Tuesday, 24 May 2011

UW Team Demonstrates Primate Exome Assembly Against Human Reference Genome


By Monica Heger

In order to overcome the challenges of using next-gen sequencing for de novo assemblies, researchers from the University of Washington demonstrated that it is possible to assemble a primate exome by aligning it to the human reference genome.

"It's feasible to sequence primate genomes, but assembly with short reads is still difficult," Renee George, a postdoctoral student in Willie Swanson's laboratory at the University of Washington, said in a presentation at this month's annual Biology of Genomes meeting in Cold Spring Harbor, NY.

To learn whether they could sequence and assemble a primate exome by aligning it to the human reference, the researchers first tested the method on the macaque monkey, which does have a reference genome. Their aim was to see if it is possible to capture primate exomes with human probes and align and assemble the resulting reads against a human reference genome.

Using Nimblegen's SeqCap EZ Exome in-solution kit, they used an Illumina Genome Analyzer to capture and sequence the exome to an average of 60-fold coverage with 76 base-paired end reads. They found good correlation after comparing the read depth of the macaque against two human controls.

"The exons that are captured well in humans are captured well in macaque," George said. Additionally, although read depths declined in the regions of the macaque genome that are more divergent from the human genome, they still remained well-covered.

The team verified the method by showing that the sequenced macaque exome was comparable to the coding regions of the macaque reference genome.

It next applied the method to two Old World monkeys — the colobus and vervet — and one New World monkey, the tamarin. None of the animals has a reference genome. 

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