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Table 1 Main features of some custom SNP genotyping platforms available

From: High-throughput genomic technology in research and clinical management of breast cancer. Evolving landscape of genetic epidemiological studies

  Assay design Multiplexing capability Throughput (no. of samples per 8 hour working day) Cost per genotype (at maximal multiplexing)a Type of study design that platform is suitable for
TaqMan® By manufacturer or flexible design by investigator No Up to 10,000+ >US$0.30 Small number of SNPs, large sample size
Pyrosequencing™ Flexible design by investigator From 1 to 3 Up to 4,000+ >US$0.30 Small number of SNPs, large sample size
Sequenom MassARRAY® Flexible design by investigator From 1 to 29-plex Up to 3,000+ US$0.05–0.10 Moderate number of SNPs, small/moderate sample size
Illumina BeadArray™ (GoldenGate® Assay) By manufacturer From 96 to 1,536-plex Up to 192 <US$0.05 Large number of SNPs, small/moderate/large sample size
Affymetrix GeneChip® By manufacturer From 1,500 to 20,000-plex Up to 16 <US$0.05 Large number of SNPs, small/moderate/large sample size
  1. aThe estimates are heavily influenced by the size of study, that is, large studies will enjoy more efficient usage of reagents and volume-based price discount from manufacturers than medium and small studies. SNP, single nucleotide polymorphism.
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