BACKGROUND The discovery of low-frequency coding variants affecting the risk of coronary artery disease has facilitated the identification of therapeutic targets. METHODS Through DNA genotyping, we tested 54,003 coding-sequence variants covering 13,715 human genes in up to 72,868 patients with coronary artery disease and 120,770 controls who did not have coronary artery disease. Through DNA sequencing, we studied the effects of loss-of-function mutations in selected genes. RESULTS We confirmed previously observed significant associations between coronary artery disease and low-frequency missense variants in the genes LPA and PCSK9. We also found significant associations between coronary artery disease and low-frequency missense variants in the genes SVEP1 (p.D2702G; minor-allele frequency, 3.60%; odds ratio for disease, 1.14; P = 4.2×10−10) and ANGPTL4 (p.E40K; minor-allele frequency, 2.01%; odds ratio, 0.86; P = 4.0×10−8), which encodes angiopoietin-like 4. Through sequencing of ANGPTL4, we identified 9 carriers of loss-of-function mutations among 6924 patients with myocardial infarction, as compared with 19 carriers among 6834 controls (odds ratio, 0.47; P = 0.04); carriers of ANGPTL4 loss-of-function alleles had triglyceride levels that were 35% lower than the levels among persons who did not carry a loss-of-function allele (P = 0.003). ANGPTL4 inhibits lipoprotein lipase; we therefore searched for mutations in LPL and identified a loss-of-function variant that was associated with an increased risk of coronary artery disease (p.D36N; minor-allele frequency, 1.9%; odds ratio, 1.13; P = 2.0×10−4) and a gain-of-function variant that was associated with protection from coronary artery disease (p.S447⋆; minor-allele frequency, 9.9%; odds ratio, 0.94; P = 2.5×10−7). CONCLUSIONS We found that carriers of loss-of-function mutations in ANGPTL4 had triglyceride levels that were lower than those among noncarriers; these mutations were also associated with protection from coronary artery disease. (Funded by the National Institutes of Health and others.)

H igh-density lipoprotein (HDL)-based therapies have yielded disappointing results, [1][2][3][4] which have led to questioning of the HDL hypothesis. Cholesteryl ester transfer protein mediates the transfer of cholesteryl esters from HDL to apolipoprotein B-containing particles, such as low-density lipoproteins (LDLs).5 Torcetrapib, the first cholesteryl ester transfer protein inhibitor to be evaluated in a large clinical trial, caused excess morbidity and mortality despite increasing HDL-cholesterol levels by ≈70% although elevations of aldosterone levels and blood pressure observed in some patients may have contributed to the negative findings.3 Dalcetrapib is another cholesteryl ester transfer protein inhibitor that raises HDL-cholesterol levels by ≈30%, without effects on circulating neurohormones. 6 The dal-OUTCOMES trial was designed to test whether dalcetrapib could modify cardiovascular risk in patients with a recent acute coronary syndrome. Background-Dalcetrapib did not improve clinical outcomes, despite increasing high-density lipoprotein cholesterol by 30%. These results differ from other evidence supporting high-density lipoprotein as a therapeutic target. Responses to dalcetrapib may vary according to patients' genetic profile. Methods and Results-We conducted a pharmacogenomic evaluation using a genome-wide approach in the dal-OUTCOMES study (discovery cohort, n=5749) and a targeted genotyping panel in the dal-PLAQUE-2 imaging trial (support cohort, n=386). The primary endpoint for the discovery cohort was a composite of cardiovascular events. The change from baseline in carotid intima-media thickness on ultrasonography at 6 and 12 months was evaluated as supporting evidence. A single-nucleotide polymorphism was found to be associated with cardiovascular events in the dalcetrapib arm, identifying the ADCY9 gene on chromosome 16 (rs1967309; P=2.41×10 -8 ), with 8 polymorphisms providing P<10 -6 in this gene. Considering patients with genotype AA at rs1967309, there was a 39% reduction in the composite cardiovascular endpoint with dalcetrapib compared with placebo (hazard ratio, 0.61; 95% confidence interval, 0.41-0.92). In patients with genotype GG, there was a 27% increase in events with dalcetrapib versus placebo. Ten single-nucleotide polymorphism in the ADCY9 gene, the majority in linkage disequilibrium with rs1967309, were associated with the effect of dalcetrapib on intima-media thickness (P<0.05). Marker rs2238448 in ADCY9, in linkage disequilibrium with rs1967309 (r 2 =0.8), was associated with both the effects of dalcetrapib on intima-media thickness in dal-PLAQUE-2 (P=0.009) and events in dal-OUTCOMES (P=8.88×10 -8 ; hazard ratio, 0.67; 95% confidence interval, 0.58-0.78). Conclusions-The Tardif et al Pharmacogenomic Determinants of Dalcetrapib 373Dalcetrapib failed to improve clinical outcomes among the 15 871 patients of the dal-OUTCOMES study, with no subgroups defined by baseline clinical or biochemical characteristics appearing to benefit from therapy. 4 These results are ...

Hematological traits are important clinical parameters. To test the role of rare and low-frequency coding variants on hematological traits, we analyzed hemoglobin, hematocrit, white blood cell (WBC) and platelet count in 31,340 individuals genotyped on an exome array. We identified several missense variants of CXCR2 associated with reduced WBC count (gene-based P=2.6×10−13). In a separate family-based re-sequencing study, we identified a novel loss-of-function CXCR2 frameshift mutation in a pedigree with congenital neutropenia that abolished ligand-induced CXCR2 signal transduction and chemotaxis. We also identified novel missense or splice site variants in key hematopoiesis regulators (EPO, TRF2, HBB, TUBB1, SH2B3) associated with blood cell traits. Finally, we were able to detect associations between the rare somatic JAK2 p.Val617Phe mutation and platelet count (P=3.9×10−22) as well as hemoglobin (P=0.002), hematocrit (P=9.5×10−7) and WBC (P=3.1×10−5). In conclusion, exome arrays complement GWAS in identifying new variants that contribute to complex human traits.

De novo mutations (DNM) are an important source of rare variants and are increasingly being linked to the development of many diseases. Recently, the paternal age effect has been the focus of a number of studies that attempt to explain the observation that increasing paternal age increases the risk for a number of diseases. Using disease-free familial quartets we show that there is a strong positive correlation between paternal age and germline DNM in healthy subjects. We also observed that germline CNVs do not follow the same trend, suggesting a different mechanism. Finally, we observed that DNM were not evenly distributed across the genome, which adds support to the existence of DNM hotspots.