NIH Awards $14.5M for DNA Sequencing Techniques

A number of micro-sized technologies - such as nanopores and microfluidics - are among the approaches researchers will use to develop high quality, low cost DNA sequencing technology through new grants from the National Institutes of Health.

The grants, which total approximately $14.5 million to eight research teams over two to four years as funds become available, are the last to be awarded by the Advanced DNA Sequencing Technology program of the National Human Genome Research Institute (NHGRI), a part of NIH.

The new group of awards - which total more than $4.5 million in the first year - is wide-ranging, and includes several research projects directed at improving the use of nanopores in DNA sequencing or creating nanopore arrays to enable large-scale DNA sequencing efforts.

Nanopore-based DNA sequencing entails threading single DNA strands through tiny pores in a membrane. Bases - the chemical letters of DNA - are read one at a time as they squeeze through the nanopore.

The different bases are identified by measuring differences in their effect on electrical current flowing through the pore. Nanopores used in DNA sequencing are extremely small, perhaps only about 2 nanometers wide, and come in several types: protein; solid state (also called synthetic); and even nanopores made of DNA. A nanometer is 1 billionth of a meter; a human hair is 100,000 nanometers wide.

One of the projects will explore the use of microfluidics in DNA library preparation. A library is a collection of stretches of physical DNA. Microfluidics can be used to capture small amounts of liquid in hair-thin channels and wells. Another team plans to test a method using an enzyme to amplify a signal that will help identify DNA bases.

“While we continue to support many research projects centered on the development of nanopore technology, some of the new grants focus on additional unique approaches to sequencing DNA,” said NHGRI Genome Technology Program Director Jeffery Schloss, Ph.D. Dr. Schloss is also director of the Division of Genome Sciences. “Despite discussion about approaching the goal of sequencing a genome for only $1,000, many challenges remain in terms of containing costs and achieving a high quality of DNA sequencing data.”

This group of awards is the last for the Advanced DNA Sequencing Technology program, which began in 2004.

“There haven’t been many programs like this anywhere else over the years,” Dr. Schloss said. “NHGRI has had a hand in supporting some very novel research, and has helped chart exciting new directions for DNA sequencing technology.”

The new grants are awarded (pending available funds) to:

• University of California Santa Cruz, $2.29 million over three years
Principal Investigator: Mark Akeson, Ph.D.

Investigators plan to sequence single DNA molecules by using a nanopore device comprised of a sensor that touches, examines and identifies each nucleotide, or DNA building block, in a DNA strand as an enzyme motor moves it through the pore. The scientists will focus on DNA “resequencing” - examining the DNA nucleotides over and over - because of the difficulty in accurately reading each strand initially.

• Illumina, Inc., San Diego, $592,000 over two years
Principal Investigator: Boyan Boyanov, Ph.D.

Dr. Boyanov and his team aim to create a hybrid protein solid-state nanopore array system that can enable scientists to sequence DNA on a large scale. Their goal is to improve the robustness of nanopore platforms by combining computer chip fabrication methods with biological nanopores to enable high-throughput sequencing. The latter refers to a very high rate of sequencing DNA by sequencing large numbers of DNA samples in parallel.

• University of Pennsylvania, Philadelphia, $880,000 over two years
Principal Investigator: Marija Drndic, Ph.D.

Investigators plan to develop a synthetic nanopore from graphene - an extremely conductive material consisting of a lattice of atoms, one atom thick - that will enable the detection of individual DNA bases without the need to slow down the DNA molecule as it passes through a pore. Researchers hope to directly identify DNA bases by measuring unique differences in current flowing through the graphene.

• Caerus Molecular Diagnostics, Inc., Mountain View, California, $701,000 over three years
Principal Investigator: Javier Farinas, Ph.D.

Researchers commonly use a system to identify DNA bases that entails making many copies of DNA and detecting a light signal from the DNA. Dr. Farinas and his co-workers plan to test a technology that uses an engineered enzyme switch to convert the product of a single molecule DNA sequencing reaction into many copies of a reporter molecule that are easily detected. The method promises to more accurately identify DNA bases.

• The Scripps Research Institute, La Jolla, California, $4.4 million over four years
Principal Investigator: M. Reza Ghadiri, Ph.D.

Investigators plan to produce protein nanopore arrays in order to sequence tens of thousands of DNA molecules in parallel, with the eventual goal of sequencing a human genome in as little as 10 minutes. They will explore three separate approaches, including arrays of lipid bilayers containing nanopores, protein pores individually embedded in synthetic films, and nanopores made of DNA that are distributed on DNA scaffolds.

• Eve Biomedical, Inc., Mountain View, California, $500,000 over two years
Principal Investigator: Theofilos Kotseroglou, Ph.D.

Researchers will study a system to sequence DNA using an enzyme (polymerase) on a carbon nanotube, in an array format. Carbon nanotubes are long, thin cylindrical tubes that are highly conductive. When an enzyme is anchored on a tube, the enzyme’s motion - while interacting with a DNA sample - changes the conductivity on the nanotube, and enables bases of the sample DNA to be identified.

• University of Washington, Seattle, $1.7 million over three years
Principal Investigator: Jay Shendure, M.D., Ph.D.

Dr. Shendure and his colleagues plan to develop new molecular biology techniques to efficiently and cost-effectively stitch together genomes across long distances. They hope this will help improve the quality of genomes that are generated by new DNA sequencing technologies.

• University of California, San Diego, $3.7 million over four years
Principal Investigators: Kun Zhang, Ph.D. and Xiaohua Huang, Ph.D.

This team plans to develop a system using microfluidics that will enable accurate genome sequencing of a single mammalian cell. Investigators will separate and sequence single chromosomal DNA strands, and then with the help of novel technology to make many copies of genomes, they will create DNA sequence libraries for DNA sequencing of single cells.