Genetic determinants of lymphocyte traits and risk of acute lymphoblastic leukemia in children with Down syndrome

摘要 急性淋巴细胞性白血病(ALL)是儿童最常见的恶性肿瘤，儿童Down 综合征(DS)患ALL(DS-ALL)的风险最高可增加30倍。DS-所有患者也都有 与治疗相关的毒性增加，复发风险增加，总体存活率比所有患者都差 没有DS。DS-ALL的预防或早期干预将需要包含遗传风险的预测模型； 然而，除了21号染色体的构成三体之外，人们对DS的遗传风险知之甚少。我们 将利用DS的极端敏感性来发现DS-ALL的风险因素。在最近的两个样本中 孟德尔随机(MR)血细胞特征分析和ALL在没有DS的儿童中，我们发现 总体上和与其他血细胞类型有关的淋巴细胞过度生产的遗传倾向是 与ALL风险增加有因果关系。基于这一发现，并考虑到我们最近的演示 所有相关的遗传风险变异似乎对患有DS的儿童产生更大的影响，我们将进行 首次全面研究血细胞性状遗传变异在DS-ALL风险中的作用，我们还将评估 与特定肿瘤改变和患者临床结果的潜在关联。这些分析将是 使用来自至少413个DS-ALL病例和超过1500个DS的全基因组测序(WGS)数据进行 通过Gabriella Miller Kids First和NIH产生的控制措施包括一些计划，这些计划将公开 可通过DBGaP和儿童第一数据门户网站获得。在目标1中，我们将使用生殖系WGS数据来执行 DS-ALL的GWA，然后使用来自该GWAS的汇总统计数据来执行两个样本的MR分析 血细胞特征和DS-ALL风险，使用我们最近在非-MR研究中已经开发的遗传工具 DS ALL。接下来，我们将为每个血细胞性状构建多基因风险评分(PR)，并检查DS的风险- ，以及评估每个PRS模型的预测性能 DS-使用拟合优度衡量的所有风险。我们还将测试单核苷酸多态(SNPs) 以前与淋巴细胞特征相关的疾病也可能与DS-ALL风险相关。在目标2中，我们将 研究血细胞性状遗传变异与躯体特征和临床结局的关系 在DS-ALL患者中。首先，我们将评估MR中是否存在肿瘤亚型特异性关联。 目标1中确定的分析、PR和候选SNP，重点是普遍存在的CRLF2-重排 和DS-ALL中的IKZF1缺失。接下来，在一项仅限病例的分析中，我们将探讨PR对血细胞特征的影响 可能与DS-ALL患者的临床结果有关，包括治疗相关的毒性，复发的风险， 以及总体存活率。这项研究将阐明DS-ALL的病因，并揭示可能 指导基因检测，并通过识别患有 DS是所有患者中风险最大的，也可能是那些DS-所有患者都有不良结局的高风险。

ABSTRACT Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, and children with Down syndrome (DS) have an up to 30-fold increased risk of developing ALL (DS-ALL). DS-ALL patients also have increased treatment-related toxicities, increased risk of relapse, and worse overall survival than ALL patients without DS. Prevention or early intervention of DS-ALL will require prediction models incorporating genetic risk; however, little is known regarding genetic risk of DS-ALL beyond the constitutive trisomy of chromosome 21. We will leverage the extreme susceptibility of DS to discover risk factors for DS-ALL. In a recent two-sample Mendelian randomization (MR) analysis of blood cell traits and ALL in children without DS, we found that a genetic propensity for overproduction of lymphocytes, overall and in relation to other blood cell types, was causally associated with an increased risk of ALL. Building on this finding, and given our recent demonstration that ALL-associated genetic risk variants appear to confer larger effects in children with DS, we will perform the first comprehensive study of the role of blood cell trait genetic variation in risk of DS-ALL, and we will also assess potential associations with particular tumor alterations and patient clinical outcomes. These analyses will be conducted using whole-genome sequencing (WGS) data from at least 413 DS-ALL cases and over 1500 DS controls, generated through the Gabriella Miller Kids First and NIH INCLUDE Programs and which will be publicly available through dbGaP and the Kids First Data Portal. In Aim 1, we will use the germline WGS data to perform a GWAS of DS-ALL, and then use summary statistics from this GWAS to perform a two-sample MR analysis of blood cell traits and DS-ALL risk, using genetic instruments already developed in our recent MR study of non- DS ALL. We will next construct polygenic risk scores (PRS) for each blood cell trait and examine the risk of DS- ALL at the tails of PRS distributions, as well as evaluating the predictive performance of each PRS model for DS-ALL risk using goodness-of-fit measures. We will also test whether single nucleotide polymorphisms (SNPs) previously associated with lymphocyte traits may also be associated with DS-ALL risk. In Aim 2, we will investigate the association between blood cell trait genetic variation and somatic features and clinical outcomes in DS-ALL patients. First, we will assess whether there may be tumor subtype-specific associations in the MR analysis, PRS, and candidate SNPs identified in Aim 1, with a focus on the prevalent CRLF2-rearrangements and IKZF1 deletions in DS-ALL. Next, in a case-only analysis we will explore whether PRS for blood cell traits may show association with DS-ALL patient clinical outcomes, including treatment-related toxicity, risk of relapse, and overall survival. This study will shed light on the etiology of DS-ALL, and reveal novel risk factors that may guide genetic testing and inform future precision prevention approaches through identification of children with DS with the greatest risk of ALL, as well as potentially those DS-ALL patients with high risk of adverse outcomes.