Gene Mapping Continues to Decrease in Price with Pre-Configured Computer
By ANNE EISENBERG
(SOURCE) February 2, 2013
THE price of sequencing a person’s genome — putting in order all three billion base pairs of DNA in a set of human chromosomes — keeps dropping. But interpreting the billions of letters in a person’s DNA blueprint for use in medicine, and keeping that highly personal information secure and anonymous, is still a complex task.
Dr. George Church, a co-founder of Knome, with its machine that can analyze and interpret human DNA in the confines of a single lab.
Dr. Peter Nagy of Columbia University says Knome Inc.’s new genomic analysis machine could help evaluate diseases that run in families.
Over the past few years, the cost of mapping one person’s genome has dropped to around $6,000 from about $250,000, and it is expected to go far lower. And, as genomic medicine quickly evolves, a powerful computer packed with software has arrived to interpret sequences privately within the walls of a lab, in contrast to systems that use the Internet and distant servers. The software parses variants in DNA, looking for ones that may be important.
The appliance, made by a human-genome interpretation company called Knome, is the size of a file cabinet and costs $125,000. Knome will begin shipping it in coming months to researchers investigating the genetic basis for cancer, rare diseases and drug response, said Jorge Conde, a co-founder of the company along with Dr. George M. Church, a geneticist and professor at Harvard Medical School.
For an additional, annual fee of $25,000, users can buy technical support and regular updates of the software for the machine, called the knoSYSTM100.
Because people can be identified by genetic data posted online, the privacy offered by the appliance, and its ability to discretely analyze data directly in a lab or office, may be an advantage. Lee Watkins Jr., director of bioinformatics at the Center for Inherited Disease Research at Johns Hopkins University, is considering buying one, in part for that reason. “You have control over it physically within your walls and logically within your network,” he said. “Everyone’s DNA is a very personal thing.”
Dr. Peter L. Nagy, a director of the personalized genomic medicine laboratory at Columbia University, is considering ordering a Knome machine for use in a clinical setting. Such machines may broaden the reach of genomic medicine, particularly in smaller labs.
“Normally you need a slew of people to maintain a center to process this data,” said Dr. Nagy, who is also an assistant professor of pathology and cell biology. “Basically this machine removes the need to maintain an expensive computational facility and a group of people who make sure the operating system is working and keep the reference data up to date.” And the appliance doesn’t tax Internet connections, he added.
The machine takes raw data from sequencers at Illumina, Complete Genomics and other DNA sequencing companies, which can be downloaded onto a hard disk. Then the machine’s software can analyze the data, selecting a list of potentially noteworthy items.
If he had the machine, Dr. Nagy said, he would go carefully through this list. “We have to validate the items, confirming or rejecting the interpretations,” he said. He would use the machine for cancer genetics, looking for specific disruptions that are driving a tumor, and in evaluating diseases that run in families.
Michael Schatz, an assistant professor at Cold Spring Harbor Laboratory on Long Island, said appliances like Knome’s weren’t needed at his lab. “We have large clusters of equipment so that we can do analysis on site,” he said. “But a smaller institution might find value in a preconfigured unit that’s alive and ready to go,” so long as there is someone at the company to answer questions and offer technical support.
The machine tackles a tedious, intensive task, searching for points of difference between a person’s genome and the standard, or “reference,” genome. “There may be hundreds of thousands of variants — or far more — that we find in the person that are different from the reference genome,” Mr. Watkins of Johns Hopkins said.
The machine’s algorithms examine these differences based on the investigator’s search criteria, looking for medically relevant ones.“You might filter down to the variants that matter for mutations known to be causative or associated with a disease,” Mr. Conde of Knome said. Programs might also compare children’s genomes to those of their parents, searching for a genetic cause of rare or inherited diseases.
Dr. Stephen Liggett, director of the Center for Personalized Medicine and Genomics at the University of South Florida, has ordered a machine from Knome. “When you would like to get genetic information quickly interpreted, and take it to the patient,” he said, “this machine is right there” to help.
Dr. Eric Topol, a professor of genomics at the Scripps Research Institute in La Jolla, Calif., and author of “The Creative Destruction of Medicine,” cautioned that appliances like Knome’s would still require personnel steeped in molecular biology and genetics to sift through and evaluate its findings.
“It’s not for your neighborhood doctor just yet,” he said, “although that time will come.”