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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.

 

Genomic coverage of many of the arrays we offer has been assessed using imputation to Phase3 of the 1000 Genomes Project and detailed in a recent publication. In general, coverage increases with increasing array density.

 

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.


Plate map design, GWAS data cleaning and dbGaP posting, imputation of GWAS datasets to 1000 Genomes, and detection of chromosomal anomalies are 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

Affymetrix UK BioBank Array

~800,000

96

Option to add custom content from the Axiom Cloud Database or other custom content. Coverage Information

Illumina HumanOmni5

~4,300,000

4

Option to add up to 500,00 custom SNPs to the array. Coverage 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. Coverage Information

Illumina Multi-Ethnic Global Array

~1,700,000

8

Multi_Ethnic genotyping array enabling genetic associations with common and rare traits. Tag SNPs maximize imputation accuracy. Coverage Information

Illumina Multi-Ethnic EUR/EAS/SAS

~1,400,000

8

Multi_Ethnic EUR/EAS/SAS genotyping array provides a multi-purpose, multi-ethnic genotyping array focused on European, East Asian and South Asian populations. Coverage Information

Illumina Multi-Ethnic AMR/AFR

~1,400,000

8

Multi_Ethnic AMR/AFR genotyping array provides a multi-purpose genotyping array focused on Hispanic and African American populations. Coverage 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. Coverage Information

Illumina Global Screening Array*

>650,000

24

The Global Screening Array combines a highly optimized, genome-wide backbone and hand curated clinical research variants. Coverage 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. Coverage Information

 

 

*minimum 276 samples

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photo of arrays

 

Illumina arrays

 

See our Services page for a full description of what is included for all study types

 

 

See our Sample Requirements page for detailed specifications for each product