Panscan I and II subsets were genotyped at the Core Genotyping Facility of the National Cancer Institute on Illumina HumanHap550 and Illumina Human610-Quad arrays, respectively. DNA extraction, genotyping and genotype calling procedures were performed in previous publications for Panscan I (Amundadottir et al., 2009 (link)) and Panscan II (Petersen et al., 2010 (link)). EPIC InterAct individuals were genotyped on the Illumina 660W- Quad BeadChip array at the Wellcome Trust Sanger Institute (sharing a large proportion of SNPs with the Illumina HumanHap550 array) (Langenberg et al., 2014 (link)). Genotyping details are given in Data Resource 7 on Mendeley Data (https://doi.org/10.17632/wcb2xsg6pj.3 ).
660w quad beadchip array
Manufactured by Illumina
Sourced in United States
The 660W-Quad BeadChip array is a laboratory equipment product designed for high-throughput genomic analysis. It provides a platform for simultaneous measurement of multiple genetic markers across a large number of samples. The core function of this product is to enable efficient and accurate data generation for various genomic research applications.
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Lab products found in correlation
2 protocols using 660w quad beadchip array
1
Genotyping Protocols for Large Genomic Datasets
2
Genome-Wide Association Study Quality Control
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The Illumina 660W-QUAD Beadchip array (Illumina, San Diego, California, USA) was used to generate genotype data on over 500 K SNPs from cases and controls. To ease automation of analysis, only data obtained from autosomes were analyzed. After filtering out SNPs with low minor allele frequency (<0.01), missing genotype data (≥0.05 of the study population with missing genotypes) or a significant departure from Hardy-Weinberg equilibrium (HWE) (p < 1E-5), there were 508,921 SNPs that passed the quality control screening and were used in subsequent analysis. For a sample to be included in the analysis, we ensured that it had at least 99% of the non-missing SNPs and for each SNP to be included in the analysis, we required that the SNP should have at least 95% of the non-missing subjects.
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