Comprehensive Integrated Genomic Perturbations Reveal Molecular Mechanisms of Red Blood Cell Trait Associations

Discovery of molecular mechanisms responsible for trait associations as discovered by genome-wide association studies (GWAS) is hampered by difficulty in identifying causal genetic variants due to linkage disequilibrium. Typical assays of genetic function are low throughput or evaluate sequences in heterologous ectopic settings. Genome editing enables perturbation of trait-associated genetic sequences within relevant genomic, chromatin and cellular context. Here we perform comprehensive analysis of genetic variants associated with red blood cell traits by pooled CRISPR screening. We performed a genome-wide Cas9 gene knockout screen in immortalized erythroid precursors (HUDEP-2 cells) during erythroid maturation to define functional erythroid genes required for cell growth or differentiation. We evaluated 952 loci associated with nine red blood cell traits (Astle et al, Cell 2016) comprising 24,843 SNPs. We linked 7,187 (28.9%) of these SNPs to genes by at least one of four routes: sharing topological associated domain, physical proximity ( Disclosures No relevant conflicts of interest to declare.