The Axiom Genotype Data Set contains billions of genotypes generated from an extensive screen on biological samples against 5.4 million validated markers in the Axiom Genomic Database.
Each variant has been been extensively validated in a larger number of biological samples to ensure that the SNP is not due to sequencing error, the minor allele can be reliably detected, and that it performs consistently in the Axiom assay. This information can be easily downloaded to aid in custom array design and other analyses.
The Axiom Genotype Data Set is the result of an ongoing screening pipeline whereby we have leveraged our production-scale infrastructure and analyzed billions of genotypes to date. These genotype calls include data generated using samples from the International HapMap Project (all phases, including 1,300 samples from Phase III). The sources of SNPs include the Single Nucleotide Polymorphism Database (dbSNP), the 1000 Genomes Project, and collaborations that have led to the discovery of novel SNPs not in the public domain, in some cases.
The files contain genotyping data on approximately 5.4 million SNPs, including ~1.8 million from HapMap and dbSNP, ~3 million from the 1000 Genomes Project 2009 release, and an additional ~0.6 million from collaborative discovery projects. Almost all of the ~1.8 million SNPs from HapMap and dbSNP were genotyped on 11 populations comprising more than 1,000 individuals, while the remaining ~3.6 million SNPs were genotyped on the three HapMap populations (CEU: Utah residents with European ancestry; CHB: Han Chinese in Beijing, China; JPT: Japanese in Tokyo, Japan; YRI: Yoruba in Ibadan, Nigeria) comprising about 270 individuals. A subset of the genotypes for the 1.8 million SNPs mentioned above is also available from HapMap and agrees with the Axiom genotypes more than 99 percent of the time.
As more discoveries occur and more SNPs are publicly available, Affymetrix will continue to screen putative SNPs and expand the overall set of information that is available to you.
Design custom arrays
With the Axiom Genomic Database of validated SNPs, researchers can create custom arrays or array plates containing 1,500 to 2.6 million SNPs. This broad spectrum of custom capabilities enables highly precise designs leveraging millions of variants from the 1000 Genomes Project as well as SNPs with low minor allele frequencies. Researchers can also combine SNPs from their discovery projects or other sources with Affymetrix' validated SNPs.
This offering delivers unparalleled flexibility for study design and maximizes the ability to generate meaningful data within a fixed budget.
Screening of millions of SNPs
To create the database, Affymetrix screened millions of SNPs from public databases and putative novel SNPs. These validated SNPs meet the following criteria:
- They have been reliably genotyped in the Axiom Genotyping Assay, meaning that they have met or exceeded stringent performance metrics, such as call rate, sample pass rate, reproducibility, and concordance
- They have been shown to be polymorphic in the given population(s) by demonstrating reliable detection of the minor allele in at least two independent chromosomes
The data release files accessible here contain genotypes and related information for approximately 5 million validated SNPs.
- CEU: Utah residents with European ancestry
- CHB: Han Chinese in Beijing, China
- YRI: Yoruba in Ibadan, Nigeria
- JPT: Japanese in Tokyo, Japan
- LWK: Luhya in Webuye, Kenya
- MKK: Maasai in Kinyawa, Kenya
- ASW: African ancestry in Southwest USA
- TSI: Toscani in Italia
- CHD: Chinese in metropolitan Denver, CO, USA
- MEX: Mexican ancestry in Los Angeles, CA, USA (sometimes referred to as MXL)
- GIH: Gujarati Indians in Houston, TX, USA
- Sample data ReadMe File (zip, 2 KB)
The enclosed ReadMe file provides more information around the sources of the samples and a detailed description of which SNPs have been genotyped across which samples.
In addition to genotype calls, these files also contain chromosome and position information. The files are in "HapMap format" (the same format used for bulk data downloads from the HapMap project).
To learn more about this data set, inquire about access to the entire data set, or obtain information about designing an Axiom custom array, please contact your Affymetrix account manager or call 888-362-2447.