Table 3 Overview of several genotyping methods used for malaria samples
Method | Marker throughput | Sample throughput | Sensitivity | Test-to-result time | Cost considerations | Accessibility | Sequencing features | Data handling |
|---|---|---|---|---|---|---|---|---|
Capillary sequencing | One gene region at a time | Low to high | Moderate at major allele, low at minor1 | Days | Not cost-effective for multiple genes in a large sample | Widely accessible. Technical expertise often available in endemic countries | Accessibility to moderately complex sequence regions. Ability to detect new variants and VNTRs2. Suitable for genotyping tri- or quadri-allelic positions | Time-consuming to review multiple sequence traces |
Microsatellite typing by capillary sequencing | One to ~ four markers at a time | Low to high | Moderate at major allele, low at minor1 | Days | Not cost-effective for multiple genes in a large sample | Widely accessible. Technical expertise often available in endemic countries | Multi-allelic nature helps to characterize polyclonal infections. Stutter and other artefacts can be problematic | Time-consuming to review multiple sequence traces |
SNP genotyping by HRM3 | One marker at a time | Low to high | Moderate at major allele, low at minor1 | Days | Not cost-effective for multiple genes in a large sample | Accessible and user-friendly technology | Accuracy in genotyping heterozygote positions is constrained. Need controls for every marker on each run | Time-consuming to review multiple sequence traces |
Real-time PCR analysis of CNVs4 | One gene region at a time | Low to high | Moderate at major allele, low at minor1 | Days | Not cost-effective for multiple genes in a large sample | Accessible and user-friendly technology | Optimal for CNVs. Need controls for every marker on each run | Time-consuming to review multiple sequence traces |
MassARRAY genotyping | One to ~ 40 markers at a time | Moderate to high | Moderate at major, low at minor1 | Weeks | Cost-effective for moderate-large sample size and multiple genes | Not highly accessible. Requires specialized technical expertise (reference lab advised) | Accuracy in genotyping heterozygote positions is constrained | Need specialized skills |
Amplicon sequencing with Illumina, and Molecular Inversion Probes | Dozens to hundreds of markers in parallel | Moderate to high | High at major and minor allele5 | Weeks6 | Cost-effective for large sample size and multiple genes | Not highly accessible. Requires specialized technical expertise (reference lab advised) | Digital allele calling. Potential to detect CNVs4. Not feasible for detecting new variants | Need specialized skills |
MinION genotyping | Dozens to hundreds of markers in parallel | Low to high | Moderate at major, low at minor1 | Days | Cost-effective for small-moderate sample size and multiple genes | Highly portable, accessible and user-friendly to run | Ability to detect new variants and VNTRs1. Accessibility to moderately complex sequence regions. High rate of sequencing errors | Need specialized skills, but amenable to more user-friendly platforms |