Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults

Physical activity (PA) may modify the genetic effects that give rise to increased risk of obesity. To identify adiposity loci whose effects are modified by PA, we performed genome-wide interaction meta-analyses of BMI and BMI-adjusted waist circumference and waist-hip ratio from up to 200,452 adults of European (n = 180,423) or other ancestry (n = 20,029). We standardized PA by categorizing it into a dichotomous variable where, on average, 23% of participants were categorized as inactive and 77% as physically active. While we replicate the interaction with PA for the strongest known obesity-risk locus in the FTO gene, of which the effect is attenuated by ~30% in physically active individuals compared to inactive individuals, we do not identify additional loci that are sensitive to PA. In additional genome-wide meta-analyses adjusting for PA and interaction with PA, we identify 11 novel adiposity loci, suggesting that accounting for PA or other environmental factors that contribute to variation in adiposity may facilitate gene discovery.

Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study

BACKGROUND

C-reactive protein (CRP) is associated with immune, cardiometabolic, and psychiatric traits and diseases. Yet it is inconclusive whether these associations are causal.

METHODS AND FINDINGS

We performed Mendelian randomization (MR) analyses using two genetic risk scores (GRSs) as instrumental variables (IVs). The first GRS consisted of four single nucleotide polymorphisms (SNPs) in the CRP gene (GRSCRP), and the second consisted of 18 SNPs that were significantly associated with CRP levels in the largest genome-wide association study (GWAS) to date (GRSGWAS). To optimize power, we used summary statistics from GWAS consortia and tested the association of these two GRSs with 32 complex somatic and psychiatric outcomes, with up to 123,865 participants per outcome from populations of European ancestry. We performed heterogeneity tests to disentangle the pleiotropic effect of IVs. A Bonferroni-corrected significance level of less than 0.0016 was considered statistically significant. An observed p-value equal to or less than 0.05 was considered nominally significant evidence for a potential causal association, yet to be confirmed. The strengths (F-statistics) of the IVs were 31.92-3,761.29 and 82.32-9,403.21 for GRSCRP and GRSGWAS, respectively. CRP GRSGWAS showed a statistically significant protective relationship of a 10% genetically elevated CRP level with the risk of schizophrenia (odds ratio [OR] 0.86 [95% CI 0.79-0.94]; p < 0.001). We validated this finding with individual-level genotype data from the schizophrenia GWAS (OR 0.96 [95% CI 0.94-0.98]; p < 1.72 × 10-6). Further, we found that a standardized CRP polygenic risk score (CRPPRS) at p-value thresholds of 1 × 10-4, 0.001, 0.01, 0.05, and 0.1 using individual-level data also showed a protective effect (OR < 1.00) against schizophrenia; the first CRPPRS (built of SNPs with p < 1 × 10-4) showed a statistically significant (p < 2.45 × 10-4) protective effect with an OR of 0.97 (95% CI 0.95-0.99). The CRP GRSGWAS showed that a 10% increase in genetically determined CRP level was significantly associated with coronary artery disease (OR 0.88 [95% CI 0.84-0.94]; p < 2.4 × 10-5) and was nominally associated with the risk of inflammatory bowel disease (OR 0.85 [95% CI 0.74-0.98]; p < 0.03), Crohn disease (OR 0.81 [95% CI 0.70-0.94]; p < 0.005), psoriatic arthritis (OR 1.36 [95% CI 1.00-1.84]; p < 0.049), knee osteoarthritis (OR 1.17 [95% CI 1.01-1.36]; p < 0.04), and bipolar disorder (OR 1.21 [95% CI 1.05-1.40]; p < 0.007) and with an increase of 0.72 (95% CI 0.11-1.34; p < 0.02) mm Hg in systolic blood pressure, 0.45 (95% CI 0.06-0.84; p < 0.02) mm Hg in diastolic blood pressure, 0.01 ml/min/1.73 m2 (95% CI 0.003-0.02; p < 0.005) in estimated glomerular filtration rate from serum creatinine, 0.01 g/dl (95% CI 0.0004-0.02; p < 0.04) in serum albumin level, and 0.03 g/dl (95% CI 0.008-0.05; p < 0.009) in serum protein level. However, after adjustment for heterogeneity, neither GRS showed a significant effect of CRP level (at p < 0.0016) on any of these outcomes, including coronary artery disease, nor on the other 20 complex outcomes studied. Our study has two potential limitations: the limited variance explained by our genetic instruments modeling CRP levels in blood and the unobserved bias introduced by the use of summary statistics in our MR analyses.

CONCLUSIONS

Genetically elevated CRP levels showed a significant potentially protective causal relationship with risk of schizophrenia. We observed nominal evidence at an observed p < 0.05 using either GRSCRP or GRSGWAS-with persistence after correction for heterogeneity-for a causal relationship of elevated CRP levels with psoriatic osteoarthritis, rheumatoid arthritis, knee osteoarthritis, systolic blood pressure, diastolic blood pressure, serum albumin, and bipolar disorder. These associations remain yet to be confirmed. We cannot verify any causal effect of CRP level on any of the other common somatic and neuropsychiatric outcomes investigated in the present study. This implies that interventions that lower CRP level are unlikely to result in decreased risk for the majority of common complex outcomes.

Abstract 3760: Associations of risk variants for 20 different malignancies with colorectal cancer in a multiethnic population

Familial clustering has been reported across different cancer sites, suggesting that cancer may be considered a broad phenotype with genetic risk factors that are shared across different malignancies. We, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study, explored the hypothesis that risk variants established for cancers at any site influence the risk of colorectal cancer. We selected 160 SNPs associated with 20 different cancer sites, including colorectal cancer, from genome-wide association studies published through May, 2009. These SNPs were genotyped in a nested case-control study of 2,077 colorectal cancer cases and 2,685 controls from five racial-ethnic groups (African American, European American, Latino, Japanese American, and Native Hawaiian) within the Multiethnic Cohort. Odds ratios and 95% Confidence Intervals were estimated by unconditional logistic regression to evaluate the association between SNPs and colorectal cancer risk, adjusting for age, sex, and race/ethnicity. We found that 22 risk variants were associated with colorectal cancer risk with P&lt;0.05: one acute lymphocytic leukemia SNP (ALL); one basal cell carcinoma SNP; two breast cancer SNPs; one chronic lymphocytic leukemia (CLL) SNP; four colorectal cancer SNPs (rs6983267, rs4939827, rs16892766, and rs10505477); five lung cancer SNPs; one nasopharyngeal cancer SNP; one neuroblastoma SNP; two pancreatic cancer SNPs; and four prostate cancer SNPs. With more associations than would be expected by chance (8 =160 tests × 0.05), these results suggest robust significant associations. The strongest association (P&lt;0.0001) was for a colorectal cancer risk variant at chromosome 8q24 (rs10505477). Other notable associations (P&lt;0.01) and their originally associated cancer site, excluding known colorectal cancer risk variants (rs6983267, rs4939827, and rs4242382), include rs17483466 (ACOXL) for CLL (P=0.003), rs4242382 (8q24) for prostate cancer (P=0.004), rs10994982 for ALL (P=0.0078), and rs4975616 (TERT-CLPTM1L) for lung cancer (P=0.0079). Future analysis will include approximately 3,600 additional colorectal cancer cases and controls from the Women's Health Initiative (WHI), Arthrosclerosis Risk In Communities Study (ARIC), and the Cardiovascular Health Study (CHS) as part of the PAGE initiative. In conclusion, these results may provide important insights into the biological pathways that are shared across different cancer sites.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3760. doi:10.1158/1538-7445.AM2011-3760

Abstract 5619: Exploration of pleiotropic effects of cancer GWAS hits with risk of endometrial cancer in the PAGE study

Introduction: Endometrial cancer is the most common gynecological cancer in developed countries. While so far no genome-wide association study (GWAS) has been published for endometrial cancer this approach has been very successful in identifying susceptibility loci for various cancer sites. Interestingly, these GWAS have discovered susceptibility loci that are associated with multiple cancer sites, such as in the 8q24 or TERT-CLPTM1L locus. To comprehensively explore such pleiotropic effects for endometrial cancer we evaluated whether GWAS hits for different cancer sites are associated with risk of endometrial cancer.

Methods: We included 965 endometrial cancer cases and 5759 controls aged 50-79 years from the Women's Health Initiative, which were genotyped as part of the Population Architecture using Genomics and Epidemiology (PAGE) study. We selected 175 single nucleotide polymorphisms (SNPs) previously shown to be associated with different cancer sites mostly in GWAS. We coded SNPs using additive genetic models and used logistic regression to estimate per allele odds ratios (OR) and 95% confidence intervals (CI). Race/ethnicity-specific models were adjusted for age and post-menopausal hormone use.

Results: Among whites the two most independent significant SNPs were rs7501939/17q12 [odds ratio (OR)=0.82; 95% confidential interval (CI)=0.74-0.92; p-value=3.4e-4], and rs4324715/5q31 (OR=0.85; 95%CI=0.76-0.94; p-value=1.5e-3). Interestingly, these two variants have been related to cancers of the male reproductive system (prostate and testicular cancer, respectively) in prior GWAS. When adjusting for multiple comparisons (p=2.86e-4) only one variant (rs7501939) remained marginally significant. The number of other ancestral groups, such as African American or Asian (n=72) was too small to allow separate analysis.

Conclusion: This first analysis suggests that susceptibility loci of the male reproductive system may be associated with endometrial cancer. The next step in this analysis will be to incorporate data from the other PAGE studies to improve the power, explore effects across different ethnicities and to expand our analysis to evaluate gene-environment interactions, particularly looking at hormone related factors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5619. doi:10.1158/1538-7445.AM2011-5619

Abstract 890: GWAS-based genetic variants and lung cancer in white postmenopausal women: The PAGE Consortium

Introduction: Lung cancer is the leading cause of cancer death in the United States, with an estimated 222,520 men and women diagnosed in 2010. While cigarette smoking is the primary causal agent in most lung cancer cases, genetic variation is known to contribute to lung cancer risk. In the present study, we aim to investigate the association between 25 single nucleotide polymorphisms (SNPs) identified in prior genome-wide association (GWA) studies of lung cancer and nicotine dependence and lung cancer in a sample of white postmenopausal women.

Methods: We selected 5,857 white subjects (1,407 cases, 4,450 controls) from the 161,808 postmenopausal women who participated in the Women's Health Initiative component of the NHGRI-funded Population Architecture using Genomics and Epidemiology (PAGE) Consortium. Lung cancer cases were identified prospectively, and confirmed via medical records review. Smoking behavior was ascertained via questionnaire at baseline. We selected 25 SNPs based on statistically significant association with either lung cancer and/or nicotine dependence in prior GWAS. We used logistic regression to estimate the association between each SNP and lung cancer assuming an additive genetic model, after adjusting for age and smoking status (current/former/never), and calculated odds ratios (OR) and 95% confidence intervals. In the subset of controls who reported any history of smoking, we used linear regression to estimate the association between each SNP and continuous pack-years of smoking.

Results: We identified nine SNPs (rs8042374, rs16969968, rs1051730, rs931794, rs8034191, rs2136100, rs578776, rs2036534, rs2836823) significantly associated with both pack-years of smoking and lung cancer adjusted for smoking status. We also identified four SNPs associated with reduced risk of lung cancer that were not significantly associated with pack-years of smoking. All four SNPs are located in CLPTM1L on Chr 5p15, a locus that has been previously associated with lung cancer in never-smokers. The A allele of rs31489 was associated with an OR of 0.79 (p = 9.03 × 10-7), the A allele of rs401681 was associated with an OR of 0.83 (p = 3.41 × 10-5), the A allele of rs402710 was associated with an OR of 0.82 (p = 5.5 × 10-5), and the G allele of rs4975616 was associated with an OR of 0.84 (p = 1.7 × 10-4).

Conclusions: These analyses confirmed prior GWAS findings of statistically significant associations between CLPTM1L and lung cancer in whites after adjustment for age and smoking status. Additional studies with larger numbers of minority lung cancer cases are needed to investigate genetic risk factors for lung cancer in non-white populations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 890. doi:10.1158/1538-7445.AM2011-890

Abstract 948: Investigation of breast cancer susceptibility loci in the PAGE study

Introduction: Recent genome-wide association studies (GWAS) of breast cancer have identified single nucleotide polymorphisms (SNPs) in more than 20 loci associated with increased risk of breast cancer, primarily in European-descent populations. Yet, the biological mechanisms underlying most of these genetic variants as well as their effect sizes in other populations differing by race/ethnicity remains unknown. We investigated breast cancer associations with previously reported SNPs in white and African American (AA) women from the Population Architecture using Genomics and Epidemiology (PAGE) study.

Methods: We selected 28 common SNPs reported in breast cancer GWAS or candidate-gene association studies representing 21 different breast cancer susceptibility loci for our analysis. These SNPs were genotyped in 5878 white and 904 AA postmenopausal women sampled from the Women's Health Initiative Study, which is part of the PAGE consortium. Invasive breast cancer cases (n = 1366 in whites and n=226 in AA) were identified prospectively and confirmed via medical records review. We coded SNPs using additive genetic models and used logistic regression to estimate per allele odds ratios (OR) and 95% confidence intervals (CI). Race/ethnicity-specific models were adjusted for age; adjustment for risk factors such as body mass index, current smoking and postmenopausal hormone therapy (HT) were also investigated.

Results: In whites, we observed statistically significant (p&lt;0.05) associations for 14 of 28 SNPs; strongest associations were seen for SNPs in 10q26.13/FGFR2 and 16q12.1/TOX3, with p&lt;0.0001. In AA, 5 of the 28 SNPs located in 1p11.2/NOTCH, 5q11.2/MAP3K1, 10q26.13/FGFR2, and 11p15.5/LSP1 were associated with breast cancer at p&lt;0.05, while an additional 4 were marginally significant at p&lt;0.07. FGFR2 has been strongly implicated as a breast cancer susceptibility locus, though a causal variant has not yet been identified (Udler et al., 2009). Our ORs of ∼1.2 in whites are consistent with prior reports. Additionally, we observed elevated odds of breast cancer, OR (95%CI) = 1.3(1.0-1.7), in AA for a SNP in this locus, rs2981578 (G allele).

Conclusions: We confirm prior breast cancer associations in postmenopausal white women and report associations in 4 loci that extend to AA women. Our next steps will be to evaluate associations by cancer subtype and expand investigations in AA to include additional genotype data and women from the other PAGE studies. These results in women differing by race/ethnicity contribute to future research on breast cancer etiology by providing data that can be used to inform the identification and fine mapping of causal breast cancer variants.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 948. doi:10.1158/1538-7445.AM2011-948

Abstract 868: Replication of melanoma GWAS hits and exploration of pleiotropic effects of cancer GWAS hits with melanoma risk in the PAGE study

Introduction: As the most serious form of skin cancer, melanoma is a considerable public health burden. Genome wide association studies (GWAS) have successfully identified several loci important to melanoma susceptibility. Some of these loci have been associated with other cancers as well, similar to the pleiotropy previously demonstrated in the 8q24 and TERT regions. Such pleiotropy can highlight important regions and may help inform variant functionality. However, the potential pleiotropic effects of gene variants identified for other cancers have not been fully explored for melanoma. This study evaluates whether GWAS hits for melanoma, as well as hits for non-melanoma cancers, are associated with melanoma risk.

Methods: We included 918 white melanoma cases and 4495 white controls in the Women's Health Initiative, which were genotyped as part of the Population Architecture using Genomics and Epidemiology (PAGE) study. We evaluated 8 single nucleotide polymorphisms (SNPs) previously shown to be associated with melanoma in GWAS as well as 175 SNPs previously shown to be associated with other cancers. These findings were mostly based on GWAS in Caucasian populations. We used logistic regression to evaluate the association between each SNP and melanoma risk, using an age-adjusted additive genetic model.

Results: Of the 8 melanoma SNPs evaluated, 7 were statistically significantly associated with melanoma risk (p&lt;0.05). These SNPs were rs1393350 (p=0.001), rs16891982 (p=3.34e-05), rs258322 (p=1.53e-9), rs4785763 (p=3.29e-4), rs7023329 (p=2.20e-5), rs910873 (p=2.38e-4), and rs4636294 (p=5.82e-5). For each of these significant SNPs, the association was in the same direction of risk as previously reported. The SNP that did not replicate was rs2284063 (p=0.38). Our analysis for pleotropic effects of other cancer GWAS hits did not yield any significant associations after adjustment for multiple comparisons (p=2.87e-4). The most significant SNP was rs710521 (p=0.006), previously associated with urinary bladder cancer.

Conclusions: This preliminary analysis demonstrates that nearly all previously discovered melanoma SNPs replicated. Our analysis did not discover any non-melanoma cancer SNPs that are also associated with melanoma. The next step in this analysis will be to incorporate data from the other three PAGE studies: the Multiethnic Cohort (MEC), Epidemiologic Architecture of Genes Linked to Environment (EAGLE), and the CALiCo Consortium (see pagestudy.org). This will substantially improve the power of our pleiotropy analyses.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 868. doi:10.1158/1538-7445.AM2011-868

Abstract 2755: Association of established risk variants for obesity and type-2 diabetes with dietary intake in the Multiethnic Cohort Study

Excess body weight is thought to account for 25 to 30% of common cancers. As the prevalence of obesity increases worldwide, the number of obesity-related cancers is expected to rise. Recent genome-wide association studies (GWAS) have identified common genetic variants associated with obesity and related metabolic conditions, such as type-2 diabetes. However, the mechanisms underlying these associations are unclear. Given that diet plays a critical role in energy balance and glucose metabolism, it is possible that some of these variants affect metabolic disease risk through an effect on food choices. As part of the Population Architecture using Genomics and Epidemiology (PAGE) initiative, we investigated the associations of 31 risk variants identified in published GWAS of obesity and type-2 diabetes with 50 dietary phenotypes (dietary patterns, macronutrients, food groups, and candidate foods) as measured by a quantitative food frequency questionnaire in the Multiethnic Cohort Study. Participants of five race/ethnic groups (African Americans, Native Hawaiians, Japanese Americans, Latinos, and Whites) were genotyped for 12 obesity (n=13,181) or 19 type-2 diabetes (n=25,273) risk variants. Linear or logistic regression was employed to test for associations, while adjusting for age, sex and ethnicity. Using an additive risk model for genotypes, we found 37 associations with dietary phenotypes (p-value&lt;0.01) for 17 of the 31 SNPs. Rs8050136, a variant located within the FTO gene which is highly expressed in the hypothalamus and is associated with obesity and type-2 diabetes, had the greatest number of associations (n=9), mostly with macronutrients. Among participants who self-reported as non-diabetic at baseline, for a per-allele change, there was a 0.23±0.076 increase in % calories from fat (p=0.002), mainly from monounsaturated fats, and a 0.29±0.095 decrease in % calories from carbohydrates (p=0.002). These associations remained even after additional adjustments for calories and physical activity. We also found that carriers of the risk allele had an increase in % calories from protein (p=0.013) and were less likely to add salt to foods (p=0.007). The directions of these associations were consistent across sexes and racial/ethnic groups. Consistent with our results, several small studies (4 in children and 3 in adults) reported higher energy intake, increased energy intake from fat, and/or diminished satiety among individuals with the risk allele. Replication studies are ongoing in PAGE. Methods to adjust for multiple comparisons among correlated phenotypes are being applied. In conclusion, these data suggest that the association of rs8050136 with obesity may at least partially be the result of a dietary preference for fat. If reproduced, these data may have relevance to the prevention of obesity and obesity-related cancers in risk allele carriers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2755. doi:10.1158/1538-7445.AM2011-2755