PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (33)
 

Clipboard (0)
None

Select a Filter Below

Year of Publication
Document Types
1.  Patterns of dental service utilization following nontraumatic dental condition visits to the emergency department in Wisconsin Medicaid 
Objectives
To examine patterns of dental service utilization for adult Medicaid enrollees in Wisconsin following nontraumatic dental condition (NTDC) visits to the emergency department (ED).
Methods
This is a retrospective, observational study of claims for NTDC visits to the ED and dental service encounters from the Wisconsin Medicaid Evaluation and Decision Support database (2001–2009). We used competing risk models to predict probabilities of returning to the ED versus obtaining follow-up care from a dentist.
Results
We observed a 43 percent increase in the rate of NTDC visits to the ED, with most of this increase occurring from 2001 to 2005. Within 30 days of an NTDC visit to the ED, ~29.6 percent of enrollees will first visit a dentist office, while ~9.9 percent will return to the ED. Young to middle-aged adults (18 to <50 years) and enrollees living in counties with a lower supply of dental providers were more likely to return to the ED following a NTDC visit. Among the enrollees that first visited a dental office following an ED visit, 37.6 percent had an extraction performed at this visit.
Conclusions
Almost one in five adult Medicaid enrollees will subsequently return to the ED following a previous NTDC visit. The provision of definitive care for these individuals appears to primarily consist of extractions.
doi:10.1111/j.1752-7325.2012.00364.x
PMCID: PMC4104605  PMID: 22882075
dental health services; dental care; emergency service; hospital; Medicaid
2.  The Effects of Bazedoxifene, Conjugated Equine Estrogens, and a Tissue Selective Estrogen Complex (TSEC) Containing Both Bazedoxifene and Conjugated Equine Estrogens on Cerebral Artery Atherosclerosis of Postmenopausal Monkeys 
Menopause (New York, N.Y.)  2014;21(1):10.1097/GME.0b013e31829370e5.
Objective
To evaluate the effects of a new selective estrogen receptor modulator (bazedoxifene acetate, BZA) and a tissue specific estrogen complex (TSEC = BZA combined with conjugated equine estrogens (CEE), on atherosclerosis extent and severity of cerebral arteries.
Methods
Ninety-eight surgically postmenopausal monkeys (Macaca fascicularis) were fed a moderately atherogenic diet and then randomized to receive no treatment, or women’s equivalent doses of BZA (20 mg/day), CEE (0.45 mg/day) or BZA+CEE. After an experimental period of 20 months (approximately equivalent to 5 years of patient experience), the extent and severity of atherosclerosis in the common carotid artery, carotid bifurcation, internal carotid artery and the basilar artery was determined. Lesion severity was determined using the American Heart Association grading system (AHA, grades 0-5).
Results
BZA had no consistent adverse effects on the extent or severity of atherosclerosis in the cerebral arteries and did not attenuate the beneficial effects of CEE on common carotid artery atherosclerosis severity. Although CEE had only modest beneficial effects on atherosclerosis extent of the carotid bifurcation, the severity of lesions and numbers of affected cases in the common carotid artery were reduced with CEE treatment. As reported previously, plasma lipid profiles did not differ among the treatment groups.
Conclusions
In this long-term (equivalent to 5 human patient years) nonhuman primate trial, BZA had no consistent adverse effect on cerebral artery atherosclerosis and did not attenuate the modest beneficial effect of CEE on common carotid arteries. Furthermore, CEE inhibited the development of complicated plaques in the common carotid artery
doi:10.1097/GME.0b013e31829370e5
PMCID: PMC3760976  PMID: 23676638
Cerebral atherosclerosis; menopause; estrogens; SERMS; bazedoxifene
3.  Host genetics and immune control of HIV-1 infection: Fine mapping for the extended human MHC region in an African cohort 
Genes and immunity  2014;15(5):275-281.
Multiple MHC loci encoding human leukocyte antigens (HLA) have allelic variants unequivocally associated with differential immune control of HIV-1 infection. Fine mapping based on single nucleotide polymorphisms (SNPs) in the extended MHC (xMHC) region is expected to reveal causal or novel factors and to justify a search for functional mechanisms. We have tested the utility of a custom fine-mapping platform (the ImmunoChip) for 172 HIV-1 seroconverters (SCs) and 449 seroprevalent individuals (SPs) from Lusaka, Zambia, with a focus on more than 6,400 informative xMHC SNPs. When conditioned on HLA and non-genetic factors previously associated with HIV-1 viral load (VL) in the study cohort, penalized approaches (HyperLasso models) identified an intergenic SNP (rs3094626 between RPP21 and HLA-E) and an intronic SNP (rs3134931 in NOTCH4) as novel correlates of early set-point VL in SCs. The minor allele of rs2857114 (downstream from HLA-DOB) was an unfavorable factor in SPs. Joint models based on demographic features, HLA alleles and the newly identified SNP variants could explain 29% and 15% of VL variance in SCs and SPs, respectively. These findings and bioinformatics strongly suggest that both classic and non-classic MHC genes deserve further investigation, especially in Africans with relatively short haplotype blocks.
doi:10.1038/gene.2014.16
PMCID: PMC4111776  PMID: 24784026
HIV-1; HLA; human MHC; SNP; viral load
4.  Increased Children's Access to Fluoride Varnish Treatment by Involving Medical Care Providers: Effect of a Medicaid Policy Change 
Health Services Research  2009;44(4):1144-1156.
Background
In 2004, the State of Wisconsin introduced a change to their Medicaid Policy allowing medical care providers to be reimbursed for fluoride varnish treatment provided to Medicaid enrolled children.
Objective
To determine the extent by which a state-level policy change impacted access to fluoride varnish treatment (FVT) for Medicaid enrolled children.
Data Source
The Electronic Data Systems of Medicaid Evaluation and Decision Support database for Wisconsin from 2002 to 2006.
Study Design
We analyzed Wisconsin Medicaid claims for FVT for children between the ages of 1 and 6 years, comparing rates in the prepolicy period (2002–2003) to the period (2004–2006) following the policy change.
Principal Findings
Medicaid claims for FVT in 2002–2003 totaled 3,631. Following the policy change, claims for FVT increased to 28,303, with 38.0 percent submitted by medical care providers. FVT rates increased for children of both sexes and all ages, rising from 1.4 per 1,000 person-years of enrollment in 2002–2003 to 6.6 per 1,000 person-years in 2004–2006. Overall, 48.6 percent of the increase in FVT was attributable to medical care providers. The largest increase was seen in children 1–2 years of age, among whom medical care providers were responsible for 83.5 percent of the increase.
Conclusions
A state-level Medicaid policy change was followed by both a significant involvement of medical care providers and an overall increase in FVT. Children between the ages of 1 and 2 years appear to benefit the most from the involvement of medical care providers.
doi:10.1111/j.1475-6773.2009.00975.x
PMCID: PMC2739021  PMID: 19453390
Medicaid-enrolled children; oral health disparities; fluoride varnish treatment; medical care providers; policy change
5.  Human Leukocyte Antigens and Cellular Immune Responses to Anthrax Vaccine Adsorbed 
Infection and Immunity  2013;81(7):2584-2591.
Interindividual variations in vaccine-induced immune responses are in part due to host genetic polymorphisms in the human leukocyte antigen (HLA) and other gene families. This study examined associations between HLA genotypes, haplotypes, and homozygosity and protective antigen (PA)-specific cellular immune responses in healthy subjects following immunization with Anthrax Vaccine Adsorbed (AVA). While limited associations were observed between individual HLA alleles or haplotypes and variable lymphocyte proliferative (LP) responses to AVA, analyses of homozygosity supported the hypothesis of a “heterozygote advantage.” Individuals who were homozygous for any HLA locus demonstrated significantly lower PA-specific LP than subjects who were heterozygous at all eight loci (median stimulation indices [SI], 1.84 versus 2.95, P = 0.009). Similarly, we found that class I (HLA-A) and class II (HLA-DQA1 and HLA-DQB1) homozygosity was significantly associated with an overall decrease in LP compared with heterozygosity at those three loci. Specifically, individuals who were homozygous at these loci had significantly lower PA-specific LP than subjects heterozygous for HLA-A (median SI, 1.48 versus 2.13, P = 0.005), HLA-DQA1 (median SI, 1.75 versus 2.11, P = 0.007), and HLA-DQB1 (median SI, 1.48 versus 2.13, P = 0.002) loci, respectively. Finally, homozygosity at an increasing number (≥4) of HLA loci was significantly correlated with a reduction in LP response (P < 0.001) in a dose-dependent manner. Additional studies are needed to reproduce these findings and determine whether HLA-heterozygous individuals generate stronger cellular immune response to other virulence factors (Bacillus anthracis LF and EF) than HLA-homozygous subjects.
doi:10.1128/IAI.00269-13
PMCID: PMC3697592  PMID: 23649091
6.  The Effect of Parental Mental Health on Proxy reports of Health-related Quality of Life in Children with Sickle Cell Disease 
Pediatric blood & cancer  2010;55(4):10.1002/pbc.22651.
Background
The objectives of this study were to evaluate factors that influence agreement between parent-proxy and child self-report of health-related quality of life (HRQL) in sickle cell disease. We hypothesized that the mental health of the parent, parental HRQL and child characteristics would affect agreement.
Procedure
In a cross-sectional study of children with sickle cell disease, HRQL of the child and the parent’s HRQL and mental health were assessed. The effect of parent and child characteristics on agreement between parent-proxy and child self-report of HRQL were determined.
Results
Rates of agreement between parent-proxy and child self-report of HRQL ranged between 42–49%. Parents with increased symptoms of distress had an increased odds of reporting a worse physical (Odds Ratio (OR) 1.12) and psychosocial HRQL (OR 1.10) compared to the child’s self-report. Severe sickle cell disease was associated with an increased odds of the parent reporting the child’s physical HRQL was worse, (OR 4.68) compared to the child’s self-report.
Conclusions
Greater symptoms of distress in the parent are associated with worse parent-proxy report of the child’s HRQL. Severe sickle cell disease is associated with greater disagreement between parent-proxy and child self-report of HRQL. These findings broaden our understanding of factors that influence proxy-reporting of a child’s HRQL.
doi:10.1002/pbc.22651
PMCID: PMC3835190  PMID: 20589646
sickle cell disease; health-related quality of life; family factors; well being
7.  Racial and Ethnic Disparities in Non-Traumatic Dental Condition Visits to Emergency Departments and Physicians’ Offices in the Wisconsin Medicaid Program 
Background
Non-traumatic dental condition (NTDC) visits frequently occur in emergency departments (EDs) and physicians’ offices (POs), but little is known about whether racial/ethnic disparities exist in Medicaid NTDC visit rates to EDs and POs.
Methods
All Medicaid dental claims in Wisconsin from 2001–2003 were analyzed to examine factors associated with NTDC visits to EDs and POs. Bivariable and multivariable analyses were performed; independent variables examined included race/ethnicity, age, gender, dental health professional shortage area (DHPSA) designation, and Urban Influence Code (UIC) for county of residence.
Results
956,774 NTDC visits made during 1,718,006 person-years were evaluated; 4.3% of visits occurred in EDs/POs. Native Americans, African-Americans, and enrollees of unknown race/ethnicity had the highest unadjusted ED/PO visit rates for NTDCs. African-Americans, Native-Americans, adults, and residence in partial or entire DHPSAs had significantly higher adjusted rates of NTDC visits to EDs. Significantly higher adjusted NTDC visit rates to POs were observed for Native-Americans, adults, and enrollees residing in entire DHPSAs, but African-Americans had a significantly lower adjusted rate.
Conclusions
Native Americans, those residing in entire DHPSAs, and adults have significantly higher risks of NTDC visits to EDs and POs; African-Americans are at increased risk of ED visits but at decreased risk of PO visits for NTDCs.
Clinical Implications
Reductions in Medicaid visits to EDs and POs and the associated costs might be achieved by improving dental care access and targeted educational strategies among minorities, DHPSA residents, and adults.
PMCID: PMC3817617  PMID: 19047672
Medicaid; racial/ethnic disparities; non-traumatic dental conditions; emergency department; DHPSAs
8.  25(OH)D3 and Cardiovascular Risk Factors in Female Nonhuman Primates 
Journal of Women's Health  2012;21(9):959-965.
Abstract
Objective
To determine if interindividual differences in plasma concentrations of 25-hydroxyvitamin D3 (25(OH)D3) have pathophysiologic significance, we evaluated a cohort of female monkeys, seeking to identify associations with clinically relevant cardiovascular risk factors, including age, abdominal obesity (waist circumference), and high-density lipoprotein cholesterol (HDL-C).
Methods
One hundred fifty-five female vervet monkeys (Chlorocebus aethiops sabaeus) aged 3–25 years consumed a typical western diet for 7–8 weeks that provided a woman's equivalent of approximately 1000 IU/day of vitamin D3. Measurements of vitamin D3 and HDL-C concentrations, as well as waist circumference, were obtained.
Results
Among young monkeys (aged 3–5 years), compared to older monkeys (aged 16–25 years), the mean plasma 25(OH)D3 concentrations were 82.3±3.2 ng/mL and 58.6±2.9 ng/mL (p<0.0001), respectively. Plasma 25(OH)D3 concentrations had a range of 19.6–142.0 ng/mL (mean±standard error [SE] 66.4±1.7 ng/mL). 25(OH)D3 concentrations were inversely associated with age (p<0.0001) and waist circumference (p=0.016) and were positively correlated with HDL-C (p=0.01). However, when statistically controlling for age, none of these relationships remained significant.
Conclusions
Higher plasma concentrations of 25(OH)D3 were associated with more favorable cardiovascular risk factors, with inverse associations observed between 25(OH)D3 and abdominal obesity, HDL-C, and age. These associations were no longer significant when controlling for age.
doi:10.1089/jwh.2011.3416
PMCID: PMC3482874  PMID: 22876774
9.  Genome-wide association analysis of juvenile idiopathic arthritis identifies a new susceptibility locus at chromosomal region 3q13 
Arthritis and rheumatism  2012;64(8):2781-2791.
Objective
We have conducted a GWAS in a Caucasian cohort of juvenile idiopathic arthritis (JIA) patients and have previously published findings limited to autoimmune loci shared with other diseases. The goal of this study was to identify novel JIA predisposing loci using genome-wide approaches.
Methods
The Discovery cohort consisted of Caucasian JIA cases (814) and local controls (658) genotyped on the Affymetrix SNP 6.0 Array along with 2400 out-of-study controls. A replication study consisted of 10 SNPs genotyped in 1744 cases and 7010 controls from the US and Europe.
Results
Analysis within the Discovery cohort provided evidence of associations at 3q13 within C3orf1 and near CD80 (rs4688011, OR=1.37, P=1.88×10−6), and 10q21 near the gene JMJD1C [rs6479891, odds ratio (OR) =1.59, P=6.1×10−8; rs12411988, OR=1.57, P=1.16×10−7 and rs10995450, OR = 1.31, P=6.74×10−5]. Meta-analysis continued to provide evidence for association for these 4 SNPs (rs4688011, P=3.6×10−7, rs6479891, P=4.33×10−5; rs12411988, P=2.71×10−5; and rs10995450, 5.39×10−5;). Gene expression data from 68 JIA cases and 23 local controls showed cis eQTL associations for C3orf1 SNP rs4688011 (P=0.024 or P=0.034, depending on probe set) and the JMJD1C SNPs rs6479891 and rs12411988 (P=0.01 and P=0.008, respectively). A variance component liability model estimated that common SNP variation accounts for ~1/3 of JIA susceptibility.
Conclusions
Genetic association results and correlated gene expression findings provide evidence of association at 3q13 and 10q21 for JIA and offer novel genes as plausible candidates in disease pathology.
doi:10.1002/art.34429
PMCID: PMC3366043  PMID: 22354554
10.  A Genome-wide Association Study of Host Genetic Determinants of the Antibody Response to Anthrax Vaccine Adsorbed 
Vaccine  2012;30(32):4778-4784.
Several lines of evidence have supported a host genetic contribution to vaccine response, but genome-wide assessments for specific determinants have been sparse. Here we describe a genome-wide association study (GWAS) of protective antigen-specific antibody (AbPA) responses among 726 European-Americans who received Anthrax Vaccine Adsorbed (AVA) as part of a clinical trial. After quality control, 736,996 SNPs were tested for association with the AbPA response to 3 or 4 AVA vaccinations given over a 6-month period. No SNP achieved the threshold of genome-wide significance (p=5x10−8), but suggestive associations (p<1x10−5) were observed for SNPs in or near the class II region of the major histocompatibility complex (MHC), in the promoter region of SPSB1, and adjacent to MEX3C. Multivariable regression modeling suggested that much of the association signal within the MHC corresponded to previously identified HLA DR-DQ haplotypes involving component HLA-DRB1 alleles of *15:01, *01:01, or *01:02. We estimated the proportion of additive genetic variance explained by common SNP variation for the AbPA response after the 6 month vaccination. This analysis indicated a significant, albeit imprecisely estimated, contribution of variation tagged by common polymorphisms (p=0.032). Future studies will be required to replicate these findings in European Americans and to further elucidate the host genetic factors underlying variable immune response to AVA.
doi:10.1016/j.vaccine.2012.05.032
PMCID: PMC3387748  PMID: 22658931
Anthrax vaccines; Bacillus anthracis; bacterial vaccines; vaccination; Genome-wide association study
11.  Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study 
European Journal of Human Genetics  2011;19(12):1271-1275.
African Americans are a genetically diverse population with a high burden of many, common heritable diseases. However, our understanding of genetic variation in African Americans is substandard because of a lack of published population-based genetic studies. We report the distribution of copy-number variation (CNV) in African Americans collected as part of the Hypertension Genetic Epidemiology Network (HyperGEN) using the Affymetrix 6.0 array and the CNV calling algorithms Birdsuite and PennCNV. We present population estimates of CNV from 446 unrelated African-American subjects randomly selected from the 451 families collected within HyperGEN. Although the majority of CNVs discovered were individually rare, we found the frequency of CNVs to be collectively high. We identified a total of 11 070 CNVs greater than 10 kb passing quality control criteria that were called by both algorithms – leading to an average of 24.8 CNVs per person covering 2214 kb (median). We identified 1541 unique copy-number variable regions, 309 of which did not overlap with the Database of Genomic Variants. These results provide further insight into the distribution of CNV in African Americans.
doi:10.1038/ejhg.2011.115
PMCID: PMC3230358  PMID: 21673747
DNA copy-number variation; African American; calling algorithm; Birdsuite; PennCNV; HyperGEN
12.  Can Rodent Longevity Studies be Both Short and Powerful? 
Many rodent experiments have assessed effects of diets, drugs, genes, and other factors on life span. A challenge with such experiments is their long duration, typically over 3.5 years given rodent life spans, thus requiring significant time costs until answers are obtained. We collected longevity data from 15 rodent studies and artificially truncated them at 2 years to assess the extent to which one will obtain the same answer regarding mortality effects. When truncated, the point estimates were not significantly different in any study, implying that in most cases, truncated studies yield similar estimates. The median ratio of variances of coefficients for truncated to full-length studies was 3.4, implying that truncated studies with roughly 3.4 times as many rodents will often have equivalent or greater power. Cost calculations suggest that shorter studies will be more expensive but perhaps not so much to not be worth the reduced time.
doi:10.1093/gerona/glq190
PMCID: PMC3041472  PMID: 21051569
Longevity; Rodent studies; Proportional hazards; Survival analysis; Sample size
13.  The Role of HLA DR-DQ Haplotypes in Variable Antibody Responses to Anthrax Vaccine Adsorbed 
Genes and immunity  2011;12(6):457-465.
Host genetic variation, particularly within the human leukocyte antigen (HLA) loci, reportedly mediates heterogeneity in immune response to certain vaccines; however, no large study of genetic determinants of anthrax vaccine response has been described. We searched for associations between the IgG antibody to protective antigen (AbPA) response to Anthrax Vaccine Adsorbed (AVA) in humans and polymorphisms at HLA class I (HLA-A, -B, and -C) and class II (HLA-DRB1, -DQA1, -DQB1, -DPB1) loci. The study included 794 European-Americans and 200 African-Americans participating in a 43-month, double-blind, placebo-controlled, clinical trial of AVA (clinicaltrials.gov identifier NCT00119067). Among European-Americans, genes from tightly linked HLA-DRB1-DQA1-DQB1 haplotypes displayed significant overall associations with longitudinal variation in AbPA levels at 4, 8, 26, and 30 weeks from baseline in response to vaccination with 3 or 4 doses of AVA (global p=6.53×10−4). In particular, carriage of the DRB1-DQA1-DQB1 haplotypes *1501-*0102-*0602 (p=1.17×10−5), *0101-*0101-*0501 (p=0.009), and *0102-*0101-*0501 (p=0.006) was associated with significantlylower AbPA levels. In carriers of two copies of these haplotypes, lower AbPA levels persisted following subsequent vaccinations. No significant associations were observed amongst African-Americans or for any HLA class I allele/haplotype. Further studies will be required to replicate these findings and to explore the role of host genetic variation outside of the HLA region.
doi:10.1038/gene.2011.15
PMCID: PMC3165112  PMID: 21368772
Anthrax vaccines; Bacillus anthracis; Bacterial vaccines; Vaccination; HLA Antigens
14.  Six Degrees of Epistasis: Statistical Network Models for GWAS 
Frontiers in Genetics  2012;2:109.
There is growing evidence that much more of the genome than previously thought is required to explain the heritability of complex phenotypes. Recent studies have demonstrated that numerous common variants from across the genome explain portions of genetic variability, spawning various avenues of research directed at explaining the remaining heritability. This polygenic structure is also the motivation for the growing application of pathway and gene set enrichment techniques, which have yielded promising results. These findings suggest that the coordination of genes in pathways that are known to occur at the gene regulatory level also can be detected at the population level. Although genes in these networks interact in complex ways, most population studies have focused on the additive contribution of common variants and the potential of rare variants to explain additional variation. In this brief review, we discuss the potential to explain additional genetic variation through the agglomeration of multiple gene–gene interactions as well as main effects of common variants in terms of a network paradigm. Just as is the case for single-locus contributions, we expect each gene–gene interaction edge in the network to have a small effect, but these effects may be reinforced through hubs and other connectivity structures in the network. We discuss some of the opportunities and challenges of network methods for analyzing genome-wide association studies (GWAS) such as the study of hubs and motifs, and integrating other types of variation and environmental interactions. Such network approaches may unveil hidden variation in GWAS, improve understanding of mechanisms of disease, and possibly fit into a network paradigm of evolutionary genetics.
doi:10.3389/fgene.2011.00109
PMCID: PMC3261632  PMID: 22303403
epistasis network; genetic association interaction network; missing heritability
15.  A Comprehensive Analysis of Shared Loci between Systemic Lupus Erythematosus (SLE) and Sixteen Autoimmune Diseases Reveals Limited Genetic Overlap 
PLoS Genetics  2011;7(12):e1002406.
In spite of the well-known clustering of multiple autoimmune disorders in families, analyses of specific shared genes and polymorphisms between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) have been limited. Therefore, we comprehensively tested autoimmune variants for association with SLE, aiming to identify pleiotropic genetic associations between these diseases. We compiled a list of 446 non–Major Histocompatibility Complex (MHC) variants identified in genome-wide association studies (GWAS) of populations of European ancestry across 17 ADs. We then tested these variants in our combined Caucasian SLE cohorts of 1,500 cases and 5,706 controls. We tested a subset of these polymorphisms in an independent Caucasian replication cohort of 2,085 SLE cases and 2,854 controls, allowing the computation of a meta-analysis between all cohorts. We have uncovered novel shared SLE loci that passed multiple comparisons adjustment, including the VTCN1 (rs12046117, P = 2.02×10−06) region. We observed that the loci shared among the most ADs include IL23R, OLIG3/TNFAIP3, and IL2RA. Given the lack of a universal autoimmune risk locus outside of the MHC and variable specificities for different diseases, our data suggests partial pleiotropy among ADs. Hierarchical clustering of ADs suggested that the most genetically related ADs appear to be type 1 diabetes with rheumatoid arthritis and Crohn's disease with ulcerative colitis. These findings support a relatively distinct genetic susceptibility for SLE. For many of the shared GWAS autoimmune loci, we found no evidence for association with SLE, including IL23R. Also, several established SLE loci are apparently not associated with other ADs, including the ITGAM-ITGAX and TNFSF4 regions. This study represents the most comprehensive evaluation of shared autoimmune loci to date, supports a relatively distinct non–MHC genetic susceptibility for SLE, provides further evidence for previously and newly identified shared genes in SLE, and highlights the value of studies of potentially pleiotropic genes in autoimmune diseases.
Author Summary
It is well known that multiple autoimmune disorders cluster in families. However, all of the genetic variants that explain this clustering have not been discovered, and the specific genetic variants shared between systemic lupus erythematosus (SLE) and other autoimmune diseases (ADs) are not known. In order to better understand the genetic factors that explain this predisposition to autoimmunity, we performed a comprehensive evaluation of shared autoimmune genetic variants. First we considered results from 17 ADs and compiled a list with 446 significant genetic variants from these studies. We identified some genetic variants extensively shared between ADs, as well as the ADs that share the most variants. The genetic overlap between SLE and other ADs was modest. Next we tested how important all the 446 genetic variants were in our collection with a minimum of 1,500 SLE patients. Among the most significant variants in SLE, the majority had already been identified in previous studies, but we also discovered variants in two important immune genes. In summary, our data identified diseases with common genetic risk factors and novel SLE effects, and this supports a relatively distinct genetic susceptibility for SLE. This study helps delineate the genetic architecture of ADs.
doi:10.1371/journal.pgen.1002406
PMCID: PMC3234215  PMID: 22174698
16.  Using the Edmonton obesity staging system to predict mortality in a population-representative cohort of people with overweight and obesity 
Background:
Anthropometric-based classification schemes for excess adiposity do not include direct assessment of obesity-related comorbidity and functional status and thus have limited clinical utility. We examined the ability of the Edmonton obesity staging system, a 5-point ordinal classification system that considers comorbidity and functional status, in predicting mortality in a nationally representative US sample.
Methods:
We analyzed data from the National Health and Human Nutrition Examination Surveys (NHANES) III (1988–1994) and the NHANES 1999–2004, with mortality follow-up through to the end of 2006. Adults (age ≥ 20 yr) with overweight or obesity who had been randomized to the morning session at the mobile examination centre were scored according to the Edmonton obesity staging system. We examined the relationship between staging system scores and mortality, and Cox proportional hazards models were adjusted for the presence of the metabolic syndrome or hypertriglyceridemic waist.
Results:
Over 75% of the cohort with overweight or obesity were given scores of 1 or 2. Scores of 4 could not be reliably assigned because specific data elements were lacking. Survival curves clearly diverged when stratified by scores of 0–3, but not when stratified by obesity class alone. Within the data from the NHANES 1988–1994, scores of 2 (hazard ratio [HR] 1.57; 95% confidence interval [CI] 1.16 to 2.13) and 3 (HR 2.69; 95% CI 1.98 to 3.67) were associated with increased mortality compared with scores of 0 or 1, even after adjustment for body mass index and the metabolic syndrome. We found similar results after adjusting for hypertriglyceridemic waist (i.e., waist circumference ≥ 90 cm and a triglyceride level ≥ 2 mmol/L for men; the corresponding values for women were ≥ 85 cm and ≥ 1.5 mmol/L), as well as in a cohort eligible for bariatric surgery.
Interpretation:
The Edmonton obesity staging system independently predicted increased mortality even after adjustment for contemporary methods of classifying adiposity. The Edmonton obesity staging system may offer improved clinical utility in assessing obesity-related risk and prioritizing treatment.
doi:10.1503/cmaj.110387
PMCID: PMC3185097  PMID: 21844111
17.  Use of self-reported height and weight biases the body mass index-mortality association 
Background
Many large-scale epidemiologic data sources used to evaluate the body mass index (BMI: kg/m2) mortality association have relied on BMI derived from self-reported height and weight. Although measured BMI (BMIM) and self-reported BMI (BMISR) correlate highly, self-reports are systematically biased.
Objective
To rigorously examine how self-reporting bias influences the association between BMI and mortality rate.
Subjects
Samples representing the US non-institutionalized civilian population.
Design and Methods
National Health and Nutrition Examination Survey data (NHANES II: 1976-80; NHANES III: 1988-94) contain BMIM and BMISR. We applied Cox regression to estimate mortality hazard ratios (HRs) for BMIM and BMISR categories, respectively, and compared results. We similarly analyzed subgroups of ostensibly healthy never-smokers.
Results
Misclassification by BMISR among the underweight and obesity ranged from 30–40% despite high correlations between BMIM and BMISR (r>0.9). The reporting bias was moderately correlated with BMIM (r>0.35), but not BMISR (r<0.15). Analyses using BMISR failed to detect six of eight significant mortality HRs detected by BMIM. Significantly biased HRs were detected in the NHANES II full dataset (χ2 = 12.49; p = 0.01) and healthy subgroup (χ2 = 9.93; p = 0.04), but not in the NHANES III full dataset (χ2 = 5.63; p = 0.23) or healthy subgroup (χ2 = 1.52; p = 0.82).
Conclusions
BMISR should not be treated as interchangeable with BMIM in BMI-mortality analyses. Bias and inconsistency introduced by using BMISR in place of BMIM in BMI-mortality estimation and hypothesis tests may account for important discrepancies in published findings.
doi:10.1038/ijo.2010.148
PMCID: PMC3040787  PMID: 20680015
self-reported BMI; measured BMI; self-reporting bias; obesity; mortality; NHANES
18.  Genome-Wide Detection of Allele Specific Copy Number Variation Associated with Insulin Resistance in African Americans from the HyperGEN Study 
PLoS ONE  2011;6(8):e24052.
African Americans have been understudied in genome wide association studies of diabetes and related traits. In the current study, we examined the joint association of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with fasting insulin and an index of insulin resistance (HOMA-IR) in the HyperGEN study, a family based study with proband ascertainment for hypertension. This analysis is restricted to 1,040 African Americans without diabetes. We generated allele specific CNV genotypes at 872,243 autosomal loci using Birdsuite, a freely available multi-stage program. Joint tests of association for SNPs and CNVs were performed using linear mixed models adjusting for covariates and familial relationships. Our results highlight SNPs associated with fasting insulin and HOMA-IR (rs6576507 and rs8026527, 3.7*10−7≤P≤1.1*10−5) near ATPase, class V, type 10A (ATP10A), and the L Type voltage dependent calcium channel (CACNA1D, rs1401492, P≤5.2*10−6). ATP10A belongs to a family of aminophospholipid-transporting ATPases and has been associated with type 2 diabetes in mice. CACNA1D has been linked to pancreatic beta cell generation in mice. The two most significant copy variable markers (rs10277702 and rs361367; P<2.0*10−4) were in the beta variable region of the T-cell receptor gene (TCRVB). Human and mouse TCR has been shown to mimic insulin and its receptor and could contribute to insulin resistance. Our findings differ from genome wide association studies of fasting insulin and other diabetes related traits in European populations, highlighting the continued need to investigate unique genetic influences for understudied populations such as African Americans.
doi:10.1371/journal.pone.0024052
PMCID: PMC3162025  PMID: 21901158
19.  Capitalizing on admixture in genome-wide association studies: a two-stage testing procedure and application to height in African-Americans 
Frontiers in genetics  2011;2:00011.
As genome-wide association studies expand beyond populations of European ancestry, the role of admixture will become increasingly important in the continued discovery and fine-mapping of variation influencing complex traits. Although admixture is commonly viewed as a confounding influence in association studies, approaches such as admixture mapping have demonstrated its ability to highlight disease susceptibility regions of the genome. In this study, we illustrate a powerful two-stage testing strategy designed to uncover trait-associated single nucleotide polymorphisms in the presence of ancestral allele frequency differentiation. In the first stage, we conduct an association scan by using predicted genotypic values based on regional admixture estimates. We then select a subset of promising markers for inclusion in a second-stage analysis, where association is tested between the observed genotype and the phenotype conditional on the predicted genotype. We prove that, under the null hypothesis, the test statistics used in each stage are orthogonal and asymptotically independent. Using simulated data designed to mimic African-American populations in the case of a quantitative trait, we show that our two-stage procedure maintains appropriate control of the family wise error rate and has higher power under realistic effect sizes than the one-stage testing procedure in which all markers are tested for association simultaneously with control of admixture. We apply the proposed procedure to a study of height in 201 African-Americans genotyped at 108 ancestry informative markers. The two-stage procedure identified two statistically significant markers rs1985080 (PTHB1/BBS9) and rs952718 (ABCA12). PTHB1/BBS9 is downregulated by parathyroid hormone in osteoblastic cells and is thought to be involved in parathyroid hormone action in bones and may play a role in height. ABCA12 is a member of the superfamily of ATP-binding cassette transporters and its potential involvement in height is unclear.
doi:10.3389/fgene.2011.00011
PMCID: PMC3132882  PMID: 21754915
two-stage; structured association testing; admixture mapping; regional admixture estimate; genome-wide association studies
20.  Provision of Fluoride Varnish Treatment by Medical and Dental Care Providers: Variation by Race/Ethnicity and Levels of Urban Influence 
Background
In 2004, Wisconsin Medicaid policy changed to allow medical care providers to be reimbursed for fluoride varnish treatment (FVT) to children’s teeth to improve access and utilization. To date, no study has been published on whether geographic and racial/ethnic variation in the provision of FVT in response to this policy change exists.
Objective
To examine the association of rates of FVT for children enrolled in Wisconsin Medicaid with race/ethnicity, Urban Influence Codes (UIC), and Dental Health Professional Shortage Area (DHPSA) designation based on county of residence.
Methods
A retrospective, pre-post design was used based on FVT claims for children in the Wisconsin Medicaid program from 2002 to 2006. Poisson Regression Models were used to evaluate the association of rates of FVT claims with race/ethnicity, UIC, and DHPSA designation.
Results
The rate of FVT claims varied by resident county-type according to UIC and DHPSA designation, age, and race/ethnicity. Post policy, the largest increases were observed for Native Americans residing in none DHPSA counties, enrollees living in rural counties and for Hispanics living in partial and entire DHPSA counties. African-Americans residing in partial DHPSA and metropolitan counties displayed the lowest rates of FVT claims.
Conclusions
Overall access and utilization of fluoride varnish treatment increased, but substantial racial/ethnic and geographic variation in the provision of FVT for children enrolled in Wisconsin Medicaid was observed. Future policies should incorporate measures that will specifically address the racial and geographic variations identified in this study.
doi:10.1111/j.1752-7325.2010.00168.x
PMCID: PMC2967666  PMID: 20459463
Fluoride varnish treatment; Children; Ethnic groups; Health services accessibility
21.  Vaso-occlusive Painful Events in Sickle Cell Disease: Impact on Child Well-Being 
Pediatric blood & cancer  2010;54(1):92-97.
Background
This study describes how painful events affect the health related quality of life (HRQL) of children with sickle cell disease (SCD) and determines the responsiveness of a generic HRQL measure in SCD. Our hypotheses were twofold: 1) HRQL is significantly impaired at presentation to the emergency department for a painful event and 2) PedsQL 4.0 Acute Version Generic Core Scales is responsive to change in the evolution of a painful event.
Procedure
This prospective cohort study included 57 children with SCD. HRQL was measured with the Acute Version of the PedsQL 4.0 Generic Core Scales, completed by child (self-report) and caregiver (proxy-report) at presentation and seven days post-discharge. Independent comparisons of HRQL scores were made between children in the study cohort and a published reference sample of children with SCD in baseline health (historical SCD controls).
Results
Median PedsQL scores at presentation were significantly lower than historical SCD controls in all domains for child self-report and all domains except social and school functioning in parent-proxy. Clinically and statistically significant changes in HRQL between presentation and post-discharge resulted in similar HRQL scores at seven days post-discharge to historical SCD controls.
Conclusions
The PedsQL is responsive to change; thus a useful tool to measure the impact of interventions in future SCD clinical trials. Painful events significantly diminish all domains of HRQL and this improves seven days post-discharge.
doi:10.1002/pbc.22222
PMCID: PMC3114448  PMID: 19653296
sickle cell disease; painful events; health related quality of life; child well-being; patient reported outcomes
22.  A method to assess linkage disequilibrium between CNVs and SNPs inside copy number variable regions 
Frontiers in genetics  2011;2(17):00017.
Since the discovery of the ubiquitous contribution of copy number variation to genetic variability, researchers have commonly used metrics such as r2 to quantify linkage disequilibrium (LD) between copy number variants (CNVs) and single nucleotide polymorphisms (SNPs). However, these reports have been restricted to SNPs outside copy number variable regions (CNVR) as current methods have not been adapted to account for SNPs displaying variable copy number. We show that traditional LD metrics inappropriately quantify SNP/CNV covariance when SNPs lie within CNVR. We derive a new method for measuring LD that solves this issue, and defaults to traditional metrics otherwise. Finally, we present a procedure to estimate CNV–SNP allele frequencies from unphased CNV–SNP genotypes. Our method allows researchers to include all SNPs in SNP/CNV LD measurements, regardless of copy number.
doi:10.3389/fgene.2011.00017
PMCID: PMC3109359  PMID: 21660233
copy number variation; linkage disequilibrium; CNV–SNP haplotype
23.  Beyond Missing Heritability: Prediction of Complex Traits 
PLoS Genetics  2011;7(4):e1002051.
Despite rapid advances in genomic technology, our ability to account for phenotypic variation using genetic information remains limited for many traits. This has unfortunately resulted in limited application of genetic data towards preventive and personalized medicine, one of the primary impetuses of genome-wide association studies. Recently, a large proportion of the “missing heritability” for human height was statistically explained by modeling thousands of single nucleotide polymorphisms concurrently. However, it is currently unclear how gains in explained genetic variance will translate to the prediction of yet-to-be observed phenotypes. Using data from the Framingham Heart Study, we explore the genomic prediction of human height in training and validation samples while varying the statistical approach used, the number of SNPs included in the model, the validation scheme, and the number of subjects used to train the model. In our training datasets, we are able to explain a large proportion of the variation in height (h2 up to 0.83, R2 up to 0.96). However, the proportion of variance accounted for in validation samples is much smaller (ranging from 0.15 to 0.36 depending on the degree of familial information used in the training dataset). While such R2 values vastly exceed what has been previously reported using a reduced number of pre-selected markers (<0.10), given the heritability of the trait (∼0.80), substantial room for improvement remains.
Author Summary
While previous genome-wide association studies have implicated numerous loci associated with complex traits, such loci typically account for a very small proportion of phenotypic variation. However, a recent study using height as a model trait has illustrated that common single nucleotide polymorphisms can explain a large amount of genetic variance when evaluated through whole-genome statistical models. However, it is unclear to what extent higher proportions of explained variance will translate into improved predictive accuracy in future populations. Here we evaluate the predictive ability of whole-genome models for human height while varying the modeling approach, the size of the training population, the validation design, and the number of SNPs. Our results suggest that whole-genome prediction models can yield higher accuracy than what is commonly attained by models based on a few selected SNPs; yet, given the heritability of the trait in question, there exists room for improving prediction accuracy. While gains in predictive accuracy are likely to be small based on more expansive genotyping, our results indicate that more substantial benefits are likely to be gained through larger training populations, as well through the inclusion of related individuals.
doi:10.1371/journal.pgen.1002051
PMCID: PMC3084207  PMID: 21552331
24.  A Method to Assess Linkage Disequilibrium between CNVs and SNPs Inside Copy Number Variable Regions 
Since the discovery of the ubiquitous contribution of copy number variation to genetic variability, researchers have commonly used metrics such as r2 to quantify linkage disequilibrium (LD) between copy number variants (CNVs) and single nucleotide polymorphisms (SNPs). However, these reports have been restricted to SNPs outside copy number variable regions (CNVR) as current methods have not been adapted to account for SNPs displaying variable copy number. We show that traditional LD metrics inappropriately quantify SNP/CNV covariance when SNPs lie within CNVR. We derive a new method for measuring LD that solves this issue, and defaults to traditional metrics otherwise. Finally, we present a procedure to estimate CNV–SNP allele frequencies from unphased CNV–SNP genotypes. Our method allows researchers to include all SNPs in SNP/CNV LD measurements, regardless of copy number.
doi:10.3389/fgene.2011.00017
PMCID: PMC3109359  PMID: 21660233
copy number variation; linkage disequilibrium; CNV–SNP haplotype
25.  A Genome-wide Association Study of Carotid Atherosclerosis in HIV-infected Men 
AIDS (London, England)  2010;24(4):583-592.
Background
The role of host genetics in the development of subclinical atherosclerosis in the context of HIV infected persons who are being treated with highly active antiretroviral therapy (HAART) is not well understood.
Methods
The present genome-wide association study (GWAS) is based on 177 HIV-positive Caucasian males receiving HAART who participated in the Fat Redistribution and Metabolic Change in HIV Infection (FRAM) Study. Common and internal carotid intima-media thicknesses (cIMT) measured by B-mode ultrasound were used as a subclinical measure of atherosclerosis. Single nucleotide polymorphisms (SNPs) were assayed using the Illumina HumanCNV370-quad beadchip. Copy Number Variants (CNV) were inferred using a hidden Markov Model (PennCNV). Regression analyses were used to assess the association of common and internal cIMT with individual SNPs and CNVs, adjusting for age, duration of antiretroviral treatment, and principal components to account for potential population stratification.
Results
Two SNPs in tight linkage disequilibrium, rs2229116 (a missense, nonsynonymous polymorphism (IIe to Val)) and rs7177922, located in the Ryanodine receptor (RYR3) gene on chromosome 15 were significantly associated with common cIMT (p-value<1.61×10−7). The RYR gene family has been known to play a role in the etiology of cardiovascular disease and has been shown to be regulated by HIV TAT protein.
Conclusions
These results suggest that in the context of HIV infection and HAART, a functional SNP in a biologically plausible candidate gene, RYR3, is associated with increased common carotid IMT, which is a surrogate for atherosclerosis.
doi:10.1097/QAD.0b013e3283353c9e
PMCID: PMC3072760  PMID: 20009918
HIV; HAART; atherosclerosis; GWAS; intima-media thickness

Results 1-25 (33)