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1.  The Fibromyalgia Family Study: A Genome-Scan Linkage Study 
Arthritis and rheumatism  2013;65(4):1122-1128.
Objective
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.
Methods
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.
Results
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.
Conclusion
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.
doi:10.1002/art.37842
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 
Purpose.
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).
Methods.
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.
Results.
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).
Conclusions.
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.
doi:10.1167/iovs.13-11918
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.
Objective
To define the relationship between Fuchs’ endothelial corneal dystrophy (FECD) severity and central corneal thickness (CCT).
Methods
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.
Results
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).
Conclusions
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.
doi:10.1001/archophthalmol.2011.1626
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.
Purpose
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).
Methods
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.
Results
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.
Conclusion
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.
doi:10.1097/ICO.0b013e31821c9b8f
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.
doi:10.1038/gene.2010.39
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.
doi:10.1007/s10519-010-9378-5
PMCID: PMC3066568  PMID: 20623172
Speech; Language; longitudinal; developmental genetics; spline fitting
7.  An association between the Calpastatin (CAST) gene and keratoconus 
Cornea  2013;32(5):696-701.
Purpose
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.
Methods
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.
Results
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.
Conclusions
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.
doi:10.1097/ICO.0b013e3182821c1c
PMCID: PMC3653445  PMID: 23449483
Linkage analysis; genetic association; common variation; keratoconus; calpains; calpastatin
8.  The Relationship of Atherosclerosis to the 10-Year Cumulative Incidence of Age-Related Macular Degeneration: The Beaver Dam Studies 
Ophthalmology  2013;120(5):1012-1019.
Objective
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.
Design
Cohort study.
Participants
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.
Methods
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
AMD.
Results
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.
Conclusions
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.
doi:10.1016/j.ophtha.2012.11.003
PMCID: PMC3646961  PMID: 23399375
9.  The Relationship between Fuchs' Endothelial Corneal Dystrophy Severity and Glaucoma and/or Ocular Hypertension 
Archives of ophthalmology  2012;130(11):1384-1388.
Objective
To investigate if Fuchs' Endothelial Corneal Dystrophy (FECD) severity is associated with glaucoma and/or ocular hypertension (G/OHTN).
Methods
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.
Results
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).
Conclusions
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.
doi:10.1001/archophthalmol.2012.1969
PMCID: PMC3954552  PMID: 22777534
10.  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 
Background
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.
Methods
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.
Results
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.
Conclusions
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.
doi:10.1002/dmrr.1031
PMCID: PMC2783577  PMID: 19795399
FIND; Type 2 Diabetes; linkage analysis; ethnicity
11.  Risk Alleles in CFH and ARMS2 and the Long Term Natural History of Age-Related Macular Degeneration. The Beaver Dam Eye Study 
JAMA ophthalmology  2013;131(3):383-392.
Objective
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.
Methods
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.
Results
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.
Conclusions
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.
doi:10.1001/jamaophthalmol.2013.713
PMCID: PMC3602927  PMID: 23494043
age-related macular degeneration; ARMS2; CFH; epidemiology
12.  Heritability of the Severity of Diabetic Retinopathy: The FIND-Eye Study 
PURPOSE
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.
METHODS
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.
RESULTS
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.
CONCLUSIONS
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.
doi:10.1167/iovs.07-1633
PMCID: PMC2583147  PMID: 18765632
13.  Speech-Sound Disorders and Attention-Deficit/Hyperactivity Disorder Symptoms 
Topics in language disorders  2012;32(3):247-263.
Purpose
The purpose of this study was to examine the association of speech-sound disorders (SSD) with symptoms of attention-deficit/hyperactivity disorder (ADHD) by the severity of the SSD and the mode of transmission of SSD within the pedigrees of children with SSD.
Participants and Methods
The participants were 412 children who were enrolled in a longitudinal family study of SSD. Children were grouped on the basis of the severity of their SSD as determined by their scores on the Goldman–Fristoe Test of Articulation and history of an SSD. Five severity groups were compared: no SSD, resolved SSD, mild SSD, mild–moderate SSD, and moderate–severe SSD. Participants were also coded for comorbid language impairment (LI), based on scores on a standardized language test. Pedigrees of children were considered to represent bilineal inheritance of disorders if there was a history for SSD on both the maternal and paternal sides of the family. Parents completed the ADHD rating scale and a developmental questionnaire for each of their children.
Results and Conclusions
Children with moderate–severe SSD had higher ratings on the inattention and hyperactive/impulsivity scales than children with no SSD. Children whose family pedigrees demonstrated bilineal inheritance had higher ratings of inattention than children without bilineal inheritance. To determine the best predictors of ADHD ratings, multiple linear regression analyses were conducted. LI was more predictive of ADHD symptoms than SSD severity, bilineal inheritance of SSD, age, or gender. Findings support that LI rather than SSD is associated with ADHD.
PMCID: PMC3868495  PMID: 24363479
ADHD; attention; genetics; language impairment; reading disorder; speech sound disorder
14.  A Genome-Wide Search for Linkage of Estimated Glomerular Filtration Rate (eGFR) in the Family Investigation of Nephropathy and Diabetes (FIND) 
PLoS ONE  2013;8(12):e81888.
Objective
Estimated glomerular filtration rate (eGFR), a measure of kidney function, is heritable, suggesting that genes influence renal function. Genes that influence eGFR have been identified through genome-wide association studies. However, family-based linkage approaches may identify loci that explain a larger proportion of the heritability. This study used genome-wide linkage and association scans to identify quantitative trait loci (QTL) that influence eGFR.
Methods
Genome-wide linkage and sparse association scans of eGFR were performed in families ascertained by probands with advanced diabetic nephropathy (DN) from the multi-ethnic Family Investigation of Nephropathy and Diabetes (FIND) study. This study included 954 African Americans (AA), 781 American Indians (AI), 614 European Americans (EA) and 1,611 Mexican Americans (MA). A total of 3,960 FIND participants were genotyped for 6,000 single nucleotide polymorphisms (SNPs) using the Illumina Linkage IVb panel. GFR was estimated by the Modification of Diet in Renal Disease (MDRD) formula.
Results
The non-parametric linkage analysis, accounting for the effects of diabetes duration and BMI, identified the strongest evidence for linkage of eGFR on chromosome 20q11 (log of the odds [LOD] = 3.34; P = 4.4×10−5) in MA and chromosome 15q12 (LOD = 2.84; P = 1.5×10−4) in EA. In all subjects, the strongest linkage signal for eGFR was detected on chromosome 10p12 (P = 5.5×10−4) at 44 cM near marker rs1339048. A subsequent association scan in both ancestry-specific groups and the entire population identified several SNPs significantly associated with eGFR across the genome.
Conclusion
The present study describes the localization of QTL influencing eGFR on 20q11 in MA, 15q21 in EA and 10p12 in the combined ethnic groups participating in the FIND study. Identification of causal genes/variants influencing eGFR, within these linkage and association loci, will open new avenues for functional analyses and development of novel diagnostic markers for DN.
doi:10.1371/journal.pone.0081888
PMCID: PMC3866106  PMID: 24358131
15.  Genetic Association of COL5A1 Variants in Keratoconus Patients Suggests a Complex Connection between Corneal Thinning and Keratoconus 
Purpose.
Single nucleotide polymorphisms (SNPs) located near or within the COL5A1 gene, at 9q34.2-q34.3 chromosomal region have been reported in association with central corneal thickness (CCT). Using family linkage analysis, we identified a keratoconus susceptibility locus at 9q34. These findings led us to perform an association study between COL5A1 variation and keratoconus susceptibility.
Methods.
A Caucasian case–control cohort of 222 keratoconus patients and 3324 controls was selected as the discovery panel. An independent case–control panel of 304 cases and 518 controls and a family panel of 186 subjects were replicated for genotyping and association. Forty-four SNPs (21 for discovery and 23 for fine-mapping) spanning 300 kilobases in and around COL5A1 were genotyped and tested for genetic association. Logistic regression models implemented in PLINK were used to test for association in case controls. Generalized estimating equation models accounting for familial correlations implemented in genome-wide interaction analyses with family data were used for association testing in families.
Results.
Two CCT associated SNPs (rs1536482 and rs7044529 near and within COL5A1) were identified in the keratoconus discovery cohort (P values of 6.5 × 10−3 and 7.4 × 10−3). SNP rs1536482 was replicated in the second case–control sample (P = 0.02), and SNP rs7044529 was replicated in a keratoconus family panel (P = 0.03). Meta P values of rs1536482 and rs7044529 in the keratoconus cohorts were 1.5 × 10−4 (odds ratio [OR] = 1.30) and 2.9 × 10−3 (OR = 1.39). After Bonferroni correction, the association of SNP rs1536482 remained significant (P = 6.5 × 10−3).
Conclusions.
SNPs in the COL5A1 region, which regulate normal variation in CCT, may play a role in the thinning associated with keratoconus.
Variants in the COL5A1 gene may contribute to genetic susceptibility to corneal thinning associated with keratoconus, in addition to their role in genetic regulation of normal variation in central corneal thickness.
doi:10.1167/iovs.13-11601
PMCID: PMC3630822  PMID: 23513063
keratoconus; association; COL5A1
16.  The Y402H Variant in the Complement Factor H Gene Affects Incidence and Progression of Age-Related Macular Degeneration: Results from Multi-State Models Applied to the Beaver Dam Eye Study 
Archives of ophthalmology  2012;130(9):1169-1176.
Objective
To investigate the impact of age, sex and the Y402H variant in the complement factor H (CFH) gene on incidence, progression and regression of age-related macular degeneration (AMD) and the impact of these factors and AMD on mortality using multi-state models (MSMs).
Methods
Analyses included 4,379 persons aged 43 to 86 years at the time of initial examination. AMD status on a 5-level severity scale was graded from retinal photographs taken at up to 5 study visits between 1988 and 2010. MSMs in continuous time were used to model the effects of age, sex and CFH genotype on incidence, progression and regression of AMD and mortality.
Results
CFH Y402H genotype CC was associated, relative to genotype TT (reported as hazard ratio, 95% confidence interval), with increased incidence of AMD (no to minimally severe early AMD: 1.98, 1.57–2.49), progression of AMD (minimally severe early to moderately severe early AMD: 1.73, 1.29–2.33; moderately severe early to severe early AMD: 1.30, 0.86–1.94; and severe early to late AMD: 1.72, 1.01–2.91), but not with regression of AMD or mortality. Late AMD was associated with increased mortality (1.37, 1.15–1.62) relative to no AMD, but earlier stages of AMD were not.
Conclusions
Using MSMs, we show that the Y402H risk variant elevates lifetime incidence of early AMD and progression of early to late AMD, and that late AMD elevates mortality risk.
doi:10.1001/archophthalmol.2012.693
PMCID: PMC3495559  PMID: 22965593
age-related macular degeneration; CFH; epidemiology
17.  Genetic Determinants of Macular Pigments in Women of the Carotenoids in Age-Related Eye Disease Study 
Purpose.
To investigate genetic determinants of macular pigment optical density in women from the Carotenoids in Age-Related Eye Disease Study (CAREDS), an ancillary study of the Women's Health Initiative Observational Study.
Methods.
1585 of 2005 CAREDS participants had macular pigment optical density (MPOD) measured noninvasively using customized heterochromatic flicker photometry and blood samples genotyped for 440 single nucleotide polymorphisms (SNPs) in 26 candidate genes related to absorption, transport, binding, and cleavage of carotenoids directly, or via lipid transport. SNPs were individually tested for associations with MPOD using least-squares linear regression.
Results.
Twenty-one SNPs from 11 genes were associated with MPOD (P ≤ 0.05) after adjusting for dietary intake of lutein and zeaxanthin. This includes variants in or near genes related to zeaxanthin binding in the macula (GSTP1), carotenoid cleavage (BCMO1), cholesterol transport or uptake (SCARB1, ABCA1, ABCG5, and LIPC), long-chain omega-3 fatty acid status (ELOVL2, FADS1, and FADS2), and various maculopathies (ALDH3A2 and RPE65). The strongest association was for rs11645428 near BCMO1 (βA = 0.029, P = 2.2 × 10−4). Conditional modeling within genes and further adjustment for other predictors of MPOD, including waist circumference, diabetes, and dietary intake of fiber, resulted in 13 SNPs from 10 genes maintaining independent association with MPOD. Variation in these single gene polymorphisms accounted for 5% of the variability in MPOD (P = 3.5 × 10−11).
Conclusions.
Our results support that MPOD is a multi-factorial phenotype associated with variation in genes related to carotenoid transport, uptake, and metabolism, independent of known dietary and health influences on MPOD.
In 1585 postmenopausal women of the Carotenoids in Age-Related Eye Disease Study sample, common genetic variants in or near genes involved in carotenoid transport, uptake, and metabolism were associated with density of lutein and zeaxanthin in the macula, independent of other known predictors, including dietary intake of carotenoids.
doi:10.1167/iovs.12-10867
PMCID: PMC3626525  PMID: 23404124
18.  Genome-wide meta-analyses of multi-ethnic cohorts identify multiple new susceptibility loci for refractive error and myopia 
Verhoeven, Virginie J.M. | Hysi, Pirro G. | Wojciechowski, Robert | Fan, Qiao | Guggenheim, Jeremy A. | Höhn, René | MacGregor, Stuart | Hewitt, Alex W. | Nag, Abhishek | Cheng, Ching-Yu | Yonova-Doing, Ekaterina | Zhou, Xin | Ikram, M. Kamran | Buitendijk, Gabriëlle H.S. | McMahon, George | Kemp, John P. | St. Pourcain, Beate | Simpson, Claire L. | Mäkelä, Kari-Matti | Lehtimäki, Terho | Kähönen, Mika | Paterson, Andrew D. | Hosseini, S. Mohsen | Wong, Hoi Suen | Xu, Liang | Jonas, Jost B. | Pärssinen, Olavi | Wedenoja, Juho | Yip, Shea Ping | Ho, Daniel W. H. | Pang, Chi Pui | Chen, Li Jia | Burdon, Kathryn P. | Craig, Jamie E. | Klein, Barbara E. K. | Klein, Ronald | Haller, Toomas | Metspalu, Andres | Khor, Chiea-Chuen | Tai, E-Shyong | Aung, Tin | Vithana, Eranga | Tay, Wan-Ting | Barathi, Veluchamy A. | Chen, Peng | Li, Ruoying | Liao, Jiemin | Zheng, Yingfeng | Ong, Rick T. | Döring, Angela | Evans, David M. | Timpson, Nicholas J. | Verkerk, Annemieke J.M.H. | Meitinger, Thomas | Raitakari, Olli | Hawthorne, Felicia | Spector, Tim D. | Karssen, Lennart C. | Pirastu, Mario | Murgia, Federico | Ang, Wei | Mishra, Aniket | Montgomery, Grant W. | Pennell, Craig E. | Cumberland, Phillippa M. | Cotlarciuc, Ioana | Mitchell, Paul | Wang, Jie Jin | Schache, Maria | Janmahasathian, Sarayut | Igo, Robert P. | Lass, Jonathan H. | Chew, Emily | Iyengar, Sudha K. | Gorgels, Theo G.M.F. | Rudan, Igor | Hayward, Caroline | Wright, Alan F. | Polasek, Ozren | Vatavuk, Zoran | Wilson, James F. | Fleck, Brian | Zeller, Tanja | Mirshahi, Alireza | Müller, Christian | Uitterlinden, Andre’ G. | Rivadeneira, Fernando | Vingerling, Johannes R. | Hofman, Albert | Oostra, Ben A. | Amin, Najaf | Bergen, Arthur A.B. | Teo, Yik-Ying | Rahi, Jugnoo S. | Vitart, Veronique | Williams, Cathy | Baird, Paul N. | Wong, Tien-Yin | Oexle, Konrad | Pfeiffer, Norbert | Mackey, David A. | Young, Terri L. | van Duijn, Cornelia M. | Saw, Seang-Mei | Wilson, Joan E. Bailey | Stambolian, Dwight | Klaver, Caroline C. | Hammond, Christopher J.
Nature genetics  2013;45(3):314-318.
Refractive error is the most common eye disorder worldwide, and a prominent cause of blindness. Myopia affects over 30% of Western populations, and up to 80% of Asians. The CREAM consortium conducted genome-wide meta-analyses including 37,382 individuals from 27 studies of European ancestry, and 8,376 from 5 Asian cohorts. We identified 16 new loci for refractive error in subjects of European ancestry, of which 8 were shared with Asians. Combined analysis revealed 8 additional loci. The new loci include genes with functions in neurotransmission (GRIA4), ion channels (KCNQ5), retinoic acid metabolism (RDH5), extracellular matrix remodeling (LAMA2, BMP2), and eye development (SIX6, PRSS56). We also confirmed previously reported associations with GJD2 and RASGRF1. Risk score analysis using associated SNPs showed a tenfold increased risk of myopia for subjects with the highest genetic load. Our results, accumulated across independent multi-ethnic studies, considerably advance understanding of mechanisms involved in refractive error and myopia.
doi:10.1038/ng.2554
PMCID: PMC3740568  PMID: 23396134
19.  The Relationship of Cataract and Cataract Extraction to Age-related Macular Degeneration: The Beaver Dam Eye Study 
Ophthalmology  2012;119(8):1628-1633.
Objective
To examine the associations of cataract and cataract surgery with early and late age-related macular degeneration (AMD) over a 20-year interval.
Design
Longitudinal population-based study of age-related eye diseases. Participants: Beaver Dam Eye Study participants.
Methods
All persons 43-84 years of age were recruited in 1987-1988. Participants were followed up at five year intervals after the baseline examination in 1988-1990. Examinations consisted of ocular examination with lens and fundus photography, medical history, measurements of blood pressure, height, and weight. Values of risk variables were updated, and incidences of early and late AMD were calculated for each 5-year interval. Odds ratios were computed using discrete linear logistic regression modeling with generalized estimating equation methods to account for correlation between the eyes and multiple intervals.
Main Outcome Measures
AMD.
Results
After controlling for age and sex, neither cataract nor cataract surgery was associated with increased odds for developing early AMD. Further controlling for high risk gene alleles (CFH and ARMS2) and other possible risk factors did not materially affect the odds ratio (OR). However, cataract surgery was associated with incidence of late AMD (OR 1.93; 95% CI 1.28, 2.90). This OR was not materially altered by further controlling for high risk alleles (CFH Y402H, ARMS2) or for other risk factors. The OR for late AMD was higher for cataract surgery performed 5 or more years prior as compared to less than 5 years prior.
Conclusions
These data strongly support the past findings of an association of cataract surgery with late AMD independent of other risk factors including high risk genetic status, and suggest the importance of considering these findings when counseling patients regarding cataract surgery. These findings should provide further impetus for the search for measures to prevent or delay the development of age-related cataract.
doi:10.1016/j.ophtha.2012.01.050
PMCID: PMC3411928  PMID: 22578823
20.  Apolipoprotein L1 gene variants associate with hypertension-attributed nephropathy and the rate of kidney function decline in African Americans 
Kidney international  2012;83(1):114-120.
Despite intensive anti-hypertensive therapy there was a high incidence of renal end-points in participants of the African American Study of Kidney Disease and Hypertension (AASK) cohort. To better understand this, coding variants in the apolipoprotein L1 (APOL1) and the non-muscle myosin heavy chain 9 (MYH9) genes were evaluated for an association with hypertension-attributed nephropathy and clinical outcomes in a case-control study. Clinical data and DNA were available for 675 AASK participant cases and 618 African American non-nephropathy control individuals. APOL1 G1 and G2, and MYH9 E1 variants along with 44 ancestry informative markers were genotyped with allele frequency differences between cases and controls analyzed by logistic regression multivariable models adjusting for ancestry, age, and gender. In recessive models, APOL1 risk variants were significantly associated with kidney disease in all cases compared to controls with an odds ratio of 2.57. In AASK cases with more advanced disease, such as a baseline urine protein to creatinine ratio over 0.6 g/g or a serum creatinine over 3 mg/dL during follow-up, the association was strengthened with odds ratios of 6.29 and 4.61, respectively. APOL1 risk variants were consistently associated with renal disease progression across medication classes and blood pressure targets. Thus, kidney disease in AASK participants was strongly associated with APOL1 renal risk variants.
doi:10.1038/ki.2012.263
PMCID: PMC3484228  PMID: 22832513
21.  Diabetic nephropathy in a sibling and albuminuria predict early GFR decline: a prospective cohort study 
BMC Nephrology  2013;14:124.
Background
Diabetic nephropathy is a growing clinical problem, and the cause for >40% of incident ESRD cases. Unfortunately, few modifiable risk factors are known. The objective is to examine if albuminuria and history of diabetic nephropathy (DN) in a sibling are associated with early DN progression or mortality.
Methods
In this longitudinal study of adults >18 yrs with diabetes monitored for up to 9 yrs (mean 4.6 ± 1.7 yrs), 435 subjects at high risk (DN family history) and 400 at low risk (diabetes >10 yrs, normoalbuminuria, no DN family history) for DN progression were evaluated for rate of eGFR change using the linear mixed effects model and progression to ESRD. All-cause mortality was evaluated by Kaplan-Meier analyses while controlling for baseline covariates in a Cox proportional hazards model. Covariates included baseline eGFR, age, gender, race, diabetes duration, blood pressure, hemoglobin A1c and urine albumin:creatinine ratio. Propensity score matching was used to identify high and low risk group pairs with balanced covariates. Sensitivity analyses were employed to test for residual confounding.
Results
Mean baseline eGFR was 74 ml/min/1.73 m2 (86% of cohort >60 ml/min/1.73 m2). Thirty high risk and no low risk subjects developed ESRD. eGFR decline was significantly greater in high compared to low risk subjects. After controlling for confounders, change in eGFR remained significantly different between groups, suggesting that DN family history independently regulates GFR progression. Mortality was also significantly greater in high versus low risk subjects, but after controlling for baseline covariates, no significant difference was observed between groups, indicating that factors other than DN family history more strongly affect mortality. Analyses of the matched pairs confirmed change in eGFR and mortality findings. Sensitivity analyses demonstrated that the eGFR results were not due to residual confounding by unmeasured covariates of a moderate effect size in the propensity matching.
Conclusions
Diabetic subjects with albuminuria and family history of DN are vulnerable for early GFR decline, whereas subjects with diabetes for longer than 10 years, normoalbuminuria and negative family history, experience slower eGFR decline, and are extremely unlikely to require dialysis. Although we would not recommend that patients with low risk characteristics be neglected, scarce resources would be more sensibly devoted to vulnerable patients, such as the high risk cases in our study, and preferably prior to the onset of albuminuria or GFR decline.
doi:10.1186/1471-2369-14-124
PMCID: PMC3703258  PMID: 23773264
Albuminuria; CKD; Diabetes; ESRD; Genetics; Progression; Proteinuria
22.  Genetic Association and Gene-Gene Interaction Analyses in African American Dialysis Patients With Nondiabetic Nephropathy 
Background
African Americans (AAs) have increased susceptibility to non-diabetic nephropathy relative to European Americans.
Study Design
Follow-up of a pooled genome-wide association study (GWAS) in AA dialysis patients with nondiabetic nephropathy; novel gene-gene interaction analyses.
Setting & Participants
Wake Forest sample: 962 AA nondiabetic nephropathy cases; 931 non-nephropathy controls. Replication sample: 668 Family Investigation of Nephropathy and Diabetes (FIND) AA nondiabetic nephropathy cases; 804 non-nephropathy controls.
Predictors
Individual genotyping of top 1420 pooled GWAS-associated single nucleotide polymorphisms (SNPs) and 54 SNPs in six nephropathy susceptibility genes.
Outcomes
APOL1 genetic association and additional candidate susceptibility loci interacting with, or independently from, APOL1.
Results
The strongest GWAS associations included two non-coding APOL1 SNPs, rs2239785 (odds ratio [OR], 0.33; dominant; p = 5.9 × 10−24) and rs136148 (OR, 0.54; additive; p = 1.1 × 10−7) with replication in FIND (p = 5.0 × 10−21 and 1.9 × 10−05, respectively). Rs2239785 remained significantly associated after controlling for the APOL1 G1 and G2 coding variants. Additional top hits included a CFH SNP(OR from meta-analysis in above 3367 AA cases and controls, 0.81; additive; p = 6.8 × 10−4). The 1420 SNPs were tested for interaction with APOL1 G1 and G2 variants. Several interactive SNPs were detected, the most significant was rs16854341 in the podocin gene (NPHS2) (p = 0.0001).
Limitations
Non-pooled GWAS have not been performed in AA nondiabetic nephropathy.
Conclusions
This follow-up of a pooled GWAS provides additional and independent evidence that APOL1 variants contribute to nondiabetic nephropathy in AAs and identified additional associated and interactive non-diabetic nephropathy susceptibility genes.
doi:10.1053/j.ajkd.2011.09.020
PMCID: PMC3259209  PMID: 22119407
African American; APOL1; CFH; end-stage renal disease; FIND; FSGS; hypertension
23.  Meta-analysis of genome-wide linkage scans for renal function traits 
Background.
Several genome scans have explored the linkage of chronic kidney disease phenotypes to chromosomic regions with disparate results. Genome scan meta-analysis (GSMA) is a quantitative method to synthesize linkage results from independent studies and assess their concordance.
Methods.
We searched PubMed to identify genome linkage analyses of renal function traits in humans, such as estimated glomerular filtration rate (GFR), albuminuria, serum creatinine concentration and creatinine clearance. We contacted authors for numerical data and extracted information from individual studies. We applied the GSMA nonparametric approach to combine results across 14 linkage studies for GFR, 11 linkage studies for albumin creatinine ratio, 11 linkage studies for serum creatinine and 4 linkage studies for creatinine clearance.
Results.
No chromosomal region reached genome-wide statistical significance in the main analysis which included all scans under each phenotype; however, regions on Chromosomes 7, 10 and 16 reached suggestive significance for linkage to two or more phenotypes. Subgroup analyses by disease status or ethnicity did not yield additional information.
Conclusions.
While heterogeneity across populations, methodologies and study designs likely explain this lack of agreement, it is possible that linkage scan methodologies lack the resolution for investigating complex traits. Combining family-based linkage studies with genome-wide association studies may be a powerful approach to detect private mutations contributing to complex renal phenotypes.
doi:10.1093/ndt/gfr255
PMCID: PMC3275782  PMID: 21622988
albuminuria; chronic kidney disease; glomerular filtration rate; linkage scans; meta-analysis
24.  A genome-wide association study identifies a potential novel gene locus for keratoconus, one of the commonest causes for corneal transplantation in developed countries 
Human Molecular Genetics  2011;21(2):421-429.
Keratoconus is a condition in which the cornea progressively thins over time, and is a major cause for cornea transplantation. To identify keratoconus susceptibility regions, we performed a comprehensive genome-wide association study (GWAS) using a discovery and replication design. A discovery panel of 222 keratoconus Caucasian patients and 3324 Caucasian controls was genotyped using Illumina 370K beadchips. Further associated and fine-mapping single nucleotide polymorphisms (SNPs) (n= 4905) were genotyped in an independent replication case–control panel of 304 cases and 518 controls and a family panel of 307 subjects in 70 families. Logistic regression models implemented in PLINK were performed to test associations in case–control samples with and without principal component (PC) adjustments. Generalized estimation equation models accounting for familial correlations implemented in GWAF were used for association testing in families. No genome-wide associations were identified in the discovery GWAS panel. From the initial testing without adjustments for PCs, the top three SNPs located at 3p26 (rs6442925), 2q21.3 (rs4954218) and 19q13.3 (rs1428642) were identified with unadjusted P-values of 6.5 × 10−8, 2.4 × 10−7 and 3.1 × 10−7, respectively. After adjustments for PCs, rs1428642 became the most significant through the genome with a P-value of 1.4 × 10−6, while rs6442925 and rs4954218 were less significant (P= 1.9 × 10−5 and 2.6 × 10−4). SNP rs4954218 was confirmed in two independent replication panels with P-values of 0.004 and 0.009, respectively. Meta-analysis revealed a highest association at rs4954218 with adjusted P= 1.6 × 10−7 (unadjusted P= 1.2 × 10−9). These findings suggest SNP rs4954218, located near the RAB3GAP1 gene, previously reported to be associated with corneal malformation, is a potential susceptibility locus for keratoconus.
doi:10.1093/hmg/ddr460
PMCID: PMC3276283  PMID: 21979947
25.  Variation in the Lysyl Oxidase (LOX) Gene Is Associated with Keratoconus in Family-Based and Case-Control Studies 
Purpose.
Keratoconus is a bilateral noninflammatory progressive corneal disorder with complex genetic inheritance and a common cause for cornea transplantation in young adults. A genomewide linkage scan in keratoconus families identified a locus at 5q23.2, overlapping the gene coding for the lysyl oxidase (LOX). LOX encodes an enzyme responsible for collagen cross-linking in a variety of tissues including the cornea. Corneal collagen cross-linking with long-wave ultraviolet light and riboflavin is a promising new treatment for keratoconus. To determine whether LOX is a genetic determinant of the pathogenesis of keratoconus, we analyzed association results of LOX polymorphisms in two independent case-control samples and in keratoconus families.
Methods.
Association results were analyzed of single-nucleotide polymorphisms (SNPs) in the LOX gene from a Genome-Wide Association Study (GWAS) investigation in two independent panels of patients with keratoconus and controls and in keratoconus families.
Results.
Evidence of association was found at SNPs rs10519694 and rs2956540 located in intron 4 of LOX in the GWAS discovery case-control panel with P values of 2.3 × 10−3 and 7 × 10−3, respectively. The same two SNPs were found to be associated with keratoconus by family-based association testing with P values of 2.7 × 10−3 and 7.7 × 10−4, respectively. Meta P values of 4.0 × 10−5 and 4.0 × 10−7 were calculated for SNPs rs10519694 and rs2956540 by analyzing case-control and family samples simultaneously. Sequencing of LOX exons in a subset of keratoconus patients identified two polymorphisms, rs1800449 and rs2288393, located in LOX transcripts I and II, associated with keratoconus in case-control and family samples with a meta P value of 0.02.
Conclusions.
Results provided strong genetic evidence that LOX variants lead to increased susceptibility to developing of keratoconus.
Keratoconus is a progressive disorder of the cornea with complex genetic inheritance, which can lead to severe visual impairment or blindness. Here we describe the association between variation in the lysyl oxidase gene and keratoconus susceptibility in case-control and family studies.
doi:10.1167/iovs.11-9268
PMCID: PMC3760233  PMID: 22661479

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