Fall 2011

Novel Methods for Genetic Testing

Can Help Eliminate Genetic Mutations

...continued from previous page.

The novelty is the method of fusing Compressed Sensing and Next Generation Sequencing, which Dr. Shental and his colleagues now call ComSeq for Compressed Sequencing.

Initially when Dr. Shental embarked on this project, he and his colleagues were interested in conducting screening using compressed sensing. They uploaded a paper on a site, frequented by their colleagues in the hopes of "learning more about what was going on." Less than a day later, Dr. Yaniv Erlich of MIT contacted them. They have been collaborating ever since.

"Initially, our focus was on screening. It took us some time to select the Next Generation Sequencing Technology, " Dr. Shental explains. "True, it's a highly accurate measurement system, however, we soon understood that you could use the same approach for research and for helping you find new disease-related mutations."

They collected three thousand samples from Dor Yeshorim and are about to screen the very same population with but 100-200 pools, instead of 3,000. As Dr. Shental suggests, "while these are just preliminary tests and the distance to clinical usage is still large, there is no doubt in my mind that this is the best method available for meeting the challenge of testing for genetic mutations in large population groups. It is virtually error-free; just increase the pool a bit and you eliminate all possibility of error."

Now, Onto Plants

The ComSeq method can be applied to other spheres of life. Their most recent grant request is to conduct a test research initiative in plant genetics. Sorghum Bicolor is an important crop in Africa (less susceptible to heat, uses smaller amounts of water, offers a large yield). As scientists cannot genetically manipulate Sorghum, they expose its seeds to a certain genetic material which causes random mutations in the genome. This process is performed over thousands of seeds which grow. To understand the genetic base of these properties, one must sequence all of these thousands of seeds, a completely unfeasible task.

Collaborating with Dr. Eyal Fridman from the Faculty of Agriculture at the Hebrew University, and Dr. Zhanguo Xin from the US Agricultural Research Service, Dr. Shental and his colleagues are interested in learning what may make the plant less susceptible to heat and subsequently more productive. As such, they have collected 6,400 such sorghum plants. These plants will be sequenced in less than 300 pools, opening the door to a new avenue of research in plant genetics which, until now, had been completely impractical.

The possibilities are endless. Nationwide carrier screens for known risk mutations can be conducted at a fraction of the cost. Screening people for many more things now becomes financially viable. Identifying large population groups at higher risk becomes easier. Deriving knowledge about mutations which were previously unknown and learn how they impact on diseases today becomes eminently more feasible.

Page: 1  2