Table 1 Inaccurate SNPs with the largest difference between SNP allele frequencies when genotyped individually vs. calculated from pooled DNA can be partially predicted. Nearly 40% of the SNPs found to be the 100 most inaccurate SNPs were also either (a) one the 500 worst performing SNPs in individual genotyping or (b) had the largest variability between replicates in the pool.
From: Identification of disease causing loci using an array-based genotyping approach on pooled DNA
All SNPs | (a) 500 worst performing SNPs Criteria: NoCalls on 3000 person database | (b) 500 worst performing SNPs Criteria: Pool variability from 3 replicates | SNPs found in (a) or (b) | Inaccuracy (predicted vs. genotyped) |
|---|---|---|---|---|
100 most inaccurate SNPs (individual genotyped vs. pooled) | 24.2% | 27.3% | 38.6% | 27.2% |
500 most inaccurate SNPs (individual genotyped vs. pooled) | 12.5% | 14.5% | 22.1% | 20.2% |
Remaining 9605 SNPs | 4.4% | 5.5% | 8.6% | 5.0% |