title: A 768-lane microfabricated system for high-throughput DNA sequencing.
abstract: A 768-lane DNA sequencing system based on microfluidic plates has been designed as a near-term successor to 96-lane capillary arrays. Electrophoretic separations are implemented for the first time in large-format (25 cm x 50 cm) microdevices, with the objective of proving realistic read length, parallelism, and the scaled sample requirements for long-read de novo sequencing. Two 384-lane plates are alternatively cycled between electrophoresis and regeneration via a robotic pipettor. A total of greater than 172000 bases, 99% accuracy (corresponding to quality score 20) is achieved for each iteration of a 384 lane plate. At current operating conditions, this implies a system throughput exceeding 4 megabases of raw sequence (Phred 20) per day on the new platform. Standard operation is at "1/32x" Sanger chemistry, equal to typical genome center operation on mature capillary array machines, and a 16-fold improvement in scaling relative to previous microfabricated devices. Experiments provide evidence that sample concentration can be further reduced to 1/256x Sanger chemistry in the microdevice. Life-testing indicates a usable life of >150 hours (more than 50 runs) for the 384 lane plates. The combined advances, particularly those in read length and sample requirement, directly address the cost model requirements for adaptation of the new technology as the next step beyond capillary array instruments.
authors.affiliation: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
authors.forename: James H
authors.initials: JH
authors.lastname: Aborn
authors.forename: Sameh A
authors.initials: SA
authors.lastname: El-Difrawy
authors.forename: Mark
authors.initials: M
authors.lastname: Novotny
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Gismondi
authors.forename: Roger
authors.initials: R
authors.lastname: Lam
authors.forename: Paul
authors.initials: P
authors.lastname: Matsudaira
authors.forename: Brian K
authors.initials: BK
authors.lastname: McKenna
authors.forename: Thomas
authors.initials: T
authors.lastname: O'Neil
authors.forename: Philip
authors.initials: P
authors.lastname: Streechon
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Ehrlich
mesh_terms: D004247:DNA / Q000032:analysis*; D046209:Electrophoresis, Microchip / Q000295:instrumentation*; D004867:Equipment Design; D044085:Microfluidics / Q000295:instrumentation*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000295:instrumentation*; D013499:Surface Properties; D013997:Time Factors
chemical_list: D004247:DNA