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Genome-Wide Human SNP Array 5.0 - Learn More

Product Specs
Number of SNPs accessible using Genotyping Console
500,568
Number of SNPs accessible using BAT 2.0
440,794
Number of Arrays
1
DNA Required
500 ng
Expected minimum BRLMM-P Call Rate (0.05)
≥97 percent
Average Minor Allele Frequency (MAF)
0.22
Average Heterozygosity
0.31
PCR Primers
1 per sample
Instrumentation
GeneChip® Scanner 3000 7G with AutoLoader
Throughput
>21 million genotypes per day per scanner with three Gene Chip® Fluidics Station 450s

Performance Data

To test the performance of the SNP Array 5.0, Affymetrix and the Broad Institute jointly ran the 270 samples from the International HapMap Project. In addition, two external sites and one internal validation group ran a plate of 44 HapMap DNAs, which includes 30 unique samples, 10 trios and five samples with multiple replicates.

The arrays that passed the QC call rate threshold were analyzed using the BRLMM-P algorithm at the default setting of 0.05. The average call rate for each set was greater than 99 percent, and the concordance with HapMap genotypes was observed to be greater than or equal to 99.5 percent. For the 10 trios, the Mendelian inheritance consistency was found to be greater than 99.9 percent. Reproducibility was measured at 99.9 percent.

 
270 HapMap
Site 1
Site 2
Internal
Call Rate
99.71
99.55
99.37
99.63
HapMap Concordance
99.69
99.67
99.56
99.69
Mendelian Consistency
99.96
99.95
99.94
99.96
Reproducibility
NA
99.9
99.9
99.9

Refer to the Affymetrix® Genome-Wide Human SNP Nsp/Sty 5.0 Assay Manual for details on the QC call rate thresholds, as well as procedures on DNA target preparation, target hybridization, fluidics setup, array scanning and data analysis.

Non-Polymorphic Probes

Learn more about the non-polymorphic probes on the Genome-Wide SNP Array 5.0

Coverage of SNPs and non-polymorphic probes on the Genome-Wide SNP Array 5.0
Figure 1
Coverage of SNPs and non-polymorphic probes on the Genome-Wide SNP Array 5.0

The SNP Array 5.0 contains 420,000 non-polymorphic probes for researchers to examine germline copy number variation (CNV) in association studies. One hundred thousand non-polymorphic probes cover 2,000 known CNVs identified in the UCSC Genome Browser database (50 probes per CNV). Another 320,000 probes were chosen to give even spacing across the genome, concentrating on areas not represented by SNPs. Current Affymetrix software does not support analysis of the non-polymorphic probes.

 

Whole-genome Sampling Assay

Learn more about the assay

Affymetrix Genome-Wide Human SNP Nsp/Sty Assay Kit 5.0/6.0