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Scientists Develop Tool to Evaluate Genome Sequencing Methods

April 11, 2013

Advances in bio-technologies and computer software have helped make genome sequencing much more common than in the past. But still in question are both the accuracy of different sequencing methods and the best ways to evaluate these efforts. Now, computer scientists have devised a tool to better measure the validity of genome sequencing.

The method, which is described in the journal PLoS One, allows for the evaluation of a wide range of genome sequencing procedures by tracking a small group of key statistical features in the basic structure of the assembled genome. Such a sequence-assembly algorithm lays out the individual short reads (strings of DNA’s four nucleic acid bases sampled from the target genome) to put together the complete genome sequence—much like a complex jigsaw puzzle. The method uses techniques from statistical inference and learning theory to select the most significant features. Surprisingly, the method concludes that many features thought by human experts to be the most important were actually highly misleading.

The work was conducted by Bud Mishra, a professor at NYU’s Courant Institute of Mathematical Sciences, as well as researchers at Sweden’s KTH Royal Institute of Technology. Mishra also holds appointments at Cold Spring Harbor Laboratory and NYU School of Medicine.

Current evaluation methods of genome sequencing are typically imprecise. They rely on what amounts to “crowd sourcing,” with scientists weighing in on the accuracy of a sequencing method. Other evaluations use apples-to-oranges comparisons in making assessments, thus limiting their value.

In the PLoS One work, the researchers expanded upon an earlier system they created, Feature Response Curve (FRCurve), which offers a global picture of how genome-sequencing methods, or assemblers, are able to deal with different regions and different structures in a large complex genome. Specifically, it points out how an assembler might have traded off one kind of quality measure at the expense of another kind. For instance, it shows how aggressively a genome assembler might have tried to pull together a group of genes into a contiguous piece of the genome, while incorrectly rearranging their correct order and copy numbers.

However, FRCurve has a significant limitation—it can only gauge the accuracy of certain kinds of assemblers at one time, thereby excluding comparisons among the range of sequencing methods currently being employed.

The work reported in PLoS One unveils a new method, FRCbam, which has the capability to evaluate a much wider class of assemblers. It does so by reverse engineering the latent structures that were obscured by error-correction and data compression; and it performs this operation rapidly by using efficient and scalable mapping algorithms.

FRCbam and FRCurve are expected to be used routinely to rank and evaluate future genome projects. This method is currently employed to evaluate the sequence assembly of the Norway Spruce, one of the largest genomes sequenced so far—it is seven times longer than the human genome.

The study was supported by grants from the Knut and Alice Wallenberg Foundation and the National Science Foundation.

Type: Article

Scientists Develop Tool to Evaluate Genome Sequencing Methods

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