Gene Sequencers: Pinpointing Psoriasis
NPF grant for equipment purchase helps accelerate research
First posted and last updated April 16, 2001
Unless you knew what it was, you might mistake the gene sequencer in the laboratory of J.T. Elder, M.D., Ph.D., for a large printer and overlook it. It's quiet. But look again. Sometimes, for 24 unattended hours a day, this sequencer is unraveling the secrets of the most precious material known to humankind: our DNA.
With a $150,000 grant from its Discovery Fund for psoriasis research, the NPF recently made it possible for Dr. Elder and his colleagues at the University of Michigan to purchase a new gene sequencer. These machines are based on technology that allows researchers to place "fluorescent tags" on strands of DNA. Prior to putting a segment of DNA through a sequencer, researchers essentially dye each of the four base molecules that bind together strands of DNA. These bases -- adenine, thymine, cytosine and guanine (A, T, C, G) -- are dyed different colors.
The first automated DNA sequencers were developed in 1987 and are made of two glass sheets separated by a layer of gel and mounted on recording instruments about the size of a microwave. The DNA is placed along the top edge of the glass sheets and electric current is used to draw the DNA through the gel. Each strand of DNA passes in front of a laser, which excites the DNA, or makes it "glow." A miniature camera captures the color of the dye expressed by the DNA, and the sequence of base pairs is determined by analyzing the order of the colors.
In 1996, however, a major breakthrough in sequencing technology occurred in the form of capillary systems. A capillary is literally a "pipe" about the size of a human hair. Instead of running the DNA between glass sheets in a gel, researchers are now able to inject segments of DNA directly into the pipe, where a laser then excites the DNA and a camera records the sequence.
The 3100 Genetic Analyzer in Dr. Elder's lab has 16 capillaries for what is called "mid-throughput" research, which is suited for individual labs targeting specific regions of the genome for genes associated with diseases.
Dr. Elder, an associate professor of dermatology at the University of Michigan and a member of the NPF Medical Advisory Board, said the sequencer can be programmed to accomplish as many as a dozen runs a day from one human action-the loading of a multi-well plate containing many DNA samples into a rack in the base of the machine. Each capillary in the sequencer can "read" approximately 500 base pairs on each run.
Search for a psoriasis gene
The sequencer is analyzing and comparing sections of chromosome 6 just "telomeric" to HLA-C (closer to the telomere, or tip, of the short arm of the chromosome), an area which he and his colleagues have demonstrated carries the PSORS1 gene, the HLA-linked component of psoriasis susceptibility. Due to the abilities of the new technology, Dr. Elder has estimated that a major breakthrough, perhaps identification of the gene, could come this year.
"Any time you see a difference between the two, it is a possible candidate (for the psoriasis gene)," Dr. Elder says.
The sequencer can detect differences between samples as minute as the replacement of a G with a T in a sequence of 100 base pairs. These differences are called single nucleotide polymorphisms (SNPs). Much of the work in the past several years has involved narrowing down the region of the suspected psoriasis mutations from 3 million base pairs in the major histocompatibility complex (MHC) on chromosome 6 to a sequence of 60,000 base pairs.
"Hundreds of SNPs are associated with psoriasis in this region," Dr. Elder says. Only some of the SNPs play a role in psoriasis, however. By comparing the psoriasis chromosome to a variety of nondisease chromosomes from other people, the irrelevant SNPs are slowly being "weeded out."
"Eventually, we will find a sequence variant that is only present on the disease chromosome, and not on any of the normal ones, and that will be our baby," Dr. Elder says.
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