The Affymetrix Axiom Genome-Wide TWB 2.0 array plates, designed jointly by the Taiwan Biobank, the National Center for Genome Medicine (Nankang, Taipei, Taiwan) and the Thermo Fisher Scientific (Waltham, MA, USA), were used for assessing ~750,000 genome-wide variants in this GWAS study. The base-calling algorithm was Affymetrix APT. The hybridization of samples onto the microarrays and the washing procedure were conducted following the manufacturer’s protocol. The Affymetrix scanner scanned the fluorescent signals and then stored them as digital images for further data processing. Associations with the phenotype were evaluated using Fisher’s exact test of allele counts.
Axiom genome wide twb 2.0 array plate
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Axiom Genome-Wide TWB 2.0 Array Plate is a high-throughput genotyping array designed for whole-genome analysis. It enables the simultaneous measurement of hundreds of thousands of genetic variants across the human genome.
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5 protocols using axiom genome wide twb 2.0 array plate
1
Genome-Wide Variant Detection Using Axiom Array
2
Genome-Wide Genotyping of Taiwan Biobank
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The Affymetrix Axiom Genome-Wide TWB 2.0 array plates, designed jointly by the Taiwan Biobank, the National Center for Genome Medicine in Taiwan and Thermo Fisher Scientific (Waltham, MA, USA), were used for assessing the genome-wide variants. Genome-wide genotyping was performed by the National Center for Genome Medicine in Taiwan, where a rigorous quality-control pipeline has been installed to process the data before release. The Affymetrix APT base-calling software was used. Associations between genotypes and phenotypes were evaluated by using the Fisher’s exact test, based on major and minor allele counts in case and control subjects. We used the Golden Helix SVS software v.8.8.3 for genome-wide comparisons of genotypes (Golden Helix, London, UK).
3
Genome-Wide Genotyping of Han Chinese
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We extracted DNA from the blood samples of the participants and genotyping was performed using Axiom Genome-Wide TWB 2.0 Array Plate (Affymetrix, Santa Clara, CA, USA), which contains 714 431 SNPs and is designed specifically for Taiwan's Han Chinese population [13 (link)]. Analysis and quality control were performed using Affymetrix Power Tools software, and markers that failed Hardy–Weinberg equilibrium tests with a P < 1.0 × 10–5, had a minor allele frequency <0.05, or had a genotype missing rate of >5% were excluded. After quality control, a total of 591 048 SNPs were retained for analysis. The use of high-coverage GWAS SNP data from large-scale Han Chinese ancestry in Taiwan using custom arrays has been previously described [14 (link)]. The samples with a missingness rate >0.02 and an inbreeding coefficient >0.15 and those with a sex mismatch were removed. Genotype data and selected SNPs were merged according to merged imputation data.
4
GWAS on Taiwan Han Chinese ApoE
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The DNA was extracted when the blood samples were obtained and then genotyped by the Genome-wide association study (GWAS) technique. We used the Axiom Genome-Wide TWB 2.0 Array Plate (Affymetrix, Santa Clara, CA, USA), which is designed for the Taiwan Han Chinese population. Affymetrix Power Tool was used for standard quality control. After excluding markers that failed Hardy–Weinberg equilibrium tests for controls (P < 1.0 × 10–4), minor allele frequency (P < 0.01), and the low call rate SNPs (<99%), there were 591,048 SNPs for analysis. This array contained two alleles of the ApoE gene: rs429358 and rs7412, which defined the three main ApoE alleles (ε2, ε3, and ε4). The ε3/ε3 carriers were used as a reference because it was the most common ApoE genotype.
5
Taiwanese Han Chinese Genotyping
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The blood DNA samples were obtained from the participants and were genotyped using the Axiom Genome-Wide TWB 2.0 Array Plate (Affymetrix, Santa Clara, CA, USA) (18 (link)). The Affymetrix TWB 2.0 SNP chip contains 653,291 SNPs and was designed specifically for Taiwan's Han Chinese population. Affymetrix Power Tools was used for analysis and a quality control procedure was performed to exclude markers that failed Hardy-Weinberg equilibrium tests with P < 1.0 × 10–5, minor allele frequency <0.05, and genotype missing rate of > 5%. A total of 591,048 SNPs were retained after the quality control.
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