CIDR offers SNP Genome Wide Association (GWAS) genotyping using a variety of arrays appropriate for a wide breadth of study design needs. Starting May 1, 2008, CIDR is offering the Affymetrix® SNP Array 6.0. We have also added the new high-density format arrays from Illumina to our service options.

Investigators must specify which array they are requesting in the application. In addition, two-stage GWAS study designs will be supported using our Custom SNP Genotyping service for the second stage. Investigators are required to have all samples collected and all subjects phenotyped before applying to CIDR.

GWAS Array    (links to product details on vendor websites)	SNPs per Sample	# of Samples per Array	Nonpolymorphic Probes per sample	Comments
Illumina Human1M-Duo	1,050,000	2	38,000	Excellent coverage of common SNPs in all 4 HapMap populations Excellent gene coverage
Affymetrix® SNP Array 6.0*	906,000	1	946,000	Excellent coverage of common SNPs in all 4 HapMap populations
Illumina Human610-Quad	597,000	4	27,000	Excellent coverage of common SNPs in Caucasian and Asian populations
Illumina HumanCNV370-Quad	345,000	4	25,000	Excellent coverage of common SNPs in Caucasian populations

Potential applicants should consult with the appropriate Institute liaison to CIDR to create a Data Dictionary (see example developed by dbGaP) and a Summary Table (see example) that describes their phenotypic dataset. This information will be used by the CIDR Access Committee as part of its assessment of the applicant's power calculations. All CIDR GWAS funded by NIH will have to abide by the conditions of the NIH data sharing policy that may require phenotypic and genotypic data (de-identified) be deposited into an NIH database (dbGaP) for release to the broader research community for analysis. For more information on the policy, please see http://grants.nih.gov/grants/guide/notice-files/NOT-OD-07-088.html.

Services include a dedicated project manager, sample pretesting with a 79 SNP ‘barcode’ panel (used to unambiguously tie DNA sample to GWAS genotyping data and to verify sample quality, gender, family relationships, and cryptic relatedness), and the opportunity to replace problematic samples. GWAS genotyping includes one repeat of 1st round failures. Assistance is provided with the preparation of a ‘cleaned’ dataset if desired.

Released data includes raw data files (.idat or .CEL files), genotypes, quality scores, intensity values, SNP and sample summary tables including quality flags and comments, and SNP cluster definition files. All raw image data is archived off-site indefinitely for future retrieval by PI if desired.