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 in...