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Table 3 Overview of several genotyping methods used for malaria samples

From: Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia–Pacific region

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
  1. 1Generally not robust to detect minor alleles at intensity lower than 10% of major allele. 2Variable Number Tandem Repeats. 3High Resolution Melt-curve analysis using quantitative PCR. 4Copy Number Variants. 5Depends in part on read depth, which is partly determined by the multiplexing level. 6Depends on sample throughput; turnaround time of weeks assumes a moderately large sample throughput for cost-efficacy