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Background: Early-life exposure to estrogenic compounds affects the development of the reproductive system in rodent models and humans. Soy products, which contain phytoestrogens such as genistein, are one source of exposure in infants fed soy formula, and they result in high serum concentrations. Objectives: Our goal was to determine whether soy exposure is associated with differential DNA methylation in vaginal cells from soy-fed infant girls. Methods: Using the Illumina HumanMethylation450 BeadChip, we evaluated epigenome-wide DNA methylation in vaginal cells from four soy formula–fed and six cow formula–fed girls from the Infant Feeding and Early Development (IFED) study. Using pyrosequencing we followed up the two most differentially methylated sites in 214 vaginal cell samples serially collected between birth and 9 months of age from 50 girls (28 soy formula–fed and 22 cow formula–fed). With a mouse model, we examined the effect of neonatal exposure to genistein on gene specific mRNA levels in vaginal tissue. Results: The epigenome-wide scan suggested differences in methylation between soy formula–fed and cow formula–fed infants at three CpGs in the gene proline rich 5 like (PRR5L) (p < 104). Pyrosequencing of the two feeding groups found that methylation levels progressively diverged with age, with pointwise differences becoming statistically significant after 126 days. Genistein-exposed mice showed a 50% decrease in vaginal Prr5l mRNA levels compared to controls. Conclusions: Girls fed soy formula have altered DNA methylation in vaginal cell DNA which may be associated with decreased expression of an estrogen-responsive gene. Citation: Harlid S, Adgent M, Jefferson WN, Panduri V, Umbach DM, Xu Z, Stallings VA, Williams CJ, Rogan WJ, Taylor JA. 2017. Soy formula and epigenetic modifications: analysis of vaginal epithelial cells from infant girls in the IFED study. Environ Health Perspect 125:447–452; http://dx.doi.org/10.1289/EHP428

Background: Factors underlying a possible excess of amyotrophic lateral sclerosis (ALS) among military veterans remain unidentified. Limitations of previous studies on this topic include reliance on ALS mortality as a surrogate for ALS incidence, low statistical power, and sparse information on military-related factors. Objectives: We evaluated associations between military-related factors and ALS using data from a case-control study of U.S. military veterans. Methods: From 2005 to 2010, we identified medical record-confirmed ALS cases via the National Registry of Veterans with ALS and controls via the Veterans Benefits Administration's Beneficiary Identification and Records Locator System database. In total, we enrolled 621 cases and 958 frequency-matched controls in the Genes and Environmental Exposures in Veterans with Amyotrophic Lateral Sclerosis study. We collected information on military service and deployments and 39 related exposures. We used unconditional logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs). We used inverse probability weighting to adjust for potential bias from confounding, missing covariate data, and selection arising from a case group that disproportionately included long-term survivors and a control group that may or may not differ from U.S. military veterans at large. Results: The odds of ALS did not differ for veterans of the Air Force, Army, Marines, and Navy. We found higher odds of ALS for veterans whose longest deployment was World War II or the Korean War and a positive trend with total years of all deployments (OR = 1.27; 95% CI: 1.06, 1.52). ALS was positively associated with exposure to herbicides for military purposes, nasopharyngeal radium, personal pesticides, exhaust from heaters or generators, high-intensity radar waves, contaminated food, explosions within one mile, herbicides in the field, mixing and application of burning agents, burning agents in the field, and Agent Orange in the field, with ORs between 1.50 and 7.75. Conclusions: Although our results need confirmation, they are potentially important given the large number of U.S. military veterans, and they provide clues to potential factors underlying the apparent increase of ALS in veteran populations. Keywords: Amyotrophic lateral sclerosis, Case-control, Deployment, Etiology, Military

Relative potency plays an important role in toxicology. Estimates of relative potency are used to rank chemicals by their effects, to calculate equivalent doses of test chemicals compared to a standard, and to weight contributions of constituent chemicals when evaluating mixtures. Typically relative potency is characterized by a constant dilution factor, even when non-similar dose-response curves indicate that constancy is inappropriate. Improperly regarding relative potency as constant may distort conclusions and potentially mislead investigators or policymakers. We consider a more general approach that allows relative potency to vary as a function of dose, response, or response quantile. Distinct functions can be defined, each generalizing different but equivalent descriptions of constant relative potency. When two chemicals have identical response limits, these functions all carry fundamentally equivalent information; otherwise, relative potency as a function of response quantile is distinct and embodies a modified definition of relative potency. Which definition is preferable depends on whether one views any differences in response limits as intrinsic to the chemicals or as extrinsic, arising from idiosyncrasies of data sources. We illustrate these ideas with constructed examples and real data. Relative potency functions offer a unified and principled description of relative potency for non-similar dose-response curves.

Objective To examine genetic associations of polymorphisms in the dopamine receptor D2 ( DRD2 ) and D3 ( DRD3 ) genes with risk of Parkinson's disease (PD). Methods The study included 1325 newly diagnosed patients with PD and 1735 controls from a consortium of five North American case–control studies. We collected risk factor information by in-person or telephone interview. Six DRD2 and two DRD3 polymorphisms were genotyped using a common laboratory. Odds ratios were estimated using logistic regression. Results Among non-Hispanic whites, homozygous carriers of Taq1A DRD2 (rs1800497) polymorphism had an increased risk of PD compared to homozygous wildtype carriers (OR = 1.5, 95% CI 1.0–2.3). In contrast, the direction of association for Taq1A polymorphism was opposite for African–Americans, showing an inverse association with PD risk (OR = 0.10, 95% CI 0.2–0.7). Among white Hispanics who carried two alleles, the Ser9Gly DRD3 (rs6280) polymorphism was associated with a decreased risk of PD (OR = 0.4, 95% CI 0.2–0.8). The inverse association of smoking with PD risk was not modified by any of the DRD2 or DRD3 polymorphisms. Conclusions DRD2 polymorphisms are unlikely to be true disease-causing variants; however, three DRD2 polymorphisms (including Taq1A) may be in linkage disequilibrium with possible disease associated variants in the DRD2-ANKK1-NCAM1-TTC12 gene cluster.

Background: An association may exist between pesticide exposure and suicide. Objective: We sought to evaluate the existence of an association between pesticide use and suicide using data from the Agricultural Health Study (AHS), a prospective cohort study of licensed pesticide applicators and their spouses in Iowa and North Carolina. Methods: Via linkage to state mortality files and the National Death Index, we identified 110 suicides occurring between enrollment in the AHS (from 1993 to 1997) and 31 May 2009, among 81,998 cohort members contributing 1,092,943 person-years of follow-up. The average length of follow-up was 13.3 years. AHS participants provided data on pesticide use and potential confounders via self-administered questionnaires at enrollment. We evaluated several measures of pesticide use: use of any pesticide, ever use of 50 specific pesticides, cumulative lifetime days of use and intensity-adjusted cumulative lifetime days of use of 22 specific pesticides, and ever use of 10 functional and chemical classes of pesticides. We used Cox proportional hazards regression models to estimate adjusted hazard ratios and 95% confidence intervals. Results: After adjusting for age at enrollment, sex, number of children in family, frequency of alcohol consumption during the past 12 months, and smoking status, we found no association between prior pesticide use and suicide in applicators and their spouses. Results were the same for applicators and spouses together or for applicators alone and were consistent across several measures of pesticide use. Conclusions: Our findings do not support an association between moderate pesticide use and suicide.

Germline TP53 mutations result in cancer proneness syndromes known as Li-Fraumeni, Li-Fraumeni-like, and nonsyndromic predisposition with or without family history. To explore genotype/phenotype associations, we previously adopted a functional classification of all germline TP53 mutant alleles based on transactivation. Severe deficiency (SD) alleles were associated with more severe cancer proneness syndromes, and a larger number of tumors, compared with partial deficiency (PD) alleles. Because mutant p53 can exert dominant-negative (DN) effects, we addressed the relationship between DN and clinical manifestations. We reasoned that DN effects might be stronger in familial cancer cases associated with germline TP53 mutations, where mutant alleles coexist with the wild-type allele since conception. We examined 104 p53 mutant alleles with single amino acid substitutions described in the IARC germline database for (i) transactivation capability and (ii) capacity to reduce the activity of the wild-type allele (i.e., DN effect) using a quantitative yeast-based assay. The functional classifications of p53 alleles were then related to clinical variables. We confirmed that a classification based on transactivation alone can identify familial cancer cases with more severe clinical features. Classification based on DN effects allowed us to highlight similar associations but did not reveal distinct clinical subclasses of SD alleles, except for a correlation with tumor tissue prevalence. We conclude that in carriers of germline TP53 mutations transactivation-based classification of TP53 alleles appears more important for genotype/phenotype correlations than DN effects and that haplo-insufficiency of the TP53 gene is an important factor in cancer proneness in humans. Mol Cancer Res; 9(3); 271–9. ©2011 AACR.

Objective In MPTP animal models of Parkinson’s disease (PD), caffeine protects neurons by blocking the adenosine receptor A2A (ADORA2A). Caffeine is primarily metabolized by cytochrome P450 1A2 (CYP1A2). Our objective was to examine whether ADORA2A and CYP1A2 polymorphisms are associated with PD risk or modify the caffeine-PD association.

Comparing agricultural cohorts with the general population is challenging because the general healthiness of farmers may mask potential adverse health effects of farming. Using data from the Agricultural Health Study, a cohort of 89,656 pesticide applicators and their spouses (N = 89, 656) in North Carolina and Iowa, the authors computed standardized mortality ratios (SMRs) comparing deaths from time of the enrollment (1993-1997) through 2007 to state-specific rates. To compensate for the cohort's overall healthiness, relative SMRs were estimated by calculating the SMR for each cause relative to the SMR for all other causes. In 1,198,129 person-years of follow-up, 6,419 deaths were observed. The all-cause mortality rate was less than expected (SMR(applicators) = 0.54, 95% confidence interval (CI): 0.52, 0.55; SMR(spouses) = 0.52, 95% CI: 0.50, 0.55). SMRs for all cancers, heart disease, and diabetes were significantly below 1.0. In contrast, applicators experienced elevated numbers of machine-related deaths (SMR = 4.15, 95% CI: 3.18, 5.31), motor vehicle nontraffic accidents (SMR = 2.80, 95% CI: 1.81, 4.14), and collisions with objects (SMR = 2.12, 95% CI: 1.25, 3.34). In the relative SMR analysis for applicators, the relative mortality ratio was elevated for lymphohematopoietic cancers, melanoma, and digestive system, prostate, kidney, and brain cancers. Among spouses, relative SMRs exceeded 1.0 for lymphohematopoietic cancers and malignancies of the digestive system, brain, breast, and ovary. Unintentional fatal injuries remain an important risk for farmers; mortality ratios from several cancers were elevated relative to other causes.

Tumor purity is the percent of cancer cells present in a sample of tumor tissue. The noncancerous cells (stromal cells) in a tumor are thought to have an important role in tumor growth, metastatic progression, and drug resistance. They also strongly influence genomic analyses of tumor samples. The Cancer Genome Atlas (TCGA) has extensive RNA-seq data from tumor tissue samples as well as assessments of tumor purity for the samples. Our goal is to select a subset of genes whose expression levels are predictive of tumor purity for each tumor type as well as a subset of genes whose expression levels are predictive of all tumor type samples when pooled together. We hope that the genes selected may provide insight about the cell-type composition of tumor samples and about the similarities and differences in tumor microenvironments. We use data from the TCGA, which covers 11 different tumor types and includes genome-wide assessments on over 3,148 samples for gene expression. To identify predictive genes, we used XGBoost, a supervised machine learning algorithm based on the idea of a boosted regression tree ensemble. We carried out 100 repeated runs of 10-fold cross-validations (total of 1,000 train-test partitions) for each tumor type and, also, for all tumor types combined. Using the training-set samples, XGBoost selects a set of genes to predict tumor purity levels; the selected genes are subsequently used to predict the purity levels of the test-set samples. Across the 1,000 train-test partitions for all 11 tumor types, the average root-mean-squared error ranged from 0.09 to 0.16 for the test sets. For each tumor type, we selected the top 250 genes based on their aggregated feature importance scores, a measure of each gene's contribution to tumor purity estimation. No single gene was among the top 250 in all 11 tumor types; however, ACAP1, AMICA1, CSF2RB, CYTIP, GGT5, GLIPR1, IRF4, and PECAM1 were not only among the top 250 in more than 6 tumor types but also in the top 250 when all tumors were combined, suggesting those genes might serve as biomarkers for tumor purity. The most common pathways from gene ontology analysis of these top genes include various immune and signaling pathways. We used XGBoost to identify genes whose expression levels were associated with tumor purity levels in each tumor type. Our results suggest that assessed tumor purity levels in tumor samples can be faithfully recapitulated using certain subsets of genes. We believe that those genes selected for each tumor type by our unbiased approach might provide insight into the biology of the tumor microenvironment, e.g., the presence of cell type-specific marker genes would indicate the presence of specific cell types. Citation Format: YuanYuan Li, Adrienna Bingham, Qi-Jing Li, Yuan Zhuang, David M. Umbach, Leping Li. Using tumor sample gene expression data to infer tumor purity levels with stochastic gradient boosting machines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2255.

To identify trends in a residual category of cancers not typically associated with tobacco, screening, or human immunodeficiency virus (HIV) infection.For persons aged 20-84, we used sex- and race-specific age-period-cohort (APC) models to describe temporal patterns of incidence (1975-2004) and mortality (1970-2004) in the U.S. for a residual cancer category that excluded non-Hodgkin lymphoma, Kaposi sarcoma, and cancer of the oral cavity and pharynx, esophagus, pancreas, larynx, lung and bronchus, urinary bladder, kidney and renal pelvis, colon and rectum, prostate, female breast, and cervix uteri.Age-specific incidence rose (0.1-0.9% per year, on average) in every sex-race group, with factors related to both time period and birth cohort membership appearing to accelerate the increases in women. Age-specific mortality fell (0.6-0.9% per year, on average) for black and white men and women, with the declines decelerating in white women but accelerating in the other sex-race groups. Extrapolations of APC models predicted higher age-adjusted incidence rates in white women (11%), black women (5%), and white men (4%) in 2005-2009, relative to 2000-2004, and lower rates in black men (-3%), accompanied by lower age-adjusted mortality rates in every sex-race group (-8% in black men, -3% in black women, -1% in white men, and -1% in white women).The possibility that increased incidence in women over time reflects changes in underlying risks, diagnostic practices, or better case ascertainment should be actively explored. Declining mortality may signify improvements in cancer care.

Vitamin D receptor (VDR) polymorphisms have been strongly associated with bone mineral density (BMD) in some studies but not in others. We used a meta-analytic approach to assess quantitatively the association between VDR and BMD and to examine the influence of specific study characteristics (e.g., skeletal site, mean age of subjects, menopausal status) on the reported results. Sixteen papers published in peer-reviewed journals through July 1996 were included. We calculated the mean difference, percent difference, and effect size (mean difference divided by standard deviation), comparing BMD between homozygous genotypes. At the hip, BMD in the BB genotype was lower than in the bb genotype (mean difference, -0.02 g/cm2; percent difference, -2.4% and effect size -0.18; p = 0.032). At the spine, the mean difference was -0.03 g/cm2; percent difference, -2.5%; and effect size, -0.19; p = 0.062. At the distal radius, the VDR effect was estimated as the mean difference, -0.01 g/cm2; percent difference, -1.7%; and effect size, -0.16; p = 0.078. The spine measurements exhibited the greatest between- and within-study variability. The difference in hip BMD between genotypes was larger (i.e., a more negative number) among the younger women and seemed to decrease with increasing age. However, statistical evidence for this trend was weak (p = 0.06). Data from the spine and the radius showed no evidence of a comparable interaction of the VDR effect with age. When we omitted data from the first report of an association between VDR polymorphisms and BMD, our analyses gave similar results, although the overall effect estimates were smaller. In the combined data from 29 study groups, the BB genotype frequency was 17.2, 4.9, and 2.3% in studies of whites, blacks, and Asians, respectively. VDR polymorphisms represent one genetic factor affecting BMD, but further research into the mechanisms, clinical significance, and its relation between other genetic and environmental factors is needed.

Objective: Joint analysis of multiple SNP markers can be informative, but studying joint effects of haplotypes and environmental exposures is challenging. Population structure can involve both genes and exposures and a case-control study is susceptible to bias from either source of stratification. We propose a procedure that uses case-parent triad data and, though not fully robust, resists bias from population structure. Methods: Our procedure assumes that haplotypes under study have no influence on propensity to exposure. Then, under a no-interaction null hypothesis (multiplicative scale), transmission of a causative haplotype from parents to affected offspring might show distortion from Mendelian proportions but should be independent of exposure. We used this insight to develop a permutation test of no haplotype-by-exposure interaction. Results: Simulations showed that our proposed test respects the nominal Type I error rate and provides good power under a variety of scenarios. We illustrate by examining whether SNP variants in GSTP1 modify the association between maternal smoking and oral clefting. Conclusion: Our procedure offers desirable features: no need for haplotype estimation, validity under unspecified genetic main effects, tolerance to Hardy-Weinberg disequilibrium, ability to handle missing genotypes and a relatively large number of SNPs. Simulations suggest resistance to bias due to exposure-related population stratification.

Background Occupation has been suggested to play a role in amyotrophic lateral sclerosis (ALS) etiology, but detailed information on the importance of specific workplace exposures is lacking. Objectives Our aim was to assess the relationship between workplace exposures and the risk of ALS and to evaluate potential interactions between these exposures and smoking. Methods We conducted a case–control study in New England between 1993 and 1996, comprising 109 cases and 253 controls who completed a structured interview covering occupations and workplace exposures. Unconditional logistic regression models were used to estimate the odds ratios (ORs) and 95% confidence intervals (CIs) for ALS. Analyses were conducted among the entire study population and after stratification by smoking. Results We observed a higher risk of ALS for construction workers excluding supervisors (OR = 2.9; 95% CI, 1.2–7.2) and precision metal workers (OR = 3.5; 95% CI, 1.2–10.5). Self-reported exposures to paint strippers; cutting, cooling, or lubricating oils; antifreeze or coolants; mineral or white spirits; and dry cleaning agents each appeared to be associated with a 60–90% higher risk. Specific chemicals related to a > 50% increase in risk of ALS included aliphatic chlorinated hydrocarbons, glycols, glycol ethers, and hexane. Relative risks associated with these workplace exposures and chemicals were greater among nonsmokers and persisted in mutually adjusted models. Conclusions Our data suggest that certain occupations and workplace exposures may be associated with increased risk of ALS. These results need to be confirmed in independent populations.

Although specific pesticides have been associated with wheeze in farmers, little is known about pesticides and asthma. Data from 19,704 male farmers in the Agricultural Health Study were used to evaluate lifetime use of 48 pesticides and prevalent adult-onset asthma, defined as doctor-diagnosed asthma after the age of 20 yrs. Asthma cases were categorised as allergic (n = 127) and nonallergic (n = 314) based on their history of eczema or hay fever. Polytomous logistic regression, controlling for age, state, smoking and body mass, was used to assess pesticide associations. High pesticide exposure events were associated with a doubling of both allergic and nonallergic asthma. For ever-use, 12 individual pesticides were associated with allergic asthma and four with nonallergic asthma. For allergic asthma, coumaphos (OR 2.34; 95% CI 1.49-3.70), heptachlor (OR 2.01; 95% CI 1.30-3.11), parathion (OR 2.05; 95% CI 1.21-3.46), 80/20 mix (carbon tetrachloride/carbon disulfide) (OR 2.15; 95% CI 1.23-3.76) and ethylene dibromide (OR 2.07; 95% CI 1.02-4.20) all showed ORs of >2.0 and significant exposure-response trends. For nonallergic asthma, DDT (dichlorodiphenyltrichloroethane) showed the strongest association (OR 1.41; 95% CI 1.09-1.84), but with little evidence of increasing asthma with increasing use. Current animal handling and farm activities did not confound these results. There was little evidence that allergy alone was driving these associations. In conclusion, pesticides may be an overlooked contributor to asthma risk among farmers.

Contains fulltext : 81314.pdf (Publisher’s version ) (Closed access) Hybrid designs arose from an effort to combine the benefits of family-based and population-based study designs. A recently proposed hybrid approach augments case-parent triads with population-based control-parent triads, genotyping everyone except the control offspring. Including parents of controls substantially improves statistical efficiency for testing and estimating both offspring and maternal genetic relative risk parameters relative to using case-parent triads alone. Moreover, it allows testing of required assumptions. Nevertheless, control fathers can be hard to recruit, whereas control offspring and their mothers may be readily available. Consequently, we propose an alternative hybrid design where offspring-mother pairs, instead of parents, serve as population-based controls. We compare the power of our proposed method with several competitors and show that it performs well in various scenarios, though it is slightly less powerful than the hybrid design that uses control parents. We describe approaches for checking whether population stratification will bias inferences that use controls and whether the mating-symmetry assumption holds. Surprisingly, if mating symmetry is violated, even though mating-type parameters cannot be directly estimated using control-mother dyads alone, and maternal effects cannot be estimated using case-parent triads alone, combining both sources of data allows estimation of all the parameters. This hybrid design can also be used to study environmental influences on disease risk and gene-by-environment interactions.

Sulfur-containing polycyclic aromatic hydrocarbons (thia-PAHs or thiaarenes) are common constituents of air pollution and cigarette smoke, but only a few have been studied for health effects. We evaluated the mutagenicity in Salmonella TA98, TA100, and TA104 of two sulfur-containing derivatives of benzo[c]phenanthrene, phenanthro[3,4-b]thiophene (P[3,4-b]T), and phenanthro[4,3-b]thiophene (P[4,3-b]T) as well as their dihydrodiol and sulfone derivatives. In addition, we assessed levels of stable DNA adducts (by (32)P-postlabeling) as well as abasic sites (by an aldehydic-site assay) produced by six of these compounds in TA100. P[3,4-b]T and its 6,7- and 8,9-diols, P[3,4-b]T sulfone, P[4,3-b]T, and its 8,9-diol were mutagenic in TA100. P[3,4-b]T sulfone, the most potent mutagen, was approximately twice as potent as benzo[a]pyrene in both TA98 and TA100. Benzo-ring dihydrodiols were much more potent than K-region dihydrodiols, which had little or no mutagenic activity in any strain. P[3,4-b]T sulfone produced abasic sites and not stable DNA adducts; the other five compounds examined, B[c]P, B[c]P 3,4-diol, P[3,4-b]T, P[3,4-b]T 8,9-diol, and P[4,3-b]T 8,9-diol, produced only stable DNA adducts. P[3,4-b]T sulfone was the only compound that produced significant levels of frameshift mutagenicity and induced mutations primarily at GC sites. In contrast, B[c]P, its 3,4-diol, and the 8,9 diols of the phenanthrothiophenes induced mutations primarily at AT sites. P[3,4-b]T was not mutagenic in TA104, whereas P[3,4-b]T sulfone was. The two isomeric forms (P[3,4-b]T and P[4,3-b]T) are apparently activated differently, with the latter, but not the former, involving a diol pathway. This study is the first illustrating the potential importance of abasic sites in the mutagenicity of thia-PAHs.

Background Reasons for the variability in survival among ALS cases are unknown but may include exposure to environmental neurotoxicants. Objectives We aimed to determine whether lead exposure, assessed by measuring blood and bone lead levels, is associated with survival in amyotrophic lateral sclerosis (ALS). Methods We evaluated the relationship of lead exposure to ALS survival in 110 cases from a case–control study conducted in New England in 1993–1996 that included measurements of blood and bone lead. We retrieved information on date and cause of death through 31 December 2003 from the National Death Index Plus and the Social Security Administration Death Index. We evaluated the relationship of survival to lead exposure using Cox proportional hazard analysis, with adjustment for age, sex, and smoking. Results We found mortality data for 100 of 110 cases; 93 of 100 death certificates mentioned ALS. Median survival from diagnosis to death was 28 months. Shorter survival was associated with older age at diagnosis, female sex, bulbar onset, shorter interval between symptom onset and diagnosis, and reduced lung function. Shorter survival from diagnosis to death had a weak inverse association with blood lead (hazard ratio = 0.9; 95% confidence interval, 0.8–1.0) and a stronger inverse association with patella lead (0.5; 0.2–1.0) and tibia lead (0.3; 0.1–0.7); similar results were found for survival from symptom onset to death. Conclusions These results suggest that lead exposure is associated with longer survival in ALS cases and, if confirmed, may shed light on mechanisms involved in disease progression.

Rationale: Risk factors for asthma among farm women are understudied. Objectives: We evaluated pesticide and other occupational exposures as risk factors for adult-onset asthma. Methods: Studying 25,814 farm women in the Agricultural Health Study, we used self-reported history of doctor-diagnosed asthma with or without eczema and/or hay fever to create two case groups: patients with atopic asthma and those with nonatopic asthma. We assessed disease-exposure associations with polytomous logistic regression. Measurements and Main Results: At enrollment (1993–1997), 702 women (2.7%) reported a doctor's diagnosis of asthma after age 19 years (282 atopic, 420 nonatopic). Growing up on a farm (61% of all farm women) was protective for atopic asthma (odds ratio [OR], 0.55; 95% confidence interval [CI], 0.43–0.70) and, to a lesser extent, for nonatopic asthma (OR, 0.83; 95%CI, 0.68–1.02; P value for difference = 0.008). Pesticide use was almost exclusively associated with atopic asthma. Any use of pesticides on the farm was associated only with atopic asthma (OR, 1.46; 95% CI, 1.14–1.87). This association with pesticides was strongest among women who had grown up on a farm. Women who grew up on farms and did not apply pesticides had the lowest overall risk of atopic asthma (OR, 0.41; 95% CI, 0.27–0.62) compared with women who neither grew up on farms nor applied pesticides. A total of 7 of 16 insecticides, 2 of 11 herbicides, and 1 of 4 fungicides were significantly associated with atopic asthma; only permethrin use on crops was associated with nonatopic asthma. Conclusions: These findings suggest that pesticides may contribute to atopic asthma, but not nonatopic asthma, among farm women.

Background Soy formula containing estrogenic isoflavones is widely used in the United States. Infants consuming soy formula exclusively have high isoflavone exposures. We wanted to study whether soy formula prolonged the physiologic estrogenization of newborns, but available quantitative descriptions of the natural history of breast and genital development are inadequate for study design. Objective We piloted techniques for assessing infants’ responses to the withdrawal from maternal estrogen and gathered data on breast and genital development in infants at different ages. Methods We studied 37 boys and 35 girls, from term pregnancies with normal birth weights, who were < 48 hr to 6 months of age, and residents of Philadelphia, Pennsylvania, during 2004–2005. One-third of the children of each sex and age interval were exclusively fed breast milk, soy formula, or cow-milk formula. Our cross-sectional study measured breast adipose tissue, breast buds, and testicular volume; observed breast and genital development; and collected vaginal wall cells and information on vaginal discharge. We assessed reliability of the measures. Results Breast tissue was maximal at birth and disappeared in older children, consistent with waning maternal estrogen. Genital development did not change by age. Breast-milk secretion and withdrawal bleeding were unusual. Vaginal wall cells showed maximal estrogen effect at birth and then reverted; girls on soy appeared to show reestrogenization at 6 months. Conclusions Examination of infants for plausible effects of estrogens is valid and repeatable. Measurement of breast tissue and characterization of vaginal wall cells could be used to evaluate exposures with estrogen-like effects.

Family-based association studies offer robustness to population stratification and can provide insight into maternally mediated and parent-of-origin effects. Usually, such studies investigate multiple markers covering a gene or chromosomal region of interest. We propose a simple and general method to test the association of a disease trait with multiple, possibly linked SNP markers and, subsequently, to nominate a set of "risk-haplotype-tagging alleles." Our test, the max_Zeta(2) test, uses only the genotypes of affected individuals and their parents without requiring the user to either know or assign haplotypes and their phases. It also accommodates sporadically missing SNP data. In the spirit of the pedigree disequilibrium test, our procedure requires only a vector of differences with expected value 0 under the null hypothesis. To enhance power against a range of alternatives when genotype data are complete, we also consider a method for combining multiple tests; here, we combine max_Zeta(2) and Hotelling's Gamma(2). To facilitate discovery of risk-related haplotypes, we develop a simple procedure for nominating risk-haplotype-tagging alleles. Our procedures can also be used to study maternally mediated genetic effects and to explore imprinting. We compare the statistical power of several competing testing procedures through simulation studies of case-parents triads, whose diplotypes are simulated on the basis of draws from the HapMap-based known haplotypes of four genes. In our simulations, the max_Zeta(2) test and the max_TDT (transmission/disequilibrium test) proposed by McIntyre et al. perform almost identically, but max_Zeta(2), unlike max_TDT, extends directly to the investigation of maternal effects. As an illustration, we reanalyze data from a previously reported orofacial cleft study, to now investigate both fetal and maternal effects of the IRF6 gene.

Targeting the first-degree relatives of people with a particular complex disease can offer a powerful approach to building a risk-based cohort for prospective studies of etiologic factors. Such a cohort provides both a sizable increase in the rate of accrual of newly incident cases, enriching for risk factors that are known or even unknown, and a high level of motivation among participants. A nationwide study of breast cancer in the United States and Puerto Rico, the Sister Study, made up of women who are each the sister of a woman with breast cancer, exemplifies this approach. In this paper, the authors provide power calculations to aid in the design of such studies and quantify their benefits for detecting both genetic variants related to risk and interactive effects of genetic and environmental factors. While the risk-based cohort can have markedly increased prevalences of rare causative alleles, most of the power advantages for this design is due to the increased rate of accrual of newly incident cases rather than the increase in any one individual allele.

The purpose of this study was to examine agricultural risk factors for chronic bronchitis among nonsmoking farm women.We used self-reported enrollment data from the 21,541 nonsmoking women in the Agricultural Health Study to evaluate occupational risk factors for prevalent chronic bronchitis among farm women. Odds ratios (ORs) for chronic bronchitis for occupational exposures were adjusted for age, state, and related agricultural exposures.Applying manure and driving combines were independently associated with chronic bronchitis. Off-farm job exposures associated with chronic bronchitis were organic dusts, asbestos, gasoline, and solvents. Five pesticides were associated with chronic bronchitis after multivariate adjustment and sensitivity analyses: dichlorvos (OR=1.63, 95% CI=1.01, 2.61), DDT (OR=1.67, 95% CI=1.13, 2.47), cyanazine (OR=1.88, 95% CI=1.00, 3.54), paraquat (OR=1.91, 95% CI=1.02, 3.55), and methyl bromide (OR=1.82, 95% CI=1.02, 3.24).Pesticides as well as grain and dust exposures were associated with chronic bronchitis among nonsmoking farm women.

In studies of case-parent triads, information is often collected about history of the condition in the parents, but typically parental phenotypes are ignored. Including that information in analyses may increase power to detect genetic association for autosomal variants. Our proposed approach uses parental phenotypes to assess association independently of the usual case-parent-based association test, enabling cross-generational internal replication for findings based on offspring and their parents. Our model for parental phenotypes also resists bias due to population stratification. We combine the information from the two generations into a single coherent model that can exploit approximate equality of parental and offspring relative risks to improve power and can also test that equality. We call the resulting procedure the Parent-phenotype Informed Likelihood Ratio Test (PPI-LRT). When some parental genotypes are missing, one can use the expectation-maximization algorithm to fit the combined model. We also develop a second composite test (PPI-CT) based on a linear combination of the parent-phenotype-based test statistic and that from the traditional log-linear, transmission-based test. We evaluate the proposed methods through non-centrality parameter calculations and simulation studies and compare them to the previously proposed approaches, parenTDT and combTDT. We show that incorporation of parental phenotype data often improves statistical power. As illustration, we apply our method to a study of young-onset breast cancer and find that it improved precision for SNPs in FGFR2 and that estimated relative risks based on triads are closely replicated using the parental data.

Objective: Drugs take effect at different times in different individuals. Consequently, researchers seek to examine how the timing of the biological response to drugs may be affected by factors such as gender, genotypes, age, or baseline symptom scores. Methods: Typically, studies measure symptoms immediately after the initiation of drug treatment and then at a sequence of later time points. In this study, we develop a statistical mixture model for analyzing such longitudinal data. Our method estimates the onset of drug effect and assesses the association between the probability distribution of the onset times and possible contributing factors. Our mixture model treats the timing of onset as missing for each individual but restricts it, for simplicity, to two possible onset points, early or late. To estimate the model, we use an expectation-maximization-based approach and provide the general formulas of the variance and covariance matrix for the estimated parameters. Results: We evaluate the model's overall utility and performance via simulation studies. In addition, we illustrate its use by application to longitudinal data from the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. The algorithm identified age and anxiety status as significant factors in affecting the onset distribution of citalopram (Celexa).

Potential reductions in laboratory assay costs afforded by pooling equal aliquots of biospecimens have long been recognized in disease surveillance and epidemiological research and, more recently, have motivated design and analytic developments in regression settings. For example, Weinberg and Umbach (1999, Biometrics 55, 718–726) provided methods for fitting set-based logistic regression models to case-control data when a continuous exposure variable (e.g., a biomarker) is assayed on pooled specimens. We focus on improving estimation efficiency by utilizing available subject-specific information at the pool allocation stage. We find that a strategy that we call “(y,c)-pooling,” which forms pooling sets of individuals within strata defined jointly by the outcome and other covariates, provides more precise estimation of the risk parameters associated with those covariates than does pooling within strata defined only by the outcome. We review the approach to set-based analysis through offsets developed by Weinberg and Umbach in a recent correction to their original paper. We propose a method for variance estimation under this design and use simulations and a real-data example to illustrate the precision benefits of (y,c)-pooling relative to y-pooling. We also note and illustrate that set-based models permit estimation of covariate interactions with exposure.

Primary and metastatic melanoma tumors share the same cell origin, making it challenging to identify genomic biomarkers that can differentiate them. Primary tumors themselves can be heterogeneous, reflecting ongoing genomic changes as they progress toward metastasizing. We developed a computational method to explore this heterogeneity and to predict metastatic progression of the primary tumors. We applied our method separately to gene expression and to microRNA (miRNA) expression data from ~450 primary and metastatic skin cutaneous melanoma (SKCM) samples from the Cancer Genome Atlas (TCGA). Metastatic progression scores from RNA-seq data were significantly associated with clinical staging of patients' lymph nodes, whereas scores from miRNA-seq data were significantly associated with Clark's level. The loss of expression of many characteristic epithelial lineage genes in primary SKCM tumor samples was highly correlated with predicted progression scores. We suggest that those genes/miRNAs might serve as putative biomarkers for SKCM metastatic progression.

Vanillin (VAN) and cinnamaldehyde (CIN) are dietary antimutagens that effectively inhibit both induced and spontaneous mutations. We have shown previously that VAN and CIN reduced the spontaneous mutant frequency in Salmonella TA104 (hisG428, rfa, DeltauvrB, pKM101) by approximately 50% and that both compounds significantly reduced mutations at GC sites but not at AT sites. Previous studies have suggested that VAN and CIN may reduce mutations in bacterial model systems by modulating DNA repair pathways, particularly by enhancing recombinational repair. To further explore the basis for inhibition of spontaneous mutation by VAN and CIN, we have determined the effects of these compounds on survival and mutant frequency in five Escherichia coli strains derived from the wild-type strain NR9102 with different DNA repair backgrounds. At nontoxic doses, both VAN and CIN significantly reduced mutant frequency in the wild-type strain NR9102, in the nucleotide excision repair-deficient strain NR11634 (uvrB), and in the recombination-proficient but SOS-deficient strain NR11475 (recA430). In contrast, in the recombination-deficient and SOS-deficient strain NR11317 (recA56), both VAN and CIN not only failed to inhibit the spontaneous mutant frequency but actually increased the mutant frequency. In the mismatch repair-defective strain NR9319 (mutL), only CIN was antimutagenic. Our results show that the antimutagenicity of VAN and CIN against spontaneous mutation required the RecA recombination function but was independent of the SOS and nucleotide excision repair pathways. Thus, we propose the counterintuitive notion that these antimutagens actually produce a type of DNA damage that elicits recombinational repair (but not mismatch, SOS, or nucleotide excision repair), which then repairs not only the damage induced by VAN and CIN but also other DNA damage-resulting in an antimutagenic effect on spontaneous mutation.

Previous studies based on limited exposure assessment have suggested that Parkinson's disease (PD) is associated with pesticide exposure. The authors used data obtained from licensed private pesticide applicators and spouses participating in the Agricultural Health Study to evaluate the relation of self-reported PD to pesticide exposure. Cohort members, who were enrolled in 1993-1997, provided detailed information on lifetime pesticide use. At follow-up in 1999-2003, 68% of the cohort was interviewed. Cases were defined as participants who reported physician-diagnosed PD at enrollment (prevalent cases, n = 83) or follow-up (incident cases, n = 78). Cases were compared with cohort members who did not report PD (n = 79,557 at enrollment and n = 55,931 at follow-up). Incident PD was associated with cumulative days of pesticide use at enrollment (for highest quartile vs. lowest, odds ratio (OR) = 2.3, 95% confidence interval: 1.2, 4.5; p-trend = 0.009), with personally applying pesticides more than half the time (OR = 1.9, 95% confidence interval: 0.7, 4.7), and with some specific pesticides (ORs > or = 1.4). Prevalent PD was not associated with overall pesticide use. This study suggests that exposure to certain pesticides may increase PD risk. Findings for specific chemicals may provide fruitful leads for further investigation.

Different degrees of a toxic response between and within the various lobes of the liver have been observed in rodents following treatment with acetaminophen. This study was designed to compare 2 sampling methods of the rat liver for gene-expression analysis. Ten male Fischer 344/N rats, 12–14 weeks of age, were treated with vehicle (0.5% aqueous ethyl cellulose) or acetaminophen (APAP, 1500 mg/kg) and sacrificed 24 hours following dose administration. Two representative sections were collected from the left liver lobe, stained with hematoxylin and eosin (H&E), and evaluated independently by 2 pathologists. The central core of the left lobe was cubed and frozen. Five random cubes were conserved, while the remaining left lobe core was pulverized. From each of the 10 animals, 2 random cubes and 2 samples from the homogeneous, pulverized samples were prepared for microarray analysis. Histopathologic evaluation revealed a variable response of centrilobular necrosis within the left lobe. Multiple methods used to analyze the microarray data indicated that sampling technique was not a major contributor to the variability observed in the gene expression data; however, only the powdered samples clustered for all animals, even those with disparate histopathologic results. Additionally, a powdered sample provided the advantages of a homogenous sample pool and the ability to use sample aliquots for other analyses to include proteomics, metabonomics, and other molecular techniques.

Correspondence to: Michael D. Shelby, PhD, NIEHS EC-32, PO Box 12233, Research Triangle Park, NC 27709. E-mail: shelby@niehs.nih.gov ‡Dr. Kesner was unable to participate in the Expert Panel meeting but participated in the drafting and review of the report before and after the meeting. Following the Expert Panel meeting, some panel members reconsidered research needs 2–5 (Drs. Bhatia, Calafat, Flaws, Hansen, Hoyer, Jeffery, Rozman, Thomas) or research need 2 alone (Dr. Marty) and concluded that they/it would not be critical to a future evaluation of genistein. †This article is a U.S. Government work and, as such, is in the public domain in the United States of America.

The National Toxicology Program (NTP) and the National Institute of Environmental Health Sciences (NIEHS) established the NTP Center for the Evaluation of Risks to Human Reproduction (CERHR) in June 1998. The purpose of the Center is to provide timely, unbiased, scientifically sound evaluations of human and experimental evidence for adverse effects on reproduction and development caused by agents to which humans may be exposed.

Studies of genetic contributions to risk can be family-based, such as the case-parents design, or population-based, such as the case-control design. Both provide powerful inference regarding associations between genetic variants and risks, but both have limitations. The case-control design requires identifying and recruiting appropriate controls, but it has the advantage that nongenetic risk factors like exposures can be assessed. For a condition with an onset early in life, such as a birth defect, one should also genotype the mothers of cases and the mothers of controls to avoid potential confounding due to maternally mediated genetic effects acting on the fetus during gestation. The case-parents approach is less vulnerable than the case-mother/control-mother approach to biases due to population structure and self-selection. The case-parents approach also allows access to epigenetic phenomena like imprinting, but it cannot evaluate the role of nongenetic cofactors like exposures. We propose a hybrid design based on augmenting a set of affected individuals and their parents with a set of unaffected, unrelated individuals and their parents. The affected individuals and their parents are all genotyped, whereas only the parents of unaffected individuals are genotyped, although exposures are ascertained for both affected and unaffected offspring. The proposed hybrid design, through log-linear, likelihood-based analysis, allows estimation of the relative risk parameters, can provide more power than either the case-parents approach or the case-mother/control-mother approach, permits straightforward likelihood-ratio tests for bias due to mating asymmetry or population stratification, and admits valid alternative analyses when mating is asymmetric or when population stratification is detected.

Pesticide exposure among farmers' wives is poorly characterized. Using questionnaire data from a cohort study of licensed pesticide applicators and their spouses, we investigated patterns of pesticide use among farmers' wives (n = 31,173). Wives reported a wide range of pesticide use: 36% never used pesticides during their lifetimes, whereas the heaviest pesticide users (10%) reported lifetime use of 3 or more agricultural pesticides plus commonly used residential pesticides. We identified 5 ordinal pesticide-use categories and studied factors associated with each category through polytomous logistic regression. Engaging in field work and household hygiene practices that could increase exposure were associated with pesticide use, and associations appeared to strengthen with increasing pesticide use category. Farm women reporting the heaviest pesticide use could exacerbate their exposure by engaging in practices that could increase pesticide contact.

Farmers engage in activities that result in exposure to diesel exhaust, solvents, welding fumes, and other respiratory irritants. Using the Agricultural Health Study, a cohort of pesticide applicators in Iowa and North Carolina, we evaluated the odds of wheeze associated with nonpesticide occupational exposures. We used logistic regression models controlling for age, state, smoking, and history of asthma or atopy to evaluate odds of wheeze in the past year among the 20898 farmers who provided complete information on all covariates. Driving diesel tractors was associated with elevated odds of wheeze (odds ratio = 1.31; 95% confidence interval = 1.13, 1.52); the odds ratio for driving gasoline tractors was 1.11 (95% confidence interval = 1.02, 1.21). A duration-response relationship was observed for driving diesel tractors but not for driving gasoline tractors. Activities involving solvent exposure, including painting and use of solvents for cleaning, were associated with an increased odds of wheeze in a duration-dependent fashion. The highest odds of wheeze for farm activities were for daily painting (odds ratio = 1.82; 95% confidence interval = 0.89, 3.73), an indication of daily solvent exposure. These results add to the growing body of evidence of adverse respiratory effects of diesel exposure on the lung and suggest exposure to solvents may contribute as well.

Microsatellite analysis is a powerful tool for the assessment of genetic instability and loss of heterozygosity in cancer cells. However, most human tumors harbor significant numbers of normal cells, which may contribute to false-negative results. Recent techniques based on fluorescently labeled primers and semiautomated capillary electrophoresis of polymerase chain reaction (PCR) products allow a reliable quantitative assessment of (PCR) products while requiring very small numbers of cells. We report a highly sensitive protocol for the semiautomated analysis of allelic imbalance based on time-release PCR and capillary electrophoresis. With this protocol, as few as 100 cells can be used to reliably assess allelic imbalance (AI) in DNA samples. Using a panel of seven microsatellite markers, we determined allelic variation in a large set of heterozygous lymphocyte DNA samples and examined the use of different statistical analysis techniques. Using these statistical approaches, we describe a calibration method to evaluate AI from microsatellite results. Using a simple formula, cutoff points at preset confidence levels are used to decide whether allelic imbalance exists in a given sample at the loci under investigation. Our method allows the reliable detection of AI with very small amounts of DNA, and is sufficiently quantitative to assess allelic ratios in nonclonal tissue specimens.

Vascular endothelial growth factor (VEGF) is a cytokine essential for angiogenesis. A recent study found that haplotypes, determined by three SNPs ( − 2,578C/A, − 1,154 G/A, and − 634G/C) in the VEGF upstream promoter/leader sequence, were associated with risk of amyotrophic lateral sclerosis (ALS). We used samples and data from a case-control study to examine the relation of ALS to VEGF haplotype. Genotypes at each of the three polymorphic sites were determined using allele-specific primer extension reactions followed by MALDI-TOF. We found a 3-fold increased risk among individuals homozygous for the AAG or AGG haplotypes (95% CI = 0.7 − 13.4), consistent with the findings of the previous study. Given the wide confidence interval, our findings should be interpreted cautiously.

Previous studies have suggested that lead exposure may be associated with increased risk of amyotrophic lateral sclerosis (ALS). Polymorphisms in the genes for delta-aminolevulinic acid dehydratase (ALAD) and the vitamin D receptor (VDR) may affect susceptibility to lead exposure. We used data from a case-control study conducted in New England from 1993 to 1996 to evaluate the relationship of ALS to polymorphisms in ALAD and VDR and the effect of these polymorphisms on the association of ALS with lead exposure. The ALAD 2 allele (177G to C; K59N) was associated with decreased lead levels in both patella and tibia, although not in blood, and with an imprecise increase in ALS risk [odds ratio (OR) = 1.9; 95% confidence interval (95% CI), 0.60-6.3]. We found a previously unreported polymorphism in ALAD at an Msp1 site in intron 2 (IVS2+299G>A) that was associated with decreased bone lead levels and with an imprecise decrease in ALS risk (OR = 0.35; 95% CI, 0.10-1.2). The VDR B allele was not associated with lead levels or ALS risk. Our ability to observe effects of genotype on associations of ALS with occupational exposure to lead or with blood or bone lead levels was limited. These findings suggest that genetic susceptibility conferred by polymorphisms in ALAD may affect ALS risk, possibly through a mechanism related to internal lead exposure.

We propose an algorithm for selecting and clustering genes according to their time-course or dose–response profiles using gene expression data. The proposed algorithm is based on the order-restricted inference methodology developed in statistics. We describe the methodology for time-course experiments although it is applicable to any ordered set of treatments. Candidate temporal profiles are defined in terms of inequalities among mean expression levels at the time points. The proposed algorithm selects genes when they meet a bootstrap-based criterion for statistical significance and assigns each selected gene to the best fitting candidate profile. We illustrate the methodology using data from a cDNA microarray experiment in which a breast cancer cell line was stimulated with estrogen for different time intervals. In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal. Contact: peddada@embryo.niehs.nih.gov * To whom correspondence should be addressed. † Present address: Amgen Inc. Thousand Oaks, CA 91320, USA.

Background Previous interview-based studies have suggested that exposure to neurotoxicants including metals might be related to ALS. Methods We evaluated the relation of lead exposure to ALS, using both biological measures and interviews, in a case-control study conducted in New England from 1993 to 1996. Cases (N = 109) were recruited at two hospitals in Boston, MA. Population controls (N = 256) identified by random-digit dialing were frequency-matched to cases by age, sex, and region of residence within New England. Results Risk of ALS was associated with self-reported occupational exposure to lead (odds ratio [OR] = 1.9; 95% confidence interval [CI] = 1.1-3.3), with a dose response for lifetime days of lead exposure. Blood and bone lead levels were measured in most cases (N = 107) and in a subset of controls (N = 41). Risk of ALS was associated with elevations in both blood and bone lead levels. ORs were 1.9 (95% CI = 1.4-2.6) for each microg/dl increase in blood lead, 3.6 (95% CI = 0.6-20.6) for each unit increase in log-transformed patella lead, and 2.3 (95% CI = 0.4-14.5) for each unit increase in log-transformed tibia lead. Conclusions These results are consistent with previous reports and suggest a potential role for lead exposure in the etiology of ALS.

Objectives. This study estimated the prevalence of medication treatment for attention deficit–hyperactivity disorder (ADHD) among elementary school children in a North Carolina county. Methods. Parents of 7333 children in grades 1 through 5 in 17 public elementary schools were asked whether their child had ever been given a diagnosis of ADHD by a psychologist or physician and whether their child was currently taking medication to treat ADHD. Parents of 6099 children (83%) responded. Results. By parental report, 607 children (10%) had been given an ADHD diagnosis and 434 (7%) were receiving ADHD medication treatment. Seventy-one % of the diagnosed children were receiving medication. Treatment rates varied by sex, race/ethnicity, and grade. Conclusions. If treatment patterns observed in this study are representative, the public health impact of ADHD may be underestimated. (Am J Public Health. 2002;92:231–234)

The Cancer Genome Atlas (TCGA) has made available comprehensive molecular profiles including gene expression using RNA-seq for many human tumor types and, thereby, provided a great opportunity to use pan-cancer gene expression patterns to identify unique features that can classify tumor types. Those features may serve as biomarkers for tumor diagnosis and potential targets for drug development. Because gender differences in cancer susceptibility are one of the most consistent findings in cancer epidemiology, knowing whether the distinguishing features differ between males and females for the same tumor types might enhance their utility as biomarkers. Our goals are: 1) to identify a set of genes whose expression levels can classify pan-cancer tumor types when gender is ignored; and 2) to identify analogous sets of genes for pan-cancer classification in sex non-specific tumors from men and from women separately. Here we analyzed the RNA-seq expression data for 9,096 TCGA tumor samples from 31 tumor types; we selected features for sample classification using a genetic algorithm, GA/KNN, which we developed. We randomly assigned half of all samples into a training set and half into a test set, proportionally allocating samples from each tumor type. We used the training set to obtain 2,000 near-optimal classifiers (each set consisting of 20 genes) from repeated GA/KNN runs. We subsequently applied each resultant near-optimal classifier to the test set. The predicted class was then compared with the true class to calculate both training- and testing-set prediction accuracies. To see if sex non-specific tumors (those that are not related to reproductive organs) differ between males and females, we repeated the analysis for 24 sex non-specific tumor types separately for males and for females. In the analysis ignoring gender, we could accurately classify 88.7% training samples and 88.1% of the testing samples on average. The top 20 genes that separated the 31 tumor types were TCF21, TBX5, EMX20S, EMX2, PA2G4P4, HNF1B, NACA2, SFTPA1, ATP5EP2, PTTG3P, FTHL3, ANXA2P3, GATA3, NAPSA, SFTA3, HSPB1P1, HOXA9, IGBP1P1, RPL19P12, and SFTPB. Not surprisingly, we achieved similar average classification accuracies for testing samples (88.2% for males and 88.4% for females). Seventy four of the 100 top-ranked genes were common between males and females. The main reasons for less than total overlap between males and females are: stochastic nature of the algorithm, training/testing partitioning (only done once) and some intrinsic differences between genders. For example, BNC1, FAT2, and MSX2 ranked 36, 84, and 94 in males but 461, 603, and 1085 in females. Conversely, HPN, POU3F3, and FOXA1 ranked 75, 78, and 91 but 421, 355, and 349, respectively. It remains unclear whether genes likes those play any role in differential cancer susceptibility between genders. In conclusion, we were able to select many sets of 20 genes that can correctly classify ~88% of the tumor samples from 31 different types for a validation set using RNA-seq gene expression alone. This accuracy is remarkable given the number of the tumor types involved. This result was largely replicated in tumors between genders. We were also identified a few genes that might play a role in gender differences among sex non-specific tumors. Citation Format: YuanYuan Li, David M. Umbach, Leping Li. A comprehensive genomic pan-cancer analysis comparing males and females using The Cancer Genome Atlas gene expression data. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr A46.

Soy-based infant formulas contain isoflavone compounds that are estrogenic. Infants exclusively fed soy formula experience high exposure to these compounds, but it is not known if infants respond t...

Pesticides have been associated with Parkinson’s disease (PD), and protective gloves and workplace hygiene can reduce pesticide exposure. We examined whether such practices modified the pesticide-P...

Current biomedical research is guided by the idea that genetic makeup and environmental exposures, broadly construed, work together through time to cause human disease. This idea is the broad essence of gene–environment interaction. The detailed assessment of gene–environment interaction using epidemiologic data involves issues such as how one defines such interactions in a statistical sense and how one might infer that interactions seen in observational studies reflect causal relationships. That gene–environment interaction is hard to detect and estimate, requiring much larger sample sizes than main effects, has prompted research into novel approaches to increase power and precision through both methods of data analysis methods and study designs. Efforts to make studies robust against hidden genetic population structure have prompted other innovations in study design. The needs of biomedical science continue to stimulate research toward improved methods for studying gene–environment interaction. Keywords: antagonism; synergism; additive model; multiplicative model; genetics; epidemiology; complex disease; causal inference; case-only design; case-parents design

To examine potential sex differences in nonmotor symptoms (NMS) among drug-naive patients with Parkinson disease (PD), and to identify NMS that can best differentiate patients with early PD from controls.Our cross-sectional analysis included 414 newly diagnosed, untreated patients with PD (269 men and 145 women) and 188 healthy controls (121 men and 67 women) in the Parkinson's Progression Markers Initiative Study. NMS were measured using well-validated instruments covering sleep, olfactory, neurobehavioral, autonomic, and neuropsychological domains.Male and female patients with PD were fairly comparable on motor presentations but differed on several nonmotor features. Male patients with PD had significantly more pronounced deficits in olfaction (p = 0.02) and in certain cognitive measurements (all p0.01) than female patients, whereas female cases experienced higher trait anxiety (p = 0.02). Multiple stepwise logistic regression analysis showed that the combination of NMS measures-University of Pennsylvania Smell Identification Test (UPSIT), Montreal Cognitive Assessment (MoCA), Scales for Outcomes in Parkinson's Disease-Autonomic (SCOPA-AUT), and state anxiety from the State-Trait Anxiety Inventory-effectively differentiated patients with PD from controls with an area under the receiver operating characteristic curve (AUC) of 0.913 (95% confidence interval [CI]: 0.89-0.94). UPSIT, MoCA, and SCOPA-AUT were the most predictive NMS measurements in men (AUC = 0.919; 95% CI: 0.89-0.95) as compared to UPSIT, MoCA, and REM Sleep Behavior Disorder Screening Questionnaire in women (AUC = 0.903; 95% CI: 0.86-0.95).Our analysis revealed notable sex differences in several nonmotor features of patients with de novo PD. Furthermore, we found a parsimonious NMS combination that could effectively differentiate de novo cases from healthy controls.

Previous epidemiological studies have generated inconsistent results regarding the associations between dietary fat intakes and risk for Parkinson's disease (PD). We therefore prospectively examined these associations in the National Institutes of Health-American Association of Retired Persons (NIH-AARP) Diet and Health Study. A 124-item food frequency questionnaire was administered at baseline in1995 to 1996, and PD diagnosis was self-reported at the follow-up survey in 2004 to 2006. A total of 1,087 cases with a PD diagnosis between 2000 and 2006 and 299,617 controls were included in the analyses. Overall, intakes of fats and other macronutrients were not associated with PD risk. However, we found a weak positive association between n-6 polyunsaturated fatty acids (PUFA) and the risk for PD. After adjusting for potential confounders, the odds ratio (OR) and 95% confidence interval (CI) between extreme quintiles of n-6 PUFA intake was 1.23 (95% CI = 1.02-1.49, P for trend = 0.02). A similar association was observed for the intake of linoleic acid. Results were similar among men and among women. Our study suggests that fat intake in general is not related to the risk for PD. The weak positive association between intake of n-6 PUFA and PD risk needs further investigation.

Increased gut permeability, inflammation, and colonic α-synuclein pathology are present in early Parkinson’s disease (PD) and have been proposed to contribute to PD pathogenesis. Peptidoglycan is a structural component of the bacterial cell wall. Peptidoglycan recognition proteins (PGRPs) maintain healthy gut microbial flora by regulating the immune response to both commensal and harmful bacteria. We tested the hypothesis that variants in genes that encode PGRPs are associated with PD risk. Participants in two independent case-control studies were genotyped for 30 single-nucleotide polymorphisms (SNPs) in the four PGLYRP genes. Using logistic regression to estimate odds ratios (OR) and 95% confidence intervals (CI) adjusted for potential confounding variables, we conducted analyses in each study, separately and pooled. One SNP failed the assay, and three had little to no variation. The ORs were similar in both study populations. In pooled analyses, three of seven PGLYRP2 SNPs (rs3813135, rs733731, rs892145), one of five PGLYRP3 SNPs (rs2987763), and six of nine PGLYRP4 SNPs (rs10888557, rs12063091, rs3006440, rs3006448, rs3006458, and rs3014864) were significantly associated with PD risk. Association was strongest for PGLYRP4 5’untranslated region (UTR) SNP rs10888557 (GG reference, CG OR 0.6 [95%CI 0.4–0.9], CC OR 0.15 [95%CI 0.04–0.6]; log-additive P-trend, 0.0004). Common variants in PGLYRP genes are associated with PD risk in two independent studies. These results require replication, but they are consistent with hypotheses of a causative role for the gut microbiota and gastrointestinal immune response in PD.

Objectives Farmers may be at increased risk for adverse respiratory outcomes compared with the general population due to their regular exposures to dusts, animals and chemicals. However, early life farm exposures to microbial agents may result in reduced risk. Understanding respiratory disease risk among farmers and identifying differences between farmers and other populations may lead to better understanding of the contribution of environmental exposures to respiratory disease risk in the general population. Methods We compared the prevalence of self-reported respiratory outcomes in 43548 participants from the Agricultural Health Study (AHS), a prospective cohort of farmers and their spouses from Iowa and North Carolina, with data from adult participants in the National Health and Nutrition Examination Survey (NHANES) over the same period (2005–2010). Results AHS participants had lower prevalences of respiratory diseases (asthma, adult-onset asthma, chronic bronchitis and emphysema), but higher prevalences of current respiratory symptoms (wheeze, cough and phlegm) even after controlling for smoking, body mass index and population characteristics. The overall prevalence of asthma in the AHS (7.2%, 95% CI 6.9 to 7.4) was 52% of that in NHANES (13.8%, 95% CI 13.3 to 14.3), although the prevalence of adult-onset asthma among men did not differ (3.6% for AHS, 3.7% for NHANES). Conversely, many respiratory symptoms were more common in the AHS than NHANES, particularly among men. Conclusions These findings suggest that farmers and their spouses have lower risk for adult-onset respiratory diseases compared with the general population, and potentially higher respiratory irritation as evidenced by increased respiratory symptoms.

Objective To estimate associations between use of specific agricultural pesticides and incident diabetes in women. Methods We used data from the Agricultural Health Study, a large prospective cohort of pesticide applicators and their spouses in Iowa and North Carolina. For comparability with previous studies of farmers, we limited analysis to 13 637 farmers’ wives who reported ever personally mixing or applying pesticides at enrolment (1993–1997), who provided complete data on required covariates and diabetes diagnosis and who reported no previous diagnosis of diabetes at enrolment. Participants reported ever-use of 50 specific pesticides at enrolment and incident diabetes at one of two follow-up interviews within an average of 12 years of enrolment. We fit Cox proportional hazards models with age as the time scale and adjusting for state and body mass index to estimate HRs and 95% CIs for each of the 45 pesticides with sufficient users. Results Five pesticides were positively associated with incident diabetes (n=688; 5%): three organophosphates, fonofos (HR=1.56, 95% CI 1.11 to 2.19), phorate (HR=1.57, 95% CI 1.14 to 2.16) and parathion (HR=1.61, 95% CI 1.05 to 2.46); the organochlorine dieldrin (HR=1.99, 95% CI 1.12 to 3.54); and the herbicide 2,4,5-T/2,4,5-TP (HR=1.59, 95% CI 1.00 to 2.51). With phorate and fonofos together in one model to account for their correlation, risks for both remained elevated, though attenuated compared with separate models. Conclusions Results are consistent with previous studies reporting an association between specific organochlorines and diabetes and add to growing evidence that certain organophosphates also may increase risk.