PacBio, RainDance to Co-Develop De Novo Whole Genome Assembly Product

May 6, 2015 | Pacific Biosciences and RainDance Technologies yesterday announced a co-development and co-marketing agreement to commercialize novel solutions for de novo whole genome assembly.

These solutions will combine the power of RainDance’s proprietary digital droplet technology and single-molecule barcoding capabilities with Pacific Biosciences’ proprietary long-range DNA amplification technology to provide sample preparation upstream of PacBio’s long-read sequencing system. This combination could provide a method to generate millions of long, single-molecule barcoded DNA fragments, averaging 10-30 kilobases that originated from much longer (~ 100 kilobase) fragments. 

PacBio has been working on de novo human genome assembly using its long read technology. 

Combining this fragmentation and labeling scheme with a sequence context-unbiased amplification method for long DNA fragments, PacBio sequencing could provide de novo, haplotype-phased assembly of complex genomes.  This would be possible even in genomic regions containing complex repeats or PCR-challenged sequences that limit performance of synthetic long-read approaches based upon short-read sequencing technologies.  Furthermore, this approach will be designed to work with low DNA input – as little as 1 ng – to address scarce or difficult-to-procure samples.

“Today, the research community is limited to technologies that ‘shred’ genomes into tiny fragments before sequencing, using computational power to assemble a genome scaffold,” said Dr. W. Richard McCombie, Professor at Cold Spring Harbor Laboratory, in a statement. “This is inefficient and error-prone. The addition of longer range sequencing information would provide even better assemblies with precise location in context. Moreover, by barcoding long fragments prepared from individual molecules, we could also get haplotype phasing information across much longer stretches of the genome assemblies.”

Dr. Michael Hunkapiller, President and CEO of Pacific Biosciences, commented: “The strength of RainDance’s proprietary technology, patent position and commercialization experience in droplets was fundamental to our decision to enter into this collaboration. We chose to work with RainDance because they are the market leader in droplet-based target enrichment and are rapidly expanding into innovative sequencing applications for long reads and single cells.  While our customers can already get industry-leading de novo genome assemblies with just PacBio, the addition of even longer-range sequencing information would provide even better assemblies.”

Roopom Banerjee, RainDance Technologies’ President and CEO, added: “This collaboration underscores the power of our proprietary droplet technology to help enable even higher quality de novo genome assembly to enhance our understanding and interpretation of the genetic basis of disease. This initiative demonstrates our commitment to continuously pushing the innovation frontier in droplet technology and sequencing applications.”