Identifying Disease Variants for Familial Crohns Disease

识别家族性克罗恩病的疾病变异

• 批准号: 7942992
• 负责人: Steven R Brant
• 金额: $ 109.22万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2013-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7942992
• 关键词: 13q; 13q13.3; 1p35; 1p35.2; 3q29; Accounting; Adult; Affect; Alleles; American; Ashkenazim; Bioinformatics; Biological Assay; Cells; Characteristics; Child; Chromosomes; Chromosomes, Human, Pair 13; Chronic; Code; Complex; Computer Simulation; Confidence Intervals; Crohn' s disease; DNA; Data; Databases; Disease; Disease Attributes; Enzyme-Linked Immunosorbent Assay; Exons; Family; Family history of; Family member; Functional disorder; Future; Gastrointestinal tract structure; Genes; Genetic; Genetic Transcription; Genome; Genotype; Hereditary Disease; Heritability; Human Genome; In Situ Hybridization; Incidence; Inflammation; Inflammatory Bowel Diseases; Intercistronic Region; Introns; Link; Linkage Disequilibrium; Lymphocyte; Minority; Mononuclear; Morbidity - disease rate; National Institute of Diabetes and Digestive and Kidney Diseases; Nucleic Acid Regulatory Sequences; Patients; Penetrance; Persons; Probability; Promoter Regions; Proteins; Proteomics; RNA; Recruitment Activity; Reverse Transcriptase Polymerase Chain Reaction; Risk; SNP genotyping; Sampling; Simulate; Societies; Susceptibility Gene; Testing; Tissues; Variant; Western Blotting; Work; cancer risk; case control; cost; density; disease phenotype; follow-up; follower of religion Jewish; genetic linkage analysis; genetic pedigree; genetic risk factor; genome-wide; genome-wide linkage; immunocytochemistry; lymphoblastoid cell line; mortality; novel; prevent; programs; protein expression; protein function; public health relevance; therapy development; transmission process

DESCRIPTION (provided by applicant): Crohn's disease (CD) is a complex genetic disorder of chronic inflammation of the gastrointestinal tract that results in increased morbidity, mortality, risk of cancer and cost to patient and society. Twenty to 30% of patients have a CD family history and the disease is four-fold increased in persons of Ashkenazi Jewish (AJ) ancestry. Multiple low penetrance susceptibility genes have been identified and confirmed, but these in total account for only 20% of CD genetic heritability. As part of the NIDDK IBD Genetics Consortium (IBDGC) the applicant performed the first SNP, high density, whole genome linkage study, four-fold larger than any prior linkage study and the only study with adequate numbers of AJ CD pairs (919 CD pairs, 196 pairs AJ). Non-parametric linkage analysis confirmed the IBD1 locus (Lod of 4.86), and identified three additional loci with genome-wide significant linkage: a novel locus at chromosome 13q13.3 (Lod 3.98, simulated whole genome p-value of 0.01) in all CD pedigrees, and loci at chromosomes 1p35.2 and 3q29, in the AJ CD pedigrees (Lod 3.50 and 3.19, respectively and simulated genome p-values of 0.02 and 0.05, respectively). Parametric linkage analysis showed that the 13q and 3q loci follow a recessive, high penetrance mode of inheritance (H-Lod 3.3 - 10% of families linked and H-Lod 3.5, 24% of AJ families linked, respectively) and 1p followed a dominant mode (H-Lod 3.4, 38% of AJ families linked). An ancillary R01 study to identify disease alleles for these three loci is proposed. The applicant will work with the IBDGC to assemble DNA samples on the AJ CD pedigrees and the non-Jewish, chromosome 13 - linked pedigrees and/or within the top quartile of non-parametric linkage evidence. Saturation genotyping will be performed across the 2-lod confidence interval for each locus, with a total of 9000 SNPs. Alleles significantly associated with CD will be identified by using within-pedigree association analysis (independent of linkage) with the program PBAT. Association will be replicated and/or extended in 722 AJ cases and controls, 200 cases to be newly recruited by the IBDGC as part of the ancillary R01, per IBDGC-coordinated plans. Deep re-sequencing of associated genes and regions will be done, in at least 50 CD cases and 50 controls, to identify potential disease alleles. The applicant will use a bioinformatics approach to analyze re-sequencing data for functional relevance. These alleles will then be characterized for association with CD in the 859 total AJ case-control pairs. Lastly, the applicant will determine expression characteristics of genes associated, both analyzing expressed RNA and protein, and how expression correlates with the disease associated versus wildtype alleles. Identifying very high penetrance disease alleles will allow us to determine the specific cause of CD in patients with the disease alleles, and eventually how these alleles cause CD pathophysiology. These discoveries will make possible predicting persons at great risk for developing CD, the potential of preventing the disease in carriers, and the development of therapies, especially for those with CD attributed to these newly identified disease alleles. PUBLIC HEALTH RELEVANCE: Nearly 500,000 Americans, both children and adults, have Crohn's disease, and in approximately one-quarter of those affected, two or more family members have the disease. We have identified three small regions of the human genome, known as "loci," that correlate with familial Crohn's disease. With this study, we will test 9000 gene markers in these regions and identify the specific genes and, by gene sequencing, the specific DNA abnormalities that result in a significant proportion of familial Crohn's disease.

描述(申请人提供)：克罗恩病(CD)是一种复杂的遗传性疾病，慢性胃肠道炎症，导致发病率、死亡率、癌症风险增加，给患者和社会带来成本。20%到30%的患者有CD家族史，在有德系犹太人(AJ)血统的人中，这种疾病增加了四倍。多个低外显性易感基因已被鉴定和证实，但这些基因总共只占CD遗传遗传力的20%。作为NIDDK IBD遗传学联合会(IBDGC)的一部分，申请人进行了第一个SNP，高密度，全基因组连锁研究，比之前的任何连锁研究都大四倍，也是唯一具有足够数量的AJ CD对的研究(919个CD对，196对AJ)。非参数连锁分析证实了IBD1基因座(LOD值为4.86)，并发现了另外三个与全基因组显著连锁的基因座：位于13q13.3(LOD3.98，模拟全基因组p值为0.01)的新基因座，以及位于AJ CD家系1p35.2和3q29(分别为LOD3.50和3.19，模拟基因组p值分别为0.02和0.05)的新基因座。参数连锁分析表明，13q和3q基因座遵循隐性、高外显的遗传方式(H-LOD3.3-10%的连锁家系和H-LOD3.5、24%的AJ家系)，1p遵循显性遗传模式(H-LOD3.4，38%的AJ家系连锁)。建议进行一项辅助的R01研究，以确定这三个基因座的疾病等位基因。申请者将与IBDGC合作，收集AJ CD家系和非犹太人13号染色体连锁家系和/或非参数连锁证据最高四分位数内的DNA样本。饱和基因分型将在每个基因座的2-Lod可信区间内进行，总共有9000个SNP。与CD显著相关的等位基因将通过使用PBAT程序的系谱内关联分析(独立于连锁)来识别。根据IBDGC协调的计划，将在722个AJ病例和对照中复制和/或推广这种关联，其中200个病例将由IBDGC作为辅助R01的一部分新招募。将对至少50个CD病例和50个对照进行相关基因和区域的深度重新测序，以确定潜在的疾病等位基因。申请者将使用生物信息学方法来分析重新测序数据的功能相关性。然后，这些等位基因将被鉴定为与859对AJ病例对照中的CD相关。最后，申请者将确定相关基因的表达特征，分析表达的RNA和蛋白质，以及表达如何与疾病相关，而不是野生型等位基因。识别非常高的外显性疾病等位基因将使我们能够确定具有疾病等位基因的患者中CD的特定原因，并最终确定这些等位基因如何导致CD的病理生理。这些发现将使预测CD高危人群、在携带者中预防疾病的潜力以及治疗方法的发展成为可能，特别是对于那些被归因于这些新发现的疾病等位基因的CD患者。 公共卫生相关性：近50万美国人，包括儿童和成人，患有克罗恩病，在大约四分之一的感染者中，有两个或更多的家庭成员患有这种疾病。我们已经确定了人类基因组的三个小区域，称为“基因座”，与家族性克罗恩病相关。在这项研究中，我们将测试这些区域的9000个基因标记物，并通过基因测序确定导致相当大比例家族性克罗恩病的特定基因和特定DNA异常。