Core facilities aim to bolster genetic research efforts
Jonathan Haines, Ph.D., directs Vanderbilt's new Program in Human Genetics. (Photo by Donna Jones Bailey)
Research into human genetics at Vanderbilt University Medical Center took a step forward recently with the formulation of the Program in Human Genetics, a research program that has developed core facilities aimed at making research into genetics easier and faster for investigators.
The program has developed four core laboratories ‹ a family ascertainment core, DNA banking and genotyping core, data analysis core, and computing core.
"There is a large base of knowledge and skills that we have developed by working on a lot of different projects with many different investigators," said Jonathan L. Haines, Ph.D., associate professor of Molecular Physiology and Biophysics and director of the program. "Many aspects of these studies are so similar that the legwork is already done."
Now that the Program in Human Genetics is up and running, Haines hopes to foster 10 to 20 new research projects with researchers throughout VUMC.
"For the last year we have been working out all the bugs in the system and we are now ready to get the word out," said Haines.
Research into the vastly complex world of human genetics can often require researchers to create new computer programs, acquire new equipment, and learn how to do complex data analysis work. VUMC's new program reduces needless replication of effort.
"The two major advantages to using any of the cores is that it saves a great deal of time and aggravation for the researcher. We help the researcher achieve his or her goals more efficiently and easily," said Haines. "We gain a lot by economies of scale, which helps reduce everyone's costs in terms of money and time," said Haines.
The first of these cores, the family ascertainment core, is new not only to Vanderbilt, but also to similar facilities nation-wide.
This core's goal is to do most of the legwork associated with studies that focus on groups of patients. The lab assists VUMC's Institutional Review Board (IRB), helps to design parts of the study that researchers may not be familiar with, and collects blood samples from patients in the clinic and other family relatives either in their homes ore remotely through the mail.
The family ascertainment lab also has a great deal of knowledge about the challenges associated with large clinical studies.
"One example is that we have all the legwork set up to send kits through the mail so that people can get their blood drawn and send it to us. It turns out that it takes a large amount of effort to figure out where to buy all the supplies you need and how to properly mark the packages," said Haines.
The second core in the Program in Human Genetics, the DNA banking and genotyping core, processes and labels all the samples gathered by individual researchers or by the family ascertainment core.
For the first element of this core, DNA genotyping, Haines uses a laser scanner to genotype DNA samples that come in.
"We can do whole genomic screens looking at 400 markers on different chromosomes fairly quickly with this machine. We can also obtain very accurate quantification of the DNA samples this way," said Haines. "Last year we processed about 3,500 samples for various projects. We have the capacity for a lot more, although exactly how many samples any project may have depends on the complexity of the project."
The DNA genotyping and banking laboratory also has the ability to store large amounts of samples and DNA material for future use by researchers.
"We have the system set up so that everything that comes in is logged and tracked with bar codes when it arrives," said Haines.
The third part of the program is the data analysis core, which does much of the statistical analysis involved with genetic studies. Some of the studies that the data analysis core often wrestle with are genetic linkage studies, association studies, and case control studies.
"In this area we can not only help researchers analyze the data that they have already gathered, but also help them design studies by making sure the sample size is correct or that the families are appropriate," said Haines.
The fourth core, the computing core, provides the basic support for all the other parts of the Program in Human Genetics.
"Although it sounds really mundane, the computing core provides all the support for the hardware, software, and the network that we use," said Haines. "Basically, without the computing core, we would be nowhere."
Haines, whose business card reads, "Fine Mapping Since 1984," hopes that the core facilities will not only foster better research in genetics, but will also help scientists and clinicians find ways to integrate their research.
"The idea of setting up cores in general is to bridge from clinical to basic science and ultimately back to clinical. We want to be able to provide support to all levels of genetic research studies and help researchers get some of those answers to the questions being asked," said Haines.