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1.  The Fibromyalgia Family Study: A Genome-Scan Linkage Study 
Arthritis and rheumatism  2013;65(4):1122-1128.
Familial aggregation of fibromyalgia has been increasingly recognized. The goal of the current study was to conduct a genome wide linkage scan to identify susceptibility loci for fibromyalgia.
We genotyped members of 116 families from the Fibromyalgia Family Study and performed a model-free genome-wide linkage analysis of fibromyalgia with 341 microsatellite markers, using the Haseman-Elston regression approach.
The estimated sibling recurrence risk ratio (λs) for fibromyalgia was 13.6 (95% CI: 10.0–18.5), based on a reported population prevalence of 2%. Genome-wide suggestive evidence of linkage was found at marker D17S2196 (Empirical P =0.00030) and D17S1294 (Empirical P =0.00035) on chromosome 17p11.2-q11.2.
The estimated sibling recurrence risk ratio suggests a strong genetic component of fibromyalgia. This is the first study to report genome-wide suggestive linkage of fibromyalgia to the chromosome 17p11.2-q11.2 region. Further investigation of these multi-case families from the Fibromyalgia Family Study is warranted to identify potential causal risk variants for fibromyalgia.
PMCID: PMC3618544  PMID: 23280346
fibromyalgia; genome scan; linkage; sibling pairs; multi-case families
2.  Association of Smoking and Other Risk Factors With Fuchs' Endothelial Corneal Dystrophy Severity and Corneal Thickness 
We investigated effects of smoking and other risk factors on the development of advanced Fuchs' endothelial corneal dystrophy (FECD) and on central corneal thickness (CCT).
Eyes from Caucasian probands, affected and unaffected family members, and unrelated controls matched for age from the FECD Genetics Multi-Center Study (n = 2044 subjects) were examined. Univariate and multivariate models, adjusted for family correlations, were used to determine the effect of smoking, sex, diabetes, and age on FECD case/control status and CCT.
In a multivariate model, sex and smoking were associated significantly with advanced FECD (grades 4–6) development (P = 0.016 and P = 0.047, respectively). Female sex increased odds by 34%. Smoking increased odds by 30%. In a multivariate model, diabetes was associated with an increase of 9.1 μm in average CCT (P = 0.021). Female sex was associated significantly with a decrease in average CCT by 6.9 μm (P = 0.015). Smoking had no significant effect on CCT in any model. As shown previously, advanced FECD was associated with large increases in CCT (31.4–94.2 μm).
Smoking was associated with an increased risk of advanced FECD and self-reported diabetes was associated with increased CCT. Further study of the impact of smoking and diabetes on FECD development and changes in corneal thickness is warranted.
This case-control analysis showed that smoking was associated significantly with advanced FECD development.
PMCID: PMC3755540  PMID: 23882692
FECD; corneal endothelial cells; smoking
3.  Relationship of Fuchs’ Endothelial Corneal Dystrophy Severity to Central Corneal Thickness 
Archives of ophthalmology  2012;130(4):10.1001/archophthalmol.2011.1626.
To define the relationship between Fuchs’ endothelial corneal dystrophy (FECD) severity and central corneal thickness (CCT).
Eyes from a subset of index cases, family members, and unrelated controls with normal corneas from the FECD Genetics Multi-Center Study (n=1610) were examined. To estimate the association between FECD severity grade (7-point severity scale based on guttae confluence) and CCT measured by ultrasonic pachymetry, a multivariable model was used that adjusted for eye, age, race, gender, glaucoma or ocular hypertension history, diabetes, contact lens wear, intraocular pressure and familial relationship to index case. An interaction between FECD severity grade and edema (stromal or epithelial) on slit lamp examination was used to investigate if the effect of FECD severity grade on CCT differed between those with and without edema.
Average CCT was thicker in index cases for all FECD grades compared to unaffected controls (p ≤ 0.003) and in affected family members with an FECD grade of 4 or greater compared to unaffected family members (p ≤ 0.04). Similar results were observed for subjects without edema. Average CCT of index cases was greater than that of affected family members for grades 4, 5 and 6 (p ≤ 0.02). Intraocular pressure was also associated with CCT (p<0.01).
An increase in CCT occurs with increasing severity of FECD, including at lower FECD grades where clinically observable edema is not present. Monitoring corneal thickness changes serially could be a more sensitive measure of disease progression with surgical therapeutic implications.
PMCID: PMC3859299  PMID: 22491913
4.  A Multi-Center Study to Map Genes for Fuchs’ Endothelial Corneal Dystrophy: Baseline Characteristics and Heritability 
Cornea  2012;31(1):26-35.
To describe the methods for family and case-control recruitment for a multi-center genetic and associated heritability analysis of Fuchs’ Endothelial Corneal Dystrophy (FECD).
Twenty-nine enrolling sites with 62 trained investigators and coordinators gathered individual and family information, graded the phenotype, and collected blood and/or saliva for genetic analysis on all individuals with and without FECD. The degree of FECD was assessed in a 0–6 semi-quantitative scale using standardized clinical methods with pathologic verification of FECD on at least one member of each family. Central corneal thickness was measured by ultrasonic pachymetry.
Three hundred twenty-two families with 330 affected sibling pairs with FECD were enrolled, and included a total of 650 sibling pairs of all disease grades. Using the entire 0–6 step FECD grading scale or a dichotomous definition of severe disease, heritability was assessed in families via sib-sib correlations. Both binary indicators of severe disease as well as semi-quantitative measures of disease severity were significantly heritable, with heritability estimates of 30% for severe disease, 37–39% for FECD score and 47% for central corneal thickness.
Genetic risk factors have a strong role in the severity of the FECD phenotype and corneal thickness. Genotyping this cohort with high-density genetic markers followed by appropriate statistical analyses should lead to novel loci for disease susceptibility.
PMCID: PMC3719980  PMID: 22045388
heritability; Fuchs’ dystrophy; corneal thickness; genetics
5.  Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration 
Genes and Immunity  2010;11(8):609-621.
Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly in the developed world. We conducted a genome-wide association study in a series of families enriched for AMD and completed a meta-analysis of this new data with results from reanalysis of an existing study of a late-stage case/control cohort. We tested the top findings for replication in 1 896 cases and 1 866 controls and identified two novel genetic protective factors for AMD. In addition to the CFH (p=2.3×10−64) and ARMS2 (p=1.2×10−60) loci, we observed a protective effect at rs429608, an intronic SNP in SKIV2L (p=5.3×10−15), a gene near the C2/BF locus, that indicates the protective effect may be mediated by variants other than the C2/BF variants previously studied. Haplotype analysis at this locus identified three protective haplotypes defined by the rs429608 protective allele. We also identified a new potentially protective effect at rs2679798 in MYRIP (p=2.9×10−4), a gene involved in retinal pigment epithelium melanosome trafficking. Interestingly, MYRIP was initially identified in the family-based scan and was confirmed in the case-control set. From these efforts, we report the identification of two novel protective factors for AMD and confirm the previously known associations at CFH, ARMS2 and C3.
PMCID: PMC3375062  PMID: 20861866
macular degeneration; association testing; melanosome trafficking
6.  Heritability Estimation for Speech-Sound Traits with Developmental Trajectories 
Behavior genetics  2010;41(2):184-191.
Numerous studies have examined genetic influences on developmental problems such as speech sound disorders, language impairment, and reading disability. Disorders such as speech sound disorder (SSD) are often analyzed using their component endophenotypes. Most studies, however, have involved comparisons of twin pairs or siblings of similar age, or have adjusted for age ignoring effects that are peculiar to age-related trajectories for phenotypic change. Such developmental changes in these skills have limited the usefulness of data from parents or siblings who differ substantially in age from the probands. Employing parent-offspring correlation in heritability estimation permits a more precise estimate of the additive component of genetic variance, but different generations have to be measured for the same trait. We report on a smoothing procedure which fits a series of lines that approximate a curve matching the developmental trajectory. This procedure adjusts for changes in measures with age, so that the adjusted values are on a similar scale for children, adolescents, and adults. We apply this method to four measures of phonological memory and articulation in order to estimate their heritability. Repetition of multisyllabic real words showed the best heritability estimate of 45% in this sample. We conclude that differences in measurement scales across the age span can be reconciled through non-linear modeling of the developmental process.
PMCID: PMC3066568  PMID: 20623172
Speech; Language; longitudinal; developmental genetics; spline fitting
7.  Genome-wide linkage scans for type 2 diabetes mellitus in four ethnically diverse populations; significant evidence for linkage on chromosome 4q in African Americans: the Family Investigation of Nephropathy and Diabetes (FIND) Research Group 
Previous studies have shown that, in addition to environmental influences, type 2 diabetes mellitus (T2DM) has a strong genetic component. The goal of the current study is to identify regions of linkage for T2DM in ethnically diverse populations.
Phenotypic and genotypic data were obtained from African American (AA; total number of individuals (N)=1004), American Indian (AI; N=883), European American (EA; N=537), and Mexican American (MA; N=1634) individuals from the Family Investigation of Nephropathy and Diabetes. Nonparametric linkage analysis, using an average of 4,404 SNPs, was performed in relative pairs affected with T2DM in each ethnic group. In addition, family-based tests were performed to detect association with T2DM.
Statistically significant evidence for linkage was observed on chromosomes 4q21.1 (LOD=3.13; genome-wide p=0.04) in AA. In addition, a total of eleven regions showed suggestive evidence for linkage (estimated at LOD>1.71), with the highest LOD scores on chromosomes 12q21.31 (LOD=2.02) and 22q12.3 (LOD=2.38) in AA, 2p11.1 (LOD=2.23) in AI, 6p12.3 (LOD=2.77) in EA, and 13q21.1 (LOD=2.24) in MA. While no region overlapped across all ethnic groups, at least five loci showing LOD>1.71 have been identified in previously published studies.
The results from this study provide evidence for the presence of genes affecting T2DM on chromosomes 4q, 12q, and 22q in AA, 6p in EA, 2p in AI, and 13q in MA. The strong evidence for linkage on chromosome 4q in AA provides important information given the paucity of diabetes genetic studies in this population.
PMCID: PMC2783577  PMID: 19795399
FIND; Type 2 Diabetes; linkage analysis; ethnicity
8.  Heritability of the Severity of Diabetic Retinopathy: The FIND-Eye Study 
Diabetic retinopathy (DR) and diabetic nephropathy (DN) are serious microvascular complications of diabetes mellitus. Correlations between severity of DR and DN and computed heritability estimates for DR were determined in a large, multiethnic sample of diabetic families. The hypothesis was that (1) the severity of DR correlates with the presence and severity of nephropathy in individuals with diabetes mellitus, and (2) the severity of DR is under significant familial influence in members of multiplex diabetic families.
The Family Investigation of Nephropathy and Diabetes (FIND) was designed to evaluate the genetic basis of DN in American Indians, European Americans, African Americans, and Mexican Americans. FIND enrolled probands with advanced DN, along with their diabetic siblings who were concordant and discordant for nephropathy. These diabetic family members were invited to participate in the FIND-Eye study to determine whether inherited factors underlie susceptibility to DR and its severity. FIND-Eye participants underwent eye examinations and had fundus photographs taken. The severity of DR was graded by using the Early Treatment Diabetic Retinopathy Study Classification (ETDRS). Sib–sib correlations were calculated with the SAGE 5.0 program FCOR, to estimate heritability of retinopathy severity.
This report summarizes the results for the first 2368 diabetic subjects from 767 families enrolled in FIND-Eye; nearly 50% were Mexican American, the largest single ethnicity within FIND. The overall prevalence of DR was high; 33.4% had proliferative DR; 7.5%, 22.8%, and 9.5% had severe, moderate, and mild nonproliferative DR, respectively; 26.6% had no DR. The severity of DR was significantly associated with severity of DN, both by phenotypic category and by increasing serum creatinine concentration (χ2 = 658.14, df = 20; P < 0.0001). The sib–sib correlation for DR severity was 0.1358 in the total sample and 0.1224 when limited to the Mexican-American sample. Broad sense heritabilities for DR were 27% overall and 24% in Mexican-American families. The polygenic heritability of liability for proliferative DR approximated 25% in this FIND-Eye sample.
These data confirm that the severity of DR parallels the presence and severity of nephropathy in individuals with diabetes mellitus. The severity of DR in members of multiplex diabetic families appears to have a significant familial connection.
PMCID: PMC2583147  PMID: 18765632
9.  Exome Array Analysis Identifies CAV1/CAV2 as a Susceptibility Locus for Intraocular Pressure 
Intraocular pressure (IOP) is an important clinical parameter in the evaluation of ocular health. Elevated IOP is a major risk factor for primary open-angle glaucoma (POAG). The goal of this study was to identify rare and less common variants that influence IOP.
We performed an exome array analysis in a subset of 1660 individuals from a population-based cohort, the Beaver Dam Eye Study. Associations with IOP were tested on 45,849 single nucleotide variants and 12,390 autosomal genes across the genome.
Intraocular pressure was suggestively associated with novel variants located in FAR2 at 12p11.22 (rs4931170, P = 1.2 × 10−5), in GGA3 at 17q25.1 (rs52809447, P = 6.7 × 10−5), and in PKDREJ at 22q13.31 (rs7291444, P = 7.4 × 10−5). Gene-based analysis found suggestive associations between IOP and the genes HAP1, MTBP, FREM3, and PHF12. We successfully replicated the associations with GAS7 (P = 7.4 × 10−3) for IOP, and also identified a previously reported POAG locus in the CAV1/CAV2 region to be associated with IOP (P = 3.3 × 10−3). This association was confirmed in a meta-analysis with three published genome-wide association studies (Pcombined = 4.0 × 10−11).
Our results suggest that novel genetic variants and genes with multiple, less common variants may play a role in the control of IOP. The implication of the caveolin genes, CAV1/CAV2, as a common genetic factor influencing both IOP variations and POAG may provide new insights of the underlying mechanism leading to glaucoma and glaucomatous visual field loss.
Using an exome array, we evaluated rare and low-frequency variants for association with intraocular pressure. We identified an association with the CAV1/CAV2 susceptibility locus, a region known to be associated with primary open angle glaucoma.
PMCID: PMC4303040  PMID: 25525164
exome; SNP; intraocular pressure
10.  Small Drusen and Age-Related Macular Degeneration: The Beaver Dam Eye Study 
Journal of clinical medicine  2015;4(3):424-440.
We tested the hypothesis that large areas of small hard drusen (diameter <63 μm) and intermediate drusen (diameter 63-124 μm) are associated with the incidence of age-related macular degeneration (AMD). Eyes of 3344 older adults with at least 2 consecutive visits spaced 5 years apart over a 20-year period were included. A 6-level severity scale including no drusen, 4 levels of increasing area (from minimal [<2596 μm2] to large [>9086 μm2]) of only small hard drusen, and intermediate drusen was used. The 5-year incidence of AMD was 3% in eyes at the start of the interval with no, minimal, small, and moderate areas of only small drusen and 5% and 25% for eyes with large area of only small drusen and intermediate drusen, respectively. Compared to eyes with a moderate area of small drusen, the odds ratio (OR) of developing AMD in eyes with a large area of only small drusen was 1.8 (P<.001). Compared to eyes with large area of only small drusen, eyes with intermediate drusen had an OR of 5.5 (P<0.001) of developing AMD. Our results are consistent with our hypothesis that large areas of only small drusen are associated with the incidence of AMD.
PMCID: PMC4402933  PMID: 25905023
Age-related macular degeneration; epidemiology; genetic risk; incidence; retinal drusen; risk factors; size and area
11.  Markers of Inflammation, Oxidative Stress, and Endothelial Dysfunction and the 20-year Cumulative Incidence of Early Age-related Macular Degeneration: The Beaver Dam Eye Study 
JAMA ophthalmology  2014;132(4):446-455.
Modifying levels of factors associated with age-related macular degeneration (AMD) may decrease risk of visual impairment in older persons.
To examine the relationships of markers of inflammation, oxidative stress, and endothelial dysfunction to the 20-year cumulative incidence of early AMD.
Longitudinal population-based cohort study.
Beaver Dam, Wisconsin.
A random sample of 975 persons in the Beaver Dam Eye Study without signs of AMD who participated in the baseline examination in 1988-1990 and up to four follow-up examinations in 1993-1995, 1998-2000, 2003-2005, and 2008-2010.
Serum markers of inflammation (high sensitivity C-reactive protein [hsCRP], tumor necrosis factor-α receptor 2 [TNF-αR2], interleukin-6 [IL-6], and white blood cell count), oxidative stress (8-isoprostane and total carbonyl content), and endothelial dysfunction (soluble vascular cell adhesion molecule-1 [sVCAM-1] and soluble intercellular adhesion molecule-1) were measured. Interactions with Complement Factor H (rs1061170) and Age-Related Maculopathy Susceptibility 2 (rs10490924), C3 (rs2230199) and C2/CFB (rs4151667) were examined using multiplicative models. AMD was assessed from fundus photographs.
Main Outcome Measure
Early AMD defined by the presence of any size drusen and the presence of pigmentary abnormalities, or by the presence of large-sized drusen (≥125 μm diameter), in the absence of late AMD.
The 20-year cumulative incidence of early AMD was 23.0%. Adjusting for age, sex, and other risk factors, hsCRP (odds ratio [OR] comparing 4th to 1st quartile 2.18, P=0.005), TNF-αR2 (1.78, P=0.04), and IL-6 (1.78, P=0.03) were associated with the incidence of early AMD. Increased incidence of early AMD was associated with sVCAM-1 (OR per standard deviation on the log ng/mL scale 1.21, P=0.04).
Conclusions and Relevance
We found modest evidence of relationships of serum hsCRP, TNF-αR2, and IL-6 and sVCAM-1 to the 20-year cumulative incidence of early AMD independent of age, smoking status, and other factors. It is not known whether these associations represent a cause and effect relationship or if other unknown confounders accounted for the findings. Even if inflammatory processes are a cause of early AMD, it is not known whether interventions that reduce systemic inflammatory processes will reduce the incidence of early AMD.
PMCID: PMC4076038  PMID: 24481424
12.  Small Drusen and Age-Related Macular Degeneration: The Beaver Dam Eye Study 
Journal of Clinical Medicine  2015;4(3):425-440.
We tested the hypothesis that large areas of small hard drusen (diameter <63 µm) and intermediate drusen (diameter 63–124 µm) are associated with the incidence of age-related macular degeneration (AMD). Eyes of 3344 older adults with at least two consecutive visits spaced five years apart over a 20-year period were included. A 6-level severity scale, including no drusen, four levels of increasing area (from minimal (<2596 µm²) to large (>9086 µm²)) of only small hard drusen, and intermediate drusen, was used. The five-year incidence of AMD was 3% in eyes at the start of the interval with no, minimal, small, and moderate areas of only small drusen and 5% and 25% for eyes with large area of only small drusen and intermediate drusen, respectively. Compared to eyes with a moderate area of small drusen, the odds ratio (OR) of developing AMD in eyes with a large area of only small drusen was 1.8 (p < 0.001). Compared to eyes with large area of only small drusen, eyes with intermediate drusen had an OR of 5.5 (p < 0.001) of developing AMD. Our results are consistent with our hypothesis that large areas of only small drusen are associated with the incidence of AMD.
PMCID: PMC4402933  PMID: 25905023
age-related macular degeneration; epidemiology; genetic risk; incidence; retinal drusen; risk factors; size and area
13.  Sunlight Exposure, Pigmentation, and Incident Age-Related Macular Degeneration 
Examine potential effects of sunlight exposure, hair color, eye color, and selected gene single-nucleotide polymorphisms (SNPs) on incidence of AMD.
Subjects participated in up to five examinations over a 20-year period. Eye color, self-reported hair color as a teenager, and sunlight exposure were ascertained at the baseline examination. Presence and severity of AMD and its lesions were determined via fundus photographs. Genetic data were available on a subset of participants. The SNPs CFH Y402H rs1061170 and ARMS2 A69S rs10490924 were used to analyze genetic risk of AMD; OCA2 rs4778241 and HERC2 rs12913832 represented genetic determinants of eye color.
Incidence of early AMD was higher in blond/red-haired persons compared with brown/black-haired persons (hazard ratio [HR] 1.25, P = 0.02) and in persons with high sun exposure in their thirties (HR 1.41, P = 0.02). However, neither was significant after adjustment for multiple comparisons. Eye (HR 1.36, P = 0.006) and hair color (HR 1.42, P = 0.003) were associated with incidence of any retinal pigmentary abnormalities (RPAs). Both remained significant after adjustment for multiple comparisons. Neither presence of alleles for light-colored eyes nor those associated with high risk of late AMD altered the association of eye or hair color with early AMD. None of the characteristics studied were significantly associated with late AMD.
Modest associations of eye color, hair color, and HERC2 genotype with any RPAs were found. Genes for AMD did not affect these associations. Eye color phenotype was more strongly associated with outcomes than HERC2 or OCA2 genotype.
Hair color and eye color were associated with increased risk of early age-related macular degeneration lesions in the context of relatively higher sunlight exposure.
PMCID: PMC4165367  PMID: 25125603
sunlight exposure; hair color; eye color; age-related macular degeneration; pigmentation
14.  Genome-wide association analyses identify three new susceptibility loci for primary angle closure glaucoma 
Vithana, Eranga N | Khor, Chiea-Chuen | Qiao, Chunyan | Nongpiur, Monisha E | George, Ronnie | Chen, Li-Jia | Do, Tan | Abu-Amero, Khaled | Huang, Chor Kai | Low, Sancy | Tajudin, Liza-Sharmini A | Perera, Shamira A | Cheng, Ching-Yu | Xu, Liang | Jia, Hongyan | Ho, Ching-Lin | Sim, Kar Seng | Wu, Ren-Yi | Tham, Clement C Y | Chew, Paul T K | Su, Daniel H | Oen, Francis T | Sarangapani, Sripriya | Soumittra, Nagaswamy | Osman, Essam A | Wong, Hon-Tym | Tang, Guangxian | Fan, Sujie | Meng, Hailin | Huong, Dao T L | Wang, Hua | Feng, Bo | Baskaran, Mani | Shantha, Balekudaru | Ramprasad, Vedam L | Kumaramanickavel, Govindasamy | Iyengar, Sudha K | How, Alicia C | Lee, Kelvin Y | Sivakumaran, Theru A | Yong, Victor H K | Ting, Serena M L | Li, Yang | Wang, Ya-Xing | Tay, Wan-Ting | Sim, Xueling | Lavanya, Raghavan | Cornes, Belinda K | Zheng, Ying-Feng | Wong, Tina T | Loon, Seng-Chee | Yong, Vernon K Y | Waseem, Naushin | Yaakub, Azhany | Chia, Kee-Seng | Allingham, R Rand | Hauser, Michael A | Lam, Dennis S C | Hibberd, Martin L | Bhattacharya, Shomi S | Zhang, Mingzhi | Teo, Yik Ying | Tan, Donald T | Jonas, Jost B | Tai, E-Shyong | Saw, Seang-Mei | Hon, Do Nhu | Al-Obeidan, Saleh A | Liu, Jianjun | Chau, Tran Nguyen Bich | Simmons, Cameron P | Bei, Jin-Xin | Zeng, Yi-Xin | Foster, Paul J | Vijaya, Lingam | Wong, Tien-Yin | Pang, Chi-Pui | Wang, Ningli | Aung, Tin
Nature genetics  2012;44(10):1142-1146.
Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study including 1,854 PACG cases and 9,608 controls across 5 sample collections in Asia. Replication experiments were conducted in 1,917 PACG cases and 8,943 controls collected from a further 6 sample collections. We report significant associations at three new loci: rs11024102 in PLEKHA7 (per-allele odds ratio (OR) = 1.22; P = 5.33 × 10−12), rs3753841 in COL11A1 (per-allele OR = 1.20; P = 9.22 × 10−10) and rs1015213 located between PCMTD1 and ST18 on chromosome 8q (per-allele OR = 1.50; P = 3.29 × 10−9). Our findings, accumulated across these independent worldwide collections, suggest possible mechanisms explaining the pathogenesis of PACG.
PMCID: PMC4333205  PMID: 22922875
15.  Mitochondrial Polymorphism A10398G and Haplogroup I Are Associated With Fuchs' Endothelial Corneal Dystrophy 
We investigated whether mitochondrial DNA (mtDNA) variants affect the susceptibility of Fuchs endothelial corneal dystrophy (FECD).
Ten mtDNA variants defining European haplogroups were genotyped in a discovery dataset consisting of 530 cases and 498 controls of European descent from the Duke FECD cohort. Association tests for mtDNA markers and haplogroups were performed using logistic regression models with adjustment of age and sex. Subset analyses included controlling for additional effects of either the TCF4 SNP rs613872 or cigarette smoking. Our replication dataset was derived from the genome-wide association study (GWAS) of the FECD Genetics Consortium, where genotypes for three of 10 mtDNA markers were available. Replication analyses were performed to compare non-Duke cases to all GWAS controls (GWAS1, N = 3200), and to non-Duke controls (GWAS2, N = 3043).
The variant A10398G was significantly associated with FECD (odds ratio [OR] = 0.72; 95% confidence interval [CI] = [0.53, 0.98]; P = 0.034), and remains significant after adjusting for smoking status (min P = 0.012). This variant was replicated in GWAS1 (P = 0.019) and GWAS2 (P = 0.036). Haplogroup I was significantly associated with FECD (OR = 0.46; 95% CI = [0.22, 0.97]; P = 0.041) and remains significant after adjusting for the effect of smoking (min P = 0.008) or rs613872 (P = 0.034).
The 10398G allele and Haplogroup I appear to confer significant protective effects for FECD. The effect of A10398G and Haplogroup I to FECD is likely independent of the known TCF4 variant. More data are needed to decipher the interaction between smoking and mtDNA haplogroups.
The nine European mitochondrial haplogroups were investigated for the susceptibility of Fuchs endothelial corneal dystrophy (FECD). A10398G and Haplogroup I were found significantly decreasing the risk of FECD.
PMCID: PMC4109404  PMID: 24917144
mitochondrial haplogroup; genetic association; oxidative stress; TCF4; smoking
16.  Prediction of Age-related Macular Degeneration in the General Population 
Ophthalmology  2013;120(12):2644-2655.
Prediction models for age-related macular degeneration (AMD) based on case-control studies have a tendency to overestimate risks. The aim of this study is to develop a prediction model for late AMD based on data from population-based studies.
Three population-based studies: the Rotterdam Study (RS), the Beaver Dam Eye Study (BDES), and the Blue Mountains Eye Study (BMES) from the Three Continent AMD Consortium (3CC).
People (n = 10106) with gradable fundus photographs, genotype data, and follow-up data without late AMD at baseline.
Features of AMD were graded on fundus photographs using the 3CC AMD severity scale. Associations with known genetic and environmental AMD risk factors were tested using Cox proportional hazard analysis. In the RS, the prediction of AMD was estimated for multivariate models by area under receiver operating characteristic curves (AUCs). The best model was validated in the BDES and BMES, and associations of variables were re-estimated in the pooled data set. Beta coefficients were used to construct a risk score, and risk of incident late AMD was calculated using Cox proportional hazard analysis. Cumulative incident risks were estimated using Kaplan–Meier product-limit analysis.
Main Outcome Measures
Incident late AMD determined per visit during a median follow-up period of 11.1 years with a total of 4 to 5 visits.
Overall, 363 participants developed incident late AMD, 3378 participants developed early AMD, and 6365 participants remained free of any AMD. The highest AUC was achieved with a model including age, sex, 26 single nucleotide polymorphisms in AMD risk genes, smoking, body mass index, and baseline AMD phenotype. The AUC of this model was 0.88 in the RS, 0.85 in the BDES and BMES at validation, and 0.87 in the pooled analysis. Individuals with low-risk scores had a hazard ratio (HR) of 0.02 (95% confidence interval [CI], 0.01–0.04) to develop late AMD, and individuals with high-risk scores had an HR of 22.0 (95% CI, 15.2–31.8). Cumulative risk of incident late AMD ranged from virtually 0 to more than 65% for those with the highest risk scores.
Our prediction model is robust and distinguishes well between those who will develop late AMD and those who will not. Estimated risks were lower in these population-based studies than in previous case-control studies.
PMCID: PMC3986722  PMID: 24120328
17.  Association between AVPR1A, DRD2, and ASPM and Endophenotypes of Communication Disorders 
Psychiatric genetics  2014;24(5):191-200.
Speech sound disorder (SSD) is one of the most common communication disorders, with prevalence rates of 16% at 3 years of age, and an estimated 3.8% of children still presenting speech difficulties at 6 years of age. Several studies have identified promising associations between communication disorders and genes in brain and neuronal pathways, but there have been few studies focusing on SSD and its associated endophenotypes. Based on the hypothesis that neuronal genes may influence endophenotypes common to communication disorders, we focused on three genes related to brain and central nervous system functioning: dopamine D2 receptor (DRD2), arginine-vassopressin receptor 1a (AVPR1A), and microcephaly gene ASPM.
We examined the association of these genes with key endophenotypes of SSD – phonological memory measured by multisyllabic and nonword repetition, vocabulary measured by Expressive One Word Picture Vocabulary Test (EOWPVT) and Peabody Picture Vocabulary Test (PPVT), and reading decoding measured by Woodcock Reading Mastery Tests Revised – as well as the clinical phenotype of SSD. We genotyped tag SNPs in these genes and examined 498 individuals from 180 families.
These data show several SNPs in all three genes were associated with phonological memory, vocabulary, and reading decoding with p<0.05. Notably, associations in AVPR1A (rs11832266) were significant after multiple testing correction. Gene-level tests showed DRD2 was associated with vocabulary, ASPM with vocabulary and reading decoding, and AVPR1A with all three endophenotypes.
Endophenotypes common to SSD, language impairment, and reading disability are all associated with these neuronal pathway genes.
PMCID: PMC4141900  PMID: 24849541
neural genes; phonology; speech impairment; language development; genetics
19.  Misclassification Can Explain Most Apparent Regression of Age-Related Macular Degeneration: Results From Multistate Models With Misclassification 
To investigate the impact of misclassification of age-related macular degeneration (AMD) on the baseline intensity and estimated effects of age, sex, and the Y402H variant in the complement factor H (CFH) gene on incidence, progression, and regression of AMD.
The Beaver Dam Eye Study, a longitudinal population-based study of age-related eye diseases conducted in the city and township of Beaver Dam, Wisconsin, performed examinations every 5 years during a 20-year period (1988–1990 through 2008–2010). Study participants (N = 4379) aged 43 to 86 years at the baseline examination had retinal photographs taken at baseline and up to four subsequent examinations. Multistate models with misclassification in continuous time were used to model the effects of age, sex, and CFH genotype on incidence, progression, and regression of AMD and mortality.
After accounting for AMD misclassification, the occurrence of any AMD regression was rare (1%–4%), while it was relatively common (14%–21%) in models that do not account for misclassification. Failure to account for misclassification attenuated estimated age effects on incidence and progression to moderately severe early AMD and attenuated estimated CFH effects on incidence and progressions to moderately severe and severe early AMD.
Apparent regression of AMD can largely, if not completely, be explained by misclassification. Estimated age effects on incidence and progression to moderately severe early AMD and estimated CFH effects on incidence and progressions to moderately severe and severe early AMD were attenuated in multistate models that did not account for misclassification.
We investigate the impact of misclassification of AMD on the baseline intensity and covariate effects on incidence, progression, and regression of AMD. Regression of AMD can largely be explained by misclassification, and effects of age and CFH were attenuated in models without misclassification.
PMCID: PMC3968926  PMID: 24550369
age-related macular degeneration; CFH; epidemiology
20.  Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes 
Ng, Maggie C. Y. | Shriner, Daniel | Chen, Brian H. | Li, Jiang | Chen, Wei-Min | Guo, Xiuqing | Liu, Jiankang | Bielinski, Suzette J. | Yanek, Lisa R. | Nalls, Michael A. | Comeau, Mary E. | Rasmussen-Torvik, Laura J. | Jensen, Richard A. | Evans, Daniel S. | Sun, Yan V. | An, Ping | Patel, Sanjay R. | Lu, Yingchang | Long, Jirong | Armstrong, Loren L. | Wagenknecht, Lynne | Yang, Lingyao | Snively, Beverly M. | Palmer, Nicholette D. | Mudgal, Poorva | Langefeld, Carl D. | Keene, Keith L. | Freedman, Barry I. | Mychaleckyj, Josyf C. | Nayak, Uma | Raffel, Leslie J. | Goodarzi, Mark O. | Chen, Y-D Ida | Taylor, Herman A. | Correa, Adolfo | Sims, Mario | Couper, David | Pankow, James S. | Boerwinkle, Eric | Adeyemo, Adebowale | Doumatey, Ayo | Chen, Guanjie | Mathias, Rasika A. | Vaidya, Dhananjay | Singleton, Andrew B. | Zonderman, Alan B. | Igo, Robert P. | Sedor, John R. | Kabagambe, Edmond K. | Siscovick, David S. | McKnight, Barbara | Rice, Kenneth | Liu, Yongmei | Hsueh, Wen-Chi | Zhao, Wei | Bielak, Lawrence F. | Kraja, Aldi | Province, Michael A. | Bottinger, Erwin P. | Gottesman, Omri | Cai, Qiuyin | Zheng, Wei | Blot, William J. | Lowe, William L. | Pacheco, Jennifer A. | Crawford, Dana C. | Grundberg, Elin | Rich, Stephen S. | Hayes, M. Geoffrey | Shu, Xiao-Ou | Loos, Ruth J. F. | Borecki, Ingrid B. | Peyser, Patricia A. | Cummings, Steven R. | Psaty, Bruce M. | Fornage, Myriam | Iyengar, Sudha K. | Evans, Michele K. | Becker, Diane M. | Kao, W. H. Linda | Wilson, James G. | Rotter, Jerome I. | Sale, Michèle M. | Liu, Simin | Rotimi, Charles N. | Bowden, Donald W.
PLoS Genetics  2014;10(8):e1004517.
Type 2 diabetes (T2D) is more prevalent in African Americans than in Europeans. However, little is known about the genetic risk in African Americans despite the recent identification of more than 70 T2D loci primarily by genome-wide association studies (GWAS) in individuals of European ancestry. In order to investigate the genetic architecture of T2D in African Americans, the MEta-analysis of type 2 DIabetes in African Americans (MEDIA) Consortium examined 17 GWAS on T2D comprising 8,284 cases and 15,543 controls in African Americans in stage 1 analysis. Single nucleotide polymorphisms (SNPs) association analysis was conducted in each study under the additive model after adjustment for age, sex, study site, and principal components. Meta-analysis of approximately 2.6 million genotyped and imputed SNPs in all studies was conducted using an inverse variance-weighted fixed effect model. Replications were performed to follow up 21 loci in up to 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry. We identified three known loci (TCF7L2, HMGA2 and KCNQ1) and two novel loci (HLA-B and INS-IGF2) at genome-wide significance (4.15×10−94
Author Summary
Despite the higher prevalence of type 2 diabetes (T2D) in African Americans than in Europeans, recent genome-wide association studies (GWAS) were examined primarily in individuals of European ancestry. In this study, we performed meta-analysis of 17 GWAS in 8,284 cases and 15,543 controls to explore the genetic architecture of T2D in African Americans. Following replication in additional 6,061 cases and 5,483 controls in African Americans, and 8,130 cases and 38,987 controls of European ancestry, we identified two novel and three previous reported T2D loci reaching genome-wide significance. We also examined 158 loci previously reported to be associated with T2D or regulating glucose homeostasis. While 56% of these loci were shared between African Americans and the other populations, the strongest associations in African Americans are often found in nearby single nucleotide polymorphisms (SNPs) instead of the original SNPs reported in other populations due to differential genetic architecture across populations. Our results highlight the importance of performing genetic studies in non-European populations to fine map the causal genetic variants.
PMCID: PMC4125087  PMID: 25102180
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).
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).
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).
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).
PMCID: PMC3908680  PMID: 24346170
macular degeneration; carotenoids; genes
Cornea  2013;32(5):696-701.
Keratoconus is a genetically heterogeneous corneal dystrophy. Previously, we performed two genome-wide linkage scans in a four generation autosomal dominant pedigree and repeatedly mapped a keratoconus locus to a genomic region located on chromosome 5q overlapping the gene encoding the inhibitor of calpains, calpastatin (CAST). To test whether variants in CAST gene are involved in genetic susceptibility to keratoconus we performed genetic testing of polymorphic markers in CAST gene in family and case-control panels of patients with keratoconus.
We genotyped SNPs (Single Nucleotide Polymorphisms) located in CAST gene in 262 patients in 40 Caucasian keratoconus families and in a Caucasian case-control panel with 304 cases and 518 controls. Generalized estimating equation models accounting for familial correlations implemented in GWAF program were used for association testing in families. Logistic regression models implemented in PLINK were performed to test associations in case-control samples.
Genetic testing of first set of seven SNPs in familial samples revealed two tentative nominally significant markers (rs4869307 p=0.03; rs27654: p=0.07). Additional genotyping of twelve tightly spaced SNPs identified CAST SNP rs4434401 to be associated with keratoconus in both familial and case-control panels with p values of 0.005 and 0.05, respectively; and with combined meta p value of familial and case-control cohorts of 0.002, or, after Bonferroni correction, 0.04.
Linkage analysis and genetic association support involvement of CAST gene in the genetic susceptibility to keratoconus. In-silico analysis of CAST expression suggests differential regulation of calpain/calpastatin system in cornea as a potential mechanism of functional defect.
PMCID: PMC3653445  PMID: 23449483
Linkage analysis; genetic association; common variation; keratoconus; calpains; calpastatin
Ophthalmology  2013;120(5):1012-1019.
To describe the relationships of intima-media layer thickness (IMT), plaque in the carotid artery, angina, myocardial infarction (MI), and stroke to the 10-year cumulative incidence of early and late age-related macular degeneration (AMD) and progression of AMD.
Cohort study.
1700 persons aged 53–96 years who participated in both the Epidemiology of Hearing Loss Study and the Beaver Dam Eye Study in 1998–2000, with photographs gradable for AMD at a 5- (2003–2005) and/or 10-year (2008–2010) follow-up examination.
IMT and presence of plaque were assessed using B-mode ultrasonography of the carotid artery. Presence of angina, MI, and stroke were defined based on a self-reported history of physician diagnosis. Presence and severity of AMD were determined by systematic grading of stereoscopic color fundus photographs.
Main Outcome Measures
The 10-year cumulative incidence of early AMD was 15.7% and the 10-year cumulative incidence of late AMD was 4.0%. Adjusting for age, sex, body mass index, smoking status, Age-Related Maculopathy Susceptibility 2 and Complement Factor H genotypes and other factors, mean IMT was associated with the 10-year incidence of early AMD (odds ratio per 0.1 mm IMT 1.11, 95% confidence interval 1.00–1.21, P value=0.03) and late AMD (1.27, 1.10–1.47, P=0.001). Mean IMT was associated with the 10-year incidence of pure geographic atrophy (1.31, 1.05–1.64, P=0.02) but not exudative AMD (1.14, 0.97–1.34, P=0.11). Similar associations were found for maximum IMT. The number of sites with plaque was related to the incidence of late AMD (2.79 for 4–6 sites vs. none, 1.06–7.37, P=0.04) but not to early AMD. A history of angina, MI, or stroke was not related to any incident AMD outcome.
In these population-based data, carotid artery IMT and carotid plaques had a weak relationship to the incidence of late AMD, independent of systemic and genetic risk factors. Angina, MI, and stroke were not related to AMD. It is unclear whether the carotid IMT is a risk indicator of processes affecting Bruch’s membrane and the retinal pigment epithelium, or a measure of atherosclerosis affecting susceptibility to AMD.
PMCID: PMC3646961  PMID: 23399375
Archives of ophthalmology  2012;130(11):1384-1388.
To investigate if Fuchs' Endothelial Corneal Dystrophy (FECD) severity is associated with glaucoma and/or ocular hypertension (G/OHTN).
A subset of eyes (n=1610) from the FECD Genetics Multi-Center Study were examined to estimate the association between FECD severity (grades 0–6 based on guttae confluence) and G/OHTN. Logistic regression models were fit that accounted for the correlation between eyes and adjusted for age, sex, central corneal thickness, intraocular pressure, presence of diabetes, and time of day of initial evaluation.
107 eyes (6.6%) had G/OHTN based on the study definition. The prevalence of G/OHTN in the control group was 6%. Prevalence was lower in index cases with an FECD grade of 1 through 3 and family members with a grade of 0 or 1 through 3 (0% and 2%, respectively) but higher in index cases and family members with a grade of 4 through 6 (11% and 9%, respectively). Adjusting for covariates, eyes with a grade of 4 through 6 were more likely to have concurrent G/OHTN than eyes with no FECD (index cases vs. controls: OR=2.10, p=0.04; affected vs. unaffected family: OR=7.06, p=0.07). Age (OR=1.06 per 1 year increase, p<0.001) and intraocular pressure (OR=1.15 per 1 mmHg increase, p<0.001) were also associated with an increased prevalence of G/OHTN. Sex, diabetes, time of day of evaluation, and central corneal thickness were not associated with the prevalence of G/OHTN (p>0.15).
Glaucoma and/or ocular hypertension occurs more often in eyes affected with severe FECD compared to unaffected eyes. Therefore, it may be beneficial to monitor for the development of glaucoma in these patients.
PMCID: PMC3954552  PMID: 22777534
JAMA ophthalmology  2013;131(3):383-392.
To describe relationships of risk alleles in complement factor H (CFH, rs1061170) and Age-Related Maculopathy susceptibility 2 (ARMS2, rs10490924) to the incidence and progression of age-related macular degeneration (AMD) over a 20-year period.
There were 4282 persons aged 43–86 years at the baseline examination in 1988–1990 enrolled in a population-based cohort study who participated in at least 1 pair of examinations spaced 5 years apart over a 20-year period and had gradable fundus photographs for AMD and genotype information on CFH and ARMS2. Low, intermediate, and high genetic risk for AMD was defined by the presence of 0–1, 2, or 3–4 risk alleles for CFH and ARMS2, respectively. Multi-state models (MSMs) were used to estimate progression of AMD over the entire age range.
There were 2820 (66%), 1129 (26%), and 333 persons (8%) with low, intermediate, and high genetic risk for AMD, respectively. The 5-year incidences of early and late AMD were 9.1% and 1.6%, respectively, and increased with age but did not differ by sex. Using the MSM, of persons aged 45 years with no AMD in the low, intermediate, and high AMD genetic risk groups, 33.0%, 39.9%, and 46.5%, respectively were estimated to develop early AMD, and 1.4%, 5.2%, and 15.3%, respectively were estimated to develop late AMD by age 80 years.
These population-based data provide estimates of the long-term risk of the incidence and progression of AMD and its lesions by age and genetic risk alleles for CFH and ARMS2.
PMCID: PMC3602927  PMID: 23494043
age-related macular degeneration; ARMS2; CFH; epidemiology

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