DNA sequencing assembly research could speed up disease identification

In the future, when physicians need to verify a patient diagnosis, they may find their answer by analyzing DNA and checking it against an online disease database.

Xiao-Long Wu, a PhD candidate in electrical and computer engineering (ECE) and a researcher at the Coordinated Science Laboratory, is working on a method to speed up DNA sequence assembly, which can re-organize many short DNA strands into a complete sequence, without having to know the proper sequence in advance.

It is fundamental in understanding evolution and disease identification. For example, if a patient is exhibiting symptoms of a disease with an uncertain diagnosis, doctors could take a DNA sample and sequence the patient’s genome. Once the disease is identified by matching its DNA sequence with those in an online library of known disease codes, doctors can see the specific genetic changes in the patient and design individualized treatment accordingly, Wu said.

Although a method for sequence assembly already exists, it is extremely expensive and time-consuming, with computation easily requiring weeks to accomplish. Wu’s team is seeking to significantly speed up the process. He describes the process as dividing multiple strands of a DNA chain and then piecing them together like a type of jigsaw puzzle.

The process aims to lower memory loads and computation time, while maintaining quality results. An additional advantage is that the process can be accomplished with low-cost commodity computers and GPU processors. This research would potentially speed up research progress in this field, Wu said.

Other research team members include ECE faculty members Wen-mei Hwu and Deming Chen, Bioengineering assistant professor Jian Ma; and CSL student researcher Yun Heo.
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Contact: Xiao-Long Wu, Coordinated Science Laboratory, 217/244-3226.

Writer: April Dahlquist, Coordinated Science Laboratory.

If you have any questions about the College of Engineering, or other story ideas, contact Rick Kubetz, Engineering Communications Office, 217/244-7716, editor. University of Illinois at Urbana-Champaign.