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Humanhap550k snp arrays

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The HumanHap550K SNP arrays are high-density genotyping microarrays designed to interrogate over 550,000 single nucleotide polymorphisms (SNPs) across the human genome. These arrays provide comprehensive genome-wide coverage and enable researchers to conduct large-scale genetic association studies.

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SNP arrays (14 citations)

2 protocols using humanhap550k snp arrays

1

Genome-wide DNA Methylation Analysis

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The blood samples were genotyped using the Illumina HumanHap550K SNP arrays in EAGLE GWAS20 (link). The SNPs with call rate >99%, minor allele frequency (MAF) >3% and Hardy-Weinberg Equilibrium (HWE) P-value >10−5 were included for analysis. Prior to meQTL analysis, each methylation trait was regressed against sex, age, batches and PCA scores based on methylation profiles. The regression residues were then quantile-normalized to the standard normal distribution N(0,1) as traits. The genetic association testing was performed using PLINK and R, adjusted for the top three PCA scores based on GWAS SNPs to control for potential population stratification.
Shi J., Marconett C.N., Duan J., Hyland P.L., Li P., Wang Z., Wheeler W., Zhou B., Campan M., Lee D.S., Huang J., Zhou W., Triche T., Amundadottir L., Warner A., Hutchinson A., Chen P.H., Chung B.S., Pesatori A.C., Consonni D., Bertazzi P.A., Bergen A.W., Freedman M., Siegmund K.D., Berman B.P., Borok Z., Chatterjee N., Tucker M.A., Caporaso N.E., Chanock S.J., Laird-Offringa I.A, & Landi M.T. (2014). Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nature communications, 5, 3365.
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2

Genome-wide DNA Methylation Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols
The blood samples were genotyped using the Illumina HumanHap550K SNP arrays in EAGLE GWAS20 (link). The SNPs with call rate >99%, minor allele frequency (MAF) >3% and Hardy-Weinberg Equilibrium (HWE) P-value >10−5 were included for analysis. Prior to meQTL analysis, each methylation trait was regressed against sex, age, batches and PCA scores based on methylation profiles. The regression residues were then quantile-normalized to the standard normal distribution N(0,1) as traits. The genetic association testing was performed using PLINK and R, adjusted for the top three PCA scores based on GWAS SNPs to control for potential population stratification.
Shi J., Marconett C.N., Duan J., Hyland P.L., Li P., Wang Z., Wheeler W., Zhou B., Campan M., Lee D.S., Huang J., Zhou W., Triche T., Amundadottir L., Warner A., Hutchinson A., Chen P.H., Chung B.S., Pesatori A.C., Consonni D., Bertazzi P.A., Bergen A.W., Freedman M., Siegmund K.D., Berman B.P., Borok Z., Chatterjee N., Tucker M.A., Caporaso N.E., Chanock S.J., Laird-Offringa I.A, & Landi M.T. (2014). Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nature communications, 5, 3365.
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