Selected Genotyping Platforms

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Written byM. Tevfik Dorak

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Related Articles Genotyping with PCR Selected Reading List

Selected Genotyping Platforms
System/Platform	Reaction Method	Pro	Con	Vendor	Relative Cost *
Luminex, Bio-Plex	ASPE (see figure), SBE, OLA	• Choice of chemistries for PCR • Multiplexing capability (up to 50-plex), especially for multiple variants from the same gene	• Optimization may be difficult • Requires dedicated instrument	Luminex, Bio-Rad	$$
Molecular inversion probes & GeneChip	Probe hybridization	• Ideal for genome-wide studies • Can be customized for smaller projects • Can be outsourced	• Without outsourcing, requires costly capital investment	Affymetrix	$
GoldenGate & BeadArray	ASPE & OLA			Illumina	$
Infinium II & BeadArray	ASPE / SBE			Illumina	$
TaqMan	FRET (see figure)	• Highly specific and sensitive • Simple closed-tube procedure	• Limited multiplexing • Relatively costly	Applied Biosystems	$$$
High-resolution melting-curve analysis	Intercalating dye, hybridization probe (labeled or unlabeled)	• Rapid, inexpensive, suitable for multiplex assays and for simultaneous screening of unknown variants • No variant-specific primer or probes • Simple closed-tube procedure	• May miss some variants in lower resolution platforms • Nonspecific amplification may interfere (but easy to rule out)	Idaho Technology, Roche Applied Science	$
MassArray	SBE (hME or iPLEX)	• Ultrahigh throughput and multiplexing with small amount of DNA • No labeling • Automated allele calling	• Expensive dedicated equipment required	Sequenom	$
Pyrosequencing	SBE & luminescence (see figure)	• Quantitative allele signal (suitability for DNA pooling studies) • Most suitable for multiplexing for closely spaced variants within 50 bases	• Limited multiplexing for independent variants • Relatively high cost for dedicated equipment • Relatively costly assay	Biotage	$$$
SNPstream	SBE	48-plex assays	• Complicated multistep procedure and not closed-tube • Not suitable for all variants • Requires a genetic analyzer (capillary electrophoresis)	Orchid Biosciences, Beckman Coulter	$$
SNaPshot	SBE	10-plex assays		Applied Biosystems	$$
SNPlex	OLA	48-plex assays		Applied Biosystems	$$
ASPE: allele-specific primer extension; SBE: single-base extension; OLA: oligonucleotide ligation assay; FRET: fluorescence resonance energy transfer; hME: homogeneous Mass EXTENT (single to 4-plex assay); iPLEX: Sequenom chemistry for up to 29-plex level).
* Cost per variant and excluding capital equipment cost