Rare Sequence Variation and Diabetes Quantitative Traits

 描述（由申请人提供）：2型糖尿病（T2 D）是一个日益严重的祸害世界各地，尽管试图预防和控制它。需要创新的方法来确定新的分子靶点的预防和护理。T2 D和相关数量性状（QT：空腹血糖[FG]、胰岛素[FI]、糖化血红蛋白[HbA 1c]）的全基因组关联研究（GWAS）极大地推进了对血糖调节的分子理解，目前有>120个常见（次要等位基因频率，MAF =1%）单核苷酸变异（SNV）和~110个基因组位点与T2 D和/或QT相关。然而，在许多基因座上，因果变异和关联的功能基础尚不清楚，大多数信号位于非编码区。需要对全基因组序列（WGS）中的罕见变异（MAF <1%）和非编码区进行更详细的扫描，以帮助将T2 D遗传学转化为更好的T2 D医疗保健。罕见变异占所有人类遗传变异的2/3。非编码区占基因组的98%以上。罕见和常见的变异都被捕获在WGS数据中，并且可以在全基因组范围内扫描性状关联，然后使用现存数据进一步测试与T2 D和其他临床表型的关联。SNV可以与详细的调控图谱（例如ENCODE，许多其他）整合以定义分子功能-性状关联。基因组注释可以指向特定的“破坏性”突变（改变基因调控或功能，产生表型变异），可能作用于一个基因座，这表明特定的体外试验可以证实注释的预测。总目标 更新2 R 01 DK 78616的目的是使用WGS扫描在来自CHARGE联盟三个队列的约3，700名白色和黑人个体中鉴定T2 D-QT相关的功能性罕见变异。我们将在“云”中管理WGS数据，并在“Commons”中分析个人数据。我们将与其他WGS研究合作复制新的发现。我们的目的是1）在大约110个已知和新的T2 D-QT基因座上检测WG范围内FG和FI罕见变异的相关性; 2）在CHARGE中使用现有的生理和分子数据检测表型T2 D-QT罕见变异，包括QT变异与T2 D风险的相关性检测; 3）使用ENCODE等注释T2 D-QT SNV，并在适当的细胞中用适当的实验在体外证实它们预测的等位基因特异性分子功能（例如，在HepG 2细胞系中用瞬时转染、凝胶移位和荧光素酶测定法测试转录因子结合位点处的等位基因特异性效应）。基于超过六年的R 01 DK 78616支持，我们的跨学科、多中心团队拥有良好的业绩记录。我们现在建议将T2 D遗传学从常见变异GWAS转移到罕见变异WGS，并进行深度注释和体外验证，以产生新的分子假设，并将T2 D遗传学转化为更好的T2 D预防和护理。

 DESCRIPTION (provided by applicant): Type 2 diabetes (T2D) is a growing scourge worldwide, despite attempts to prevent and control it. Innovative approaches are needed to identify new molecular targets for prevention and care. Genome-wide association studies (GWAS) for T2D and related quantitative traits (QTs: fasting glucose [FG], insulin [FI], glycated hemoglobin [HbA1c]) have dramatically advanced molecular understanding of glycemic regulation, with >120 common (minor allele frequency, MAF =1%) single nucleotide variants (SNV) and ~110 genomic loci now associated with T2D and-or QTs. However, the causal variant and the functional basis of associations are unclear at many loci, and most signals reside in non-coding regions. More detailed scans of rare variants (MAF <1%) and non-coding regions available from whole genome sequence (WGS) are needed to help translate T2D genetics into better T2D healthcare. Rare variation makes up ~2/3 of all human genetic variation. Non-coding regions occupy >98% of the genome. Both rare and common variants are captured in WGS data and can be scanned genome-wide for trait associations, then further tested for association with T2D and other clinical phenotypes using extant data. SNVs can be integrated with detailed regulatory maps (e.g. ENCODE, many others) to define molecular function-trait associations. Genomic annotation can point to specific "disruptive" mutations (altering gene regulation or function, producing phenotype variation) potentially acting at a locus, suggesting specific in vitro assays to confirm the annotation's prediction. The overall goal to renew 2R01DK78616 is to identify T2D-QT- associated functional rare variants using WGS scans in ~3,700 white and black individuals from three cohorts in the CHARGE consortium. We will manage WGS data in the "cloud" and analyze individual data in a "Commons". We will replicate new findings in collaboration with other WGS studies. Our Aims are 1) test WGS-wide for FG and FI rare variant associations at ~110 known and new T2D-QT loci; 2) Phenotype T2D-QT rare variants with existing physiological and molecular data in CHARGE, including tests of QT variant associations with T2D risk; 3) Annotate T2D-QT SNVs using ENCODE and others, and confirm their predicted allele-specific molecular function in vitro with appropriate experiments in appropriate cells (For instance, test allele-specific effects at transcription facto binding sites with transient transfection, gel shift and luciferase assays in HepG2 cell lines). Ou interdisciplinary, multicenter team has a proven track record based on over six years of R01DK78616 support. We now propose to move T2D genetics from common variant GWAS to rare variant WGS with deep annotation and in vitro validation to generate new molecular hypotheses and advance translation of T2D genetics into better T2D prevention and care.