Prof. Shepard Wins Two NIH/NHGRI Grants

Electrical Engineering Professor Ken Shepard has been awarded two grants from the National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), to develop nanoscale technologies that will dramatically reduce the cost of DNA sequencing.

Watch Shepard discuss his research in his new Bioelectronic Systems Lab

Shepard (at left) is the principal investigator on “Integrated, Mutiplexed High-Frequency Electronic Analysis of DNA in Nanopores,” a project that will receive $1.5 million over three years to develop much faster and more sensitive electronics to enable sequencing based on arrays of nanopores. With Marija Drndic, Ph.D., University of Pennsylvania, Shepard is focusing on significantly improving the noise-limited bandwidth of the detection electronics for nanopores. This approach will enable their full potential to be realized through close integration of the electronics and the pores while simultaneously supporting high levels of parallelism with multiple nanopores on the same detection substrate.

He is also part of a consortium led by Intel Corp on a project—“Single-Molecule, Real-Time Electronic Sequencing”—to develop a real-time, single-molecule sequencer that detects specifically engineered, electrically active tags that will be attached to each of the four DNA nucleotides. This project will receive $5 million over five years.

"I'm delighted to be working on these projects as part of the $1000 genome effort at the NHGRI,” says Shepard. “They recognize the growing importance of CMOS [complementary metal–oxide–semiconductor] electronics in changing the shape of molecular diagnostics in the 21st century."

During the past decade, DNA sequencing costs have fallen dramatically (see www.genome.gov/sequencingcosts), fueled by tools, technologies and process improvements developed by genomics researchers. In 2004, NHGRI launched the Advanced DNA Sequencing Technology Program to accelerate improvements in DNA sequencing technologies. By 2009, the program had surpassed its initial goal of producing high-quality genome sequences of roughly six billion base pairs—the amount of DNA found in humans and other mammals that receive roughly three billion base pairs from each of their parents—for $100,000 each. Today, the cost of sequencing a human genome using these next-generation DNA sequencing technologies has dipped to just under $8,000.

Price is one hurdle in the way of widespread use of genomics in research and clinical care. Speed and accuracy are among other factors. These grants will attempt to address all of these challenges.

“We can now access data we could not dream of getting in 2004 when we started this program – tens of thousands of human genome sequences have been generated," says Eric D. Green, M.D., Ph.D., NHGRI director.  “And yet, the information we would truly like to get for understanding disease and, eventually, for treating patients, requires much better quality sequence data. That is the direction we would like to go with these grants.”

To read the grant abstracts and for more details about the NHGRI genome technology program, visit: www.genome.gov/10000368. Additional information about NHGRI can be found at www.genome.gov.

—by Holly Evarts