Axiom customized biobank genotyping arrays

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Axiom® Customized Biobank Genotyping Arrays are high-throughput genotyping platforms designed for large-scale genetic studies. These arrays enable the simultaneous analysis of thousands of genomic markers across multiple samples, facilitating comprehensive genetic profiling.

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Axiom Biobank Genotyping Array Axiom Biobank array BioBank Array Axiom array

5 protocols using axiom customized biobank genotyping arrays

Genome-wide association study quality control

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We collected donated blood samples from the remaining 3608 subjects and analyzed them using the Affymetrix Axiom^® Customized Biobank Genotyping Arrays (Affymetrix, Santa Clara, CA, USA), and the PLINK program (ver. 1.07) was used for quality control. Specimens with the following characteristics were excluded from the analyses: low genotype call rate (<97%), sex inconsistency, and related and cryptically related individuals (identical by descent >0.9). SNPs with low call rates (<97%), low minor allele frequency (MAF ≤ 0.05%), or significant deviation from the Hardy-Weinberg equilibrium permutation test (HWE P < 1.0 × 10⁻⁵) were excluded. After performing the quality control evaluations for this study, 345,072 autosomal SNPs were retained for the association analyses.

Lee Y.J., Choi S., Kwon S.Y., Lee Y., Lee J.K., Heo E.Y., Chung H.S, & Kim D.K. (2020). A Genome-Wide Association Study in Early COPD: Identification of One Major Susceptibility Loci. International Journal of Chronic Obstructive Pulmonary Disease, 15, 2967-2975.

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Genomic DNA Genotyping and Quality Control

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Genomic DNA was isolated from venous blood samples and 200 ng of DNA from each patient was genotyped using Affymetrix Axiom^® Customized Biobank Genotyping Arrays (Affymetrix, Santa Clara, CA, USA). The PLINK program (version 1.90, Free Software Foundation Inc., Boston, MA, USA) was used for quality control procedures. Samples meeting any of the following criteria were removed: (i) gender inconsistency, (ii) call rate ≤ 97% and (iii) related and cryptically related individuals (identical by descent >0.185). SNPs were filtered if (1) the call rate was <95%, (2) the minor allele frequency (MAF) was ≤ 0.01, or (3) there was a significant deviation from the Hardy-Weinberg equilibrium permutation test (P<1x10^-4).

Seo J.Y., Lee J.E., Chung G.E., Shin E., Kwak M.S., Yang J.I, & Yim J.Y. (2020). A genome-wide association study on liver enzymes in Korean population. PLoS ONE, 15(2), e0229374.

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Genome-Wide Genotyping Quality Control

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Genomic DNA was extracted from venous blood samples genotyped using Affymetrix Axiom® Customized Biobank Genotyping Arrays (Affymetrix, Santa Clara, CA, USA), and the PLINK program (ver. 1.07) was used for quality control procedures. Specimens with the following characteristics were excluded from the analysis: low genotyping call rate (≤ 97%), sex inconsistency, and related and cryptically related individuals (identical by descent > 0.9). Small nucleotide polymorphisms (SNPs) with low call rates (< 97%), low minor allele frequency (MAF ≤ 0.05%), or significant deviation from the Hardy-Weinberg equilibrium permutation test (HWE P < 1.0 × 10⁻⁵) were excluded (S1 Table). After performing the quality control evaluations, 345,072 autosomal SNPs were retained for the association analysis. S2–S5 Tables summarize the HWE, MAF, and missing rates of each SNP. Targeted imputation was performed in the validation set when SNP information could not be confirmed as significant in the discovery set. Imputation was performed as follows: genotypes were pre-phased using SHAPEIT2, imputed with IMPUTE2, and analyzed using 1000 genome phase 3 haplotypes as the reference panel.

Lee J., Lee Y., Park B., Won S., Han J.S, & Heo N.J. (2018). Genome-wide association analysis identifies multiple loci associated with kidney disease-related traits in Korean populations. PLoS ONE, 13(3), e0194044.

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Genetic Variant Profiling in Blood Samples

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Genomic DNA was isolated from venous blood samples and 200 ng of DNA from each patient was genotyped using Axiom^® Customized Biobank Genotyping Arrays (Affymetrix, Santa Clara, CA, USA). The PLINK program version 1.07 (Free Software Foundation Inc., Boston, MA, USA) was used for quality control procedures. Samples meeting any of the following criteria were removed: (1) gender inconsistency, (2) call rate ≤97%, and (3) related and cryptically related individuals (identical by descent >0.185). SNPs were filtered if (1) the call rate was <95%, (2) the minor allele frequency was ≤0.01 (n=172,546), or (3) there was a significant deviation from the Hardy-Weinberg equilibrium permutation test (p<0.0001). After quality control, 584,061 autosomal SNPs remained for the association analysis.

Chung G.E., Lee Y., Yim J.Y., Choe E.K., Kwak M.S., Yang J.I., Park B., Lee J.E., Kim J.A, & Kim J.S. (2017). Genetic Polymorphisms of PNPLA3 and SAMM50 Are Associated with Nonalcoholic Fatty Liver Disease in a Korean Population. Gut and Liver, 12(3), 316-323.

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Genotyping and Quality Control in GWAS

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Genomic DNA was extracted from blood samples and 200 ng of DNA from each patient was genotyped using Affymetrix Axiom® Customized Biobank Genotyping Arrays (Affymetrix, Santa Clara, CA, USA). Genotype data were produced using the Korean Chip, designed by the Center for Genome Science, Korea National Institute of Health, Korea (4845–301, 3000–3031). The quality control measures were performed using the PLINK program (version 1.07; Free Software Foundation Inc., Boston, MA, USA). Samples meeting any of the following criteria were removed: (i) gender discrepancy, (ii) call rate ≤ 97%, and (iii) related and cryptically related individuals (identical by state > 90%). SNPs were filtered if (1) the call rate was < 95%, (2) minor allele frequency was ≤ 0.05, or (3) deviation from the Hardy–Weinberg equilibrium permutation test (P < 1.00 × 10⁻⁵) was observed. SHAPEIT2 v2.r904 and IMPUTE2 version 2.3.2 were used for pre-phasing the data and genotype imputations in GWAS.^{20 (link),21 (link)} As a reference panel, we used 1000 Genomes Phase 3 haplotypes. Any imputed SNPs with imputation quality scores < 0.5 were excluded. After quality control, 3,631,724 SNPs in the discovery set and 3,587,584 SNPs in the validation set remained for association analysis.

Lee Y., Cho E.J., Choe E.K., Kwak M.S., Yang J.I., Oh S.W., Yim J.Y, & Chung G.E. (2024). Genome-wide association study of metabolic dysfunction-associated fatty liver disease in a Korean population. Scientific Reports, 14, 9753.

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