Facilitating personalized medicine of monogenic stone patients by genetic characterization

通过基因特征促进单基因结石患者的个体化用药 下一代测序（NGS），包括采用已知和候选的靶向（t）NGS组， 基因，是强调严重的，遗传性形式的泌尿系结石病（USD）是更常见的， 以前被认识到，现在涉及到约40个基因。这些单基因美元是在最前沿的 个体化用药在肾脏病学中的应用。治疗可以靶向酶/mRNA编码的关键 缺陷代谢途径中导致有害中间体积累或通过伴侣的步骤 帮助折叠和正确运输突变蛋白质的治疗方法。基因和等位基因信息越来越成为 这是参与这些有针对性的临床试验的先决条件。在过去的10年里，罕见的肾结石 联盟（RKSC）专注于招募和表征单基因USD患者人群， 目的是了解疾病的自然史，进行基因型/表型研究， 对患者进行临床研究。这最初涉及桑格测序，但最近tNGS与 ~100个基因面板。作为筛查的一部分，假定患者患有原发性高尿酸（PH）或 Dent病（两种常见的USD），但桑格在这些疾病的典型基因中没有突变 测序，在面板上筛选。在分析的297例患者中， 30例（10.1%），在11个不同的基因中发现突变。在过去一年，所有RKSC招募病人 采用这种tNGS方法对102个家庭进行了初步的遗传筛选， (32.4%）已被遗传解析，鉴定了8种不同的基因。有趣的是，在约15%的情况下， 在第二个单基因基因中鉴定出遗传复杂性和另外的可能致病的变异。 不幸的是，RKSC最近失去了资金，但我们计划保持财团的完整性， 建议对通过RKSC群体招募的单基因USD进行遗传特征分析，主要是为了识别 患者纳入临床试验。该提案有两个具体目标：1。对患有A的患者进行基因分型 表型与使用全局NGS的单基因型肾结石或肾钙质沉着症一致 方法和2。表征和分析致病基因以外的变异阵列， 单基因结石患者。该项目有共同PI，一位是USD临床和生化方面的专家 (Dr. Lieske博士）和一位单基因肾病遗传学专家（Harris博士）。测试的tNGS 方法将采用沿着与一个发达和成熟的生物信息学管道，以确定可能的 使役变体这些结果将返回给转诊医生，并提供咨询和 变异构象，提供诊断信息，允许个性化治疗，并鼓励临床 试招募。为研究积累的基因变异和变异组合知识 将允许更好地了解这些疾病，并提供对遗传因素的见解， 表型修饰

Facilitating personalized medicine of monogenic stone patients by genetic characterization Next generation sequencing (NGS), including employing a targeted (t)NGS panel of known and candidate genes, is highlighting that severe, inherited forms of urinary stone disease (USD) are more common than previously appreciated, with ~40 genes now implicated. These monogenic USD are at the forefront of the application of personalized medicine in nephrology. Treatments can target enzymes/mRNAs encoding key steps in the defective metabolic pathway that lead to accumulation of harmful intermediates or via chaperone treatments to help fold and correctly traffic the mutated proteins. Genic and allelic information is increasingly a prerequisite for involvement in these targeted clinical trials. Over the past 10 years, the Rare Kidney Stone Consortium (RKSC) has focused on recruiting and characterizing patient populations with monogenic USD with the aims to understand the natural history of the disorders, conduct genotype/phenotype studies, and categorize patients for clinical studies. This initially involved Sanger sequencing but more recently tNGS with a ~100 gene panel. As part of this screening, patients presumed to have either primary hyperoxaluria (PH) or Dent disease (two common USD), but without mutations in the canonical genes for these disorders by Sanger sequencing, were screened on the panel. Out of 297 analyzed patients, a monogenic cause was detected in 30 cases (10.1%), with mutations identified in 11 different genes. In the past year, all RKSC recruited patients have been primarily genetically screened employing this tNGS approach and of 102 families screened 33 (32.4%) have been genetically resolved with 8 different genes identified. Interestingly, in ~15% of cases genetic complexity was identified with an additional likely pathogenic variant in a second monogenic gene. Unfortunately, funding for the RKSC was recently lost but we plan to keep the consortium intact and here propose to genetically characterize monogenic USD recruited through the RKSC groups, primarily to identify patients for inclusion in clinical trials. The proposal has two specific aims: 1. Genotype patients with a phenotype consistent with a monogenic form of nephrolithiasis or nephrocalcinosis using global NGS approaches and 2. Characterize and analyze the array of variants beyond the causative gene in monogenic stone patients. The project has co-PIs, one an expert in clinical and biochemical aspects of USD (Dr. Lieske), and one an expert in the genetics of monogenic kidney diseases (Dr. Harris). Tested tNGS approached will be employed along with a developed and proven bioinformatics pipeline to identify likely causative variants. These results will be returned to the referring physician, with safeguards of counseling and variant conformation, to provide diagnostic information, to allow personalized treatment, and encourage clinical trial recruitment. The accumulated knowledge of gene variants and variant combinations derived for the study will allow for better understanding of these diseases and provide insights into genetic factors causing phenotypic modification.