Genomic research: Faster, cheaper, more hope

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A child affected by the Lundell family disorder, from the American Journal of Human Genetics paper published about the case.

Over the course of two generations, the Lundell family of Ogden, Utah, lost five boys to a mysterious genetic disease that kills infants before the age of 6 months. In the past, it was the kind of shadowy medical problem that doctors were powerless to do much of anything about. The Lundell women didn't even know how likely they were to give birth to affected boys.

Now, that's changed. In the span of just 16 months, researchers were able to identify the gene responsible for the deaths. The discovery will help members of the Lundell family know whether they are carriers, and it could even help them avoid more tragic losses—by allowing for in vitro fertilization that selects against affected embryos. But here's the really amazing part: All of this cost only about $10,000. Dirt cheap by the standards of scientific research. Forbes' Matthew Herper explains:

Three new technologies allowed Lyon to find the gene that was causing the boys to die. The cost of sequencing a human genome has been dropping precipitously, from $100 million in 2001 to $10,000 last year, according to Macquarie Securities, an investment advisor. Other new technologies allowed Lyon to focus on just 1% of human genetic material that was likely to provide him answers. And a brand new kind of software allowed him to use information about the family and their genetic material to find the defective gene.

A key clue was that only boys had been affected by the genetic defect. That meant the mutation was almost certainly on a gene on the X chromosome. Chromosomes are the bundles in human cells that contain the DNA code; every person gets two very similar sets from each parent. A defective gene on a chromosome from a mother is often masked by a correct one from the father. But boys have only one X chromosome, leaving them more vulnerable to defects like this.

His team read the chemical bases of the DNA with a machine made by Illumina, the San Diego company that has led the way in decreasing the cost of DNA sequencing. Then came the hard part: discovering an explanation for the boys' sickness in that code, a series of As, Ts, Cs, and Gs (short of the chemical names of DNA bases). He tried several methods, but among the most effective was a new computer progam called the Variant Annotation, Analysis and Selection Tool, or VAAST. VAAST was developed by Mark Yandell, a scientist at the University of Utah who had worked at Celera Genomics during the heyday when it was run by maverick gene mapper J. Craig Venter. "To go from something like sequencing, to be able to say, this kid is sick because of this, it's almost too real," says Yandell.

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