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PacBio, RainDance Technologies Partner to Commercialize Whole-Genome Assembly Solution

NEW YORK (GenomeWeb) – Pacific Biosciences and RainDance Technologies plan to co-develop and commercialize solutions for de novo whole-genome assembly, the companies said today.

The solutions will combine RainDance's digital droplet technology and single-molecule barcoding technology with PacBio's proprietary long-range DNA amplification technology to provide a sample prep solution that can be used prior to sequencing on the PacBio RS II.

The goal is to be able to provide a method for generating millions of single-molecule barcoded DNA fragments that are 10 kb to 30 kb in length that originated from fragments around 100 kb in length.

PacBio CEO Mike Hunkapiller said during a conference call discussing PacBio's first quarter results that the approach essentially creates synthetic reads — piecing back together the DNA fragments into 100-kb and longer reads.

The approach should allow "haplotype phas[ing] and assembly of complex regions even in genomic regions containing complex repeats or PCR-challenged sequences that limit the performance of other synthetic long read approaches based on short read sequencing technologies," he said during the call.

Richard McCombie, a professor at Cold Spring Harbor Laboratory, said in a statement that current techniques that "shred genomes into tiny fragments before sequencing" and rely on informatics to piece it back together are "inefficient and error-prone." Longer range sequencing information would "provide even better assemblies with precise location in context," he said. "Moreover, by barcoding long fragments prepared from individual molecules, we could also get haplotype phasing information across much longer stretches of the genome assemblies."

The approach will be designed to work with DNA inputs as low as 1 ng.

The companies did not disclose a timeline for commercialization.

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