Discovery of low-frequency ulcerative colitis risk variants using whole-genome sequencing

溃疡性结肠炎(UC)和克罗恩病(CD)是炎症性肠病(IBD)最常见的两种形式。在英国，每10万人中约有400人受到影响。它们的特点是慢性和痛苦的胃肠道炎症，被认为是由遗传易感个体对正常肠道微生物的过度免疫反应引起的。目前的治疗方法昂贵，并不总是有效，而且可能有严重的副作用，需要定期临床监测。目前临床上迫切需要一种更个性化的IBD治疗方法，同时开发更有效和更具成本效益的治疗方法。来自家庭研究的数据表明，IBD风险有很大的可遗传成分。与没有受影响的兄弟姐妹相比，患有UC的兄弟姐妹的患病风险增加了7-17倍，而CD患者的兄弟姐妹的患病风险增加了15-42倍。对常见遗传变异的大规模调查已经确定了基因组的99个区域，这些区域解释了IBD风险增加的一部分。对位于这些区域内的基因的仔细研究进一步发展了我们对IBD生物学的理解，并强调了作为新型治疗干预的潜在靶点的生物学途径。进一步的基因区域仍然与IBD风险相关是毫无疑问的，因为到目前为止确认的那些增加的兄弟姐妹风险中，只有大约20%可以解释。一些无法解释的风险变异可能得到中等效应大小的低频遗传变异的支持，因为现有的全基因组扫描还没有很好地调查这些变异。最近在高通量DNA测序方面的技术进步使这些变异体首次能够在一定范围内获得，使它们能够被彻底调查与常见疾病如IBD的关联。在这里，我建议使用全基因组测序进行第一次大规模搜索与UC相关的低频变异体。来自2000名英国血统UC患者的DNA将被全基因组测序，并与来自普通英国人的4000人的序列进行比较。在观察到显著差异的地方，我们将在另外3000例UC患者和对照中对这些基因变异进行基因分型，以确认它们与UC有关，而不是人工制品。此外，我们将进行类似的测试，在UC序列中搜索支持临床相关疾病亚类的基因变异，如对治疗的反应、疾病严重程度和发病年龄。这项研究的数据还将与威康信托桑格研究所正在进行的CD上的类似研究的数据结合起来，以实现对更广泛地支持IBD的基因组区域的强大搜索。这些联合数据还将使我们能够更好地了解两种常见形式的IBD之间的遗传差异。识别新的基因区域可能会进一步阐明疾病的生物学基础，并产生关于疾病病因学的进一步假说。随着时间的推移，已确定的生物途径可能成为新的疗法和预防的目标。根据研究中确定的标记物对IBD风险进行更准确的评估也是可能的，这取决于确定的地区解释的疾病易感性变异的比例。我们将使用疾病风险的临床和遗传标记来建立和测试预测算法，希望开发一种对IBD状态和/或疾病严重程度和治疗反应的临床有用的测试。

Ulcerative colitis (UC) and Crohn's disease (CD) are the two most common forms of inflammatory bowel disease (IBD). Together they affect approximately 400 in every 100,000 people in the UK. They are characterised by chronic and painful inflammation of the gastrointestinal tract that is thought to be caused by an over-reactive immune response to normal intestinal microbes in genetically susceptible individuals. Current therapies are expensive, don't always work, and can have severe side effects that necessitate regular clinical monitoring. There is currently an urgent clinical need for a more personalized approach to IBD therapy coupled with the development of more efficacious and cost-effective treatments.Data from family studies have demonstrated that there is a large heritable component to IBD risk. Siblings of individuals with UC have a 7-17 fold increased risk of disease compared to individuals without an affected sibling, for CD the increased risk to siblings is 15-42 fold. Large-scale surveys of common genetic variants have identified 99 regions of the genome that explain a proportion of this increased risk of IBD. Scrutiny of the genes that lie within these regions has further developed our understanding of IBD biology and highlighted biological pathways that are potential targets for novel therapeutic interventions.That further genetic regions remain to be correlated with IBD risk is beyond doubt because only around 20% of the increased sibling risk is explained by those confirmed to date. Some of unexplained risk variation is likely to be underpinned by low-frequency genetic variants of intermediate effect size as these have not been well surveyed by existing genome-wide scans. Recent technological advances in high-throughput DNA sequencing make these variants accessible for the first time on a scale that allows them to be thoroughly surveyed for association to common diseases such as IBD.Here, I propose to conduct the first large-scale search for low-frequency variants associated with UC using whole-genome sequencing. DNA from 2000 UC patients of UK ancestry will be whole-genome sequenced and compared to sequences from 4000 individuals from the general UK population. Where significant differences are observed we will genotype these genetic variants in an additional 3000 UC cases and controls to confirm they are associated with UC and are not artefacts. Furthermore, we will conduct similar tests to search within UC sequences for genetic variants that underpin clinically relevant disease subclasses such as response to therapy, disease severity and age at onset. Data from the study will also be combined with that from a similar study in CD, underway at the Wellcome Trust Sanger Institute, to enable powerful searches for regions of the genome underlying IBD more broadly. This combined data will also allow us to better understand the genetic differences between the two common forms of IBD.The identification of novel genetic regions is likely to shed further light on the biology underlying the disease and generate further hypotheses regarding disease aetiology. In time, the identified biological pathways may become targets for novel therapeutics and preventions. More accurate assessments of IBD risk, based on the markers identified in the study, may also be possible depending on the proportion of disease susceptibility variation explained by the identified regions. We will use both clinical and genetic markers of disease risk to build, and test, predictive algorithms in the hope of developing a clinically useful test for IBD status and/or disease severity and response to therapy.