Disruptive technology drops the cost of DNA methylation sequencing by 100-fold

As sequencing of individual human genomes becomes more affordable and useful, the next big hurdle in genetic science will be to map the human epigenome. While DNA provides the blueprint for building a human being, the epigenome determines the details of how that blueprint is expressed in an individual. Pathologists and clinical laboratory administrators will want to track efforts to map and understand the human epigenome.

The epigenome is a set of chemical modifications to the genome that are not encoded in the DNA but which modulate how and when genes are expressed. Methylation is only one marker in the complex epigenetic map, but it is an important one. Methylation suppresses gene activity, and is thought to be responsible for suppressing some genes that prevent cancer. Though researchers are a long way from using this knowledge to cure cancer or other diseases, faster, more affordable DNA methylation sequencing will help move that research forward.

Pacific Biosciences is using its game-changing technology to drop the cost of sequencing DNA methylation from $100,000 per individual to less than $1,000. Researchers say DNA methylation is a key genetic component in development of many cancers, and the drop in cost will accelerate understanding of how and why some cancers develop. Research findings may lead to new clinical pathology laboratory tests.

Pacific Bioscience, Inc., of Menlo Park, California, is one company that is focused on methylation as it develops next-generation sequencing technology to that is capable of fast, affordable sequencing of an individual’s epigenetic markers. The technology is called single-molecule, real-time (SMRT) sequencing, and the company is using it to detect DNA methylation during DNA sequencing. The company expects to have this new technology commercially available in late 2011.

Previously the only method for sequencing DNA methylation was through bisulfite conversion, which can cost up to $100,000 per individual. The new technology is expected to bring that down to less than $1,000 per individual.

Pacific Biosciences announced that it will be shipping its first sequencers using SMRT technology later this year, and will add the ability to sequence DNA methylation next year. The company received a grant last October of $1.9 million through the National Human Genome Research Institute to support development of the technology. More importantly, the company raised $69 million in capital last August on the basis of its SMRT sequencing technology.

In February, Pacific Biosciences announced that 10 institutions have signed up for its “early access” purchase program. These customers will be the first to receive shipment on the SMRT DNA sequencing system and include: Baylor College of Medicine, the Broad Institute of MIT and Harvard, Cold Spring Harbor Laboratory, the U.S. Department of Energy Joint Genome Institute, The Genome Center at Washington University, Monsanto Company, the National Cancer Institute/SAIC-Frederick, the National Center for Genome Resources, the Ontario Institute for Cancer Research, and Stanford University.

In the June 2010 issue of Nature Methods, Pacific Biosciences researchers described their technology: “In SMRT sequencing, DNA polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands.

“The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the DNA template, including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine. Measurement of polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect determination of primary DNA sequence. The various modifications affect polymerase kinetics differently, allowing discrimination between them.”

The company admits that there are still technical problems to be solved before the technology will reach its full potential. Currently, SMRT sequencing can distinguish methylated adenosine from unmethylated adenosine in DNA, but has not perfected the technique for methylated and unmethylated cytosine.

Two things must happen before DNA methylation technology is likely to be used by clinical laboratories and pathology groups. First, there must be continued reduction in the cost to perform DNA methylation sequencing. Second, not until ongoing research into the role of DNA methylization in various cancers provides useful knowledge will it be possible to develop different assays for clinical applications.

If scientists are able to identify how and when DNA methylation leads to cancer, a host of new diagnostic tests is likely to be developed and made available to pathologists and clinical laboratory scientists.

-K. Branz


Related Information


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