A new technique that combines gene chip technology with the latest generation of gene sequencing machines to allow fast and accurate sequencing of selected parts of the genome has been developed by researchers from the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine in Houston and NimbleGen Systems, Inc., a Wisconsin-based company recently purchased by Roche Applied Science.
“This new technology will replace polymerase chain reaction (PCR) for many purposes,” said Dr. Richard Gibbs, director of the HGSC and senior author of the report. “If the aim is to sequence a whole genome for everybody, this is a huge step in that direction.”
The report, which appears in the current issue of Nature Methods, describes the use of microarrays to enrich or increase the volume of specific genomic sequences. High throughput DNA sequencing machines made by 454 Life Sciences then determine the exact genetic code of the material.
For example, if scientists were looking for a mutation in a particular cancer-causing gene (such as BRCA1 that is associated with breast and ovarian cancer), they could make a microarray that is complementary to the part of the genome in which one is interested. This takes advantage of the fact that the adenine (A) bases always attach to the thymine (T) and the cytosine (C) always attaches to the guanine (G) in reactions.
“You take the DNA and you hybridize it (allow the DNA to stick to its complement) on the chip,” said Dr. George Weinstock, co-director of the HGSC. “Then you wash away everything that doesn’t stick. This can enrich the portion of the genome to be studied by factors of three hundred or more.”
The new process is simpler, more accurate and efficient than the multiplex PCR that was previously used to sequence portions of the genome. In one experiment, more than 6,400 exons (the part of the genetic code that carries the instructions for making proteins), were analyzed. Using the old technology this would have taken at least six months.
“We hope to be able to use this to sequence all the exons in the genome,” Gibbs said.
Others who took part in this study include David Wheeler, Donna Muzny and Xingzhi Song of BCM and Thomas J. Albert, Michael N. Molla, Lynne Nazareth, Todd. A. Richmond, Chris M. Middle, Matthew J. Rodesch and Charles J. Packard of NimbleGen.
Funding for this work came from the U.S. National Human Genome Research Institute and the National Cancer Institute.
Journal
Nature Methods