Identifying Pathogenic Non-Coding Mutations in Rare Mendelian Disease

摘要 确定罕见和常见疾病的新原因将带来重大和直接的好处 通过改进基因检测、遗传咨询、保险等方式， 最后是更有效的治疗方案。我们的长期目标是 颠覆性地改善和扩大罕见和常见疾病的基因检测。电流诊断 测试仅考虑蛋白质编码基因中的致病性变体。然而，我们现在有证据表明 很大一部分罕见疾病是由于未知的非编码遗传变异， 影响这些基因的调节。本提案的目标是识别和量化 致病性非编码基因变异对基因功能和表达的影响 导致罕见疾病的基因这一初始步骤将使治疗在生命的早期，当它仍然是 可以阻止疾病最严重的后果，包括死亡。我们将专注于 严重早发性儿科疾病，包括糖原累积病（GSD I、II、III、IV和IV） IX）、脂肪酸氧化障碍、极长链酰基辅酶A脱氢酶缺乏 （VLCAD）和多重酰基辅酶A脱氢酶缺乏症（MADD）。迄今为止， 这些和其它疾病限于蛋白质编码突变。然而，我们的临床团队 我收集了大量病例，这些病例在两个基因中的一个上只有一个致病性编码变异， 在这些隐性疾病中必须同时受到影响的等位基因。我们也有生物化学和 支持诊断的生物标志物证据。这些病例是识别的理想机会 其他致病变种。我们的假设是隐性遗传的遗传原因 疾病包括新的遗传变异，可以改变蛋白质序列（Aim 1），剪接 (Aim 2），或疾病基因的基因表达（Aim 3）。我们组建了一个儿科团队 GSD、VLCAD和MADD方面的专家临床医生，以及 在遗传学，基因组学，表观遗传调控，生物医学工程和统计学。这支球队 已获得患者样本并获得杜克IRB批准立即开始。我们预计 这项研究将确定和验证影响疾病的新的遗传变异。在我们提议 为了研究一个相对较小的罕见疾病子集，这些策略将立即 可推广到任何患者样本的任何隐性疾病，具有不确定的遗传 测试结果这一结果将提供全面的基因检测，更好地了解 疾病机制，最终更好的治疗方案。

ABSTRACT Determining new causes for rare and common disease would have major and immediate benefits for patients and their families by improved genetic testing, genetic counseling, insurance reimbursement, and ultimately more effective treatment options. Our long term goal is to disruptively improve and expand genetic testing for rare and common disease. Current diagnostic tests only consider pathogenic variants in protein-coding genes. However, we now have evidence that a substantial fraction of rare disease is due to unknown non-coding genetic variants that influence the regulation of those genes. The goal of this proposal is to identify and quantify the effect of pathogenic non-coding genetic variants on the function and expression of genes that cause rare disease. This initial step will enable treatment early in life when it is still possible to stop the most severe consequences of disease, including death. We will focus on severe early-onset pediatric disorders, including glycogen storage diseases (GSD I, II, III, IV, and IX), and the fatty acid oxidation disorders, very long-chain acyl-CoA dehydrogenase deficiency (VLCAD), and multiple acyl-CoA dehydrogenase deficiency (MADD). To date, genetic tests for these and other diseases are limited to protein-coding mutations. However, our clinical team has collected numerous cases that have a single pathogenic coding variant on only one of the two alleles that must be both affected in these recessive disorders. We also have biochemical and biomarker evidence that supports the diagnosis. Those cases are an ideal opportunity to identify additional disease-causing variants. Our hypothesis is that the genetic causes of recessive disorders include novel genetic variants that can alter either protein sequence (Aim 1), splicing (Aim 2), or gene expression (Aim 3) of disease genes. We have assembled a team of Pediatric clinicians who are experts in GSDs, VLCAD, and MADD, as well as researchers who are experts in genetics, genomics, epigenetic regulation, biomedical engineering, and statistics. This team has obtained patient samples and received Duke IRB approval to begin immediately. We expect this study will identify and validate novel genetic variants that influence disease. While we propose to study a relatively small subset of rare disorders, these strategies will be immediately generalizable to any patient sample with any recessive disorder that has inconclusive genetic testing results. That outcome will provide comprehensive genetic testing, better understanding of disease mechanisms, and ultimately better treatment options.