Definition of chromosomal abnormalities by next generation sequencing

通过下一代测序定义染色体异常

• 批准号: 8063822
• 负责人: Nara Sobreira
• 金额: $ 3.84万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-04-01 至 2014-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8063822
• 关键词: 10q21; 10q21.1; 17q; Base Pairing; Candidate Disease Gene; Chromosomal Rearrangement; Chromosome abnormality; Chromosomes; Cleidocranial Dysplasia; Clinic; Complex; Craniofacial Abnormalities; Cytogenetics; DNA Sequence Rearrangement; Detection; Development; Developmental Delay Disorders; Disease; Equilibrium; Evaluation; Family; Fluorescent in Situ Hybridization; Functional disorder; Generations; Genes; Genetic; Genetic Medicine; Genomics; Hereditary Disease; Heterogeneity; Human; Human Genetics; Hybridization Array; Institutes; Inverse Polymerase Chain Reaction; Karyotype; Lead; Mental disorders; Methods; Molecular; Molecular Abnormality; Molecular Cytogenetics; Mutation; NRG3 gene; Online Mendelian Inheritance In Man; Patients; Phenotype; Predisposition; Psychotic Disorders; Reading; Reporting; Resolution; Resources; Retinitis Pigmentosa; SNP genotyping; Schizophrenia; Series; Susceptibility Gene; Syndrome; Testing; Translocation Breakpoint; Usher Syndrome; base; campomelic dysplasia; clinical phenotype; comparative genomic hybridization; hearing impairment; interest; malformation; next generation; novel strategies; positional cloning; proband

DESCRIPTION (provided by applicant): Historically, chromosomal rearrangements have been investigated by conventional karyotype followed by arduous positional-cloning projects. More recently, molecular cytogenetic characterizations using fluorescence in situ hybridization, array comparative genomic hybridization, and SNP genotyping together with molecular methods such as inverse PCR and quantitative PCR have allowed an increasingly more precise evaluation of chromosome abnormalities with the result that some presumably balanced rearrangements have been found to include deletions, duplications, insertions or inversions. I will test a new approach: targeted genomic capture followed by next generation sequencing to rapidly and precisely define the molecular abnormalities in a set of clinically interesting cases followed in the Genetics clinics of the Johns Hopkins Institute of Genetic Medicine. 3 cases with complex dysmorphic syndromes already known to have translocations: the first (family L982181) is segregating an apparently balanced t(2;3)(p15;q12) translocation over 3 generations associated with craniofacial abnormalities; the second (patient JHU2010) has a t(2;6)(q22;p12.3) translocation and a breakpoint in the region of RUNX2 on chromosome 6p, associated with cleidocranial dysplasia (OMIM 119600); and the third (patient L08-2709) has a t(5;17)(q23.2;q24) translocation, with a breakpoint in the region upstream of the SOX9 on chromosome 17q, associated with the clinical phenotype of acampomelic campomelic dysplasia (OMIM 114290). Additionally, I will study three cases with deletions in the 10q21-q23 region that have been collected by the Valle lab as part of their ongoing interest in identification of schizophrenia susceptibility genes in this region. They include the fourth patient in my series (JHU2020), who has a 10q23.1 deletion associated with multiple anomalies and development delay; the fifth and sixth involve 2 families (JHU2000 and JHU88293) with overlapping deletions both of which inactivate PCDH15 on 10q21.1 and are associated with schizophrenia. The delineation of these complex rearrangements will lead to a better understanding of the molecular bases of their clinical phenotypes. In cases 5 and 6, the study of PCDH15 as a candidate gene for psychiatric disease is of interest because it is the only annotated gene that is deleted in both families (JHU2000 and JHU88293). Recessive truncating mutations in PCDH15 cause Usher type 1F (OMIM 602083) characterized by congenital hearing loss, vestibular dysfunction and pigmentary retinopathy. Interestingly, an early report, pre-appreciation of locus heterogeneity, suggested nearly 20% of patients with Usher syndrome develop psychosis [4]. PUBLIC HEALTH RELEVANCE: New methods have shown that chromosomal aberrations are more frequent than previously realized (e.g. CNV); and are often more complex than previously appreciated by examination, apparently balanced translocations by karyotype often have associated deletion or duplications at the margins. I am interested in taking advantage of chromosomal aberrations to identify genes responsible for human genetic disease and have been using methods such as FISH, SNP genotyping, qRT-PCR, inverse PCR, long range PCR, and others to define the exactly breakpoints of translocations and deletions but sometimes they do not allow the identification of breakpoints at the resolution of 1 base pair. I will test a new approach: targeted genomic capture followed by next generation sequencing (100 bp paired end reads) of the captured material to rapidly and precisely define the molecular abnormalities in a set of clinically interesting cases followed in the Genetics clinics of the Johns Hopkins McKusick-Nathans Institute of Genetic Medicine (IGM).

描述（由申请人提供）：历史上，染色体重排一直是通过传统的核型研究，然后是艰巨的位置克隆项目。最近，使用荧光原位杂交、阵列比较基因组杂交和SNP基因分型的分子细胞遗传学表征，以及诸如反PCR和定量PCR等分子方法，使得对染色体异常的评估越来越精确，结果发现一些可能平衡的重排包括缺失、重复、插入或反转。我将测试一种新方法：靶向基因组捕获，然后进行下一代测序，以快速准确地定义约翰霍普金斯遗传医学研究所遗传学诊所的一组临床有趣病例中的分子异常。已知有易位的3例复杂畸形综合征：第一例（家族L982181）分离明显平衡的t(2;3)(p15；Q12) 3代以上易位与颅面异常相关；第二例（患者JHU2010）有t(2;6)（q22;p12.3）易位和6p染色体RUNX2区域的断点，与锁骨颅发育不良相关（OMIM 119600）；第三例患者（患者L08-2709）有t(5;17)（q23.2;q24）易位，断点位于染色体17q上SOX9上游区域，与非染色体型同源性染色体发育不良（OMIM 114290）的临床表型相关。此外，我将研究三个10q21-q23区域缺失的病例，这些病例由Valle实验室收集，作为他们对该区域精神分裂症易感基因鉴定的持续兴趣的一部分。其中包括我的系列研究中的第4例患者（JHU2020），其10q23.1缺失与多种异常和发育延迟相关；第五个和第六个涉及两个家族（JHU2000和JHU88293），它们都有重叠缺失，这两个家族都在10q21.1上使PCDH15失活，并与精神分裂症有关。对这些复杂重排的描述将有助于更好地理解其临床表型的分子基础。在病例5和病例6中，PCDH15作为精神疾病的候选基因的研究引起了人们的兴趣，因为它是两个家族中唯一缺失的注释基因（JHU2000和JHU88293）。PCDH15的隐性截短突变导致先天性听力损失、前庭功能障碍和色素视网膜病变为特征的Usher型1F （OMIM 602083）。有趣的是，一份早期的报告，对基因座异质性的预评价，表明近20%的Usher综合征患者会发展为精神病。