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September 20, 2009

Gene Sequencing Price Improvement Update

Melanie Swan's broader perspective blog has an update on genome sequencing

Leading third-generation sequencing company Pacific Biosciences affirmed at the Cold Springs Harbor Laboratory Personal Genomes meeting September 14-17, 2009 that the company has 12 prototype instruments in operation and continues to be on track for ~$100 (“the cost of a nice dinner”) whole human genome sequencing to be commercially available in the second half of 2010. NimbleGen indicated that they may have a $2,000 exome sequencer available in 2010. Complete Genomics hopes to sequence 10,000, in 2010 at a minimum cost of $5,000 per genome.


It seems that 2010 should have genome sequencing in the $500-2000 price at the end of the year. 2011-2013 should see the $100 pricing for genome sequencing.

This site covered Pacific Biosciences on Aug 11, 2009 Via email from Pacific Biosciences I was told that the 2010 device would be more expensive than $100 per genome sequence, but they did not have a price at that time.

Pacific Biosciences has a Single Molecule Real-Time (SMRT) DNA sequencing, due to be released commercially in 2010 and could enable $100 genome sequencing in 15 minutes in 2013. The second generation real time DNA reader in 2013 is the one that is expected to hit the $100 genome sequencing price. They will release a product in 2010 but it will not be that cheap.


Roche NimbleGen introduces NimbleGen HD2 microarrays for Comparative Genomic Hybridization (CGH) and ChIP-chip analysis of eukaryotic organisms. With 2.1 million probes, NimbleGen HD2 arrays offer the opportunity to fully interrogate copy number variation, transcription factor binding, and chromatin structure.

Advantages of NimbleGen HD2 Arrays

More Probes Enable Increased Resolution and Cost-Effective Analysis

With 2.1 million probes, NimbleGen HD2 arrays offer the highest density microarray platform currently available for CGH and ChIP-chip analysis. NimbleGen HD2 arrays enable genome-wide detection of copy number variation down to ~5 kb resolution (human) and transcription factor binding at 100bp resolution. Fewer HD2 arrays and less total sample are required to perform genome-wide ChIP-chip studies, which leads to a significant reduction in cost to perform such analyses.

Long Oligonucleotide Probes Enhance the Accuracy of Your Analysis

NimbleGen HD2 arrays utilize long oligo probes, which have been shown to provide increased sensitivity, specificity, and reproducibility. Depending on the specific array design, HD2 arrays are synthesized with oligos between 50 and 75 bases in length.

Only the Most Current Genomes

The inherent flexibility of the Roche NimbleGen technology enables the rapid creation of array designs using the most current genomic sequence from any eukaryotic genome. NimbleGen HD2 arrays will deliver the highest resolution and highest quality CGH and ChIP-chip data on the latest genomic build.




NimbleGen Gene Synthesis System

proprietary Maskless Array Synthesizer (MAS) technology. The MAS system is a bench top, solid-state, high-density DNA array fabrication instrument comprised of a maskless light projector, a reaction chamber, a personal computer, and a DNA synthesizer. Roche NimbleGen builds its arrays using photo-mediated synthesis chemistry with its MAS system.

At the heart of the system is a Digital Micromirror Device (DMD), similar to Texas Instruments' Digital Light Processor (DLP), employing a solid-state array of miniature aluminum mirrors to pattern 786,000 to 4.2 million individual pixels of light. The DMD creates "virtual masks" that replace the physical chromium masks used in traditional arrays.

These "virtual masks" reflect the desired pattern of UV light with individually addressable aluminum mirrors controlled by the computer. The DMD controls the pattern of UV light projected on the microscope slide in the reaction chamber, which is coupled to the DNA synthesizer. The UV light selectively cleaves a UV-labile protecting group at the precise location where the next nucleotide will be coupled. The patterns are coordinated with the DNA synthesis chemistry in a parallel, combinatorial manner such that 385,000 to 2.1 million unique probe features are synthesized in a single array.



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