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Affymetrix 6.0 platform

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The Affymetrix 6.0 platform is a high-density genotyping array designed for genome-wide association studies (GWAS) and copy number variation (CNV) analysis. It features over 1.8 million genetic markers, including more than 906,000 single nucleotide polymorphisms (SNPs) and 946,000 probes for the detection of copy number variations. The platform allows for the simultaneous analysis of hundreds of thousands of genetic markers across the entire human genome.

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Lab products found in correlation

Abi snplex platform, by Thermo Fisher Scientific (2 mentions) Infinium custom gwas chip, by Illumina (2 mentions)

Close spelling variants of this product

Affymetrix SNP 6.0 platform Affymetrix 6.0 Array Set Platform 6.0 platform Affymetrix platform

6 protocols using affymetrix 6.0 platform

1

Genetic Variants Regulating Blood Pressure

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SCNN1A, SCNN1G and SCNN1B genes were identified based on their potential biological effect on BP regulation. Seventeen SNPs were genotyped using ABI SNPlex platform (Applied Biosystems, Foster City, CA) and additional 42 SNPs were genotyped on the Affymetrix 6.0 platform (Affymetrix, Santa Clara, CA) in a subsample of GenSalt participants (N=1,881). SNPs with minor allele frequency (MAF) less than 1%, genotyping call rate less than 90% and deviation from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction for multiple testing were excluded. After quality control, we selected tag-SNPs from these genes with pairwise r2 thresholds of less than 0.9. A total of 44 tag-SNPs were included in the current analysis. Haploview software (version 4.2, http://www.broad.mit.edu/mpg/haploview) was used to conduct quality control and tag-SNPs selection. 18 (link) Detailed information on all tag-SNPs, including the gene symbol, chromosome, physical position, major/minor alleles, call rate, MAF, HWE P value and genotyping platform, has been shown in Supplementary Table 1.
Liu F., Yang X., Mo X., Huang J., Chen J., Kelly T.N., Hixson J.E., Rao D.C., Gu C.C., Shimmin L.C., Chen J., Rice T.K., Li J., Schwander K., He J., Liu D.P, & D.o.n.g.f.e.n.g.G.u. (2014). Associations of epithelial sodium channel genes with blood pressure: the GenSalt study. Journal of human hypertension, 29(4), 224-228.
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2

Genotyping of NCBT Gene SNPs

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SNPs located within the five NCBT genes (including about 5kb flanking regions each upstream and downstream of the genes) were genotyped among all participants using chip-based hybridization assays Affymetrix 6.0 platform (Affymetrix, Santa Clara, CA). SNPs were excluded if they had a call rate less than 95%, or significantly deviated from Hardy-Weinberg equilibrium (HWE) after adjustment for multiple comparisons (false discovery rate [FDR], P<0.05), or had a minor allele frequency (MAF) less than 1%. Within the five NCBT genes, 133 SNPs met the quality control criteria, and 76 SNPs were tagged (r2<0.9) using Haploview software (version4.2, http://www.broad.mit.edu/mpg/haploview) for inclusion in the current analysis. Detailed characteristics of the NCBT genes including the gene symbol, physical position, number of tag SNPs and encoded protein were presented in Table 1. Quality control information on the tagged 76 SNPs was listed in Supplemental Table 1.
Guo L., Liu F., Chen S., Yang X., Huang J., He J., Jaquish C.E., Zhao Q., Gu C.C., Hixson J.E, & Gu D. (2015). Common Variants in the Na+-coupled Bicarbonate Transporter Genes and Salt Sensitivity of Blood Pressure: The GenSalt Study. Journal of human hypertension, 30(9), 543-548.
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3

Genotyping of NCBT Gene SNPs

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SNPs located within the five NCBT genes (including about 5kb flanking regions each upstream and downstream of the genes) were genotyped among all participants using chip-based hybridization assays Affymetrix 6.0 platform (Affymetrix, Santa Clara, CA). SNPs were excluded if they had a call rate less than 95%, or significantly deviated from Hardy-Weinberg equilibrium (HWE) after adjustment for multiple comparisons (false discovery rate [FDR], P<0.05), or had a minor allele frequency (MAF) less than 1%. Within the five NCBT genes, 133 SNPs met the quality control criteria, and 76 SNPs were tagged (r2<0.9) using Haploview software (version4.2, http://www.broad.mit.edu/mpg/haploview) for inclusion in the current analysis. Detailed characteristics of the NCBT genes including the gene symbol, physical position, number of tag SNPs and encoded protein were presented in Table 1. Quality control information on the tagged 76 SNPs was listed in Supplemental Table 1.
Guo L., Liu F., Chen S., Yang X., Huang J., He J., Jaquish C.E., Zhao Q., Gu C.C., Hixson J.E, & Gu D. (2015). Common Variants in the Na+-coupled Bicarbonate Transporter Genes and Salt Sensitivity of Blood Pressure: The GenSalt Study. Journal of human hypertension, 30(9), 543-548.
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4

Genotype Data Integration and Imputation

Cited 1 time
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Genotype data was available from 4 platforms: Illumina HumanOmni Express -12VI platform (Illumina), Affymetrix 6.0 platform (Affymetrix), Illumina Infinium custom GWAS chip (Illumina), and the Global Screening Arrays (GSA) version 2 (Illumina). Imputation of nongenotyped single-nucleotide variations (SNVs, formerly known as single-nucleotide polymorphisms [SNP]) was performed using IMPUTE2 and MINIMAC4 against the haplotype reference consortium (17 (link)); calls made with an imputation score of less than 95% were discarded.
Soto-Pedre E., Newey P.J., Srinivasan S., Siddiqui M.K., Palmer C.N, & Leese G.P. (2022). Identification of 4 New Loci Associated With Primary Hyperparathyroidism (PHPT) and a Polygenic Risk Score for PHPT. The Journal of Clinical Endocrinology and Metabolism, 107(12), 3302-3308.
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5

Genetic Variants Regulating Blood Pressure

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SCNN1A, SCNN1G and SCNN1B genes were identified based on their potential biological effect on BP regulation. Seventeen SNPs were genotyped using ABI SNPlex platform (Applied Biosystems, Foster City, CA) and additional 42 SNPs were genotyped on the Affymetrix 6.0 platform (Affymetrix, Santa Clara, CA) in a subsample of GenSalt participants (N=1,881). SNPs with minor allele frequency (MAF) less than 1%, genotyping call rate less than 90% and deviation from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction for multiple testing were excluded. After quality control, we selected tag-SNPs from these genes with pairwise r2 thresholds of less than 0.9. A total of 44 tag-SNPs were included in the current analysis. Haploview software (version 4.2, http://www.broad.mit.edu/mpg/haploview) was used to conduct quality control and tag-SNPs selection. 18 (link) Detailed information on all tag-SNPs, including the gene symbol, chromosome, physical position, major/minor alleles, call rate, MAF, HWE P value and genotyping platform, has been shown in Supplementary Table 1.
Liu F., Yang X., Mo X., Huang J., Chen J., Kelly T.N., Hixson J.E., Rao D.C., Gu C.C., Shimmin L.C., Chen J., Rice T.K., Li J., Schwander K., He J., Liu D.P, & D.o.n.g.f.e.n.g.G.u. (2014). Associations of epithelial sodium channel genes with blood pressure: the GenSalt study. Journal of human hypertension, 29(4), 224-228.
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6

Genotype Data Integration and Imputation

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Genotype data was available from the following platforms: the Human Exome -12
VI_A_chip, the Metabohip (10) , Illumina HumanOmni Express -12VI platform (Illumina, San Diego), Affymetrix 6.0 platform (Affymetrix, Santa Clara) and the Illumina Infinium custom GWAS chip (Illumina, San Diego). Imputation was performed against 1000G Phase I V3 reference panel using Impute2 (11) and using the haplotype reference consortium (12) ; calls made with imputation quality below 90% were discarded. All SNPs were in Hardy-Weinberg equilibrium (P<10e-04).
Soto-Pedre E., Siddiqui M.K., Doney A.S., Palmer C.N.A., Pearson E.R, & Leese G.P. (2017). Replication confirms the association of loci in FOXE1, PDE8B, CAPZB and PDE10A with thyroid traits: a Genetics of Diabetes Audit and Research Tayside study (GoDARTS). Pharmacogenetics and genomics, 27(10).
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