Using the NHGRI catalog, we identified 157 SNPs with a published risk allele and a p-value less than or equal to 10-7
for the association with cardiovascular disease or an intermediate phenotype which were able to be matched in our geneotyped or imputed data. An additional 5 SNPs were not able to be matched (rs1746563722
gene region, rs2892768023
in the APOA1/C3/A4/A5
in the MLXIPL
gene region, and rs471252425
in the KCNQ1
gene region). After pruning to eliminate correlated SNPs in high linkage disequilibrium, the remaining 101 SNPs were used in the construction of the primary genetic risk score. The second score, limited to SNPs with a published association with incident CVD, included 12 SNPs after pruning.
The resulting genetic scores were evaluated in the 19,313 white participants from the WGHS. At baseline the participants had a median age of 52.8 years (25th -75th percentile: 48.9 - 58.9), a median systolic blood pressure of 125 mm Hg (25th -75th percentile: 115 - 135), a median total cholesterol of 208 mg/dL (25th -75th percentile:184 - 235), a median high density lipoprotein cholesterol of 52 mg\dL (25th -75th percentile: 43.3 - 62.5), and a median high-sensitivity C-reactive protein of 2 mg/dL (25th -75th percentile: 0.8 - 4.3). Also at baseline, 12% (2248) were current smokers and 2% (479) were diabetic. In the diabetics, the median hemoglobin A1c level was 6.9% (25th -75th percentile: 5.9 - 8.3). Thirteen percent of the women (2499) reported a parental history of MI before 60 years. Over the follow-up period (median 12.3 years), 777 incident cardiovascular events (199 myocardial infarctions, 203 strokes, 63 cardiovascular deaths, 312 revascularizations) were reported by the study participants and confirmed by the endpoints committee (634 in the first 10 years).
The 101 SNPs used in the genetic risk score are shown in eTable1
arranged by the category of the phenotype for the published association. The 12 SNPs used for the score based only on SNPs known to be associated with cardiovascular disease are listed in the phenotype category “Cardiovascular Disease”. Each SNP was tested for association with the previously published phenotype as well as for association with incident CVD in the WGHS. These results, along the candidate gene, the published cardiovascular risk allele, and the frequency of the risk allele in the WGHS, are also included in . Of the101 SNPs, 72 replicated the published phenotype association in the WGHS with a p-value less than 0.05 and 5 were significantly associated with incident CVD (rs17249754 in the ATP2B1
gene region, rs1333049 in the chromosome 9p21.3 region, rs10830963 in the MTNR1B
gene region, rs4607103 in the ADAMTS9
gene region, and rs1883025 in the ABCA1
gene region). Only rs1333049 in the chromosome 9p21.3 region has a previously published genome-wide association with cardiovascular disease.
Association of Genetic Risk Score and Family History with Cardiovascular Disease
Among the 19,313 WGHS participants, the mean score (or number of risk alleles) using the 101 SNPs was 102.1, with a standard deviation of 6.4 and a range of 73 to 125. The mean score using the 12 SNPs was 10.7, with a standard deviation of 1.9 and a range of 4 to 19. As anticipated, the 101 SNP score was positively correlated with total cholesterol, systolic blood pressure, and C-reactive protein, and negatively associated with high density lipoprotein (eTable2
). The 12 SNP score was also positively correlated with total cholesterol, but the relationship was sharply attenuated when the one SNP with a published association with cholesterol levels (rs599839 in the CELSR2/PSRC1/SORT1
region) was removed. The odds of a family history of premature MI also increased with increasing scores, with an odds ratio of 1.01 per allele for the 101 SNP score and 1.04 per allele for the 12 SNP score, both with p-values less than 0.001.
The shows the unadjusted survival curves by tertile of each genetic risk score and for family history (top row), as well as the distribution of risk alleles by event status at 10 years of follow-up for the genetic risk scores (bottom row). While there is a trend towards increasing risk with greater number of risk alleles for both scores, only the highest tertile of the 101 SNP score had a significant hazard ratio (HR 1.22 compared to the lowest risk group, p = 0.027). This corresponds to an absolute CVD risk of 3% over 10 years in the lowest tertile of genetic risk (73-99 risk alleles) and 3.7% in the highest tertile (106-125 risk alleles). As suggested by the overlap in the distributions by event status, neither genetic risk score alone had discriminatory capabilities for CVD risk (c-index 0.523 for 101 SNP score and 0.517 for 12 SNP score).
Cumulative Incidence of Cardiovascular Events by Genetic Risk Score Tertile and Family History and Distribution of Genetic Risk Scores by 10 Year Cardiovascular Event Status
Both the 101 and 12 SNP genetic risk scores were associated with increased risk of CVD after adjusting for age (). Specifically, the age-adjusted hazard ratio for CVD per allele for the 101 SNP score was 1.015 (95% confidence interval: 1.00-1.03, p value 0.006) and was 1.05 (95% confidence interval: 1.01-1.09, p value 0.014) for the 12 SNP score. Neither score remained independently associated once the ATP III or Reynolds covariates were adjusted for. The ATP III adjusted HR per allele for the 101 SNP score was 1.00 (95% CI 0.99-1.01) and was 1.04 (95% CI 1.00-1.08) for the 12 SNP score. In contrast, family history of premature MI remained an independent risk factor for incident cardiovascular disease even after adjustment (HR 1.57, 95% CI 1.31-1.89). The effects of the standard risk factors were unaffected by the addition of the genetic markers (models shown in eTables 3 and 4
All of the models were calibrated with and without with the addition of the genetic risk scores or family history. Neither genetic risk score improved prediction when added the ATP III or Reynolds covariates, as shown in . Adding the 101 SNP score to the ATP III covariates changed the c-index 0.000 with an NRI of 0.5% (p=0.24), whereas adding the 12 SNP score changed the c-index 0.001 (p=0.12) with an NRI of 0.5% (p=0.59) The 12 SNP risk score and family history did show some improvement in prediction beyond age alone. When the reclassification calibration was examined (), only family history showed an improvement in fit when added to the base models.
Discrimination and Reclassification after Addition of Genetic Risk Score or Family History to Base Model
Reclassification Calibration for the Addition of Genetic Risk Score or Family History to Base Model
Repeating our analysis with only the directly genotyped SNPs had no appreciable effect on our results, nor did excluding the SNPs associated only with C-reactive protein, hemoglobin A1c or triglycerides.