TABLE 3.
Sensitivity and specificity of pyrosequencing in detecting SNPs of a single strain
| Strain | Amino acid at codon (dhfr genotypes):
|
Sensitivityb
|
Amino acid at codon (dhps genotypes):
|
Sensitivity
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 50 | 51 | 59 | 108 | 164 | 4Pa | 2P | 436 | 437 | 540 | 581 | 613 | 4P | 2P | |
| 3D7 | C | N | C | S | I | + | + | S | G | K | A | A | + | − |
| V1/S | C | I | R | N | L | + | +/− | F | G | K | A | T | + | +/− |
| FCR3 | C | N | C | T | I | + | + | S | A | K | A | A | + | +/− |
| HB3 | C | N | C | N | I | + | + | S | A | K | A | A | + | +/− |
| K1 | C | N | N | N | I | + | + | S | G | K | G | A | + | +/− |
| W2 | C | I | R | N | I | + | + | F | G | K | A | S | + | + |
| Peru | NA | S | G | E | G | A | NA | NA | ||||||
| P. vivax SV4 | − | − | − | − | ||||||||||
| P. malariae Uganda I | − | − | − | − | ||||||||||
| P. ovale Nigeria I | − | − | − | − | ||||||||||
a
Parasite genome equivalents of DNA.
b
Positive (+) or negative (−) PCR results are indicated. +/−, the results were variable in repeat experiments; NA, not tested. The DNA sequences of all of the laboratory strains were reconfirmed by direct sequencing. The results were consistent between the different codons within the same gene. We tested each strain at DNA concentrations equivalent to 40,000, 4,000, 400, 40, 4, and 2 parasites. Genotyping results for dhfr and dhps were positive for all P. falciparum strains from 40,000 to 40 parasites and negative for P. vivax SV4, P. malariae Uganda I, and P. ovale Nigeria I at all six concentrations (data not shown).