基于快速和常规全外显子组分析技术对遗传性疾病的诊断程序比较
|
摘要
目的探索可被临床医生直接应用的全外显子测序(WES)数据分析平台及方法。方法选择复旦大学附属儿科医院(我院)临床诊断不明疾病的核心家系3例(例1～3)和仅先证者2例(例4和5)行WES分析,采用Wu Xi NextCODE临床测序数据分析系统(简称NextCODE平台)进行快速数据分析,并与我院分子诊断中心已建立的高通量数据分析流程(简称常规数据分析流程)进行参与人员及耗时的比较。结果例1～3基于表型相关候选基因联合遗传模式的分析方法,分别检测到FGFR2基因杂合突变、GBE1基因复合杂合突变及TBX1基因杂合突变;例4和5通过表型相关候选基因分析,分别检测到IL10RA基因纯合突变和复合杂合突变。NextCODE平台自动完成3/7个步骤,从输入表型至生成报告,WES数据分析用时30 min以内。常规数据分析流程自动完成1/7个步骤,6个人工完成步骤需要多个专业人员进行数据的筛选及解读,从输入表型至生成报告,熟练的专业人员用时2～8 h。结论 5例临床诊断不明病例通过WES明确了诊断;NextCODE是直接为临床医生所用、简单快速的WES数据分析平台,有助于协助临床医生直接利用高通量测序数据,准确锁定致病突变,提高诊断效率。
Objective A difficult hurdle in whole exome sequencing application is rapid data interpretation. In this study,wholeexome sequencing and Wu Xi Next CODE software were used to rapidly identify pathogenic mutations in 5 undiagnosed cases. Methods The exome targets of the patient' s DNA were captured with the Sure Selct Human All Exon kit followed by sequencing with the Illumina Hi Seq2000 platform. The Wu Xi Next CODE software was used for the data analysis. The detected variant was confirmed with Sanger direct sequencing. Results 5 trio families with undiagnosed probands were recruited. A heterozygous missense mutation was identified in FGFR2 gene in proband 1,compound heterozygous missense mutations in GBE1 gene in proband 2,and a heterozygous missense mutation in TBX1 gene in proband 3 by whole-exome sequencing of trio samples. A homozygous missense mutation was identified in IL10 RA gene in proband 4,and compound heterozygous missense mutations in IL10 RA gene in proband 5by whole-exome sequencing of proband only. Conclusion This study clearly showed the efficacy of whole-exome sequencing and was helpful to rapid genetic diagnosis for undiagnosed cases.
Objective A difficult hurdle in whole exome sequencing application is rapid data interpretation. In this study,wholeexome sequencing and Wu Xi Next CODE software were used to rapidly identify pathogenic mutations in 5 undiagnosed cases. Methods The exome targets of the patient' s DNA were captured with the Sure Selct Human All Exon kit followed by sequencing with the Illumina Hi Seq2000 platform. The Wu Xi Next CODE software was used for the data analysis. The detected variant was confirmed with Sanger direct sequencing. Results 5 trio families with undiagnosed probands were recruited. A heterozygous missense mutation was identified in FGFR2 gene in proband 1,compound heterozygous missense mutations in GBE1 gene in proband 2,and a heterozygous missense mutation in TBX1 gene in proband 3 by whole-exome sequencing of trio samples. A homozygous missense mutation was identified in IL10 RA gene in proband 4,and compound heterozygous missense mutations in IL10 RA gene in proband 5by whole-exome sequencing of proband only. Conclusion This study clearly showed the efficacy of whole-exome sequencing and was helpful to rapid genetic diagnosis for undiagnosed cases.
引文
[1]Schorderet DF.Using OMIM(On-line Mendelian Inheritance in Man)as an expert system in medical genetics.Am J Med Genet,1991,39(3):278-284
[2]Choi M,Scholl UI,Ji W,et al.Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.Proc Natl Acad Sci U S A,2009,106(45):19096-19101
[3]Grody WW,Thompson BH,Hudgins L.Whole-exome/genome sequencing and genomics.Pediatrics,2013,132(S3):211-215
[4]Need AC,Shashi V,Hitomi Y,et al.Clinical application of exome sequencing in undiagnosed genetic conditions.J Med Genet,2012,49(6):353-361
[5]Hane Lee P,Joshua L.Deignan P,Naghmeh Dorrani M,CGC,et al.Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders.JAMA,2014,312(18):1880-1887
[6]Frederick E.Dewey M,Megan E.Grove M,Cuiping Pan P,et al.Clinical Interpretation and Implications of Whole-Genome Sequencing.JAMA,2014,311(10):1035-1044
[7]黎籽秀,刘博,徐凌丽,等.高通量测序数据分析和临床诊断流程的解读.中国循证儿科杂志,2015,10(1):19-24
[8]Yang Y,Muzny DM,Reid JG,et al.Clinical whole-exome sequencing for the diagnosis of mendelian disorders.N Engl J Med,2013,369(16):1502-1511
[9]Jang JH,Shin KH,Park JG.Mutations in fibroblast growth factor receptor 2 and fibroblast growth factor receptor 3 genes associated with human gastric and colorectal cancers.Cancer Res,2001,61(9):3541-3543
[10]Schell U,Hehr A,Feldman GJ,et al.Mutations in FGFR1and FGFR2 cause familial and sporadic Pfeiffer syndrome.Hum Mol Genet,1995,4(3):323-328
[11]Plomp AS,Hamel BC,Cobben JM,et al.Pfeiffer syndrome type 2:further delineation and review of the literature.Am J Med Genet,1998,75(3):245-251
[12]Xu YJ,Chen S,Zhang J,et al.Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion.BMC Med Genet,2014,15:78
[13]Bartsch O,Nemeckova M,Kocarek E,et al.Di George/velocardiofacial syndrome:FISH studies of chromosomes 22q11and 10p14,and clinical reports on the proximal 22q11deletion.Am J Med Genet A,2003,117A(1):1-5
[14]Yagi H,Furutani Y,Hamada H,et al.Role of TBX1 in human del22q11.2 syndrome.Lancet,2003,362(9393):1366-1373
[15]Green RC,Berg JS,Grody WW,et al.ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.Genet Med,2013,15(7):565-574
[16]Kingsmore S.Comprehensive carrier screening and molecular diagnostic testing for recessive childhood diseases.PLo S Curr,2012,e4f9877ab8ffa9
[17]Bao Y,Kishnani P,Wu JY,et al.Hepatic and neuromuscular forms of glycogen storage disease type IV caused by mutations in the same glycogen-branching enzyme gene.J Clin Invest,1996,97(4):941-948
[18]Gasche C,Grundtner P,Zwirn P,et al.Novel variants of the IL-10 receptor 1 affect inhibition of monocyte TNF-alpha production.J Immunol,2003,170(11):5578-5582
[19]Mao H,Yang W,Lee PP,et al.Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease.Genes Immun,2012,13(5):437-442
[2]Choi M,Scholl UI,Ji W,et al.Genetic diagnosis by whole exome capture and massively parallel DNA sequencing.Proc Natl Acad Sci U S A,2009,106(45):19096-19101
[3]Grody WW,Thompson BH,Hudgins L.Whole-exome/genome sequencing and genomics.Pediatrics,2013,132(S3):211-215
[4]Need AC,Shashi V,Hitomi Y,et al.Clinical application of exome sequencing in undiagnosed genetic conditions.J Med Genet,2012,49(6):353-361
[5]Hane Lee P,Joshua L.Deignan P,Naghmeh Dorrani M,CGC,et al.Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders.JAMA,2014,312(18):1880-1887
[6]Frederick E.Dewey M,Megan E.Grove M,Cuiping Pan P,et al.Clinical Interpretation and Implications of Whole-Genome Sequencing.JAMA,2014,311(10):1035-1044
[7]黎籽秀,刘博,徐凌丽,等.高通量测序数据分析和临床诊断流程的解读.中国循证儿科杂志,2015,10(1):19-24
[8]Yang Y,Muzny DM,Reid JG,et al.Clinical whole-exome sequencing for the diagnosis of mendelian disorders.N Engl J Med,2013,369(16):1502-1511
[9]Jang JH,Shin KH,Park JG.Mutations in fibroblast growth factor receptor 2 and fibroblast growth factor receptor 3 genes associated with human gastric and colorectal cancers.Cancer Res,2001,61(9):3541-3543
[10]Schell U,Hehr A,Feldman GJ,et al.Mutations in FGFR1and FGFR2 cause familial and sporadic Pfeiffer syndrome.Hum Mol Genet,1995,4(3):323-328
[11]Plomp AS,Hamel BC,Cobben JM,et al.Pfeiffer syndrome type 2:further delineation and review of the literature.Am J Med Genet,1998,75(3):245-251
[12]Xu YJ,Chen S,Zhang J,et al.Novel TBX1 loss-of-function mutation causes isolated conotruncal heart defects in Chinese patients without 22q11.2 deletion.BMC Med Genet,2014,15:78
[13]Bartsch O,Nemeckova M,Kocarek E,et al.Di George/velocardiofacial syndrome:FISH studies of chromosomes 22q11and 10p14,and clinical reports on the proximal 22q11deletion.Am J Med Genet A,2003,117A(1):1-5
[14]Yagi H,Furutani Y,Hamada H,et al.Role of TBX1 in human del22q11.2 syndrome.Lancet,2003,362(9393):1366-1373
[15]Green RC,Berg JS,Grody WW,et al.ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.Genet Med,2013,15(7):565-574
[16]Kingsmore S.Comprehensive carrier screening and molecular diagnostic testing for recessive childhood diseases.PLo S Curr,2012,e4f9877ab8ffa9
[17]Bao Y,Kishnani P,Wu JY,et al.Hepatic and neuromuscular forms of glycogen storage disease type IV caused by mutations in the same glycogen-branching enzyme gene.J Clin Invest,1996,97(4):941-948
[18]Gasche C,Grundtner P,Zwirn P,et al.Novel variants of the IL-10 receptor 1 affect inhibition of monocyte TNF-alpha production.J Immunol,2003,170(11):5578-5582
[19]Mao H,Yang W,Lee PP,et al.Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease.Genes Immun,2012,13(5):437-442
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |