Table 1.
Comparison of various DNA methods (adapted from [135, 237, 245, 247])
| SCAR | ARMS | SSR | PCR-RFLP | RP-PCR | ISSR | AFLP | Sequencing | Hybridization | |
| Development cost | medium | medium | high | medium a | low | low | low | medium | medium |
| Running cost | low | low | medium | medium a | low | low | medium | medium | medium |
| Polymorphism | low b | low c | high d | low e | medium f | medium f | medium f | medium-low g | only for detection h |
| Detection of contamination by DNA of the same target species (mixture) | no | no | yes | yes/noi | no | no | no | yes/nok | yes/nok |
| Detection of contamination by non-target species DNA (mixture) | no | no | no | yes j | no | no | no | yes/nok | yes/nok |
| Detection of contamination by DNA of the same target species (mixture) | no | no | yes | yes/no i | no | no | no | yes/nok | yes/nok |
| Detection of contamination by non-target species DNA (mixture) | no | No | no | yesj | No | no | no | yes/nok | yes/nok |
| Multi-locus/single locus | single locus | single locus | single locus | single locus | multi-loci | multi-loci | multi-loci | single locus | single locus |
| Level of identification (taxonomic level) | species | species to strain | strain | species to strain | species to strain | species to strain | species to strain | family to strain | genus to subspecies |
| Quality of DNA required (integrity) | medium | medium | low | medium | high | high | high | medium | medium |
| Quality of DNA required (purity) | high l | high l | medium | high | high | high | high | high l | high |
| Prior sequence knowledge requirement (including universal primer sequence) | yes | yes | yes | no | no | no | no | yes | yes |
| Throughput | low | low | high | low | high | high | high | low | high |
| Level of skills required | low | low | low-medium | low | low | low | medium | medium | medium |
| Automation | yes | yes | yes | difficult | yes | yes | yes | yes | difficult |
| Reliability | high | high | high | high | low | medium | high | high | medium |
Development cost: cost for developing standardized reference results for target samples
Running cost: cost for routine testing
Detection of contamination: same target species = samples of the same strain or locality; non-target species = adulterants or substitutes
Multi-locus: simultaneous amplification of multiple regions in the genome in a single PCR
Prior sequence requirement: sequence requirement to design primers for amplification or probes for hybridization
Throughput: number of samples that can be handled within a given period of time
Reliability: giving reproducible and accurate results under the same conditions
a: enzyme dependent
b: band/no band, or size polymorphism
c: band or no band
d: null allele or size polymorphism
e: band number and size polymorphism
f: presence/absence of all the bands in a pattern
g: sequence dependent; nucleotide difference
h: presence or absence of sample DNA
i: restriction enzyme dependent
j: primer dependent
k: sequence dependent
l: crude tolerated