Neurology Research International

Review Article

From Genetics to Genomics of Epilepsy

Table 8

Comparison of commercially available sequencing platforms.


	(a) Massive parallel clonal amplification with optical detection

	Roche 454	Life Technologies SOLiD	Illumina

Library amplification	emPCR*	emPCR*	On glass
Sequencing	Incorporation of unlabeled dNTPs	Ligase-mediated addition of fluorescent oligoNTPs (2bp)	Incorporation of end-blocked fluorescent dNTPs
Detection	Light emission from release of PPi	Fluorescence emission from ligated dye-labeled oligoNTPs	Fluorescence emission from incorporated labeled oligoNTPs
Progression	Unlabeled dNTPS added in base-specific fashion	Chemical cleavage removes dye and oligoNTP	Chemical cleavage fluorescent dye and blocking group
Errors	Insertion/deletion	End of read	End of read
Length	400 bp	75 bp	150 bp
Overall yield/run	500 Mbp	>100 Gbp	200 Gbp

	(b) Fluorescent and semiconductor single molecule sequencing

	Helicos	Pacific biosystem	Iontorrent

Library amplification	N/A-tSMS**	N/A-SMRT*** sequencing	Optional PCR
Sequencing	Incorporation of fluorescent labeled dNTPs	Polymerase incorporation terminal phosphate labeled dNTPs	Polymerase incorporation of dNTPs releases H⁺
Detection	Laser-induced emission from incorporated dNTP	Real time detection of fluorescent dye in polymerase active site	Semiconductor ion sensor detects H⁺ released during dNTPs incorporation
Progression	Chemical cleavage of dNTP fluorescent group	N/A fluorescent dyes are removed as PPi with dNTPs incorporation	H⁺ signal during each dNTP incorporation is converted in voltage signal
Errors	Insertion/deletion	Insertion/deletion	Insertion/deletion
Length	35 bp	1000 bp	200–400 bp
Overall yield/run	21–37 Gbp	>100 Gbp	1 Gbp

*emPCR (emulsion PCR) is an amplification method where DNA library fragments are mixed with beads and PCR reagents in an oil emulsion that allows massive amplification of bead-DNA in a single reaction.
**tSMS: true Single Molecule Sequencing.
***SMRT (Single Molecule Real Time)
bp: base pair, Mbp: Mega base pair (10⁶ bp), Gbp: Giga base pair (10⁹ bp), dNTP: deoxynucleotide-tri-phosphate, PPi: pyrophosphate.