Genotyping was performed with all patients. Genomic DNA was prepared from leukocytes of peripheral blood with a QuickGene-610L DNA extraction kit (Fujifilm, Tokyo, Japan). During the discovery stage, genome-wide genotyping was performed using the HumanOmni2.5–8 BeadChip Kit (Illumina Inc., San Diego, CA). To ensure high-quality genotype data, a series of quality control filters were applied to the raw data, including a MAF cutoff of >0.01 and genotyping success rate of >95%. Genome-wide imputation was performed using the Michigan Imputation Server (https://imputationserver.sph.umich.edu/index.html ) with ASN population haplotypes from the 1000 Genomes project (phase 3) as reference sequences. Series of quality-control filters were applied again to the post-imputed dataset, including a MAF cutoff of >0.01, a genotyping success rate of >90%, and an individual call rate of >90%. Quality control was performed using PLINK (version 1.07; http://pngu.mgh.harvard.edu/~purcell/plink ; accessed April 11, 2015). During the replication stage, samples were genotyped using TaqMan SNP assays with the ABI PRISM 7700 system (Applied Biosystems Inc., Foster City, CA). We did not consider deviations in genotype distributions from the Hardy–Weinberg equilibrium because all samples were from patients with AMD.
Humanomni2.5 8 beadchip kit
Manufactured by Illumina
Sourced in United States
The HumanOmni2.5–8 BeadChip Kit is a high-density genotyping microarray produced by Illumina. It is designed to interrogate over 2.5 million genetic markers across the human genome. The kit provides a comprehensive genomic coverage for large-scale genetic studies.
Automatically generated - may contain errors
4 protocols using humanomni2.5 8 beadchip kit
1
Genotyping and Genome-wide Imputation
2
SNP Array Analysis of BT474 Cells
3
South Indian Families Genotyping Protocol
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Genotyping for the South Indian families was performed at the Ocular Genomics Institute at the Massachusetts Eye and Ear Infirmary using the Illumina HumanOmni2.5-8 Beadchip kit (2,379,855 markers; Illumina, Inc., San Diego, CA, USA). Genotypes were called using GenomeStudio (v2011.1, Illumina, Inc.). The genetic sex of all individuals was consistent with the reported sex. Two samples were removed because genotyping call rates were <99%. The average call rate per sample was >99.8%. QC for 2,352,697 (98.9%) well-clustered SNPs was performed with PLINK (v1.07, provided in the public domain, http://pngu.mgh.harvard.edu/∼purcell/plink/ ).28 25,088 (1.1%) SNPs with call frequency <90% and 881,678 (37.5%) SNPs with minor allele frequency (MAF) <0.01 were removed from the analysis. 164,174 (7.0%) SNPs with Mendelian errors and 58,443 (2.5%) SNPs on chromosome X or Y, or on the mitochondrial chromosome were also excluded. After QC, 1,223,314 SNPs were included in the final analysis. Genotyping for replication cohorts is described in the Supplementary Methods .
4
High-throughput Genetic Profiling of SCAALA Cohort
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DNA extraction was performed from the peripheral blood samples of 1246 SCAALA subjects, according to the protocols of QIAGEN kit (Gentra Puregene Blood Kit, Hilden, Germany). All samples to be genotyped were standardized at a concentration of 50 ng/μL and identified in bar code tubes. The samples were genotyped using the Illumina Human Omni 2.5-8 Bead Chip Kit, which consists of a large platform with approximately 2.5 million markers of the human genome (www. ilummina.com). For this study, the RORA genetic information was extracted between positions 60781040 and 61517218 on chromosome 15.
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