高级检索
中华医学遗传学杂志
期刊首页
过刊列表
高级检索
稿件发表
• 综述 •
ENGLISH ABSTRACT
转录组测序技术在遗传病诊断中的应用
安君
郭可欣
胡平
作者及单位信息
·
DOI： 10.3760/cma.j.cn511374-20240821-00452
Advancements in the application of RNA sequencing for genetic disorder diagnosis
An Jun
Guo Kexin
Hu Ping
Authors Info & Affiliations
An Jun
Department of Prenatal Diagnosis, Women′s Hospital of Nanjing Medical University, Nanjing Women and Children′s Health Care Hospital, Nanjing, Jiangsu 210004, China
State Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
Guo Kexin
Department of Prenatal Diagnosis, Women′s Hospital of Nanjing Medical University, Nanjing Women and Children′s Health Care Hospital, Nanjing, Jiangsu 210004, China
Hu Ping
Department of Prenatal Diagnosis, Women′s Hospital of Nanjing Medical University, Nanjing Women and Children′s Health Care Hospital, Nanjing, Jiangsu 210004, China
·
DOI： 10.3760/cma.j.cn511374-20240821-00452
0
0
0
0
0
0
PDF下载
APP内阅读
摘要

全外显子组测序(WES)和全基因组测序(WGS)等高通量测序技术极大地提高了遗传病的诊断率，但在解释意义不明变异(VUS)、非编码区变异以及这些变异对下游基因的影响方面仍存在巨大的挑战，其诊断率通常在25% ～ 57%。转录组测序(RNA-seq)可以作为DNA测序的补充检测，通过检测基因的异常表达、异常剪接、等位基因特异性表达和融合基因表达等揭示遗传变异的功能影响，进一步提高遗传病的诊断率并为其拓宽了诊断策略，有望成为新的诊断工具。本文总结了RNA-seq的方法及技术特点，重点探讨了其在遗传病诊断方面的应用进展、未诊断遗传病中的应用策略、以及在遗传病诊断过程中所面临的主要挑战。

遗传病;孟德尔病;遗传学诊断;转录组测序;外显子组测序;全基因组测序
ABSTRACT

Next generation sequencing (NGS) technologies, including whole exome sequencing (WES) and whole genome sequencing (WGS), have greatly increased the diagnostic rates for genetic disorders. However, challenges still remain with the interpretation of variants of uncertain significance (VUS), variants in non-coding regions, and understanding of the effects of such variants on downstream genes. As a result, the diagnostic rates have typically ranged from 25% to 57%. RNA sequencing (RNA-seq) can complement DNA sequencing by revealing the functional consequences of genetic variants through the detection of aberrant gene expression, abnormal splicing events, allele-specific expression, and fusion gene expression. This has further increased the diagnostic rate of genetic disorders and enriched their therapeutic strategies. By broadening the scope of conventional genomic diagnostic methods, RNA-seq is poised to become a novel tool for the diagnosis of genetic disorders. This review has explored the methodologies and technical characteristics of RNA-seq by focusing on its recent advancement in clinical diagnosis, applications in undiagnosed genetic disorders, and the main challenges encountered.

Genetic disorder;Mendelian disorder;Genetic diagnosis;RNA sequencing;Exome sequencing;Whole genome sequencing
Hu Ping, Email: mocdef.3ab61gnipuhyjbyfjn
Guo Kexin, Email: mocdef.3ab61ougxk_oib
Copyright by Chinese Medical Association
No content published by the journals of Chinese Medical Association may be reproduced or abridged without authorization. Please do not use or copy the layout and design of the journals without permission.
All articles published represent the opinions of the authors, and do not reflect the official policy of the Chinese Medical Association or the Editorial Board, unless this is clearly specified.
引用本文

安君,郭可欣,胡平. 转录组测序技术在遗传病诊断中的应用[J]. 中华医学遗传学杂志,2025,42(02)：238-243.

DOI:10.3760/cma.j.cn511374-20240821-00452

PERMISSIONS

Request permissions for this article from CCC.

评价本文
*以上评分为匿名评价

版权归中华医学会所有。

未经授权，不得转载、摘编本刊文章，不得使用本刊的版式设计。

除非特别声明，本刊刊出的所有文章不代表中华医学会和本刊编委会的观点。

遗传病是由遗传物质改变所导致的疾病 [ 1 ]，主要包括单基因病、多基因病、染色体病和线粒体病。经典的单基因病又称孟德尔病(Mendelian disorders)。人类在线孟德尔遗传(Online Mendelian Inheritance in Man，OMIM)数据库目前已收录约7000种孟德尔病。全外显子组测序(whole exome sequencing，WES)和全基因组测序(whole genome sequencing，WGS)等高通量测序技术的广泛应用，显著提高了罕见孟德尔病的诊断率，从而为疾病的精准治疗和个体化管理奠定了基础。然而，大多数研究者报告的诊断率仅为25% ～ 57% [ 2 , 3 , 4 , 5 , 6 ]，并且在解释意义不明变异(variants of uncertain significance，VUS)、非编码区变异以及这类变异对下游基因的影响等方面仍存在巨大的挑战。近年来，转录组测序(RNA sequencing，RNA-seq)技术在基因组学研究中发挥着越来越重要的作用。作为DNA测序的重要补充，RNA-seq能够通过揭示遗传变异的功能后果，进一步提高遗传病的诊断和治疗能力。
试读结束，您可以通过登录机构账户或个人账户后获取全文阅读权限。
参考文献
[1]
张学. 我国遗传病致病基因研究的回顾和展望[J]. 海南医学， 2019,30(S1):41-46. DOI: CNKI:SUN:HAIN.0.2019-S1-008 .
返回引文位置Google Scholar
百度学术
万方数据
Zhang X . Disease gene discovery in China: a historical overview and future perspective[J]. Hainan Med J, 2019,30(S1):41-46. DOI: CNKI:SUN:HAIN.0.2019-S1-008 .
Goto CitationGoogle Scholar
Baidu Scholar
Wanfang Data
[2]
Yang Y , Muzny DM , Xia F ,et al. Molecular findings among patients referred for clinical whole-exome sequencing[J]. JAMA, 2014,312(18):1870-1879. DOI: 10.1001/jama.2014.14601 .
返回引文位置Google Scholar
百度学术
万方数据
[3]
Kress W , Rost S , Kolokotronis K ,et al. The genetic approach: Next-generation sequencing-based diagnosis of congenital and infantile myopathies/muscle dystrophies[J]. Neuropediatrics, 2017,48(4):242-246. DOI: 10.1055/s-0037-1602660 .
返回引文位置Google Scholar
百度学术
万方数据
[4]
Powis Z , Farwell Hagman KD , Speare V ,et al. Exome sequencing in neonates: diagnostic rates, characteristics, and time to diagnosis[J]. Genet Med, 2018,20(11):1468-1471. DOI: 10.1038/gim.2018.11 .
返回引文位置Google Scholar
百度学术
万方数据
[5]
Topa A , Rohlin A , Fehr A ,et al. The value of genome-wide analysis in craniosynostosis[J]. Front Genet, 2023,14:1322462. DOI: 10.3389/fgene.2023.1322462 .
返回引文位置Google Scholar
百度学术
万方数据
[6]
Migliavacca MP , Sobreira J , Bermeo D ,et al. Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil[J]. Am J Med Genet A, 2024,194(6):e63544. DOI: 10.1002/ajmg.a.63544 .
返回引文位置Google Scholar
百度学术
万方数据
[7]
Wang Z , Gerstein M , Snyder M . RNA-Seq: a revolutionary tool for transcriptomics[J]. Nat Rev Genet, 2009,10(1):57-63. DOI: 10.1038/nrg2484 .
返回引文位置Google Scholar
百度学术
万方数据
[8]
Zhang H , He L , Cai L . Transcriptome sequencing: RNA-Seq[J]. Methods Mol Biol, 2018,1754:15-27. DOI: 10.1007/978-1-4939-7717-8_2 .
返回引文位置Google Scholar
百度学术
万方数据
[9]
Ku CS , Wu M , Cooper DN ,et al. Exome versus transcriptome sequencing in identifying coding region variants[J]. Expert Rev Mol Diagn, 2012,12(3):241-251. DOI: 10.1586/erm.12.10 .
返回引文位置Google Scholar
百度学术
万方数据
[10]
Consortium SM-I . A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium[J]. Nat Biotechnol, 2014,32(9):903-914. DOI: 10.1038/nbt.2957 .
返回引文位置Google Scholar
百度学术
万方数据
[11]
Stark R , Grzelak M , Hadfield J . RNA sequencing: the teenage years[J]. Nat Rev Genet, 2019,20(11):631-656. DOI: 10.1038/s41576-019-0150-2 .
返回引文位置Google Scholar
百度学术
万方数据
[12]
Oikonomopoulos S , Wang YC , Djambazian H ,et al. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations[J]. Sci Rep, 2016,6:31602. DOI: 10.1038/srep31602 .
返回引文位置Google Scholar
百度学术
万方数据
[13]
Garalde DR , Snell EA , Jachimowicz D ,et al. Highly parallel direct RNA sequencing on an array of nanopores[J]. Nat Methods, 2018,15(3):201-206. DOI: 10.1038/nmeth.4577 .
返回引文位置Google Scholar
百度学术
万方数据
[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. DOI: 10.1038/gim.2015.30 .
返回引文位置Google Scholar
百度学术
万方数据
[15]
Brnich SE , Rivera-Munoz EA , Berg JS . Quantifying the potential of functional evidence to reclassify variants of uncertain significance in the categorical and Bayesian interpretation frameworks[J]. Hum Mutat, 2018,39(11):1531-1541. DOI: 10.1002/humu.23609 .
返回引文位置Google Scholar
百度学术
万方数据
[16]
Gelman H , Dines JN , Berg J ,et al. Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation[J]. Genome Med, 2019,11(1):85. DOI: 10.1186/s13073-019-0698-7 .
返回引文位置Google Scholar
百度学术
万方数据
[17]
Montgomery SB , Lappalainen T , Gutierrez-Arcelus M ,et al. Rare and common regulatory variation in population-scale sequenced human genomes[J]. PLoS Genet, 2011,7(7):e1002144. DOI: 10.1371/journal.pgen.1002144 .
返回引文位置Google Scholar
百度学术
万方数据
[18]
Kremer LS , Bader DM , Mertes C ,et al. Genetic diagnosis of Mendelian disorders via RNA sequencing[J]. Nat Commun, 2017,8:15824. DOI: 10.1038/ncomms15824 .
返回引文位置Google Scholar
百度学术
万方数据
[19]
Youssefian L , Vahidnezhad H , Saeidian AH ,et al. Autosomal recessive congenital ichthyosis: Genomic landscape and phenotypic spectrum in a cohort of 125 consanguineous families[J]. Hum Mutat, 2019,40(3):288-298. DOI: 10.1002/humu.23695 .
返回引文位置Google Scholar
百度学术
万方数据
[20]
Abramowicz A , Gos M . Splicing mutations in human genetic disorders: examples, detection, and confirmation[J]. J Appl Genet, 2018,59(3):253-268. DOI: 10.1007/s13353-018-0444-7 .
返回引文位置Google Scholar
百度学术
万方数据
[21]
Tazi J , Bakkour N , Stamm S . Alternative splicing and disease[J]. Biochim Biophys Acta, 2009,1792(1):14-26. DOI: 10.1016/j.bbadis.2008.09.017 .
返回引文位置Google Scholar
百度学术
万方数据
[22]
Scotti MM , Swanson MS . RNA mis-splicing in disease[J]. Nat Rev Genet, 2016,17(1):19-32. DOI: 10.1038/nrg.2015.3 .
返回引文位置Google Scholar
百度学术
万方数据
[23]
Singh RK , Cooper TA . Pre-mRNA splicing in disease and therapeutics[J]. Trends Mol Med, 2012,18(8):472-482. DOI: 10.1016/j.molmed.2012.06.006 .
返回引文位置Google Scholar
百度学术
万方数据
[24]
Abou Tayoun AN , Pesaran T , DiStefano MT ,et al. Recommendations for interpreting the loss of function PVS1 ACMG/AMP variant criterion[J]. Hum Mutat, 2018,39(11):1517-1524. DOI: 10.1002/humu.23626 .
返回引文位置Google Scholar
百度学术
万方数据
[25]
Vahidnezhad H , Youssefian L , Daneshpazhooh M ,et al. Biallelic KRT5 mutations in autosomal recessive epidermolysis bullosa simplex, including a complete human keratin 5 " knock-out " [J]. Matrix Biol, 2019,83:48-59. DOI: 10.1016/j.matbio.2019.07.002 .
返回引文位置Google Scholar
百度学术
万方数据
[26]
Lee M , Kwong AKY , Chui MMC ,et al. Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept[J]. NPJ Genom Med, 2022,7(1):74. DOI: 10.1038/s41525-022-00347-4 .
返回引文位置Google Scholar
百度学术
万方数据
[27]
Wimmer K , Roca X , Beiglbock H ,et al. Extensive in silico analysis of NF1 splicing defects uncovers determinants for splicing outcome upon 5′ splice-site disruption [J]. Hum Mutat, 2007,28(6):599-612. DOI: 10.1002/humu.20493 .
返回引文位置Google Scholar
百度学术
万方数据
[28]
Cummings BB , Marshall JL , Tukiainen T ,et al. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing[J]. Sci Transl Med, 2017,9(386):eaal5209. DOI: 10.1126/scitranslmed.aal5209 .
返回引文位置Google Scholar
百度学术
万方数据
[29]
Fresard L , Smail C , Ferraro NM ,et al. Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts[J]. Nat Med, 2019,25(6):911-919. DOI: 10.1038/s41591-019-0457-8 .
返回引文位置Google Scholar
百度学术
万方数据
[30]
Hiraide T , Shimizu K , Miyamoto S ,et al. Genome sequencing and RNA sequencing of urinary cells reveal an intronic FBN1 variant causing aberrant splicing [J]. J Hum Genet, 2022,67(7):387-392. DOI: 10.1038/s10038-022-01016-1 .
返回引文位置Google Scholar
百度学术
万方数据
[31]
Benayed R , Offin M , Mullaney K ,et al. High yield of RNA sequencing for targetable kinase fusions in lung adenocarcinomas with no mitogenic driver alteration detected by DNA sequencing and low tumor mutation burden[J]. Clin Cancer Res, 2019,25(15):4712-4722. DOI: 10.1158/1078-0432.CCR-19-0225 .
返回引文位置Google Scholar
百度学术
万方数据
[32]
Davies KD , Lomboy A , Lawrence CA ,et al. DNA-based versus RNA-based detection of MET exon 14 skipping events in lung cancer [J]. J Thorac Oncol, 2019,14(4):737-741. DOI: 10.1016/j.jtho.2018.12.020 .
返回引文位置Google Scholar
百度学术
万方数据
[33]
Beaubier N , Bontrager M , Huether R ,et al. Integrated genomic profiling expands clinical options for patients with cancer[J]. Nat Biotechnol, 2019,37(11):1351-1360. DOI: 10.1038/s41587-019-0259-z .
返回引文位置Google Scholar
百度学术
万方数据
[34]
Kerbs P , Vosberg S , Krebs S ,et al. Fusion gene detection by RNA-sequencing complements diagnostics of acute myeloid leukemia and identifies recurring NRIP1-MIR99AHG rearrangements [J]. Haematologica, 2022,107(1):100-111. DOI: 10.3324/haematol.2021.278436 .
返回引文位置Google Scholar
百度学术
万方数据
[35]
Xiao B , Luo X , Liu Y ,et al. Combining optical genome mapping and RNA-seq for structural variants detection and interpretation in unsolv ed neurodevelopmental disorders [J]. Genome Med, 2024,16(1):113. DOI: 10.1186/s13073-024-01382-9 .
返回引文位置Google Scholar
百度学术
万方数据
[36]
肖慧，周文浩. 转录组测序在孟德尔病临床诊断中的应用进展[J]. 中国当代儿科杂志， 2020,22(10):1138-1143. DOI: 10.7499/j.issn.1008-8830.2005004 .
返回引文位置Google Scholar
百度学术
万方数据
Xiao H , Zhou WH . Application of RNA sequencing in clinical diagnosis of Mendelian disease[J]. Chin J Contemp Pediatr, 2020,22(10):1138-1143. DOI: 10.7499/j.issn.1008-8830.2005004 .
Goto CitationGoogle Scholar
Baidu Scholar
Wanfang Data
[37]
Chepelev I , Wei G , Tang Q ,et al. Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq[J]. Nucleic Acids Res, 2009,37(16):e106. DOI: 10.1093/nar/gkp507 .
返回引文位置Google Scholar
百度学术
万方数据
[38]
Cirulli ET , Singh A , Shianna KV ,et al. Screening the human exome: a comparison of whole genome and whole transcriptome sequencing[J]. Genome Biol, 2010,11(5):R57. DOI: 10.1186/gb-2010-11-5-r57 .
返回引文位置Google Scholar
百度学术
万方数据
[39]
Yépez VA , Gusic M , Kopajtich R ,et al. Clinical implementation of RNA seq uencing for Mendelian disease diagnostics [J]. Genome Med, 2022,14(1):38. DOI: 10.1186/s13073-022-01019-9 .
返回引文位置Google Scholar
百度学术
万方数据
[40]
Alfares A , Aloraini T , Subaie LA ,et al. Whole-genome sequencing offers additional but limited clinical utility compared with reanalysis of whole-exome sequencing[J]. Genet Med, 2018,20(11):1328-1333. DOI: 10.1038/gim.2018.41 .
返回引文位置Google Scholar
百度学术
万方数据
[41]
Lee H , Huang AY , Wang LK ,et al. Diagnostic utility of transcriptome sequencing for rare Mendelian diseases[J]. Genet Med, 2020,22(3):490-499. DOI: 10.1038/s41436-019-0672-1 .
返回引文位置Google Scholar
百度学术
万方数据
[42]
Blake B , Brady LI , Rouse NA ,et al. The efficacy of whole genome sequencing and RNA-Seq in the diagnosis of whole exome sequencing negative patients with complex neurological phenotypes[J]. J Pediatr Genet, 2023,12(3):206-212. DOI: 10.1055/s-0041-1736610 .
返回引文位置Google Scholar
百度学术
万方数据
[43]
Murdock DR , Dai H , Burrage LC ,et al. Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing[J]. J Clin Invest, 2021,131(1):e141500. DOI: 10.1172/JCI141500 .
返回引文位置Google Scholar
百度学术
万方数据
[44]
Kawakami R , Hiraide T , Watanabe K ,et al. RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing[J]. J Hum Genet, 2024,69(2):91-99. DOI: 10.1038/s10038-023-01211-8 .
返回引文位置Google Scholar
百度学术
万方数据
[45]
Smirnov D , Schlieben LD , Peymani F ,et al. Guidelines for clinical interpretation of variant pathogenicity using RNA phenotypes[J]. Hum Mutat, 2022,43(8):1056-1070. DOI: 10.1002/humu.24416 .
返回引文位置Google Scholar
百度学术
万方数据
[46]
Dionnet E , Defour A , Da Silva N ,et al. Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay [J]. Hum Mutat, 2020,41(10):1797-1810. DOI: 10.1002/humu.24083 .
返回引文位置Google Scholar
百度学术
万方数据
[47]
Savisaar R , Hurst LD . Estimating the prevalence of functional exonic splice regulatory information[J]. Hum Genet, 2017,136(9):1059-1078. DOI: 10.1007/s00439-017-1798-3 .
返回引文位置Google Scholar
百度学术
万方数据
[48]
Rentas S , Rathi KS , Kaur M ,et al. Diagnosing Cornelia de Lange syndrome and related neurodevelopmental disorders using RNA sequencing [J]. Genet Med, 2020,22(5):927-936. DOI: 10.1038/s41436-019-0741-5 .
返回引文位置Google Scholar
百度学术
万方数据
[49]
Peymani F , Farzeen A , Prokisch H . RNA sequencing role and application in clinical diagnostic[J]. Pediatr Investig, 2022,6(1):29-35. DOI: 10.1002/ped4.12314 .
返回引文位置Google Scholar
百度学术
万方数据
[50]
Li S , Zhao S , Sinson JC ,et al. The clinical utility and diagnostic implementation of human subject cell transdifferentiation followed by RNA sequencing[J]. Am J Hum Genet, 2024,111(5):841-862. DOI: 10.1016/j.ajhg.2024.03.007 .
返回引文位置Google Scholar
百度学术
万方数据
[51]
Gu W , Crawford ED , O′Donovan BD ,et al. Depletion of Abundant Sequences by Hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications[J]. Genome Biol, 2016,17:41. DOI: 10.1186/s13059-016-0904-5 .
返回引文位置Google Scholar
百度学术
万方数据
备注信息
A
胡平，Email： mocdef.3ab61gnipuhyjbyfjn
B
郭可欣，Email： mocdef.3ab61ougxk_oib
C

安君：起草文章；郭可欣：对文章知识性内容作批评性审阅、指导；胡平：对文章知识性内容作批评性审阅、获取研究经费、行政/技术/材料支持、指导、支持性贡献

D
所有作者均声明不存在利益冲突
E
国家自然科学基金 (82371862)
国家重点研发计划 (2022YFC2703400)
南京医科大学科技发展基金 (NMUB20240073)
评论 （0条）
注册
登录
时间排序
暂无评论，发表第一条评论抢沙发
最新推荐
更多
TRDN基因变异所致Triadin敲除综合征1例的临床及遗传学分析并文献复习
李环 等
中华医学遗传学杂志 2024,41(11)
ABCC9基因变异所致Cantú综合征1例患儿的临床特征及遗传学分析
肖梦君 等
中华医学遗传学杂志 2024,41(10)
SLC9A7基因变异所致X连锁精神发育迟滞1例患儿的临床特征及遗传学分析
李维 等
中华医学遗传学杂志 2024,41(06)
X连锁α-地中海贫血精神发育迟滞综合征一个家系的临床及ATRX基因变异分析
董睿 等
中华医学遗传学杂志 2023,40(12)
MedAI助手（体验版）
文档即答
智问智答
机器翻译
回答内容由人工智能生成，我社无法保证其准确性和完整性，该生成内容不代表我们的态度或观点，仅供参考。
生成快照
文献快照

你好，我可以帮助您更好的了解本文，请向我提问您关注的问题。

0/2000

《中华医学会杂志社用户协议》 | 《隐私政策》

《SparkDesk 用户协议》 | 《SparkDesk 隐私政策》

网信算备340104764864601230055号 | 网信算备340104726288401230013号

技术支持：

历史对话
本文全部
还没有聊天记录
设置
模式
纯净模式沉浸模式
字号
小中大