By Kirell Lakhman

"Nobody will tell you how to, but your lab directors will love you if you learn how to use a genome browser."

That was Hutton Kearney, who oversees cytogenetics at the Fullerton Genetics Laboratory at Mission Hospitals in Asheville, NC. She made those remarks during the closing day of the AGT conference, held in Jacksonville., Fla., late last month.

In her talk, Kearney described how lab techs can make use of genome browsers, which illustrate genome builds, particularly to help them identify what genes are present in a sample or to confirm where a FISH clone map sits in relation to a sequence.

The intro-level presentation — she called it Genome Databases 101 — underscored just how novel certain otherwise-core genomic technologies and techniques remain among members of the Association of Genetic Technologists. (Here's additional evidence from that conference.)

This isn't meant as a jab at them: As Kearney herself noted at the outset of her talk, the human genome was completed after her fellowship, which meant she "had to self-teach. Probably most of us [haven't taken] specific courses to teach us how to interrogate the genome thoroughly. You probably know very little about this because I knew very little about this."

Besides the fact that she is one such director, a quick glance around the room while Kearney spoke added heft to the observation: About a hundred heads snapped down in unison to keep track of notes. And Kearney's reverence for browser-empowerment underscored the growing clinical importance of genomic tools once limited to research labs.

"All of this I've learned through clicking around on the browsers," Kearney forewarned, and urged participants to learn by doing.

During her talk, Kearney kept it simple by describing generally that she uses genome browsers — there are three principle sites — to interrogate copy-number imbalances, map clones, and visualize where her FISH probes map.

She said cytogeneticists "typically think about chromosomes in terms of band positions," which she called a "very gross approximation." A browser can enable lab techs to bore into genomes by the kilobase rather than hover at megabase altitudes — an ability that could help confirm whether a sequence being interrogated is associated with a disease polymorphism.

"You're really guessing with gross mapping," she said.

Genome builds are released every year or so, and the most current version — NCBI 36, curated by the National Center for Biotechnology Information — was released in 2006. A new one is due any time by the Genome Reference Consortium.

Generally, a build, which is consistent between browsers, simply catalogs the number of base pairs in a genome together with their orientation. By comparison, an annotation uncover a genome's genes, segmented duplications, promoters, exons, and introns, and other components.

Kearney described the three principle browsers: NCBI's Map Viewer, the assembly at the University of California, Santa Cruz, and the international Ensembl browser. She said she uses all three "every day" and encouraged attendees to log on, dive in, and start exploring them, starting with a chromosome of interest and entering the coordinates of the segment in which you're interested.

Kearney said Map Viewer is the "most limited as far as looking at the genome [and viewing its] content, but it is the best browser to look at genes, and that's often your most important question." NCBI also provides a link to the Online Mendelean Inheritance in Man, or OMIM, server, a Johns Hopkins University service that she said is "a very nice clinical synopsis for most genes and syndromes."

The browser also makes it "very easy" to e-mail genes to prescribing physicians, she said. This could be a bonus to lab directors and the techs responsible for the work. Accolades, like other biological emanations, flow downhill.

UCSC's browser, on the other hand, is "by far the ugliest — they didn't do a lot in the way of bells and whistles in the way that it looks," Kearney said. "But it's the simplest and easiest to customize, and it is actually my favorite."

Lastly, Ensemble "is by far the most complex," she said. "It has the most bells and whistles you could ever ask for in a browser. Sometimes it just gets to be too much for me; I just feel like I can't see what I need to see."

However, Kearney admitted she turns to Ensembl whenever she needs an image for a publication: "It's prettier," she said.