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Sociology of Genomics Research, TCGA Glioblastoma Data, DNA Barcoding Efforts, more


Ten years ago, Joan Fujimura told Genome Technology that "biologists need computational assistance and computational scientists need biological expertise." Now a professor of sociology at the University of Wisconsin-Madison, Fujimura continues to study the culture of large-scale genomics research and is writing a book that chronicles "the role of race in recent biomedical genetics studies."

In April 2006, GT organized a panel discussion on automation featuring researchers from "four tech-driven labs," including Susan Perkins at the American Museum of Natural History's Sackler Institute for Comparative Genomics. At the time, she joked that she wished her lab would one day obtain "the thing that they have on CSI, where they get their sample and have their sequence seven minutes later." While technological advancements to date have not afforded such speedy results, Perkins says she now is "excited about ... some of the new sequencing technologies that are allowing for longer reads in massively high-throughput ways." She is also enthusiastic about recent improvements in "methods to isolate single cells for genomics and transcriptomics," which will "allow us to catapult our knowledge of microbial diversity and function into places we never thought possible."

For its sixth annual cancer issue last year, GT spoke with David Neil Hayes at the University of North Carolina, Chapel Hill, who, along with his colleagues at the National Cancer Institute-funded The Cancer Genome Atlas project, identified subtypes of glioblastoma based on expression, copy number, and mutation status data. Since then, researchers have published more than 25 studies in which they made use of data and other resources generated by TCGA efforts. In particular, a trio of investigators at Stanford University reports its use of TCGA glioblastoma data to estimate parent-specific DNA copy number in tumor samples with high-density genotyping arrays in a January 2011 PLoS Computational Biology paper.

Elsewhere in its April 2010 issue, GT profiled the Moorea Biocode Project team's efforts to sequence the genomes of every non-microbial species on the small island in French Polynesia. In December, the Moorea Biocode team made its laboratory information management system — a project-specific plug-in for Biomatters' Geneious Pro sequence analysis software — available online as a public tool for DNA barcoding initiatives.

The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.