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Genome Wide Association

Human SNP Genome Wide Association Studies (GWAS) can be accomplished using a variety of arrays appropriate for a wide breadth of study design needs.

All GWAS arrays listed below support the addition of the Exome array content and/or the addition of custom SNPs. There is a minimum experimental sample number of 1,104 for the addition of custom content.

Released data includes raw data files (.idat files), genotypes, quality scores, intensity values, SNP and sample summary tables including quality flags and comments, and SNP cluster definition files.

CIDR has a collaboration with the University of Washington Genetics Coordinating Center (GCC). Plate map design, GWAS data cleaning and dbGaP posting, imputation of GWAS datasets to 1000 Genomes, and detection of chromosomal anomalies are new services offered at NO ADDITIONAL COST to study investigators with GWAS projects supported by the NIH CIDR Program. Investigators working with CIDR through the SNP Center may also utilize these services through a fee-for-service mechanism.

Under the NIH CIDR Program, a single application can be submitted for both the initial GWAS study as well as replication using our custom SNP service. Investigators are required to have all samples collected and all subjects phenotyped before applying.

Array *	SNPs per Sample	Samples per Array	Comments
Illumina HumanOmni5	~4,300,000	4	Cosmopolitan array providing coverage of 3 main HapMap populations down to MAF 1% based on 1000 Genomes. Option to add up to 500,00 custom SNPs to the array. Additional Information
Illumina HumanOmni2.5	~2,500,000	8	Coverage of SNPs down to MAF 2.5% based on 1000 Genomes Project pilot data in all 3 populations. Additional Information
Illumina HumanOmniExpress	>700,000	12	Coverage of common SNPs in Caucasian and Asian populations. 60% overlap in rs numbers with previous Illumina arrays. FFPE samples are supported on this array. Additional Information
Illumina HumanCore	>250,000	12	Includes an informative base of tag SNPs and is appropriate for common variant. mtDNA ancestry, sex confirmation, loss-of-function, variant, indel and CNV studies. Additional Information

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