AsianScientist (Mar. 14, 2013) – Scientists have developed a method to study the evolution of microbes and cancer cells by detecting mutations as they happen.
By watching the changes happening in a microbe or cancer cell, scientists hope to understand how drug resistance develops, which would lead to more precise investigations of therapeutic treatments.
The team of scientists from the Genome Institute of Singapore (GIS), led by Dr. Niranjan Nagarajan and Dr. Martin Hibberd, developed the novel method, known as LoFreq, by combining deep sequencing of DNA with computational analysis to detect mutations at extremely “LOw FREQuency”, or in as few as one in 1,000 cells.
Limitations in available technology prompted the scientists to develop this new method.
“This work came out of an interest in looking at the evolution and transmission of the dengue virus. We were using high-throughput sequencing to look at intra-sample diversity in the virus and realized that computational tools to analyze such data were still limited,” said Dr. Nagarajan.
Microbes and cancer cells evolve more quickly than normal human cells because they have rapid life-cycles, which enable faster selection of advantageous mutations. Previously, scientists had to wait for the selection process to reach maturity before they could observe mutations and assess their impact.
The LoFreq method significantly increases the sensitivity of detecting mutations, making it possible to “catch evolution in real time.” This means that scientists can now observe the process of mutation as it happens in organisms to investigate whether new drugs designed to kill them are working and to catch how drug resistance develops.
“LoFreq has really allowed us to look at viral genome evolution in fine detail and we hope to use it construct better models for transmission of the dengue virus. We can also now identify key functional regions in viral genomes by highlighting spots that never mutate or mutate rapidly. In ongoing work, we are developing extensions to LoFreq that can better characterize mutations in cancer,” Dr. Nagarajan explained.
The LoFreq method is now freely available as a software package with an accompanying wiki giving step-by-step instructions. The GIS scientists are continuing to develop the software and improve it with new features.
With their new method, Dr Nagarajan’s team is studying the dengue virus, characterizing subtle shifts in the viral genome in response to new antiviral drugs.
“The method was used in a collaboration with Roche for studying the impact of a new anti-viral drug for dengue. We are also using this approach to study HCV (hepatits C virus) and plan to apply it to study new anti-viral drugs for dengue undergoing clinical trials in Singapore,” he said.
The article can be found at: Wilm A et al. (2013) LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.
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Source: A*STAR; Photo: Sanofi Pasteur/Flickr/CC.
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