SNP Discovery through Next-Generation Sequencing and Its Applications

Table 3

Commonly used genotyping platforms.

Name	Assay type	Technology	Throughput; (samples)	Multiplexing	Relative scale; (no. of SNP/no. of individuals)
Genechip	Hybridization	Oligo nucleotide array	96/5 days	Up to 18×10^6	Small/large
Infinium II	Hybridization	Bead array	Up to 128/5 days	Up to 13×10^6	Large/small-large
Goldengate	Primer extension-ligation	Bead array	172/3 days	Up to 3,072	Medium/large
iPlex	Primer extension	Mass spectrometry (MALDI-TOF)	3840/2.5 days	Up to 40	Medium/large
Taqman	PCR	Taqman probe	Up to 1536/day	Up to 256	Medium/medium
SNPlex	PCR	Capillary electrophoresis	Up to 1536/3 days	Up to 48	Medium/large
KASPar	PCR	FRET quenching oligos	Up to 96/day	—	Medium/large
Invader	Primer annealing/endonuclease digestion	FRET quenching oligos	Up to 384/day	Up to 200,000	Medium/large
HRM	PCR	Melting curve analysis	Up to 1536/day	—	Medium/large