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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.