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Gene Fusions and Transcriptome Sequencing


Christopher Maher
Title: Research Investigator, University of Michigan Medical School
Education: PhD, Cold Spring Harbor Laboratory and Stony Brook University, 2006
Recommended by: Arul Chinnaiyan

For Christopher Maher, an innovative undergraduate program at Cornell University made all the difference in shaping his scientific career. As a Presidential Research Scholar in the biomedical engineering department, Maher says he was given the freedom to explore whatever research direction interested him. After an initial interest in biology, he found himself gravitating toward computational work and wound up earning his master's and PhD degrees under the tutelage of Lincoln Stein and Doreen Ware.

His graduate school work focused largely on transcriptional and post-transcriptional regulation in plants and nematodes. He followed that up with a short postdoctoral stint at the South African National Bioinformatics Institute where he worked on a cancer bioinformatics project; later, he took on a longer research fellowship at the University of Michigan with Arul Chinnaiyan in the school's pathology department.

The Michigan fellowship connected Maher to research focused on human disease and set him on his current scientific path. As a postdoc at the Michigan Center for Translational Pathology, he worked extensively with next-gen sequencing data and focused on optimizing an approach the Chinnaiyan lab had come up with to identify fusion genes. Maher used 454 and Illumina sequencing instruments for the research and, more recently, developed a method for performing the identification using paired-end sequences.

The work started out in prostate cancer and has since branched out to other types of cancer, he says. In addition to validating known gene fusions, the technique was also able to identify novel examples as well, indicating that it is better suited to detecting these events than previous technologies such as array CGH or fluorescence in situ hybridization, which have also been used in gene fusion studies.

Chinnaiyan, who recommended Maher for this series, says that his former postdoc's work "establishes a robust pipeline for the discovery of novel gene chimeras using high-throughput sequencing that opens up an important class of cancer-related mutations for comprehensive characterization."

After completing his fellowship work in the Chinnaiyan lab this year, Maher was promoted in September to his new position as a research investigator in the pathology department at Michigan's medical school.

Looking ahead

As a newly minted research investigator, Maher says he is "very much interested in continuing to work with gene fusions. I think we're not only going to see the discovery of many novel gene fusions but also ... see things that we've missed" with ones that are already known. He also expects to branch out to studying the cancer transcriptome with next-gen sequencing and use that to find novel noncoding RNAs.

Publications of note

Maher says a paper published in Nature in January 2009 entitled "Transcriptome sequencing to detect gene fusions in cancer" illustrates the kind of work he's done. The paper provides validation for the approach of using next-gen sequencing to find gene fusions in cancer, he adds. "That highlights what I've been doing over the last few years," says Maher, who was first author on the publication.

That paper was followed by another, in Proceedings of the National Academy of Sciences in July, which demonstrated the gene fusion concept using paired-end transcriptome sequencing.

And the Nobel goes to...

Maher was especially impressed by how the discovery of micro-RNAs reshaped much of the conversation surrounding cancer biology, so his dream for a Nobel Prize would center around discovering a novel mechanism that would promote our "understanding and ability to cure cancer" and also serve as "a tool to understand biology in general," he says.

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