Rare Sequence Variation and Diabetes Quantitative Traits

 描述(申请人提供)：2型糖尿病(T2D)是世界范围内日益严重的疾病，尽管人们试图预防和控制它。需要创新的方法来确定预防和护理的新分子目标。T2D及其相关数量性状(QTS：空腹血糖[FG]、胰岛素[FI]、糖化血红蛋白[HbA1c])的全基因组关联研究(GWAS)已经极大地提高了对血糖调节的分子理解，目前有120个常见的(次要等位基因频率，MAF=1%)单核苷酸变异(SNV)和约110个基因组座位与T2D和-或QTS相关。然而，关联的因果变异和功能基础在许多基因座上并不清楚，而且大多数信号存在于非编码区。需要对稀有变异(MAF&lt；1%)和全基因组序列(WGS)中可用的非编码区进行更详细的扫描，以帮助将T2D遗传学转化为更好的T2D医疗保健。罕见变异约占人类全部遗传变异的2/3。非编码区占据了基因组的98%。罕见和常见的变异都被捕获在WGS数据中，并可以在全基因组范围内扫描特征关联，然后使用现有数据进一步测试与T2D和其他临床表型的关联。SNV可以与详细的调控图(例如，ENCODE等)相结合，以定义分子功能-特性关联。基因组注释可以指向特定的“破坏性”突变(改变基因调节或功能，产生表型变异)，潜在地作用于一个基因座，建议进行特定的体外分析来证实注释的预测。总目标 更新2R01DK78616是通过WGS扫描从Charge联合体的三个队列中的约3,700名白人和黑人个体中识别与T2D-QT相关的功能罕见变异。我们将在“云”中管理WGS数据，并在“公地”中分析单个数据。我们将与WGS的其他研究合作，复制新的发现。我们的目标是1)在WGS范围内测试约110个已知和新的T2D-QT基因座上的FG和FI罕见变异关联；2)负责现有生理和分子数据的表型T2D-QT罕见变异，包括QT变异与T2D风险的测试；3)使用ENCODE和其他方法注释T2D-QT SNV，并在适当的细胞中通过适当的实验证实它们在体外预测的等位基因特异的分子功能(例如，通过瞬时转染、凝胶漂移和荧光素酶分析在HepG2细胞系中测试转录事实结合部位的等位基因特异性效应)。基于超过六年的R01DK78616支持，OU跨学科、多中心团队拥有良好的跟踪记录。我们现在建议将T2D遗传学从常见的变异型GWA转移到罕见的变异型WGS，并进行深入的注释和体外验证，以产生新的分子假说，并将T2D遗传学转化为更好的T2D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.