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.
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.
We are pleased to announce that CIDR has entered into a collaboration with the University of Washington Center for Biomedical Statistics (CBS). 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 |
Samples |
Non- |
Comments |
~4,300,000 |
4 |
0 |
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 |
|
~4,300,000 |
4 |
0 |
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. Option to add Custom SNP content, including exome array content. Additional Information |
|
~2,500,000 |
8 |
0 |
Coverage of SNPs down to MAF 2.5% based on 1000 Genomes Project pilot data in all 3 populations. Additional Information |
|
>2,500,000 |
8 |
0 |
Coverage of SNPs down to MAF 2.5% based on 1000 Genomes Project pilot data in all 3 populations. Option to add up to 200,000 custom beadtypes |
|
>1,000,000 |
4 |
124,000 |
Coverage of common SNPs in all 3 HapMap populations. 60% overlap in rs numbers with previous Illumina arrays. Additional Information |
|
>700,000 |
12 |
0 |
Coverage of common SNPs in Caucasian and Asian populations. 60% overlap in rs numbers with previous Illumina arrays |
>650,000 |
12 |
0 |
Coverage of common SNPs in Caucasian and Asian populations. 60% overlap in rs numbers with previous Illumina arrays. SNP manifest and assay optimized for special needs of FFPE samples |
>700,000 |
8 |
0 |
Coverage of common SNPs in Caucasian and Asian populations. 60% overlap in rs numbers with previous Illumina arrays. Option to add up to 200,000 custom SNPs including exome array content. |
~2,500,000 |
8 |
0 |
Available option for previous studies which have utilized the 2.5 array. This supplemental array provides additional assays required to approximate Omni5 coverage. |
|
~1,250,000 |
8 |
0 |
Available option for previous studies which have utilized the Omni1-Quad or OmniExpress BeadChip. This supplemental array provides the additional assays required to approximate Omni2.5 coverage |
* Number of overlapping markers across Illumina GWAS arrays
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Research Technologist, Jeremy Rife, loads carriers onto an iScan
See our Services page for a full description of what is included for all study types