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Cancer, Text Mining, Synthetic Biology, and Early Days of Consumer Genomics


In April of last year, we featured our fourth annual special issue devoted to cancer research. We highlighted the growing use of profiling miRNAs in tumors for possible use as biomarkers or in therapeutics. GWAS also held center stage, with scientists having found major associations in breast, prostate, and colon cancer in 2008. We featured work from NCI's Aaron Schetter, NIH's Stephen Chanock, and Brigham and Women's Hospital's David Sugarbaker, among others. This year, we again look at advances from the past 12 months to profile some of the most outstanding research and discoveries in cancer.

A year ago we also featured a story on the emergence of text-mining tools like iHop, EBIMed, GoPubMed, and PubGene, which utilize algorithms to extract the most useful bits of information out of the growing databases of literature. Companies like Madrid-based Bioalma and Cambridge, UK-based Linguamatics are both looking to use their text-mining technology to help researchers make sense of all those articles. Linguamatics' plans for this year are to continue building a customer base among big pharma, while Bioalma has its eye on the academic market.

Another feature looked into synthetic biology, focusing on work out of Christina Smolke's lab at Caltech and Chris Anderson's at the University of California, Berkeley. Both scientists were using synthetic biology constructs to design disease-sensing smart cells. Smolke has since moved to Stanford, where she's an assistant professor in the bioengineering department. Anderson continues to lead synBERC's Tumor Killing Bacterium Project. Ongoing work on all fronts aims to bring synthetic biology to the forefront of drug discovery research and drug production, such as Amyris Biotechnologies' collaboration with Sanofi-Aventis to produce its synthetic artemisinin on production-scale levels.

In April 2004, GT's cover story focused on genomics in the consumer market, spanning everything from skin creams designed to fit your personal genotype to anti-counterfeiting devices on clothing and currency to microchips made of custom-structured plant DNA. One featured scientist was the US Department of Agriculture's Ray Schnell, who at the time was working with scientists at chocolate manufacturer Mars to protect cacao trees from diseases like witches' broom, frosty pod, and black pod. Last summer, Mars announced a partnership with IBM and the Agricultural Research Service Subtropical Horticultural Research Station in Miami to sequence the entire cacao genome. It's anticipated that this public data will allow scientists to further study cacao's disease susceptibility as well as to compare it to that of other plants.

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.