Bioinformatics: Inspiration ahead

By Maureen Aylward

We asked our Zintro experts to tell us what they think is the most inspiring and important discoveries coming out of bioinformatics today.

Kenneth Rubenstein , PhD, an executive in vitro diagnostic industry and consultant specializing in dx/bioanalytics for start-ups and emerging companies, says that next-generation DNA sequencing (NGS) technologies have taken the life sciences research world by storm. The first human genome sequence was completed in 2001 after five years and an expenditure of several billion US dollars. Intensive bioinformatics input was essential since tens of thousands of small fragments of DNA were sequenced and assembled into their proper order, explains Rubenstein.

“NGS technologies came on the scene in 2005. Since they produce even smaller sequenced fragments than older methods, bioinformatics for assembly, mapping, and data interpretation have gotten more complex and elaborate,” he says. “Given that tens of thousands of genomes have now been sequenced, the informatics task is shifting toward deriving actionable biological information from sequence data. The human genome and those of other organisms are not well understood in many ways. Indeed, the more we learn the more questions that open up to be addressed.”

Rubenstein says that several companies, notably Ingenuity Systems and a host of academic contributors, are working on ways to link established knowledge bases to new sequence data to provide clues to suggest downstream biological investigations. “Although a great many NGS informatics challenges remain, the main ones center on how to make sense of all this data, especially with regard to cancer applications where ten thousand or more tumor genomes will soon have sequences,” Rubenstein explains.

Ramon-Garcia, PhD, a researcher and expert in cellular and molecular biology of virus infection, says that the most important discoveries in the field of biomedicine are new tools that allow for the interpretation of raw data obtained in next-generation sequencing. However, Garcia sees challenges in the generation of new predictive tools to integrate high-throughput genomic data (gene expression, genome structure, miRNA, gene mutation, and methylation), clinical data, and environmental data to predict outcome or response to treatment for patients.

CompBioExpert, a computational biologist and senior scientist, says that an area of application in bioinformatics that is getting more interesting is the metagenomics of microbial communities, particularly the metagenomics of the human biome (basically what’s living in your gut) and other extreme or important environments. He recommends the recent article in the The New York Times that reports the human biome falls into one of three types of enterotypes, human gut ecosystems.

Paul Shapiro, PhD, an expert in molecular cell biology, molecular biology, and biochemistry, says that important bioinformatics applications continue to be developed to support the staggering pace of developments in genome sequencing hardware, especially for determining human genomic sequence variations (single nucleotide level, large insertions/deletions, duplications/CNVs, in/dels and structural variations). “These are areas that may be associated with disease risk and other phenotypes, most notably pharmacogenomics and for identifying all microbial species in environmental metagenomic samples using culture independent methods,” says Shapiro.

By Maureen Aylward

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