Lesley M. Butler

Ancestry Informative Marker Sets for Determining Continental Origin and Admixture Proportions in Common Populations in America

To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome‐wide distribution, and genotype reproducibility on two platforms (TaqMan® assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations. Hum Mutat 0,1–10, 2008.

Tea and cancer prevention: Epidemiological studies

Experimental studies have consistently shown the inhibitory activities of tea extracts on tumorigenesis in multiple model systems. Epidemiological studies, however, have produced inconclusive results in humans. A comprehensive review was conducted to assess the current knowledge on tea consumption and risk of cancers in humans. In general, consumption of black tea was not associated with lower risk of cancer. High intake of green tea was consistently associated with reduced risk of upper gastrointestinal tract cancers after sufficient control for confounders. Limited data support a protective effect of green tea on lung and hepatocellular carcinogenesis. Although observational studies do not support a beneficial role of tea intake on prostate cancer risk, phase II clinical trials have demonstrated an inhibitory effect of green tea extract against the progression of prostate pre-malignant lesions. Green tea may exert beneficial effects against mammary carcinogenesis in premenopausal women and recurrence of breast cancer. There is no sufficient evidence that supports a protective role of tea intake on the development of cancers of the colorectum, pancreas, urinary tract, glioma, lymphoma, and leukemia. Future prospective observational studies with biomarkers of exposure and phase III clinical trials are required to provide definitive evidence for the hypothesized beneficial effect of tea consumption on cancer formation in humans.

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

BackgroundCase-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.ResultsIn this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.ConclusionThese data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.

Dietary patterns and incident type 2 diabetes in chinese men and women: the singapore chinese health study.

OBJECTIVE To empirically derive dietary patterns and examine their association with incident type 2 diabetes. RESEARCH DESIGN AND METHODS We used data from the Singapore Chinese Health Study, including 43,176 Chinese men and women (aged 45–74 years), free of diabetes, cardiovascular disease, and cancer at baseline (1993–1998) and followed up through 2004. Two major dietary patterns were identified using principal components analysis: a vegetable, fruit, and soy-rich pattern (VFS) and a dim sum and meat-rich pattern (DSM). Pattern scores for each participant were calculated and examined with type 2 diabetes risk using Cox regression. RESULTS The associations of the two dietary patterns with diabetes risk were modified by smoking status. Neither pattern was associated with risk of diabetes in ever smokers. In never smokers, the VFS dietary pattern was inversely associated with risk of type 2 diabetes. Compared with the lowest quintile of the VFS dietary pattern score, the hazard ratios (HRs) for quintiles 2–5 were 0.91, 0.82, 0.73, and 0.75 (P = 0.0005 for trend). The DSM dietary pattern was positively associated with risk of type 2 diabetes in never smokers, with HRs for quintiles 2–5 of 1.07, 1.25, 1.18, and 1.47 (P < 0.0001 for trend). CONCLUSIONS A dietary pattern with higher intake of vegetables, fruits, and soy foods was inversely associated with risk of incident type 2 diabetes, and a pattern with higher intake of dim sum, meat and processed meat, sweetened foods and beverages, and fried foods was associated with a significantly increased risk of type 2 diabetes in Chinese men and women in Singapore.

Ovarian Cancer Risk Factors by Histologic Subtype: An Analysis From the Ovarian Cancer Cohort Consortium

PURPOSE An understanding of the etiologic heterogeneity of ovarian cancer is important for improving prevention, early detection, and therapeutic approaches. We evaluated 14 hormonal, reproductive, and lifestyle factors by histologic subtype in the Ovarian Cancer Cohort Consortium (OC3). PATIENTS AND METHODS Among 1.3 million women from 21 studies, 5,584 invasive epithelial ovarian cancers were identified (3,378 serous, 606 endometrioid, 331 mucinous, 269 clear cell, 1,000 other). By using competing-risks Cox proportional hazards regression stratified by study and birth year and adjusted for age, parity, and oral contraceptive use, we assessed associations for all invasive cancers by histology. Heterogeneity was evaluated by likelihood ratio test. RESULTS Most risk factors exhibited significant heterogeneity by histology. Higher parity was most strongly associated with endometrioid (relative risk [RR] per birth, 0.78; 95% CI, 0.74 to 0.83) and clear cell (RR, 0.68; 95% CI, 0.61 to 0.76) carcinomas (P value for heterogeneity [P-het] < .001). Similarly, age at menopause, endometriosis, and tubal ligation were only associated with endometrioid and clear cell tumors (P-het ≤ .01). Family history of breast cancer (P-het = .008) had modest heterogeneity. Smoking was associated with an increased risk of mucinous (RR per 20 pack-years, 1.26; 95% CI, 1.08 to 1.46) but a decreased risk of clear cell (RR, 0.72; 95% CI, 0.55 to 0.94) tumors (P-het = .004). Unsupervised clustering by risk factors separated endometrioid, clear cell, and low-grade serous carcinomas from high-grade serous and mucinous carcinomas. CONCLUSION The heterogeneous associations of risk factors with ovarian cancer subtypes emphasize the importance of conducting etiologic studies by ovarian cancer subtypes. Most established risk factors were more strongly associated with nonserous carcinomas, which demonstrate challenges for risk prediction of serous cancers, the most fatal subtype.

Joint effects between UDP-glucuronosyltransferase 1A7 genotype and dietary carcinogen exposure on risk of colon cancer.

The UDP-glucuronosyltransferase 1A7 (UGT1A7) gene is polymorphic and encodes an enzyme involved in the detoxification of heterocyclic amines (HCA) and polycyclic aromatic hydrocarbons (PAH). Consumption of pan-fried and well-done meat are surrogates for HCA and PAH exposure and are possibly associated with colon cancer. We have evaluated whether UGT1A7 allelic variations are associated with colon cancer and whether UGT1A7 genotype modified associations among meat intake, exposure to HCAs and PAHs, and colon cancer in a population-based case-control study of African Americans (197 cases and 202 controls) and whites (203 cases and 210 controls). As part of a 150-item food frequency questionnaire, meat intake was assessed by cooking method and doneness and used to estimate individual HCA and PAH exposure. UGT1A7 alleles (UGT1A7*1, UGT1A7*2, UGT1A7*3, and UGT1A7*4) were measured and genotypes were categorized into predicted activity groups (high: *1/*1, *1/*2, *2/*2; intermediate: *1/*3, *1/*4, *2/*3; low: *3/*3, *3/*4, *4/*4). There was no association with UGT1A7 low versus high/intermediate genotype [odds ratio (OR), 1.1; 95% confidence interval (95% CI), 0.7-1.8], regardless of race. Greater than additive joint effects were observed for UGT1A7 low genotype and HCA-related factors. For example, equal to or greater than the median daily intake of the HCA, 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (DiMeIQx) and having UGT1A7 low genotype was positively associated with colon cancer (OR, 2.4; 95% CI, 1.2-4.8), compared with less than the median daily intake and UGT1A7 high/intermediate genotypes. These data suggest that the associations among cooked meat–derived compound exposure, and colon cancer are modified by the UGT1A7 genotype.

An Aging Workforce and Injury in the Construction Industry

The relatively large birth cohort between 1946 and 1964, combined with the economic recession in the first decade of the 21st century, have led to an increase in the proportion of older workers in the US workplace. Understanding the health and safety needs of an aging workforce will be critical, especially in the construction industry, where physical job demands are high. This paper reviews the epidemiologic literature on the impact of age on injury among workers in the construction industry in terms of cause, type, and cost. PubMed was searched by using the following terms: older workers, construction, construction industry, injury, and age. The available studies reported that, among the construction industry workforce, older age at injury was related to higher injury costs but not to number of injuries. The higher injury costs associated with worker age are likely due in part to the severity of the injuries sustained by older workers. Identification of injury trends and subsequent analytical research efforts designed to ascertain factors associated with injury among older construction workers are needed for employers to effectively manage a health and safety program that addresses the needs of the aging worker.

Calcium Intake Increases Risk of Prostate Cancer among Singapore Chinese

Consumption of dairy products, the primary source of calcium in Western diets, has been found to be positively associated with prostate cancer. In an Asian diet, nondairy foods are the major contributors of calcium. Thus, a study of dietary calcium and prostate cancer in Asians can better inform on whether calcium, as opposed to other dairy components, is responsible for the dairy foods-prostate cancer association. We examined calcium intake and prostate cancer risk among 27,293 men in the Singapore Chinese Health Study that was established between 1993 and 1998. As of December 31, 2007, 298 incident prostate cancer cases had been diagnosed among the cohort members. Diet was assessed at baseline with a validated 165-item food-frequency questionnaire. It is hypothesized that there is greater net absorption of calcium in smaller individuals. Therefore, the calcium-prostate cancer association was also assessed in stratified analyses by median body mass index. Vegetables were the largest contributor of daily calcium intake in the study population. Overall, we observed a modest, statistically nonsignificant 25% increase in prostate cancer risk for the 4th (median = 659 mg/d) versus 1st (median = 211 mg/d) quartiles of calcium intake after adjustment for potential confounders. The association became considerably stronger and achieved statistical significance (hazard ratio, 2.03; 95% confidence interval, 1.23-3.34; P for trend = 0.01) for men with a below median body mass index (22.9 kg/m(2)). Dietary calcium might be a risk factor for prostate cancer even at relatively low intake.

UGT1A1 and UGT1A9 functional variants, meat intake, and colon cancer, among Caucasians and African-Americans

Glucuronidation by the UDP-glucuronosyltransferase enzymes (UGTs) is one of the primary detoxification pathways of dietary heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PAHs). In a population-based case-control study of 537 cases and 866 controls, we investigated whether colon cancer was associated with genetic variations in UGT1A1 and UGT1A9 genes and we determined if those variations modify the association between colon cancer and dietary HCA and PAH exposure. We measured functional UGT1A1 polymorphisms at positions -53 (28; A(TA)6TAA to A(TA)7TAA), -3156 (G>A), -3279 (T>G) and the UGT1A9-275(T>A) polymorphism, and found no association with colon cancer overall. However, when stratified by race, the UGT1A1-3279 GG/TG intermediate/low activity genotypes were associated with an increased risk of colon cancer (odds ratio (OR)=1.5, 95% confidence interval (CI)=1.1-2.0) in Caucasians. This finding is also supported by haplotype analyses where the UGT1A1-3279G-allele-bearing haplotype is overrepresented in case group. Overall, UGT1A1-53 and -3156 genotypes modified the association between dietary benzo(a)pyrene (BaP) and colon cancer (P for interaction=0.02 and 0.03, respectively). The strongest association was observed for those with <7.7 ng/day BaP exposure and the low activity genotypes, for both UGT1A1 28/28 (OR=1.8, 95% CI=1.1-2.9) and -3156AA (OR=1.7, 95% CI=1.0-3.0), compared to >or=7.7 ng/day and combined high/intermediate genotypes. These data support a hypothesis that UGTs modify the association between meat-derived PAH exposure and colon cancer by their role in the elimination of dietary carcinogens.

Marine n‐3 and saturated fatty acids in relation to risk of colorectal cancer in Singapore Chinese: A prospective study

Experimental data support multiple roles for fatty acids in colorectal carcinogenesis. We examined dietary fatty acids and incidence of colorectal cancer, and evaluated effect modification by sex and stage of disease among a population‐based cohort of 61,321 Singapore Chinese that was established between 1993 and 1998. As of December 31, 2005, 961 incident colorectal cancers were diagnosed. Presented hazard ratios (HRs) are for highest versus lowest quartiles with adjustment for potential confounders. Among women, we observed a dose‐dependent, positive association between saturated fat and localized colorectal cancer (Dukes A or B) [(HR = 1.69, 95% confidence interval (CI) = 1.08–2.63, p for trend = 0.01)]. No such associations were noted in men (p for interaction by sex = 0.04). Marine n‐3 polyunsaturated fatty acid (PUFA) intake was positively associated with advanced disease (Dukes C or D) (HR = 1.33, 95% CI = 1.05–1.70, p for trend = 0.01), regardless of sex. The association with marine n‐3 PUFAs was strongest among those with the shortest (≤5 years) duration of follow‐up (HR = 1.49, 95% CI = 1.00–2.21, p for trend = 0.04). In contrast, we observed a small, albeit imprecise, inverse association with marine n‐3 PUFAs for localized colorectal cancer among those with the longest duration of follow‐up (>10 years) (HR = 0.62, 95% CI = 0.29–1.34, p for trend = 0.55). Our findings suggest that subtypes of fatty acids may differentially influence risk of colorectal cancer of a specified stage.