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Of maps and microarrays


Most everyone would agree that it’s important to have a good map, but there are certain times in life that we are bluntly reminded of that. Last year on a trip to Greece, I rented a car to drive from Athens to Delphi and got a map from the rental dealership. It wasn’t until the trip was well underway that I opened the map to discover an alarmingly white page featuring a vague outline of the country spotted with large stars indicating the location of each franchise of this particular rental agency. And that was it. Not a town, highway, or landmark on the entire thing.

Good maps are indeed crucial, and nobody knows that as well as the scientists trying to traverse biological pathways. The problem with pathway maps is that it’s not clear yet which data will serve as the highways and cities and which data are the highly unnecessary rental agencies. That’s resulted in a horde of public-sector databases and informatic tools as well as a number of vendors vying to be the best pathway analysis technology. It’s too early to tell which of these will be around for the long haul, but GT’s senior editor Jen Crebs presents an overview of some current tools to help you parse out which ones may be most relevant to your work. Recognizing the problem of many standards in the field, she also includes a chart showing which tools and databases adhere to each pathway standard.

In our cover story this month, we look at new applications for microarrays. I remember the days when you could just say “chip” and everyone would understand that you were working on gene expression. Not so today, as scientists come up with increasingly creative ways to put all sorts of biological content in array format. This story takes you on a tour of emerging uses for arrays that appear most promising, including microRNAs, DNA methylation, protein-based arrays, and ChIP-on-chip.

If you read any of our sister publications — GenomeWeb Daily News or our newsletters — you’ve seen that all of their websites have been redesigned recently to promote easier navigation between sites, a better search function, and simpler access to your own account. Genome Technology’s site is up next, and we’ll be getting more than a facelift. Our new site will be chock full of features designed to keep you on top of the latest news and events in the field. The site’s highlights will include more frequent content updates, tools to keep you connected to the community, and plenty of other cool widgets. We’ll let you know when it’s live.

Finally, GT has a new reporter on our roster. Please welcome Matthew Dublin, who has previously worked for Newsweek, among other publications.

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.