Wholesale genomes

Since the unveiling of the first draft of the human genome in June 2000, you’ve probably heard a lot about the potential power of genomic data for diagnosing, preventing and even curing disease.

Progress was slow at first, partly because of money: The first sequencing efforts cost hundreds of millions of dollars. But with the price tag now at less than $5,000 per person, researchers can begin building large collections of DNA data.

In October, for example, the autism science and advocacy organization Autism Speaks announced its plans to sequence whole genomes of 10,000 individuals —children with the disorder and their family members — over the next two years.

The organization is partnering with BGI, a sequencing powerhouse in Shenzhen, China, that reportedly holds 20 percent of the world’s sequencing machines.

Participants will come mainly from the Autism Genetic Resource Exchange, a biobank that holds thousands of blood samples and clinical information from families in which at least two children have autism. But the researchers also plan to sequence 1,000 samples from China.

That’s the plan, anyway. Autism Speaks has pledged $250,000 for initial sequencing. Because BGI is offering the project a 50 percent discount, that amount will cover the sequencing cost for 100 people, according to Andy Shih, vice president of scientific affairs at Autism Speaks. BGI and Autism Speaks will work together to raise the remaining funds, Shih says.

Every geneticist I’ve ever interviewed would probably be downright giddy to be able to dive into that much data. But it’s important to be realistic, particularly in this economy.

Until costs come down substantially, many researchers have pursued a cheaper option: sequencing of the exome, or protein-coding part of the genome, which costs less than half what it does to decode a whole genome.

Earlier this year, Evan Eichler‘s team used this approach to identify four spontaneous point mutations linked to autism, and Matthew State‘s group reported similar unpublished findings at the World Congress of Psychiatric Genetics in September.

But as Shih points out, the exome represents only 1.5 percent of the genome. The rest, once dismissed as ‘junk DNA,’ holds important regulatory levers that control the genes in the exome.

“We believe there is tremendous potential for discovery and a more complete understanding of the genetic architecture of autism that simply will not be captured by whole-exome sequencing,” Shih told me. That’s no doubt true. I just hope this project raises the funds to achieve that goal.