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.
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