1/2 Genomic Strategies to Identify High-impact Psychiatric Risk Variants

 描述(申请人提供)：精神分裂症(SCZ)和双相情感障碍(BP)是主要的成人精神障碍；他们之间的关系的不确定性是精神病学的中心问题。通过发现对任何一种或两种疾病(或对其内在表型)具有高度影响的变异，我们可以改变我们对它们生物学的理解。这个多站点项目由有成功合作记录的研究人员完成，将利用特殊的、广泛的表型谱系和人口样本，并结合生物信息学和实验基因组学方法来识别这些变异，并证明它们与这些疾病的关系。我们将通过三个步骤进行：(1)通过对种族均一群体中发现的样本进行全基因组测序(WGS)来检测新的变异；(2)利用生物信息学和功能基因组学分析，为进一步研究这些变异确定基因组区域的优先顺序；(3)通过(A)在来自相同群体的非常大的病例/对照样本中进行基于归因的关联分析，以及(B)使用新的高通量功能分析来验证相关和预测有害的变异，从而识别与疾病相关的变异。WGS发现样本包括来自芬兰(FIN)和荷兰(NL)的SCZ、BP和对照人员。我们将使用我们团队已经实施的管道来分析他们的变体，以分析最近出现瓶颈的拉丁美洲创始人群体中BP家系的完整WGS。我们的大多数WGS样本都来自这样的创始人群体；正如我们之前所展示的那样，这使得在这些样本中检测到有害变异的可能性很高。WGS将检测到大量的变体，其中大多数功能意义未知。因此，我们将使用两种方法，将重点缩小到与SCZ和BP最有可能相关的区域(编码和非编码)：(1)生物信息学，以确定先前与这些疾病相关的区域(例如，GWAS或CNV基因座，或先前测序研究中突出显示的变异，包括我们的BP家系)和候选调控区域(通过分析ENCODE或其他参考数据)；(2)基于测序的评估，我们将在两个与我们的表型相关的独特样本中进行转录和表观基因组变异：来自受影响和未受影响的BP家系成员的成纤维细胞；以及来自参考个体的神经元和神经前体细胞。然后，我们将利用从与我们的发现样本(或密切相关的样本)相同的人群中获得的非常大的、基因分型的病例/对照样本，来准确地推测我们优先考虑的区域的新变异；这将使我们能够识别与SCZ的关联， BP和/或内表型。最后，在初步的验证研究中，我们将使用一种新型的高通量基于序列的报告分析来评估我们的生物信息学管道或关联分析所强调的假定调控变异体的功能。

 DESCRIPTION (provided by applicant): Schizophrenia (SCZ) and bipolar disorder (BP) are the major adult psychotic disorders; uncertainty about their relationship is a central issue in psychiatry. By discovering variants with a high impact on either or both disorders (or on their endophenotypes) we can transform our understanding of their biology. This multisite project, from investigators with a track record of successful collaboration, will leverage exceptional, extensively phenotyped pedigree and population samples and integrate a combination of bioinformatics and experimental genomics approaches to identify such variants and demonstrate their relationship to these diseases. We will proceed through three steps: (1) Detect novel variants by whole genome sequencing (WGS) of discovery samples from ethnically homogenous populations; (2) Prioritize genome regions for further studies of these variants, using bioinformatics and functional genomics analyses; (3) Identify disease related variants through (a) imputation-based association analyses in very large case/control samples from the same populations and (b) validation of associated and predicted-deleterious variants using novel high-throughput functional assays. The WGS discovery sample includes SCZ, BP, and control individuals from Finland (FIN) and the Netherlands (NL). We will analyze their variants using a pipeline already implemented by our group to analyze the completed WGS of BP pedigrees from recently bottlenecked Latin American founder populations. The majority of our WGS samples derive from such founder populations; as we have shown previously this creates a high probability of detecting deleterious variants in these samples. WGS will detect a huge number of variants, most of unknown functional significance. We will thus narrow our focus to regions (coding and non-coding) most likely relevant to SCZ and BP, using two approaches: (1) Bioinformatics to prioritize regions previously implicated in these disorders (e.g. GWAS or CNV loci, or variants highlighted in prior sequencing studies including that of our BP pedigrees) and candidate regulatory regions (through analyses of ENCODE or other reference data); (2) Sequencing-based assessments of transcriptomic and epigenomic variation that we will conduct in two unique samples relevant to our phenotypes: fibroblasts from affected and unaffected members of our BP pedigrees; and neuronal and neuronal progenitor cells from reference individuals. We will then leverage very large, genotyped case/control samples available from the same populations as our discovery samples (or closely related ones) to accurately impute the novel variants from our prioritized regions; this will enable us to identify associations with SCZ, BP, and/or endophenotypes. Finally, in an initial validation study, we will use a novel high-throughput sequence-based reporter assay to evaluate the function of putative regulatory variants highlighted by our bioinformatics pipeline or by our association analyses.