Computational protocol: Progression Rate From Intermediate to Advanced Age-Related Macular Degeneration Is Correlated With the Number of Risk Alleles at the CFH Locus

Similar protocols

Protocol publication

[…] A total of 392 individuals were genotyped at ARMS2:rs10490924, CFH:rs10737680, C2:rs429608, C2:rs9332739, and C3:rs2230199 by at least one of three methods: (1) a 19 SNV Sequenom MassARRAY (Sequenom, Inc., San Diego, CA, USA) (n = 210 individuals); (2) HumanCoreExome chip genotyping (Illumina, San Diego, CA, USA) (n = 257 samples genotyped using a custom-modified Illumina HumanCoreExome chip as part of 50,000 individuals genotyped at the Center for Inherited Disease Research (CIDR) by the International AMD Gene Consortium, IAMDGC, and n = 127 samples genotyped at the University of Miami); and (3) Taqman (Applied Biosystems, Foster City, CA, USA) (n = 32). All SNVs had call rates > 98%. Genotypes at the CFH:rs1061170 and CFB:rs641153 single nucleotide polymorphisms (SNPs) were imputed from the exome-chip data using the 1000 Genomes reference panel, SHAPEIT for phasing, and IMPUTE2 for imputation; both variants were imputed with info quality scores > 0.99.Samples genotyped on multiple platforms were checked for concordance and excluded if mismatches occurred at any SNP. Analyses were restricted to unrelated individuals of (self-reported) European ancestry since the allele frequency of genetic risk variants varies with ethnicity. Ethnicity of samples with exome-chip data was confirmed using Eigenstrat; any samples that did not cluster with individuals of Northern European ancestry from the 1000 Genomes database (CEU population) were excluded. In total, 20 individuals were excluded from analyses, leaving a final sample of 372 genotyped individuals (547 eyes); 14 individuals did not cluster with the CEU population, 2 showed mismatches between genotyping platforms, and 4 showed a mismatch between X-chromosome homozygosity in PLINK and recorded sex. […]

Pipeline specifications

Software tools SHAPEIT, IMPUTE, PLINK
Application GWAS