New method to fulfill the promise of the original Human Genome Project

Copy number variants are believed to be linked to a number of diseases. For the first time, scientists have figured out how to map the variations of the other elusive copies.
Written by Boonsri Dickinson, Contributing Editor

University of Washington geneticist Evan Eichler uncovered the secret to identifying neglected genes called copy number variants. You see, most genes have two copies: one from the mom and one from the dad. But a gene might have three or four copies.

Before, scientists had to estimate the copies.

The devil is in the details, as changes in the genome are important in making associations to diseases. However, it hasn't been technically possible to identify those copies until now.

Eichler developed a method to look at the 1000 Genome Project data.

"We have peered into the dark matter of the human genome to identify genes that most have alluded to. It's a dream come true," said Eichler. "This time next year, we will have thousands of genomes available," he added.

(When I got my DNA tested a couple of years ago, the companies happily probed my genome for single-nucleotide polymorphism (SNP) changes. But the SNP platform wasn't designed to look for copy number variants.

It's like being given a map of the city with some of the key details missing, but being expected to find some sort of treasure chest. No doubt, you'd most likely get lost and not know which regions you were supposed to be looking for.

For technical reasons, copy number variants have been a particularly troublesome bunch to identify. When regions of the genome have copies in them, it's hard to sequence them.

"It will fulfill the promise of the original Human Genome Project to discover all forms of genetic changes and to link them to diseases. I'm excited to apply this method to study human disease and human health," said Eichler.

In the study published in Science, the researchers looked at 159 individuals. They were able to identify copy number variants and distinguish 1000 duplicated genes that can be used for genetic studies.

"These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species," Eichler wrote in the study.

Evolutionarily speaking, our ancestors acquired some of these copy number variants to fight off foreign molecules. "They help us interact with our environment, so we can withstand the plague and detoxify compounds associated with eating a bit of bad fruit," said Eichler.

Now, Eichler really wants to apply this new method to disease studies to show how important (or unimportant) the copies are in the grand scheme of things. Soon, scientists will look at how the copies present themselves in groups of people with diabetes, autism and other diseases.

Photo: As appeared in Science, courtesy of Evan Eichler

This post was originally published on Smartplanet.com

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