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First-Of-Its-Kind Ultrafast Detection Of Microbe And Cancer Cell Mutations Could Lead To More Precise Investigations Of Therapeutic Treatments

Scientists at A*STAR’s Genome Institute of (GIS) have developed a novel technique to precisely monitor and study the evolution of micro-organisms such as viruses and bacteria. This is an extremely important capability as it allows scientists to investigate if new drugs designed to kill them are working, and catch the development of resistance early on.

Micro-organisms and cancer cells evolve more quickly than normal human cells as their rapid life-cycles enable faster selection of advantageous mutations. Previously, scientists have had to wait for the selection process to reach maturity before they can observe mutations and assess their impact.

In this new work, led by GIS Principal Investigators and , the sensitivity of detecting mutations has been significantly increased, thus making it possible to “catch evolution in real time”. Being able to do this means that scientists can now observe the process of mutation as it happens, and catch how the organism or develops resistance to drugs used.

The novel method, known as LoFreq, was achieved by combining deep sequencing of DNA with computational analysis to detect mutations at extremely “LOw FREQuency” – in as few as one in 1000 cells. This approach is currently being used at the GIS to study the , characterizing subtle shifts in the viral genome in response to new antiviral drugs.

said, “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.”

Executive Director of GIS, Prof Ng Huck Hui said, “This innovation in the computational space highlights GIS’s effort in developing unique capabilities in analyzing increasingly complex next-generation sequencing datasets. We expect that LoFreq will have wide utility in the analysis of viral, bacterial and cancer genome data.”


Research publication:
The research findings described in the press release was published in the December 2012 issue of Nucleic Acids Research under the title “LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets”.

Andreas Wilm1, Pauline Poh Kim Aw1, Denis Bertrand1, Grace Hui Ting Yeo1,
Swee Hoe Ong1, Chang Hua Wong1, Chiea Chuen Khor1, Rosemary Petric2,
Martin Lloyd Hibberd1 and Niranjan Nagarajan1

1. Genome Institute of Singapore, 60 Biopolis Street, Genome, #02-01, Singapore 138672, Singapore and
2. Hoffmann-La Roche, Bldg 85/521340 Kingsland Street, Nutley, NJ 07110, USA

Agency for Science, Technology and Research (A*STAR), Singapore