Table 1. Chip size, the lowest MAF covered by the chip, the number of non-synonymous SNPs, and design notes of recent Illumina and Affymetrix chips according to their datasheets provided by the companies.
| Chip size in number (SNPs) | Lowest MAF captured | Number (non-synonymous SNPs) | Based on | Note | |
|---|---|---|---|---|---|
| Affymetrix | |||||
| Axiom Genome-Wide Human EU (Axiom GW EU) | ∼600 000 | 1% | 10 648 | HapMap, Single Nucleotide Polymorphism database (dbSNP), 1000 GP | Targeting European population |
| Axiom Genome-Wide Human ASI (Axiom GW ASI) | ∼600 000 | 1% | 10 346 | HapMap, dbSNP, 1000 GP | Targeting Asian population |
| Axiom Genome-Wide Human CHB (Axiom GW CHB) | ∼1 200 000 | 2% | 10 560 | HapMap, dbSNP, 1000 GP | Targeting CHB subpopulation |
| Axiom Genome-Wide Human PanAFR (Axiom GW PanAFR) | ∼2 200 000 | 2% | 12 250 | HapMap, dbSNP, 1000 GP, Southern African Genomes Project | Targeting African population |
| Illumina | |||||
| Human OmniExpress | ∼700 000 | 5% | 15 062 | HapMap | Optimized tag SNP |
| Human Omni1S-8 | ∼1 000 000 | 5% | 5641 | 1000GP | Optimized tag SNP |
| Human Omni2.5-8 | ∼2 500 000 | 2.5% | 41 900 | 1000GP | Targeting common and rare variants |
| Human Omni2.5S-8 | ∼2 500 000 | 1% | 57 360 | 1000GP | Targeting rare variants |
http://www.affymetrix.com/support/technical/datasheets/axiom_ceu_arrayplate_datasheet.pdf, http://www.affymetrix.com/support/technical/datasheets/axiom_asi_arrayplate_datasheet.pdf, http://www.affymetrix.com/support/technical/datasheets/axiom_chb_1_2_array_plate_set_datasheet.pdf, http://www.affymetrix.com/support/technical/datasheets/axiom_panafr_arrayplate_datasheet.pdf, http://www.illumina.com/documents/products/datasheets/datasheet_human_omni_express.pdf, http://res.illumina.com/documents/products/datasheets/datasheet_human_omni1s.pdf, http://res.illumina.com/documents/products/datasheets/datasheet_human_omni2.5.pdf, http://res.illumina.com/documents/products/datasheets/datasheet_omni25s.pdf.