Answer by okubo

okubo — Tue, 01 Mar 2011 00:38:04 +0900

http://seqanswers.com/forums/archive/index.php

Single-Molecule DNA Sequencing of a Viral Genome

Timothy D. Harris,1* Phillip R. Buzby,1 Hazen Babcock,1 Eric Beer,1 Jayson Bowers,1 Ido Braslavsky,2 Marie Causey,1 Jennifer Colonell,1 James DiMeo,1 J. William Efcavitch,1 Eldar Giladi,1 Jaime Gill,1 John Healy,1 Mirna Jarosz,1 Dan Lapen,1 Keith Moulton,1 Stephen R. Quake,3 Kathleen Steinmann,1 Edward Thayer,1 Anastasia Tyurina,1 Rebecca Ward,1 Howard Weiss,1 Zheng Xie1

The full promise of human genomics will be realized only when the genomes of thousands of individuals can be sequenced for comparative analysis. A reference sequence enables the use of short read length. We report an amplification-free method for determining the nucleotide sequence of more than 280,000 individual DNA molecules simultaneously. A DNA polymerase adds labeled nucleotides to surface-immobilized primer-template duplexes in stepwise fashion, and the asynchronous growth of individual DNA molecules was monitored by fluorescence imaging. Read lengths of >25 bases and equivalent phred software program quality scores approaching 30 were achieved. We used this method to sequence the M13 virus to an average depth of >150x and with 100% coverage; thus, we resequenced the M13 genome with high-sensitivity mutation detection. This demonstrates a strategy for high-throughput low-cost resequencing.

1 Helicos BioSciences Corporation, One Kendall Square, Cambridge, MA 02139, USA. 2 Department of Physics and Astronomy, Ohio University, Athens, OH 45701, USA. 3 Department of Bioengineering, Stanford University, and Howard Hughes Medical Institute, Stanford, CA 94305, USA. The paper abstract and full text (for subscribers) is located here: http://www.sciencemag.org/cgi/content/abstract/320/5872/106

Answer by okubo

okubo — Tue, 01 Mar 2011 00:34:01 +0900

Here's a list George Church uses, I think.

Illumina-GA SbP Fluorescent read-length 2*110 bp
AB-SOLiD SbL Longest ligation reads
CGI SbL $2000 genome, rolony grid, 100Kb haplotypes
Polonator SbL/P Open-source, $170K device, 100Mb haplotypes
Roche-454 SbP Long reads (>0.4 kb)
Helicos SbP-sm Hi h parallelism & quantitation
Ion Torrent SbP $50K, small device
Pacific Bio SbP-sm Long reads (>2.0 kb) 9 Intelligent Bio SbP hexagonal grid
Halcyon EM-sm Long reads (>Mb), $100 genome
Genizon BioSci SbH in situ sequencing
LightSpeed SbL 16X higher density >10X speed
Bionanomatrix SbP-sm Fluorescent mapping
OxfordNanopore Pore-protein-sm small device
Visigen SbP-sm Pol <> dNTP FRET
ZS Genetics EM-sm Iodine labels
Nabsys Pore-SbH-sm small device
GE Global SbP-sm
IBM Pore Si-sm small device
Electronic Biosci Pore-protein-sm
GnuBio SbP-picoliter droplets

The few additions are: CGI Polonator (it's a company?) Roche-454 Ion Torrent GeniZon BioSci GE Global IBM Electroni Biosci

Answers to: シーケンサー出力の伸びの予測ってどのくらいわかってますか？

Answer by okubo

Answer by okubo