DNA sequencing and bioinformatics, part I: a case study from the classroom

What happens when high school students clone and sequence genomic DNA?

Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.

Of course, without bioinformatics there's no way to know what's been cloned or sequenced.

This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of our iFinch product to support the Bio-Rad cloning and sequencing kit. Now teachers and students get to use one of the same bioinformatics systems that professionals use for genetic analysis.

Naturally, we've wondered how well this project would work in the hands of inexperienced users. Our normal customers are laboratory professionals who already know what they're doing in the lab and what they want to see when they turn on a computer.

Now that it's almost fall, we're about to find the answer. The school year is fast approaching. Soon teachers will be back in class and hopefully, lots of students will be sequencing DNA. I've been using iFinch with my own college bioinformatics classes for over a year, working on a metagenomics project, but this is different. These are not my students and I will not be present. These are students in the wild. Many will have had very little lab experience, some will be in college, some in high school, and all will be pretty new to the whole practice of sequencing and analyzing genomic DNA.

Test driving iFinch
Last week, one of our first high school collaborators started using iFinch to carry out the bioinformatics portion of their summer sequencing project. In the project, they attempted to clone and sequence GAPDH genes from snapdragons. GAPDH stands for Glyceraldehyde 3-phosphate dehydrogenase, an essential enzyme that helps metabolize glucose. After they finished, I looked through their iFinch reports to see what I could learned from their data. Just a bit of laboratory forensics, to satisfy my curiosity.

Don't worry, I won't give away anything about gene structure or new discoveries. I'm only going to discuss the things that I could easily learn from iFinch reports.

Uploading and filtering the data
The first thing that our class needed to do was to get their data into the system. Most laboratories upload data directly from their analytical instruments. As soon as the data are finished, they go right into the system. Classrooms use a slightly different technique and upload their data through an iFinch web page.

What happens next, depends on the kind of file that was uploaded and the choice that was selected on the upload page. If a file is a chromatogram, iFinch sends it to pipeline where different programs analyze it, extract information, and present the information in a collection of reports. If a file is not a chromatogram, its fate depends on the menu choice. If it was identified as a generic file, the file goes to the selected folder. If not, then it goes to a holding place for non-chromatogram data.

Why is this important? DNA sequencing instruments can produce other files in addition to chromatograms. In this case, our test classroom had 206 .phd files and .seq files that they tried to upload along with their chromatograms. I found these when I clicked the Undistributed Data link. iFinch recognized that these were not chromatogram files and sent them off to the holding tank. The chromatograms were sent onward into the pipeline. This feature was helpful because it allowed the class to go ahead and upload all the files from their DNA sequencing instrument without having to sort them out beforehand.

Did the experiment work? Did the class clone any GAP genes?

I guess you'll have to come back tomorrow to find out.

or read the rest of the series: Part II, Part III.