Affymetrix 6.0 array

Manufactured by Thermo Fisher Scientific

Sourced in United States

The Affymetrix 6.0 array is a high-density genotyping microarray platform designed for genome-wide association studies (GWAS). It provides comprehensive coverage of common genetic variations across the human genome, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs).

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Lab products found in correlation

Axiom world array 3 platform, by Thermo Fisher Scientific (2 mentions) Picogreen, by Thermo Fisher Scientific (2 mentions) Axiom biobank array, by Thermo Fisher Scientific (1 mentions) 610k quad array, by Illumina (1 mentions)

Close spelling variants of this product

Affymetrix SNP 6.0 arrays Affymetrix GeneChip Human Mapping 6.0 array Affymetrix 6.0 SNP Array Affymetrix 6.0 SNP Array in WHI Affymetrix Genome-Wide Human SNP 6.0 Array Affymetrix 6.0 Array Set Platform 6.0 array Array 6.0

7 protocols using affymetrix 6.0 array

Genotyping CARDIA and BioVU Cohorts

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CARDIA AA participants were genotyped as part of the Candidate Gene Association Resource (CARe) study using the Affymetrix 6.0 array (Affymetrix, Santa Clara, CA). BioVU AA participants were genotyped using the Affymetrix Axiom Biobank array (Affymetrix, Inc., Santa Clara, CA) and on the Axiom World Array 3 platform (Affymetrix, Inc., Santa Clara, CA). DNA was purified and quantitated by PicoGreen (Invitrogen, Inc., Grand Island, NY).

Bray M.J., Edwards T.L., Wellons M.F., Jones S.H., Hartmann K.E, & Velez Edwards D.R. (2017). Admixture mapping of uterine fibroid size and number in African American women. Fertility and sterility, 108(6), 1034-1042.e26.

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Polygenic Risk Score for Type 2 Diabetes

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ARIC participants were genotyped using the Affymetrix 6.0 array (Affymetrix Inc). Genotyping in the RS was done using the Illumina 550K and 610K quad array (Illumina Inc). Genotyped variants were imputed to the Haplotype Reference Consortium (r1.1 2016).²¹ Haplotype phasing and imputation was performed using the Michigan Imputation Server, which is available at https://imputationserver.sph.umich.edu.
A recent GWAS based on individuals of European ancestry identified 403 independent genetic variants associated with type 2 diabetes.⁵ Using the 403 genetic variants identified in this study, we created weighted polygenic score by multiplying the risk allele dosage with the effect estimates reported in the GWAS of type 2 diabetes. An additive weighted polygenic score was calculated by summing the weighted dosages for each individual.²² Separately in ARIC and the RS, all individuals were categorized into low (quintile 1), intermediate (quintiles 2–4) and high (quintile 5) genetic risk categories, with the low genetic risk category as the reference.

Ligthart S., Hasbani N.R., Ahmadizar F., van Herpt T.T., Leening M.J., Uitterlinden A.G., Sijbrands E.J., Morrison A.C., Boerwinkle E., Pankow J.S., Selvin E., Ikram M.A., Kavousi M., de Vries P.S, & Dehghan A. (2021). Genetic susceptibility, obesity and lifetime risk of type 2 diabetes: The ARIC study and Rotterdam Study. Diabetic Medicine, 38(10), e14639.

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Genotyping of BioVU and CARDIA Cohorts

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Individuals from BioVU were genotyped on the on the Affymetrix Axiom Biobank array (Affymetrix, Inc., Santa Clara, CA), and BioVU AAs were further genotyped on the Axiom World Array 3 platform (Affymetrix, Inc., Santa Clara, CA) (Supplemental Table 1). Purification and quantification of DNA for BioVU was performed by PicoGreen (Invitrogen, Inc., Grand Island, NY). Individuals from CARDIA were genotyped at the Broad Institute of MIT and Harvard (Cambridge, MA) on the Affymetrix 6.0 array (Affymetrix, Santa Clara, CA).

Bray M.J., Wellons M.F., Jones S.H., Torstenson E.S., Edwards T.L, & Velez Edwards D.R. (2018). Transethnic and race-stratified genome-wide association study meta-analyses of fibroid characteristics in African and European American women. Fertility and sterility, 110(4), 737-745.e34.

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Polygenic Risk Score for Coronary Heart Disease

Cited 2 times

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Participants were genotyped using the Affymetrix 6.0 array (Affymetrix Inc, Santa Clara, CA, USA). Genotyped variants were used to impute to the TOPMed (version R2) reference panel. Haplotype phasing and imputation was performed using the Michigan Imputation Server,^{28 (link)} which is available at https://imputationserver.sph.umich.edu.
A PRS for CHD, based on over six million genetic variants, was developed using the LDPred algorithm on individuals of European ancestry in UK Biobank by Khera et al.^{8 (link)} Based on the publicly available weights from this published score, a PRS was created by multiplying the risk allele dosage with the weights. After restricting to single nucleotide polymorphisms (SNPs) with an imputation quality r² greater than 0.3 in ARIC, 6,483,355 SNPs were included in an additive weighted genetic risk score calculated by summing the weighted dosages for each individual. A residual PRS was then created after adjusting for the first eleven principal components for ancestry. Individuals were further categorized into low (<20^th percentile), intermediate (20^th-80^th percentile), and high (>80^th percentile) genetic risk categories according to their self-reported race. To maximize the statistical precision and analyze the effects of low and high polygenic risk, the intermediate genetic risk category was used as the reference.

Hasbani N.R., Ligthart S., Brown M.R., Heath A.S., Bebo A., Ashley K.E., Boerwinkle E., Morrison A.C., Folsom A.R., Aguilar D, & de Vries P.S. (2022). American Heart Association’s Life’s Simple 7: Lifestyle Recommendations, Polygenic Risk, and Lifetime Risk of Coronary Heart Disease. Circulation, 145(11), 808-818.

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Polygenic Risk Score for Coronary Heart Disease

Cited 2 times

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Participants were genotyped using the Affymetrix 6.0 array (Affymetrix Inc, Santa Clara, CA). Genotyped variants were used to impute to the TOPMed (version R2) reference panel. Haplotype phasing and imputation was performed using the Michigan Imputation Server^{28 (link)} (available at https://imputationserver.sph.umich.edu).
A PRS for CHD, on the basis of more than 6 million genetic variants, was developed using the LDPred algorithm on individuals of European ancestry in UK Biobank by Khera et al.^{8 (link)} On the basis of the publicly available weights from this published score, a PRS was created by multiplying the risk allele dosage with the weights. After restricting to single nucleotide polymorphisms with an imputation quality r² >0.3 in ARIC, 6 483 355 single nucleotide polymorphisms were included in an additive weighted genetic risk score calculated by summing the weighted dosages for each individual. A residual PRS was then created after adjusting for the first 11 principal components for ancestry. Individuals were further categorized into low (<20th percentile), intermediate (20th–80th percentile), and high (>80th percentile) genetic risk categories according to their self-reported race. To maximize the statistical precision and analyze the effects of low and high polygenic risk, the intermediate genetic risk category was used as the reference.

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Genetic Risk Prediction for Type 2 Diabetes

Cited 2 times

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ARIC participants were genotyped using the Affymetrix 6.0 array (Affymetrix Inc, Santa Clara, CA, USA). Genotyping in the Rotterdam Study was done using the Illumina 550K and 610K quad array (Illumina Inc, San Diego, CA, USA). Genotyped variants were imputed to the Haplotype Reference Consortium (r1.1 2016) (21 (link)). Haplotype phasing and imputation was performed using the Michigan Imputation Server, which is available at https://imputationserver.sph.umich.edu.
A recent GWAS based on individuals of European ancestry identified 403 independent genetic variants associated with type 2 diabetes (5 (link)). Using the 403 genetic variants identified in this study, we created weighted polygenic score by multiplying the risk allele dosage with the effect estimates reported in the GWAS of type 2 diabetes. An additive weighted polygenic score was calculated by summing the weighted dosages for each individual (22 (link)). Separately in ARIC and the Rotterdam Study, all individuals were categorized into low (quintile 1), intermediate (quintiles 2–4), and high (quintile 5) genetic risk categories, with the low genetic risk category as the reference.

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Genotyping Platforms for Genetic Analyses

Cited 1 time

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BioVU samples were genotyped using both the Affymetrix BioBank array and the Axiom World array 2 (Affymetrix Inc., Santa Clara, CA, USA) to attain better coverage for African-derived variants. BioME and the Mt. Sinai eMERGE site used the Illumina 1 M (Illumina Inc., San Diego, CA, USA) platform, with an exome chip backbone included for BioME samples. CARDIA-WS was genotyped on the Affymetrix 6.0 array (Affymetrix Inc., Santa Clara, CA, USA) as part of the Candidate-gene Association Resource which has been previously described in detail (Lettre et al. 2011 (link)).
The Stage 2 23andMe samples (1744 cases and 2906 controls) were genotyped on a custom GWAS panel across four versions. Stage 2 participants from BWHS (382 cases and 392 controls) were genotyped on the Illumina Infinium Expanded Multi-Ethnic Genotyping Array (MEGA; Illumina, Inc., San Diego, CA, USA) at Vanderbilt University VANTAGE Core Genotyping facility.

Hellwege J.N., Jeff J.M., Wise L.A., Gallagher C.S., Wellons M., Hartmann K.E., Jones S.F., Torstenson E.S., Dickinson S., Ruiz-Narváez E.A., Rohland N., Allen A., Reich D., Tandon A., Pasaniuc B., Mancuso N., Im H.K., Hinds D.A., Palmer J.R., Rosenberg L., Denny J.C., Roden D.M., Stewart E.A., Morton C.C., Kenny E.E., Edwards T.L, & Velez Edwards D.R. (2017). A multi-stage genome-wide association study of uterine fibroids in African Americans. Human Genetics, 136(10), 1363-1373.

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