May 18, 2007

Investigators navigate the zebrafish genome

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Jeffrey Smith, M.D., Ph.D., center, and colleagues Bradford Elmore, left, and Kevin Bradley are working to map the zebrafish genome.
(photo by Susan Urmy)

Investigators navigate the zebrafish genome

Finding a friend's house in a neighborhood without street names or house numbers could be next to impossible.

For geneticists, locating a gene that causes a particular trait or disease can be as difficult as navigating unfamiliar territory without a map or landmarks. This is especially true for researchers using zebrafish as a model system.

Compared to the old standards of mice and fruit flies, zebrafish are relative newcomers to genetics research. As such, most of their genetic “landmarks” remain unmapped.

Researchers at Vanderbilt University Medical Center recently identified more than a half million of these landmarks, which could be used as a resource to help geneticists quickly locate their gene of interest.

In the most recent edition of Genome Biology, Jeffrey Smith, M.D., Ph.D., and colleagues report the identification of 645,088 polymorphisms — common variations in the genome — and their location on genetic and physical maps of zebrafish chromosomes.

Zebrafish are popular model organisms for the study of development, owing to their transparent embryos that allow researchers to easily see abnormalities that arise during this period. Increasingly, the fish are being used to study specific diseases and identify disease-linked genes.

But since they are relatively new to the genetics world, “the development of genetic resources (for zebrafish) are about 10 years behind other model organisms,” said Smith, an assistant professor of Medicine and Cancer Biology and senior author on the paper.

The zebrafish genome is currently being sequenced by the Wellcome Trust Sanger Institute in England — one of the centers that participated in the Human Genome Project — but the sequence is not yet complete.

Smith and colleagues set out to identify markers in the zebrafish genome by looking for common variations in the DNA sequence, or polymorphisms.

In any population, Smith said, there are mutations that occur over time. Some mutations cause an abnormality or disease and others are simply innocuous “bystanders.”

“Most of the variation present in a genome of a given population — whether zebrafish or humans — is in the bystander category,” he said.

“Most of those don't do anything in terms of causing a disease or trait, but are very useful in distinguishing chromosomes. And zebrafish have a lot of them.”

Using “computers the size of refrigerators,” Kevin Bradley, an analyst in Smith's lab and lead author on the paper, sorted through DNA sequence determined by the Sanger Institute.

By lining up several different sequences of the same region of DNA, the researchers could identify different types of polymorphisms: single nucleotide polymorphisms (SNPs), a change in a single “letter” in the DNA sequence; short tandem repeats (STRs), a short genetic “stutter” resulting in a repetition of a short stretch of DNA sequence; and small insertions/deletions (InDels), in which a small DNA fragment gets deleted or inserted into the wrong location.

To the few thousand polymorphisms that had been previously identified, Smith's group added more than a half million new markers — approximately 550,000 SNPs, 80,000 InDels, and 18,000 STRs.

The researchers then determined the position of a subset (about 260,000) of the newly identified SNPs on zebrafish genetic maps. To demonstrate the utility of using the SNPs to map a trait, Smith picked a gene whose location in the zebrafish genome was known and used the new SNP-based process to verify that it would identify the gene in the same location. It did.

The increased density of “tick marks” represented by the SNPs on the genetic maps should allow researchers to more quickly and easily locate their gene of interest.

Although a large number of SNPs still need to be positioned on the map, Smith suggests that continued development of this resource “will empower disease gene identification and complex trait mapping” for researchers using zebrafish as a model system.

Interestingly, the variations identified in this study account for 2.4 percent of the known genetic variation in the world, Smith noted.

“It's a small piece, but of a very large pie.”

Other Vanderbilt authors on the paper were Bradford Elmore, Joan Breyer, Brian Yaspan, Jasson Jessen, Ph.D., and Ela Knapik, M.D. The study was supported by a grant from the National Institutes of Health.