec.content}}
参考文献
[1] 中华医学会儿科学分会神经学组,中国医师协会神经内科分会儿童神经疾病专业委员会.儿童智力障碍或全面发育迟缓病因诊断策略专家共识[J].中华儿科杂志,2018,56(11):806-810.
Group of Neurology,Society of Pediatrics,Chinese Medical Association,Committee of Pediatric Neurological Diseases,Chinese Medical Doctor Association.Expert consensus on the etiological diagnosis strategy of intellectual disability or global developmental delay in children[J].Chin J Pediatr,2018,56(11):806-810.(in Chinese)
[2] Pauper M, Kucuk E, Wenger AM, et al. Correction:Long-read trio sequencing of individuals with unsolved intellectual disability[J]. Eur J Hum Genet, 2021,29(4):720.
[3] Jang W, Kim Y, Han E, et al. Chromosomal microarray analysis as a first-tier clinical diagnostic test in patients with developmental delay/intellectual disability, autism spectrum disorders, and multiple congenital anomalies:A prospective multicenter study in Korea[J]. Ann Lab Med, 2019,39(3):299-310.
[4] Lee CL, Lee CH, Chuang CK, et al.Array-CGH increased the diagnostic rate of developmental delay or intellectual disability in Taiwan[J]. Pediatr Neonatol, 2019,60(4):453-460.
[5] Wang R, Lei T, Fu F, et al. Application of chromosome microarray analysis in patients with unexplained developmental delay/intellectual disability in South China[J].Pediatr Neonatol, 2019,60(1):35-42.
[6] 孙昱,傅启华,余永国.高通量测序技术在智力障碍/全面发育迟缓中的临床应用[J].中华检验医学杂志,2019,42(2):84-88.
Sun Y,Fu QH,Yu YG.Clinical application of next generation sequencing in molecular diagnosis of intellectual disability/global developmental delay[J].Chin J Lab Med, 2019,42(2):84-88.(in Chinese)
[7] Vissers LE, Gilissen C, Veltman JA. Genetic studies in intellectual disability and related disorders[J]. Nat Rev Genet, 2016,17(1):9-18.
[8] Malinowski J, Miller DT,Demmer L, et al. Systematic evidence-based review: outcomes from exome and genome sequencing for pediatric patients with congenital anomalies or intellectual disability[J]. Genet Med, 2020, 22(6):986-1004.
[9] Enomoto Y, Tsurusaki Y, Yokoi T, et al. CNV analysis using whole exome sequencing identified biallelic CNVs of VPS13B in siblings with intellectual disability[J]. Eur J Med Genet, 2020,63(1):103610.
[10] Shashi V,Mcconkie-Rosell A, Rosell B, et al. The utility of the traditional medical genetics diagnostic evaluation in the context of next-generation sequencing for undiagnosed genetic disorders[J]. Genet Med, 2014,16(2):176-182.
[11] 王以文,陈功勋,朱登纳,等.基于共识选择健康测量工具对粗大运动功能评估88项和66项测量学属性的系统评价[J].中国循证儿科杂志,2022,17(5):336-342.
Wang YW, Chen GX, Zhu DN, et al. Psychometric properties of gross motor function measure-88 and 66 based on consensus-based standards for the selection of health measurement instruments:A systematic review[J]. Chin J Evid Based Pediatr, 2022,17(5):336-342.(in Chinese)
[12] Strom SP, Hossain WA, Grigorian M, et al. A streamlined approach to prader-willi and angelman syndrome molecular diagnostics[J]. Front Genet, 2021,12:608889.
[13] Lee CY, Yen HY, Zhong AW, et al. Resolving misalignment interference for NGS-based clinical diagnostics[J]. Hum Genet, 2021,140(3):477-492.
[14] Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants:A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology[J]. Genet Med, 2015,17(5):405-424.
[15] Dong X, Liu B, Yang L, et al. Clinical exome sequencing as the first-tier test for diagnosing developmental disorders covering both CNV and SNV:A Chinese cohort[J]. J Med Genet, 2020,57(8):558-566.
[16] Chen JS, Yu WH, Tsai MC, et al. Comorbidities associated with genetic abnormalities in children with intellectual disability[J]. Sci Rep, 2021,11(1):6563.
[17] Keenan TR, Crowley S. An introduction to child development[M]. Sage Publications, America, Los Angeles, 2016.
[18] Onnis L, Truzzi A, Ma X. Language development and disorders:Possible genes and environment interactions[J]. Res Dev Disabil, 2018,82:132-146.
[19] Xiao B, Qiu W, Ji X, et al. Marked yield of re-evaluating phenotype and exome/target sequencing data in 33 individuals with intellectual disabilities[J]. Am J Med Genet A, 2018,176(1):107-115.
[20] Liu P, Meng L, Normand EA, et al. Reanalysis of clinical exome sequencing data[J]. N Engl J Med, 2019,380(25):2478-2480.
[21] Hu WF, Chahrour MH, Walsh CA. The diverse genetic landscape of neurodevelopmental disorders[J]. Annu Rev Genomics Hum Genet, 2014,15:195-213.
[22] Hamdan FF, Srour M, Capo-Chichi JM, et al. De novo mutations in moderate or severe intellectual disability[J]. PLoS Genet, 2014, 10(10):e1004772.
[23] Bowling KM, Thompson ML, Amaral MD, et al. Genomic diagnosis for children with intellectual disability and/or developmental delay[J]. Genome Med, 2017,9(1):43.
[24] Sanders SJ, Murtha MT, Gupta AR, et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism[J]. Nature, 2012,485(7397):237-241.
[25] Liu J, Tong L, Song S, et al. Novel and de novo mutations in pediatric refractory epilepsy[J]. Mol Brain, 2018,11(1):48.
[26] McCormack M, McGinty RN, Zhu X, et al. De-novo mutations in patients with chronic ultra-refractory epilepsy with onset after age five years[J]. Eur J Med Genet, 2020,63(1):103625.
[27] Chintalapati M, Moorjani P. Evolution of the mutation rate across primates[J]. Curr Opin Genet Dev, 2020,62:58-64.
[28] Tan TY, Lunke S, Chong B, et al. A head-to-head evaluation of the diagnostic efficacy and costs of trio versus singleton exome sequencing analysis[J]. Eur J Hum Genet, 2019,27(12):1791-1799.
[29] Du X, Gao X, Liu X, et al. Genetic diagnostic evaluation of trio-based whole exome sequencing among children with diagnosed or suspected autism spectrum disorder[J]. Front Genet, 2018(9):594.
[30] Geisheker MR, Heymann G, Wang T, et al. Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains[J]. Nat Neurosci, 2017,20(8):1043-1051.
[31] Reichow B, George-Puskar A, Lutz T, et al. Brief report: systematic review of Rett syndrome in males[J]. J Autism Dev Disord, 2015,45(10):3377-3383.
[32] Wen Z, Cheng TL, Li GZ, et al. Identification of autism-related MECP2 mutations by whole-exome sequencing and functional validation[J]. Mol Autism, 2017(8):43.
基金
上海申康医院发展中心临床三年行动计划(SHDC2020CR1047B,SHDC2020CR6028);上海交通大学“转化医学国家重大科技基础设施(上海)开放课题项目”(TMSK-2021-142)
PDF(751 KB)
