A review of software for microarray genotyping

Table 1 The arrays that are currently available for the human genome from Affymetrix and Illumina

	#Arrays	#SNPs	Software
Affymetrix
GeneChip Human Mapping 10 K 2.0 Array	1	10,204	MPAM
GeneChip Human Mapping 100 K Set	2	116,204	DM
GeneChip Human Mapping 500 K Array Set	2	500,568	BRLMM
Genome-Wide Human SNP Array 5.0	1	500,568^a	BRLMM-P
Genome-Wide Human SNP Array 6.0	1	906,600^b	Birdseed
Illumina	#Samples	#Markers	Software
HumanCytoSNP-12 DNA Analysis BeadChip	12	299,140	^d
Human660W-Quad v1 DNA Analysis BeadChip	4	657,366	^d
HumanOmniExpress BeadChip	12	731,442	^d
Human1M-Duo DNA Analysis BeadChip	2	1,199,187	^d
HumanOmni1-Quad BeadChip	4	1,140,419	^d
HumanOmni1S-8 BeadChip	8	1,200,000^c	^d
HumanOmni2.5-Quad BeadChip	4	2,450,000^c	^d

For Affymetrix, #Arrays reflects the physical number of arrays to use to obtain genotypes for all SNPs. For Illumina, #Samples gives the number of samples that can be run using the same BeadChip
^aAdditional 420,000 non-polymorphic probes for copy number analysis.
^bAdditional 946,000 non-polymorphic probes for copy number analysis.
^cAlso includes probes for CNVs.
^dThe BeadStudio and the GenomeStudio applications can handle all Illumina's arrays.

ISSN: 1479-7364