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1.  Epidemiologic study of the C-3 epimer of 25-hydroxyvitamin D3 in a population-based sample 
Background & aims
Vitamin D is associated with many health outcomes and the blood concentration of 25-hydroxyvitamin D [25(OH)D] is commonly measured in clinical practice. A C-3 epimer of this compound, 3-epi-25(OH)D3, has recently been detected in blood samples. Few clinical assays currently detect this epimer and its physiological function is unknown, as are the demographic, behavioral, and physiologic factors that may be correlated with it. We sought to determine the correlation between these factors and 3-epi-25(OH)D3.
Methods
We conducted a cross-sectional population-based study of 303 non-Hispanic white participants in the Survey of the Health of Wisconsin. Serum 25(OH)D2, 25(OH)D3 and 3-epi-25(OH)D3 were measured by high-performance liquid chromatography tandem mass spectrometry. We measured vitamin D intake from foods and supplements via a food frequency questionnaire, sun exposure by spectrophotometry, waist circumference during a physical exam, and additional demographic and behavioral factors by questionnaire. We calculated the percent of 3-epi-25(OH)D3 out of the total 25(OH)D3.
Results
Summer P=0.009), higher alcohol intake (season (P=0.007), and higher vitamin D intake from supplements (P=0.0004), but not food (P=0.20), were significantly associated with a higher percent of 3-epi-25(OH)D3 relative to the total 25(OH)D3, although these associations appear to be partially driven by individuals with low 3-epi-25(OH)D3. Moreover, the percent of 3-epi-25(OH)D3 was significantly correlated with the total 25(OH)D3 (r=0.37, P<0.0001).
Conclusions
We report findings from an epidemiologic study of 3-epi-25(OH)D3 and show that individuals with lower total 25(OH)D3 tend to have a lower percent of 3-epi-25(OH)D3 relative to the total. While this is the largest reported sample of adults with measured 3-epi-25(OH)D3, the sample size of 303 is relatively small and replication of our findings is necessary.
doi:10.1016/j.clnu.2013.06.005
PMCID: PMC3884039  PMID: 23831447
3-epi-25(OH)D3; 25(OH)D2; 25(OH)D3; epimer; vitamin D; sun exposure
2.  Investigation of TREM2 variant in the Wisconsin Registry for Alzheimer’s Prevention 
Neurobiology of aging  2013;35(6):1252-1254.
Recent studies have found an association between a variant in TREM2 (rs75932628-T) and both Alzheimer’s disease (AD) and cognitive function in individuals age 80–100. The role of TREM2 in younger, asymptomatic individuals is unknown. We examined this variant in 1,148 participants from the Wisconsin Registry for Alzheimer’s Prevention, a longitudinal study of middle-aged adults enriched for a parental history of AD. Thirteen individuals carried the T risk allele. Carriers were more likely to have a parental history of AD (100% of carriers versus 70% of non-carriers; p=0.01) and, among the parental history subset, families with a TREM2 carrier had a younger maternal age of AD onset than non-carriers (67.9 versus 75.6 years; p=0.03). There was no significant association between TREM2 carrier status and cognitive function or decline. In conclusion, the association between TREM2 and both parental history of AD and younger maternal age of AD onset provide additional support for the role of TREM2 in AD and illustrate the importance of considering family history in AD study design.
doi:10.1016/j.neurobiolaging.2013.11.013
PMCID: PMC3961539  PMID: 24378087
TREM2; family history; Alzheimer’s disease; memory; cognition; longitudinal
3.  Heritability of Cognitive Traits Among Siblings with a Parental History of Alzheimer’s Disease 
Journal of Alzheimer's disease : JAD  2015;45(4):1149-1155.
Cognitive decline is one of the hallmark features of Alzheimer’s disease, but many studies struggle to find strong associations between cognitive function and genetic variants. In order to identify which aspects of cognition are more likely to have a strong genetic component, we assessed the heritability of various cognitive functions related to Alzheimer’s in 303 initially asymptomatic middle-aged adult siblings with a parental history of Alzheimer’s from the Wisconsin Registry for Alzheimer’s Prevention. Participants underwent extensive cognitive testing and six cognitive factors were identified via factor analysis. Working Memory and Visual Learning & Memory had the highest heritability (52% and 41%, respectively). Inclusion of APOE allele counts did not notably change heritability estimates, indicating that there are likely additional genetic variants contributing to cognition. These findings suggest that future genetic studies should focus on the cognitive domains of Working Memory and Visual Learning & Memory.
doi:10.3233/JAD-142658
PMCID: PMC4398625  PMID: 25649654
Alzheimer’s Disease; Heritability; Genetics; Cognitive Function; WRAP; APOE
4.  Stressful Events, Social Support, and Cognitive Function in Middle-aged Adults with a Family History of Alzheimer’s Disease 
Journal of aging and health  2013;25(6):944-959.
Objectives
To examine the associations of stressful experiences and social support with cognitive function in a sample of middle-aged adults with a family history of Alzheimer’s disease (AD).
Methods
Using data from the Wisconsin Registry for Alzheimer’s Prevention (WRAP; N=623), we evaluated relationships between stressful events experienced in the past year, as well as social support, and cognitive performance in four domains: speed and flexibility, immediate memory, verbal learning and memory, and working memory. We assessed interactions between psychosocial predictors, and with APOE ε4 status.
Results
Greater number of stressful events was associated with poorer performance on tests of speed and flexibility. Greater social support was associated with better performance in the same domain; this relationship was diminished by presence of the ε4 allele. No associations were seen in the remaining three domains.
Discussion
Psychosocial factors may influence cognition in at-risk individuals; influence varies by cognitive domain and ε4 status.
doi:10.1177/0898264313498416
PMCID: PMC3769466  PMID: 23945762
Cognitive function; geriatrics; social factors; stressful events; gene-environment interaction
5.  Interaction between two cholesterol metabolism genes influences memory: findings from the Wisconsin Registry for Alzheimer’s Prevention 
The strongest genetic factor for late-onset Alzheimer’s disease (AD) is APOE; nine additional susceptibility genes have recently been identified. The effect of these genes is often assumed to be additive and polygenic scores are formed as a summary measure of risk. However, interactions between these genes are likely to be important. We sought to examine the role of interactions between the nine recently identified AD susceptibility genes and APOE in cognitive function and decline in 1,153 participants from the Wisconsin Registry for Alzheimer’s Prevention, a longitudinal study of middle-aged adults enriched for a parental history of AD. Participants underwent extensive cognitive testing at baseline and up to two additional visits approximately 4 and 6 years later. The influence of the interaction between APOE and each of 14 single nucleotide polymorphisms (SNPs) in the nine recently identified genes on three cognitive factor scores (Verbal Learning and Memory, Working Memory, and Immediate Memory) was examined using linear mixed models adjusting for age, gender and ancestry. Interactions between the APOE ε4 allele and both of the genotyped ABCA7 SNPs, rs3764650 and rs3752246, were associated with all three cognitive factor scores (P-values ≤0.01). Both of these genes are in the cholesterol metabolism pathway leading to AD. This research supports the importance of considering non-additive effects of AD susceptibility genes.
doi:10.3233/JAD-130482
PMCID: PMC3759032  PMID: 23669301
gene-gene interaction; memory; cognition; Alzheimer’s disease; cholesterol
6.  Detecting Multiple Causal Rare Variants in Exome Sequence Data 
Genetic Epidemiology  2011;35(Suppl 1):S18-S21.
Recent advances in sequencing technology have presented both opportunities and challenges, with limited statistical power to detect a single causal rare variant with practical sample sizes. To overcome this, the contributors to Group 1 of Genetic Analysis Workshop 17 sought to develop methods to detect the combined signal of multiple causal rare variants in a biologically meaningful way. The contributors used genes, genome location proximity, or genetic pathways as the basic unit in combining the information from multiple variants. Weaknesses of the exome sequence data and the relative strengths and weaknesses of the five approaches are discussed.
doi:10.1002/gepi.20644
PMCID: PMC3271433  PMID: 22128053
Bayesian; pathways; simulated
7.  Genome-wide association study of vitamin D concentrations in Hispanic Americans: The IRAS Family Study 
Vitamin D deficiency is associated with many adverse health outcomes. There are several well established environmental predictors of vitamin D concentrations, yet studies of the genetic determinants of vitamin D concentrations are in their infancy. Our objective was to conduct a pilot genome-wide association (GWA) study of 25-hydroxyvitamin D (25[OH]D) and 1,25-dihydroxyvitamin D (1,25[OH]2D) concentrations in a subset of 229 Hispanic subjects, followed by replication genotyping of 50 single nucleotide polymorphisms (SNPs) in the entire sample of 1,190 Hispanics from San Antonio, Texas and San Luis Valley, Colorado. Of the 309,200 SNPs that met all quality control criteria, three SNPs in high linkage disequilibrium (LD) with each other were significantly associated with 1,25[OH]2D (rs6680429, rs9970802, and rs10889028) at a Bonferroni corrected P-value threshold of 1.62 × 10−7, however none met the threshold for 25[OH]D. Of the 50 SNPs selected for replication genotyping, five for 25[OH]D (rs2806508, rs10141935, rs4778359, rs1507023, and rs9937918) and eight for 1,25[OH]2D (rs6680429, rs1348864, rs4559029, rs12667374, rs7781309, rs10505337, rs2486443, and rs2154175) were replicated in the entire sample of Hispanics (P < 0.01). In conclusion, we identified several SNPs that were associated with vitamin D metabolite concentrations in Hispanics. These candidate polymorphisms merit further investigation in independent populations and other ethnicities.
doi:10.1016/j.jsbmb.2010.06.013
PMCID: PMC2949505  PMID: 20600896
Vitamin D; 25-hydroxyvitamin D; 1,25-dihydroxyvitamin D; genome-wide association study; Hispanic
8.  Detecting Gene-Environment Interactions in Genome-Wide Association Data 
Genetic epidemiology  2009;33(Suppl 1):S68-S73.
Despite the importance of gene-environment (G×E) interactions in the etiology of common diseases, little work has been done to develop methods for detecting these types of interactions in genome-wide association study data. This was the focus of Genetic Analysis Workshop 16 Group 10 contributions, which introduced a variety of new methods for the detection of G×E interactions in both case-control and family-based data using both cross-sectional and longitudinal study designs. Many of these contributions detected significant G×E interactions. Although these interactions have not yet been confirmed, the results suggest the importance of testing for interactions. Issues of sample size, quantifying the environmental exposure, longitudinal data analysis, family-based analysis, selection of the most powerful analysis method, population stratification, and computational expense with respect to testing G×E interactions are discussed.
doi:10.1002/gepi.20475
PMCID: PMC2924567  PMID: 19924704
GAW; case-control; family-based; cross-sectional; longitudinal; rheumatoid arthritis; Framingham Heart Study
9.  Association of 25-hydroxyvitamin D with Blood Pressure in Predominantly 25-hydroxyvitamin D Deficient Hispanic and African Americans 
American journal of hypertension  2009;22(8):867-870.
Background
Several observational studies have recently suggested an inverse association of circulating levels of vitamin D with blood pressure. These findings have been based mainly on Caucasian populations; whether this association also exists among Hispanic and African Americans has yet to be definitively determined. This study investigates the association of 25-hydroxyvitamin D (25[OH]D) with blood pressure in Hispanic and African Americans.
Methods
The data source for this study is the Insulin Resistance Atherosclerosis Family Study (IRASFS), which consists of Hispanic- and African-American families from three U.S. recruitment centers (n=1334). A variance components model was used to analyze the association of plasma 25[OH]D levels with blood pressure.
Results
An inverse association was found between 25[OH]D and both systolic (β for 10 ng/mL difference= −2.05; p<0.01) and diastolic (β for 10 ng/mL difference= −1.35; p<0.001) blood pressure in all populations combined, after adjusting for age, sex, ethnicity and season of blood draw. Further adjustment for body mass index (BMI) weakened this association (β for 10 ng/mL difference= −0.94; p=0.14 and β for 10 ng/mL difference = −0.64; p=0.09, respectively).
Conclusions
25[OH]D levels are significantly inversely associated with blood pressure in Hispanic and African Americans from the IRASFS. However, this association was not significant after adjustment for BMI. Further research is needed to determine the role of BMI in this association. Large, well-designed prospective studies of the effect of vitamin D supplementation on blood pressure may be warranted.
doi:10.1038/ajh.2009.88
PMCID: PMC2865679  PMID: 19444222
Vitamin D; 25-hydroxyvitamin D; blood pressure; hypertension; race; ethnic groups; Hispanic; African American
10.  Association Between Informal Caregiving and Cellular Aging in the Survey of the Health of Wisconsin: The Role of Caregiving Characteristics, Stress, and Strain 
American Journal of Epidemiology  2014;179(11):1340-1352.
The pathophysiological consequences of caregiving have not been fully elucidated. We evaluated how caregiving, stress, and caregiver strain were associated with shorter relative telomere length (RTL), a marker of cellular aging. Caregivers (n = 240) and some noncaregivers (n = 98) in the 2008–2010 Survey of the Health of Wisconsin, comprising a representative sample of Wisconsin adults aged 21–74 years, reported their sociodemographic, health, and psychological characteristics. RTL was assayed from blood or saliva samples. Median T and S values were used to determine the telomere-to-single copy gene ratio (T/S) for each sample, and log(T/S) was used as the dependent variable in analyses. Multivariable generalized additive models showed that RTL did not differ between caregivers and noncaregivers (difference in log(T/S) = −0.03; P > 0.05), but moderate-to-high levels of stress versus low stress were associated with longer RTL (difference = 0.15; P = 0.04). Among caregivers, more hours per week of care, caring for a young person, and greater strain were associated with shorter RTL (P < 0.05). Caregivers with discordant levels of stress and strain (i.e., low perceived stress/high strain) compared with low stress/low strain had the shortest RTL (difference = −0.24; P = 0.02, Pinteraction = 0.13), corresponding to approximately 10–15 additional years of aging. Caregivers with these characteristics may be at increased risk for accelerated aging. Future work is necessary to better elucidate these relationships and develop interventions to improve the long-term health and well-being of caregivers.
doi:10.1093/aje/kwu066
PMCID: PMC4036217  PMID: 24780842
caregivers; caregiver strain; population-based studies; stress, psychological; Survey of the Health of Wisconsin
11.  Reproductive windows, genetic loci and breast cancer risk. 
Annals of epidemiology  2014;24(5):376-382.
Purpose
The reproductive windows between age at menarche and first childbirth (standardized AFB) and from menarche to menopause (reproductive lifespan) may interact with genetic variants in association with breast cancer risk.
Methods
We assessed this hypothesis in 6131 breast cancer cases and 7274 controls who participated in the population-based Collaborative Breast Cancer Study. Risk factor information was collected through telephone interviews and DNA samples were collected on a sub-sample (N=1484 cases, 1307 controls) to genotype for 13 genome-wide association study-identified loci. Adjusted odds ratios (OR) and 95% confidence intervals (CI) were calculated and P-values for the interaction between reproductive windows and genotypes were obtained by adding cross-product terms to statistical models.
Results
For standardized AFB, the OR was 1.52 (CI:1.36-1.71) comparing the highest to lowest quintile. Carrier status for rs10941679 (5p12) and rs10483813 (RAD51B) appeared to modify this relationship (P=0.04 and P=0.02, respectively). For reproductive lifespan, the OR comparing the highest and lowest quintiles was 1.62 (CI:1.35-1.95). No interactions were detected between genotype and reproductive lifespan (all P>0.05). All results were similar regardless of ductal versus lobular breast cancer subtype.
Conclusions
Our results suggest reproductive windows are associated with breast cancer risk, and that associations may vary by genetic variants.
doi:10.1016/j.annepidem.2014.02.007
PMCID: PMC4164346  PMID: 24792587
breast neoplasms; epidemiology; menarche; menopause; genetic loci; histology
12.  PREDICTORS OF DISCORDANCE BETWEEN PERCEIVED AND OBJECTIVE NEIGHBORHOOD DATA 
Annals of epidemiology  2013;24(3):214-221.
Purpose
Pathways by which the social and built environments affect health can be influenced by differences between perception and reality. This discordance is an important for understanding health impacts of the built environment. This study examines associations between perceived and objective measures of 12 non-residential destinations, as well as previously unexplored sociodemographic, lifestyle, neighborhood and urbanicity predictors of discordance.
Methods
Perceived neighborhood data were collected from participants of the Survey of the Health of Wisconsin (SHOW), using a self-administered questionnaire. Objective data were collected using the Wisconsin Assessment of the Social and Built Environment, an audit-based instrument assessing built environment features around each participant’s residence.
Results
Overall, there was relatively high agreement, ranging from 50% for proximity to parks to >90% for golf courses. Education, positive neighborhood perceptions, and rurality were negatively associated with discordance. Associations between discordance and depression, disease status, and lifestyle factors appeared to be modified by urbanicity level.
Conclusions
These data show perceived and objective neighborhood environment data are not interchangeable and the level of discordance is associated with or modified by individual and neighborhood factors, including level of urbanicity. These results suggest that consideration should be given to including both types of measures in future studies.
doi:10.1016/j.annepidem.2013.12.007
PMCID: PMC3947547  PMID: 24467991
Epidemiological methods; Environment Design; Obesity; Perception; Validity (Epidemiology); Rural Population; Urban Population
13.  The Wisconsin Assessment of the Social and Built Environment (WASABE): a multi-dimensional objective audit instrument for examining neighborhood effects on health 
BMC Public Health  2014;14:1165.
Background
Growing evidence suggests that mixed methods approaches to measuring neighborhood effects on health are needed. The Wisconsin Assessment of the Social and Built Environment (WASABE) is an objective audit tool designed as an addition to a statewide household-based health examination survey, the Survey of the Health of Wisconsin (SHOW), to objectively measure participant’s neighborhoods.
Methods
This paper describes the development and implementation of the WASABE and examines the instrument’s ability to capture a range of social and built environment features in urban and rural communities. A systematic literature review and formative research were used to create the tool. Inter-rater reliability parameters across items were calculated. Prevalence and density of features were estimated for strata formed according to several sociodemographic and urbanicity factors.
Results
The tool is highly reliable with over 81% of 115 derived items having percent agreement above 95%. It captured variance in neighborhood features in for a diverse sample of SHOW participants. Sidewalk density in neighborhoods surrounding households of participants living at less than 100% of the poverty level was 67% (95% confidence interval, 55-80%) compared to 34% (25-44%) for those living at greater than 400% of the poverty level. Walking and biking trails were present in 29% (19-39%) of participant buffer in urban areas compared to only 7% (2-12%) in rural communities. Significant environmental differences were also observed for white versus non-white, high versus low income, and college graduates versus individuals with lower level of education.
Conclusions
The WASABE has strong inter-rater reliability and validity properties. It builds on previous work to provide a rigorous and standardized method for systematically gathering objective built and social environmental data in a number of geographic settings. Findings illustrate the complex milieu of built environment features found in participants neighborhoods and have relevance for future research, policy, and community engagement purposes.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2458-14-1165) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2458-14-1165
PMCID: PMC4289353  PMID: 25391283
Neighborhoods; Built environment; Social environment; Population health; Measurement; Urban; Rural; Chronic disease; Prevention; Physical activity; Methods; Audit tool
14.  Telomere length varies by DNA extraction method: Implications for epidemiologic research 
Background
Both shorter and longer telomeres in peripheral blood leukocyte (PBL) DNA have been associated with cancer risk. However, associations remain inconsistent across studies of the same cancer type. This study compares DNA preparation methods to determine telomere length from colorectal cancer patients.
Methods
We examined PBL relative telomere length (RTL) measured by quantitative PCR (qPCR) in 1,033 colorectal cancer patients and 2,952 healthy controls. DNA was extracted with Phenol/Chloroform, PureGene or QIAamp.
Results
We observed differences in RTL depending on DNA extraction method (p<0.001). Phenol/Chloroform extracted DNA had a mean RTL (T/S ratio) of 0.78 (range 0.01-6.54) ) compared to PureGene extracted DNA (mean RTL of 0.75; range 0.00-12.33). DNA extracted by QIAamp yielded a mean RTL of 0.38 (range 0.02-3.69). We subsequently compared RTL measured by qPCR from an independent set of 20 colorectal cancer cases and 24 normal controls in PBL DNA extracted by each of the three extraction methods. The range of RTL measured by qPCR from QIAamp-extracted DNA (0.17-0.58-) was smaller than from either PureGene or Phenol/Chloroform (ranges:0.04-2.67 and 0.32-2.81, respectively).
Conclusions
RTL measured by qPCR from QIAamp-extracted DNA was smaller than from either PureGene or Phenol/Chloroform (p<0.001).
Impact
Differences in DNA extraction method may contribute to the discrepancies between studies seeking to find an association between the risk of cancer or other diseases and RTL.
doi:10.1158/1055-9965.EPI-13-0409
PMCID: PMC3827976  PMID: 24019396
Telomere length; extraction methods; colorectal cancer
15.  The associations between a polygenic score, reproductive and menstrual risk factors and breast cancer risk 
We evaluated whether 13 single nucleotide polymorphisms (SNPs) identified in genome-wide association studies interact with one another and with reproductive and menstrual risk factors in association with breast cancer risk. DNA samples and information on parity, breastfeeding, age at menarche, age at first birth, and age at menopause were collected through structured interviews from 1484 breast cancer cases and 1307 controls who participated in a population-based case-control study conducted in three U.S. states. A polygenic score was created as the sum of risk allele copies multiplied by the corresponding log odds estimate. Logistic regression was used to test associations between SNPs, the score, reproductive and menstrual factors and breast cancer risk. Nonlinearity of the score was assessed by the inclusion of a quadratic term for polygenic score. Interactions between the aforementioned variables were tested by including a cross-product term in models. We confirmed associations between rs13387042 (2q35), rs4973768 (SLC4A7), rs10941679 (5p12), rs2981582 (FGFR2), rs3817198 (LSP1), rs3803662 (TOX3) and rs6504950 (STXBP4) with breast cancer. Women in the score’s highest quintile had 2.2-fold increased risk when compared to women in the lowest quintile (95% confidence interval:1.67–2.88). The quadratic polygenic score term was not significant in the model (p=0.85), suggesting established breast cancer loci are not associated with increased risk more than the sum of risk alleles. Modifications of menstrual and reproductive risk factors associations with breast cancer risk by polygenic score were not observed. Our results suggest interactions between breast cancer susceptibility loci and reproductive factors are not strong contributors to breast cancer risk.
doi:10.1007/s10549-013-2646-3
PMCID: PMC3799826  PMID: 23893088
Epidemiology; reproductive and menstrual factors; breast cancer; breast cancer susceptibility loci
16.  Genetic Evidence for Role of Carotenoids in Age-Related Macular Degeneration in the Carotenoids in Age-Related Eye Disease Study (CAREDS) 
Purpose.
We tested variants in genes related to lutein and zeaxanthin status for association with age-related macular degeneration (AMD) in the Carotenoids in Age-Related Eye Disease Study (CAREDS).
Methods.
Of 2005 CAREDS participants, 1663 were graded for AMD from fundus photography and genotyped for 424 single nucleotide polymorphisms (SNPs) from 24 candidate genes for carotenoid status. Of 337 AMD cases 91% had early or intermediate AMD. The SNPs were tested individually for association with AMD using logistic regression. A carotenoid-related genetic risk model was built using backward selection and compared to existing AMD risk factors using the area under the receiver operating characteristic curve (AUC).
Results.
A total of 24 variants from five genes (BCMO1, BCO2, NPCL1L1, ABCG8, and FADS2) not previously related to AMD and four genes related to AMD in previous studies (SCARB1, ABCA1, APOE, and ALDH3A2) were associated independently with AMD, after adjusting for age and ancestry. Variants in all genes (not always the identical SNPs) were associated with lutein and zeaxanthin in serum and/or macula, in this or other samples, except for BCO2 and FADS2. A genetic risk score including nine variants significantly (P = 0.002) discriminated between AMD cases and controls beyond age, smoking, CFH Y402H, and ARMS2 A69S. The odds ratio (95% confidence interval) for AMD among women in the highest versus lowest quintile for the risk score was 3.1 (2.0–4.9).
Conclusions.
Variants in genes related to lutein and zeaxanthin status were associated with AMD in CAREDS, adding to the body of evidence supporting a protective role of lutein and zeaxanthin in risk of AMD.
In this study of over 1600 postmenopausal women of the CAREDS, we describe the first evidence that variation in multiple genes related to carotenoid status in the blood and macula are associated with age-related macular degeneration (AMD).
doi:10.1167/iovs.13-13216
PMCID: PMC3908680  PMID: 24346170
macular degeneration; carotenoids; genes
17.  Prediction of genetic contributions to complex traits using whole genome sequencing data 
BMC Proceedings  2014;8(Suppl 1):S68.
Although markers identified by genome-wide association studies have individually strong statistical significance, their performance in prediction remains limited. Our goal was to use animal breeding genomic prediction models to predict additive genetic contributions for systolic blood pressure (SBP) using whole genome sequencing data with different validation designs.
The additive genetic contributions of SBP were estimated via linear mixed model. Rare variants (MAF<0.05) were collapsed through the k-means method to create a "collapsed single-nucleotide polymorphisms." Prediction of the additive genomic contributions of SBP was conducted using genomic Best Linear Unbiased Predictor (GBLUP) and BayesCπ. Estimates of predictive accuracy were compared using common single-nucleotide polymorphisms (SNPs) versus common and collapsed SNPs, and for prediction within and across families.
The additive genetic variance of SBP contributed to 18% of the phenotypic variance (h2 = 0.18). BayesCπ had slightly better prediction accuracies than GBLUP. In both models, within-family predictions had higher accuracies both in the training and testing set than didacross-family design. Collapsing rare variants via the k-means method and adding to the common SNPs did not improve prediction accuracies. The prediction model, including both pedigree and genomic information, achieved a slightly higher accuracy than using either source of information alone.
Prediction of genetic contributions to complex traits is feasible using whole genome sequencing and statistical methods borrowed from animal breeding. The relatedness of individuals between the training and testing set strongly affected the performance of prediction models. Methods for inclusion of rare variants in these models need more development.
doi:10.1186/1753-6561-8-S1-S68
PMCID: PMC4143683  PMID: 25519339
18.  Genetic Analysis Workshop 18: Methods and strategies for analyzing human sequence and phenotype data in members of extended pedigrees 
BMC Proceedings  2014;8(Suppl 1):S1.
Genetic Analysis Workshop 18 provided a platform for developing and evaluating statistical methods to analyze whole-genome sequence data from a pedigree-based sample. In this article we present an overview of the data sets and the contributions that analyzed these data. The family data, donated by the Type 2 Diabetes Genetic Exploration by Next-Generation Sequencing in Ethnic Samples Consortium, included sequence-level genotypes based on sequencing and imputation, genome-wide association genotypes from prior genotyping arrays, and phenotypes from longitudinal assessments. The contributions from individual research groups were extensively discussed before, during, and after the workshop in theme-based discussion groups before being submitted for publication.
doi:10.1186/1753-6561-8-S1-S1
PMCID: PMC4143625  PMID: 25519310
19.  The Association of Telomere Length with Colorectal Cancer Differs by the Age of Cancer Onset 
OBJECTIVES:
Telomeres are nucleoprotein structures that cap the end of chromosomes and shorten with sequential cell divisions in normal aging. Short telomeres are also implicated in the incidence of many cancers, but the evidence is not conclusive for colorectal cancer (CRC). Therefore, the aim of this study was to assess the association of CRC and telomere length.
METHODS:
In this case–control study, we measured relative telomere length from peripheral blood leukocytes (PBLs) DNA with quantitative PCR in 598 CRC patients and 2,212 healthy controls.
RESULTS:
Multivariate analysis indicated that telomere length was associated with risk for CRC, and this association varied in an age-related manner; younger individuals (≤50 years of age) with longer telomeres (80–99 percentiles) had a 2–6 times higher risk of CRC, while older individuals (>50 years of age) with shortened telomeres (1–10 percentiles) had 2–12 times the risk for CRC. The risk for CRC varies with extremes in telomere length in an age-associated manner.
CONCLUSIONS:
Younger individuals with longer telomeres or older individuals with shorter telomeres are at higher risk for CRC. These findings indicate that the association of PBL telomere length varies according to the age of cancer onset and that CRC is likely associated with at minimum two different mechanisms of telomere dynamics.
doi:10.1038/ctg.2014.3
PMCID: PMC3972691  PMID: 24598784
20.  Perceived neighborhood quality, sleep quality, and health status: Evidence from the Survey of the Health of Wisconsin 
Why does living in a disadvantaged neighborhood predict poorer mental and physical health? Recent research focusing on the Southwestern United States suggests that disadvantaged neighborhoods favor poor health, in part, because they undermine sleep quality. Building on previous research, we test whether this process extends to the Midwestern United States. Specifically, we use cross-sectional data from the Survey of the Health of Wisconsin (SHOW), a statewide probability sample of Wisconsin adults, to examine whether associations among perceived neighborhood quality (e.g., perceptions of crime, litter, and pleasantness in the neighborhood) and health status (overall self-rated health and depression) are mediated by overall sleep quality (measured as self-rated sleep quality and physician diagnosis of sleep apnea). We find that perceptions of low neighborhood quality are associated with poorer self-rated sleep quality, poorer self-rated health, and more depressive symptoms. We also observe that poorer self-rated sleep quality is associated with poorer self-rated health and more depressive symptoms. Our mediation analyses indicate that self-rated sleep quality partially mediates the link between perceived neighborhood quality and health status. Specifically, self-rated sleep quality explains approximately 20% of the association between neighborhood quality and self-rated health and nearly 19% of the association between neighborhood quality and depression. Taken together, these results confirm previous research and extend the generalizability of the indirect effect of perceived neighborhood context on health status through sleep quality.
doi:10.1016/j.socscimed.2012.07.021
PMCID: PMC3733364  PMID: 22901794
Sleep; Sleep quality; Neighborhood context; Neighborhood quality; Self-rated health; Depression; Wisconsin; USA
21.  Correlation of Chromosomal Instability, Telomere Length and Telomere Maintenance in Microsatellite Stable Rectal Cancer: A Molecular Subclass of Rectal Cancer 
PLoS ONE  2013;8(11):e80015.
Introduction
Colorectal cancer (CRC) tumor DNA is characterized by chromosomal damage termed chromosomal instability (CIN) and excessively shortened telomeres. Up to 80% of CRC is microsatellite stable (MSS) and is historically considered to be chromosomally unstable (CIN+). However, tumor phenotyping depicts some MSS CRC with little or no genetic changes, thus being chromosomally stable (CIN-). MSS CIN- tumors have not been assessed for telomere attrition.
Experimental Design
MSS rectal cancers from patients ≤50 years old with Stage II (B2 or higher) or Stage III disease were assessed for CIN, telomere length and telomere maintenance mechanism (telomerase activation [TA]; alternative lengthening of telomeres [ALT]). Relative telomere length was measured by qPCR in somatic epithelial and cancer DNA. TA was measured with the TRAPeze assay, and tumors were evaluated for the presence of C-circles indicative of ALT. p53 mutation status was assessed in all available samples. DNA copy number changes were evaluated with Spectral Genomics aCGH.
Results
Tumors were classified as chromosomally stable (CIN-) and chromosomally instable (CIN+) by degree of DNA copy number changes. CIN- tumors (35%; n=6) had fewer copy number changes (<17% of their clones with DNA copy number changes) than CIN+ tumors (65%; n=13) which had high levels of copy number changes in 20% to 49% of clones. Telomere lengths were longer in CIN- compared to CIN+ tumors (p=0.0066) and in those in which telomerase was not activated (p=0.004). Tumors exhibiting activation of telomerase had shorter tumor telomeres (p=0.0040); and tended to be CIN+ (p=0.0949).
Conclusions
MSS rectal cancer appears to represent a heterogeneous group of tumors that may be categorized both on the basis of CIN status and telomere maintenance mechanism. MSS CIN- rectal cancers appear to have longer telomeres than those of MSS CIN+ rectal cancers and to utilize ALT rather than activation of telomerase.
doi:10.1371/journal.pone.0080015
PMCID: PMC3836975  PMID: 24278232
22.  Genetic Determinants of Macular Pigments in Women of the Carotenoids in Age-Related Eye Disease Study 
Purpose.
To investigate genetic determinants of macular pigment optical density in women from the Carotenoids in Age-Related Eye Disease Study (CAREDS), an ancillary study of the Women's Health Initiative Observational Study.
Methods.
1585 of 2005 CAREDS participants had macular pigment optical density (MPOD) measured noninvasively using customized heterochromatic flicker photometry and blood samples genotyped for 440 single nucleotide polymorphisms (SNPs) in 26 candidate genes related to absorption, transport, binding, and cleavage of carotenoids directly, or via lipid transport. SNPs were individually tested for associations with MPOD using least-squares linear regression.
Results.
Twenty-one SNPs from 11 genes were associated with MPOD (P ≤ 0.05) after adjusting for dietary intake of lutein and zeaxanthin. This includes variants in or near genes related to zeaxanthin binding in the macula (GSTP1), carotenoid cleavage (BCMO1), cholesterol transport or uptake (SCARB1, ABCA1, ABCG5, and LIPC), long-chain omega-3 fatty acid status (ELOVL2, FADS1, and FADS2), and various maculopathies (ALDH3A2 and RPE65). The strongest association was for rs11645428 near BCMO1 (βA = 0.029, P = 2.2 × 10−4). Conditional modeling within genes and further adjustment for other predictors of MPOD, including waist circumference, diabetes, and dietary intake of fiber, resulted in 13 SNPs from 10 genes maintaining independent association with MPOD. Variation in these single gene polymorphisms accounted for 5% of the variability in MPOD (P = 3.5 × 10−11).
Conclusions.
Our results support that MPOD is a multi-factorial phenotype associated with variation in genes related to carotenoid transport, uptake, and metabolism, independent of known dietary and health influences on MPOD.
In 1585 postmenopausal women of the Carotenoids in Age-Related Eye Disease Study sample, common genetic variants in or near genes involved in carotenoid transport, uptake, and metabolism were associated with density of lutein and zeaxanthin in the macula, independent of other known predictors, including dietary intake of carotenoids.
doi:10.1167/iovs.12-10867
PMCID: PMC3626525  PMID: 23404124
23.  The Challenge of Detecting Epistasis (G×G Interactions): Genetic Analysis Workshop 16 
Genetic epidemiology  2009;33(0 1):S58-S67.
Interest is increasing in epistasis as a possible source of the unexplained variance missed by genome-wide association studies. The Genetic Analysis Workshop 16 Group 9 participants evaluated a wide variety of classical and novel analytical methods for detecting epistasis, in both the statistical and machine learning paradigms, applied to both real and simulated data. Because the magnitude of epistasis is clearly relative to scale of penetrance, and therefore to some extent, to the choice of model framework, it is not surprising that strong interactions under one model might be minimized or even disappear entirely under a different modeling framework.
doi:10.1002/gepi.20474
PMCID: PMC3692280  PMID: 19924703
generalized linear model; machine learning methods
24.  Duration of Physical Activity and Serum 25-hydroxyvitamin D Status of Postmenopausal Women 
Annals of epidemiology  2011;21(6):440-449.
Purpose
To investigate whether the association between physical activity and serum 25-hydroxyvitamin D (25(OH)D) concentrations is independent of sun exposure, body size, and other potential explanatory variables.
Methods
Using data from a sample of 1,343 postmenopausal women, from the Women’s Health Initiative, linear regression was used to examine the associations of duration (minutes/week) of recreational activity and of yard work with 25(OH)D concentrations (nmol/L).
Results
In age-adjusted analyses, positive associations were observed between 25(OH)D concentrations and both duration of recreational physical activity (β=0.71, SE(0.09), P<0.001) and yard work (β=0.36, SE(0.10), P=0.004). After further adjustment for vitamin D intake, self-reported sunlight exposure, waist circumference, and season of blood draw, 25(OH)D was significantly associated with recreational activity (β=0.21, SE(0.09), P=0.014) but not with yard work (β=0.18, SE(0.09), P=0.061). Interactions were observed between season and both recreational activity (Pinteraction=0.082) and yard work (Pinteraction=0.038) such that these activity-25(OH)D associations were greater during summer/fall compared to winter/spring. Self-reported sunlight exposure and measures of body size did not modify the associations.
Conclusion
The observed age-adjusted activity-25(OH)D associations were attenuated after adjusting for explanatory variables and were modified by season of blood draw. Adopting a lifestyle that incorporates outdoor physical activity during summer/fall, consuming recommended amounts of vitamin D, and maintaining a healthy weight may improve or maintain vitamin D status in postmenopausal women.
doi:10.1016/j.annepidem.2010.11.011
PMCID: PMC3090482  PMID: 21414803
25-hydroxyvitamin D; vitamin D; serum; sunlight exposure; physical activity; epidemiology; women
25.  Identifying rare variants from exome scans: the GAW17 experience 
BMC Proceedings  2011;5(Suppl 9):S1.
Genetic Analysis Workshop 17 (GAW17) provided a platform for evaluating existing statistical genetic methods and for developing novel methods to analyze rare variants that modulate complex traits. In this article, we present an overview of the 1000 Genomes Project exome data and simulated phenotype data that were distributed to GAW17 participants for analyses, the different issues addressed by the participants, and the process of preparation of manuscripts resulting from the discussions during the workshop.
doi:10.1186/1753-6561-5-S9-S1
PMCID: PMC3287821  PMID: 22373325

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