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Infinium custom gwas chip

Manufactured by Illumina
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The Illumina Infinium custom GWAS chip is a high-throughput genotyping array designed for genome-wide association studies (GWAS). It enables the simultaneous analysis of a large number of genetic variants across the human genome. The chip is customizable, allowing researchers to select specific markers of interest for their study.

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Lab products found in correlation

Affymetrix 6.0 platform, by Thermo Fisher Scientific (2 mentions)

Close spelling variants of this product

GWAS chips (3 citations) Infinium chips (3 citations)

2 protocols using infinium custom gwas chip

1

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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2

Genotype Data Integration and Imputation

Check if the same lab product or an alternative is used in the 5 most similar protocols
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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