Dataset Information

Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry.

ABSTRACT:

Importance

Primary open-angle glaucoma presents with increased prevalence and a higher degree of clinical severity in populations of African ancestry compared with European or Asian ancestry. Despite this, individuals of African ancestry remain understudied in genomic research for blinding disorders.

Objectives

To perform a genome-wide association study (GWAS) of African ancestry populations and evaluate potential mechanisms of pathogenesis for loci associated with primary open-angle glaucoma.

Design, settings, and participants

A 2-stage GWAS with a discovery data set of 2320 individuals with primary open-angle glaucoma and 2121 control individuals without primary open-angle glaucoma. The validation stage included an additional 6937 affected individuals and 14 917 unaffected individuals using multicenter clinic- and population-based participant recruitment approaches. Study participants were recruited from Ghana, Nigeria, South Africa, the United States, Tanzania, Britain, Cameroon, Saudi Arabia, Brazil, the Democratic Republic of the Congo, Morocco, Peru, and Mali from 2003 to 2018. Individuals with primary open-angle glaucoma had open iridocorneal angles and displayed glaucomatous optic neuropathy with visual field defects. Elevated intraocular pressure was not included in the case definition. Control individuals had no elevated intraocular pressure and no signs of glaucoma.

Exposures

Genetic variants associated with primary open-angle glaucoma.

Main outcomes and measures

Presence of primary open-angle glaucoma. Genome-wide significance was defined as P < 5 × 10-8 in the discovery stage and in the meta-analysis of combined discovery and validation data.

Results

A total of 2320 individuals with primary open-angle glaucoma (mean [interquartile range] age, 64.6 [56-74] years; 1055 [45.5%] women) and 2121 individuals without primary open-angle glaucoma (mean [interquartile range] age, 63.4 [55-71] years; 1025 [48.3%] women) were included in the discovery GWAS. The GWAS discovery meta-analysis demonstrated association of variants at amyloid-β A4 precursor protein-binding family B member 2 (APBB2; chromosome 4, rs59892895T>C) with primary open-angle glaucoma (odds ratio [OR], 1.32 [95% CI, 1.20-1.46]; P = 2 × 10-8). The association was validated in an analysis of an additional 6937 affected individuals and 14 917 unaffected individuals (OR, 1.15 [95% CI, 1.09-1.21]; P < .001). Each copy of the rs59892895*C risk allele was associated with increased risk of primary open-angle glaucoma when all data were included in a meta-analysis (OR, 1.19 [95% CI, 1.14-1.25]; P = 4 × 10-13). The rs59892895*C risk allele was present at appreciable frequency only in African ancestry populations. In contrast, the rs59892895*C risk allele had a frequency of less than 0.1% in individuals of European or Asian ancestry.

Conclusions and relevance

In this genome-wide association study, variants at the APBB2 locus demonstrated differential association with primary open-angle glaucoma by ancestry. If validated in additional populations this finding may have implications for risk assessment and therapeutic strategies.

SUBMITTER: Genetics of Glaucoma in People of African Descent (GGLAD) Consortium

PROVIDER: S-EPMC6865235 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry.

Hauser Michael A MA Allingham R Rand RR Aung Tin T Van Der Heide Carly J CJ Taylor Kent D KD Rotter Jerome I JI Wang Shih-Hsiu J SJ Bonnemaijer Pieter W M PWM Williams Susan E SE Abdullahi Sadiq M SM Abu-Amero Khaled K KK Anderson Michael G MG Akafo Stephen S Alhassan Mahmoud B MB Asimadu Ifeoma I Ayyagari Radha R Bakayoko Saydou S Nyamsi Prisca Biangoup PB Bowden Donald W DW Bromley William C WC Budenz Donald L DL Carmichael Trevor R TR Challa Pratap P Chen Yii-Der Ida YI Chuka-Okosa Chimdi M CM Cooke Bailey Jessica N JN Costa Vital Paulino VP Cruz Dianne A DA DuBiner Harvey H Ervin John F JF Feldman Robert M RM Flamme-Wiese Miles M Gaasterland Douglas E DE Garnai Sarah J SJ Girkin Christopher A CA Guirou Nouhoum N Guo Xiuqing X Haines Jonathan L JL Hammond Christopher J CJ Herndon Leon L Hoffmann Thomas J TJ Hulette Christine M CM Hydara Abba A Igo Robert P RP Jorgenson Eric E Kabwe Joyce J Kilangalanga Ngoy Janvier NJ Kizor-Akaraiwe Nkiru N Kuchtey Rachel W RW Lamari Hasnaa H Li Zheng Z Liebmann Jeffrey M JM Liu Yutao Y Loos Ruth J F RJF Melo Monica B MB Moroi Sayoko E SE Msosa Joseph M JM Mullins Robert F RF Nadkarni Girish G Napo Abdoulaye A Ng Maggie C Y MCY Nunes Hugo Freire HF Obeng-Nyarkoh Ebenezer E Okeke Anthony A Okeke Suhanya S Olaniyi Olusegun O Olawoye Olusola O Oliveira Mariana Borges MB Pasquale Louise R LR Perez-Grossmann Rodolfo A RA Pericak-Vance Margaret A MA Qin Xue X Ramsay Michele M Resnikoff Serge S Richards Julia E JE Schimiti Rui Barroso RB Sim Kar Seng KS Sponsel William E WE Svidnicki Paulo Vinicius PV Thiadens Alberta A H J AAHJ Uche Nkechinyere J NJ van Duijn Cornelia M CM de Vasconcellos José Paulo Cabral JPC Wiggs Janey L JL Zangwill Linda M LM Risch Neil N Milea Dan D Ashaye Adeyinka A Klaver Caroline C W CCW Weinreb Robert N RN Ashley Koch Allison E AE Fingert John H JH Khor Chiea Chuen CC

JAMA 20191101 17

<h4>Importance</h4>Primary open-angle glaucoma presents with increased prevalence and a higher degree of clinical severity in populations of African ancestry compared with European or Asian ancestry. Despite this, individuals of African ancestry remain understudied in genomic research for blinding disorders.<h4>Objectives</h4>To perform a genome-wide association study (GWAS) of African ancestry populations and evaluate potential mechanisms of pathogenesis for loci associated with primary open-an ...[more]

PMID: 31688885

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Project description:PurposeTo find genetic contributions to glaucoma in African Americans.DesignCross-sectional, case-control study.ParticipantsOne thousand eight hundred seventy-five primary open-angle glaucoma (POAG) patients and 1709 controls, self-identified as being of African descent (AD), from the African Descent and Glaucoma Evaluation Study (ADAGES) III and Wake Forest School of Medicine.MethodsMegaChip genotypes were imputed to Thousand Genomes data. Association of single nucleotide polymorphisms (SNPs) with POAG and advanced POAG was tested by linear mixed model correcting for relatedness and population stratification. Genetic risk scores were tested by receiver operator characteristic curves (ROC-AUCs).Main outcome measuresPrimary open-angle glaucoma defined by visual field loss without other nonocular conditions (n = 1875). Advanced POAG was defined by age-based mean deviation of visual field (n = 946).ResultsEighteen million two hundred eighty-one thousand nine hundred twenty SNPs met imputation quality of r2 > 0.7 and minor allele frequency > 0.005. Association of a novel locus, EN04, was observed for advanced POAG (rs185815146 β, 0.36; standard error, 0.065; P < 3×10-8). For POAG, an AD signal was observed at the 9p21 European descent (ED) POAG signal (rs79721419; P < 6.5×10-5) independent of the previously observed 9p21 ED signal (rs2383204; P < 2.3×10-5) by conditional analyses. An association with POAG in FNDC3B (rs111698934; P < 3.9×10-5) was observed, not in linkage disequilibrium (LD) with the previously reported ED SNP. Additional previously identified loci associated with POAG in persons of AD were: 8q22, AFAP1, and TMC01. An AUC of 0.62 was observed with an unweighted genetic risk score comprising 11 SNPs in candidate genes. Two additional risk scores were studied by using a penalized matrix decomposition with cross-validation; risk scores of 50 and 400 SNPs were identified with ROC of AUC = 0.74 and AUC = 0.94, respectively.ConclusionsA novel association with advanced POAG in the EN04 locus was identified putatively in persons of AD. In addition to this finding, this genome-wide association study in POAG patients of AD contributes to POAG genetics by identification of novel signals in prior loci (9p21), as well as advancing the fine mapping of regions because of shorter average LD (FNDC3B). Although not useful without confirmation and clinical trials, the use of genetic risk scores demonstrated that considerable AD-specific genetic information remains in these data.

Project description:PurposeTo estimate the population frequencies of all common mitochondrial variants and ancestral haplogroups among 1,999 subjects recruited for the Primary Open-Angle African American Glaucoma Genetics (POAAGG) Study, including 1,217 primary open-angle glaucoma (POAG) cases and 782 controls, and to identify ancestral subpopulations and mitochondrial mutations as potential risk factors for POAG susceptibility.MethodsSubject classification by characteristic glaucomatous optic nerve findings and corresponding visual field defects, as defined by enrolling glaucoma specialists, stereo disc photography, phlebotomy, extraction of total DNA from peripheral blood or saliva, DNA quantification and normalization, PCR amplification of whole mitochondrial genomes, Ion Torrent deep semiconductor DNA sequencing on DNA pools ("Pool-seq"), Sanger sequencing of 3,479 individual mitochondrial DNAs, and bioinformatic analysis.ResultsThe distribution of common African haplogroups within the POAAGG study population was broadly similar to prior surveys of African Americans. However, the POAG case population was found to be enriched in L1c2 haplogroups, which are defined in part by missense mutations m.6150G>A (Val83Ile, odds ratio [OR] 1.8, p=0.01), m.6253C>T (Met117Thr, rs200165736, OR 1.6, p=0.04), and m.6480G>A (Val193Ile, rs199476128, OR 4.6, p=0.04) in the cytochrome c oxidase subunit 1 (MT-CO1) gene and by a variant, m.2220A>G (OR 2.0, p=0.01), in MT-RNR2, which encodes the mitochondrial ribosomal 16s RNA gene. L2 haplogroups were predicted to be overrepresented in the POAG case population by Pool-seq, and the difference was confirmed to be significant with Sanger sequencing, that targeted the L2-associated variants m.2416T>C (rs28358580, OR 1.2, p=0.02) and m.2332C>T (OR 1.2, p=.02) in MT-RNR2. Another variant within MT-RNR2, m.3010G>A (rs3928306), previously implicated in sensitivity to the optic neuropathy-associated antibiotic linezolid, and arising on D4 and J1 lineages, associated with Leber hereditary optic neuropathy (LHON) severity, was confirmed to be common (>5%) but was not significantly enriched in the POAG cases. Two variants linked to the composition of the gut microbiome, m.15784T>C (rs527236194, haplogroup L2a1) and m.16390G>A (rs41378955, L2 haplogroups), were also enriched in the case DNA pools.ConclusionsThese results implicate African mtDNA haplogroups L1c2, L1c2b, and L2 as risk factors for POAG. Approximately one in four African Americans have these mitochondrial ancestries, which may contribute to their elevated glaucoma risk. These haplogroups are defined in part by ancestral variants in the MT-RNR2 and/or MT-CO1 genes, several of which have prior disease associations, such as MT-CO1 missense variants that have been implicated in prostate cancer.

Dataset Information

Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry.

Importance

Objectives

Design, settings, and participants

Exposures

Main outcomes and measures

Results

Conclusions and relevance

Publications

Association of Genetic Variants With Primary Open-Angle Glaucoma Among Individuals With African Ancestry.

Similar Datasets

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