Faraz Hach, SFU Computing Science PhD student, and one of the two lead authors of the award-winning paper.

Computing Science

Molecular study of cancer cells leads to award

July 16, 2012

A paper co-authored by an SFU Computing Science PhD student and recent SFU grad won the outstanding student paper award at the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).

The paper “Dissect: Detection and Characterization of Novel Structural Alterations in Transcribed Sequences,” was presented by Deniz Yorukoglu, who completed his MSc at SFU’s Lab for Computational Biology in 2011, and is now working on his PhD at MIT. Yorukoglu and Faraz Hach, an SFU Computing Science PhD student, are the joint lead authors of the paper; Cenk Sahinalp, SFU Computing Science professor and director of the SFU Lab for Computational Biology, directed the research.

The study involved developed a computational tool to see if the RNA strings in cancer cells reflect a common pattern of aberrations from those of non-cancerous cells. The RNA in normal cells of a given tissue type will be roughly the same from individual to individual; in cancer cells, the RNA strings are majorly altered—pieces may be removed, inverted, or duplicated. The discovery of a common pattern of RNA aberrations among multiple samples of cancer cells could lead to a valuable diagnostic tool.

“This study is the first time people have looked at these aberrations in RNA in cancer samples,” explains Sahinalp. “This research is moving the diagnostic process to the molecular level.”

Inanc Birol of the BC Genome Science Centre provided the assembly tool for the research; Colin Collins of the Vancouver Prostate Centre provided the cell samples. Lucas Swanson, an SFU MSc student based in the BC Genome Science Centre, assembled the samples, which Yorukoglu and Hach then analysed in order to develop the computational tool. Birol, Colins and Swanson are listed as additional authors on the paper. 

This research was conducted on cells from one prostate cancer patient; the next step, which is already underway in Sahinalp’s lab, is to test the process on the cells from ten different patients.

The ISBM conference is the annual meeting of the International Society of Computational Biology, held this year from July 15 to 17 in Long Beach, California. The conference attracted 1500-2000 attendants; hundreds of papers were submitted, with only 35 selected for presentation. Yorukoglu and Hach’s paper won the Ian Lawson Van Toch Memorial Award for Outstanding Student Paper.