TABLE 4.
Comparison of different methods for detecting dhfr SNPs in mixed populations of P. falciparum parasites with different genotypes (DNA stock equal to 40 parasites/μl for each strain)a
| Codon | Parasite proportion (%)b
|
Pyroic
|
RFLP
|
DSd
|
||||
|---|---|---|---|---|---|---|---|---|
| 3D7 | V1/S | Amino acid code | No. of expts with positive reactions | Amino acid code | No. of expts with positive reactions | Amino acid code | No. of expts with positive reactions | |
| 51 | 100 | 0 | N | 3/3 | N | 3/3 | N | 3/3 |
| 95 | 5 | N | 3/3 | N | 3/3 | N | 3/3 | |
| 90 | 10 | N | 2/3 | N | 3/3 | N | 3/3 | |
| N/I | 1/3 | |||||||
| 85 | 15 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 80 | 20 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 70 | 30 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 60 | 40 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 50 | 50 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 40 | 60 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 30 | 70 | N/I | 3/3 | N/I | 3/3 | N/I | 3/3 | |
| 20 | 80 | N/I | 3/3 | N/I | 2/3 | I | 3/3 | |
| I | 1/3 | |||||||
| 15 | 85 | N/I | 3/3 | N/I | 2/3 | I | 3/3 | |
| I | 1/3 | |||||||
| 10 | 90 | N/I | 2/3 | N/I | 2/3 | I | 3/3 | |
| I | 1/3 | I | 1/3 | |||||
| 5 | 95 | N/I | 1/3 | I | 3/3 | I | 3/3 | |
| I | 2/3 | |||||||
| 0 | 00 | I | 3/3 | I | 3/3 | I | 3/3 | |
| 59 | 100 | 0 | C | 3/3 | C | 3/3 | C | 3/3 |
| 95 | 5 | C | 3/3 | C | 3/3 | C | 3/3 | |
| 90 | 10 | C | 2/3 | C/R | 3/3 | C | 3/3 | |
| C/R | 1/3 | |||||||
| 85 | 15 | C/R | 2/3 | C/R | 3/3 | C/R | 3/3 | |
| 80 | 20 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 70 | 30 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 60 | 40 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 50 | 50 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 40 | 60 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 30 | 70 | C/R | 3/3 | C/R | 3/3 | C/R | 3/3 | |
| 20 | 80 | C/R | 3/3 | C/R | 2/3 | R | 3/3 | |
| R | 1/3 | |||||||
| 15 | 85 | C/R | 2/3 | C/R | 2/3 | R | 3/3 | |
| R | 1/3 | |||||||
| 10 | 90 | C/R | 1/3 | C/R | 2/3 | R | 3/3 | |
| R | 2/3 | R | 1/3 | |||||
| 5 | 95 | R | 3/3 | R | 3/3 | R | 3/3 | |
| 0 | 00 | R | 3/3 | R | 3/3 | R | 3/3 | |
| 108 | 100 | 0 | S | 3/3 | S | 3/3 | S | 3/3 |
| 95 | 5 | S | 3/3 | S | 3/3 | S | 3/3 | |
| 90 | 10 | S | 2/3 | S | 3/3 | S | 3/3 | |
| S/N | 1/3 | |||||||
| 85 | 15 | S/N | 2/3 | S/N | 3/3 | S/N | 3/3 | |
| 80 | 20 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 70 | 30 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 60 | 40 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 50 | 50 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 40 | 60 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 30 | 70 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 20 | 80 | S/N | 3/3 | S/N | 3/3 | S/N | 3/3 | |
| 15 | 85 | S/N | 2/3 | S/N | 3/3 | N | 3/3 | |
| N | 1/3 | |||||||
| 10 | 90 | S/N | 1/3 | S/N | 2/3 | N | 3/3 | |
| N | 2/3 | N | 1/3 | |||||
| 5 | 95 | N | 3/3 | S/N | 1/3 | N | 3/3 | |
| N | 2/3 | |||||||
| 0 | 00 | N | 3/3 | N | 3/3 | N | 3/3 | |
| 164 | 100 | 0 | I | 3/3 | I | 3/3 | I | 3/3 |
| 95 | 5 | I | 3/3 | I | 3/3 | I | 3/3 | |
| 90 | 10 | I | 3/3 | I | 3/3 | I | 3/3 | |
| 85 | 15 | I | 3/3 | I/L | 3/3 | I | 3/3 | |
| 80 | 20 | I | 3/3 | I/L | 3/3 | I | 3/3 | |
| 70 | 30 | I/L | 3/3 | I/L | 3/3 | I/L | 3/3 | |
| 60 | 40 | I/L | 3/3 | I/L | 3/3 | I/L | 3/3 | |
| 50 | 50 | I/L | 3/3 | I/L | 3/3 | I/L | 3/3 | |
| 40 | 60 | I/L | 3/3 | I/L | 3/3 | I/L | 3/3 | |
| 30 | 70 | I/L | 3/3 | I/L | 3/3 | I/L | 3/3 | |
| 20 | 80 | I/L | 3/3 | I/L | 3/3 | L | 3/3 | |
| 15 | 85 | I/L | 2/3 | I/L | 3/3 | L | 3/3 | |
| L | 1/3 | |||||||
| 10 | 90 | I/L | 2/3 | L | 3/3 | L | 3/3 | |
| L | 1/3 | |||||||
| 5 | 95 | L | 3/3 | L | 3/3 | L | 3/3 | |
| 0 | 00 | L | 3/3 | L | 3/3 | L | 3/3 | |
a
Each concentration was tested in triplicate.
b
DNA proportion of wild-type parasites (3D7) and mutant parasites (V1/S).
c
Pyro, Pyrosequencing.
d
DS, direct sequencing.