INTRODUCTION: Clonal Hematopoiesis of Indeterminate Potential (CHIP) is a clonal expansion of blood cells arising from a leukemogenic somatic mutation in hematopoietic stem cells. CHIP increases with age and has been associated with hematologic malignancy and coronary artery disease.

OBJECTIVES: Simultaneous somatic and germline whole genome sequence analysis now provides the opportunity to identify root causes of CHIP. Here, we analyze genomes from 100,002 participants of diverse ancestries in the NHLBI TOPMed program to identify inherited variation associated with CHIP and its clinical consequences.

METHODS: We identified CHIP through somatic variant calling with MuTect2 followed by filtering on known leukemogenic CHIP driver mutations. We analyzed associations between CHIP and clinical phenotypes including blood traits, inflammatory markers and stroke. We performed a genome-wide association study to identify common inherited germline variation associated with the development of CHIP. We applied burden tests to rare loss-of-function (LOF) variation in coding genes, and rare regulatory variation in hematopoietic stem cell enhancers.

RESULTS: We identified 4,587 individuals with CHIP, 90% of whom had a single driver mutation. >75% of the driver mutations were in one of three CHIP driver genes (DNMT3A, TET2, and ASXL1). CHIP prevalence was strongly associated with age (p<10-300).

CHIP associated with blood cell trait RDW (p=1.3 x 10-4), and inflammatory markers IL-6 (p=4.6 x 10?5) and Lp-PLA2 (p=1.8 x 10?7). We found an increased risk for the first nononcologic incident event conferred by CHIP – ischemic stroke (Adjusted HR: 1.1, p=0.047), with larger CHIP clones (VAF>20%) conferring increased risk (HR: 1.2, p=0.008). CHIP driver gene specific phenotypic profiles were also observed.

Four genome-wide significant risk loci were associated with CHIP, including one locus at TET2 that was African ancestry specific. Computational analyses of the TET2 locus implicated rs79901204 as the causal variant which disrupts a hematopoietic stem cell specific enhancer element. Rare LOF variants in CHEK2, a DNA damage repair gene, and rare regulatory variation in HAPLN1 enhancers, a bone marrow stromal cell protein, were the top associations with CHIP in rare variant analyses (p=2.1 x 10-5 and p=2.0 x10-5 respectively).

CONCLUSION: Heritable variation altering hematopoietic stem cell function and the fidelity of DNA-damage repair increased the likelihood of developing CHIP.

Aspirin is often used in primary and secondary prevention of cardiovascular disease (CVD). The efficacy of aspirin and other anti-platelet treatments is linked to their ability to suppress platelet activation, a key component in thrombosis. The concept of aspirin resistance is controversial, with unknown prevalence and many studies finding on re-testing that suspected aspirin resistance was due to non-compliance or self-report error. Thus, the extent of differences in aspirin efficacy in the population due to genetic or environmental effects remains to be determined. To study the genetic factors influencing on-aspirin platelet aggregation in the European ancestry Offspring cohort of the Framingham Heart Study, we used a gold standard platelet activation assay (light transmission aggregometry) after addition of arachidonic acid as a sensitive determinant of aspirin takers. Then we conducted WGS-imputed GWAS analysis in a subset of individuals who were taking aspirin at the time of platelet activation measurement. We focused on QTL analysis of platelet activation via 3 agonist pathways (ADP, epinephrine and collagen) that partially escape aspirin inactivation. From these analyses we found 2 genome-wide significant loci (P<5E-8), and 2 borderline loci (P<1E-7) for platelet activation. All four loci (ABAT, MMD2, CSH1, ACYP2) had a minor allele associated with decreased epinephrine-induced platelet activation, indicating those individuals had greater platelet suppression on aspirin treatment. We attempted replication in a smaller, diverse sample – the Framingham Omni cohort – and a Welsh population sample – the Caerphilly Prospective Study in Men – and found evidence for association in the same direction in aspirin takers in the region of ACYP2. In interaction models including non-aspirin takers there was a significant interaction with the ACYP2 peak SNP (P<0.03 interaction). This sentinel SNP is ~6kb upstream of the consensus start site and overlaps an area of epigenetic activity in megakaryocytes, the precursor cell for platelets. Acylphoshpatase-2 (ACYP2) hydrolyzes calcium channel intermediates, and calcium signaling plays a critical role in platelet activation, particularly for epinephrine-based stimulation. Efforts are currently underway to evaluate whether the identified SNPs contribute to future risk of CVD or bleeding in the Women’s Genome Health Study, a randomized trial of aspirin, vitamin E and placebo with >20 years follow-up.