Table 3.
Pairwise Correlations Between Mutant Allele Frequency Estimates in Clinical Specimens Generated by Various Methodsa
| Sanger | Sanger-MLE | Pooled gDNA (1) | Pooled gDNA (2) | Pooled gDNA (3)b | Pooled gDNA (4)b | Pooled DBS (1) | Pooled DBS (2) | |
|---|---|---|---|---|---|---|---|---|
| Sanger | … | <.0001 | .0002 | .0001 | .2004 | .2686 | .0008 | 1 |
| Sanger-MLE | 0.9992 | … | .0005 | .0003 | .2935 | .3629 | .0017 | 1 |
| Pooled gDNA (1) | 0.9929 | 0.9902 | … | <.0001 | .0126 | .0219 | <.0001 | 1 |
| Pooled gDNA (2) | 0.9943 | 0.9916 | 0.9994 | … | .0130 | .0296 | <.0001 | 1 |
| Pooled gDNA (3)b | 0.9928 | 0.9895 | 0.9995 | 0.9995 | … | .0056 | .0067 | 1 |
| Pooled gDNA (4)b | 0.9904 | 0.9870 | 0.9992 | 0.9989 | 0.9998 | … | .0011 | 1 |
| Pooled DBS (1) | 0.9880 | 0.9842 | 0.9991 | 0.9983 | 0.9998 | 1 | … | 1 |
| Pooled DBS (2) | 0.6264 | 0.6503 | 0.6370 | 0.6257 | 0.5482 | 0.5510 | 0.6259 | … |
Abbreviations: DBS, dried blood spot; gDNA, genomic DNA; MLE, maximum likelihood estimation;
a Numbers in lower half are correlation coefficients between estimates of mutant allele frequencies in dhfr (codons 51, 59, 108, and 164) and dhps (codons 437, 540, and 581); numbers close to 1 indicate a positive correlation, those close to −1 indicate a negative correlation, and those close to 0 indicate no correlation between values in the 2 groups. Correlation coefficients that were significant at P < .05 after Bonferroni correction are bolded and italicized. Numbers in upper half of table are P values for the correlation coefficients. Numbers in parentheses indicate technical replicates of the second-generation sequencing reactions.
b Frequencies are available only for the 4 dhfr loci, because dhps was sequenced in only only 2 replicates.