Photograph by Matt KaplanWolfgang Haak discusses genotyping protocol.
Posted by Nirav Merchant.
Barcodes are everywhere you look, from products on a store shelf to express mail and books. You are always a glance away from the omnipresent black and white bands. So what do barcodes have to do with Genographic work in the field?
Scientists from each Genographic regional center travel to remote locations to gather DNA samples which they collect and transport in small vials and tubes. To ensure that there are no mix ups or data entry errors, the vials and accompanying forms are given matching barcodes, similar to labels and GPIDs in the public participation kits. Once the samples arrive back at the regional center, they are scanned using a barcode reader and they are ready to begin testing. As the DNA travels through the various testing stages, the barcode allows us to track its progress and location.
Photograph by Matt Kaplan.Amanda Owings (North American Genographic research center) and Daniela Rodriguez Lacerda (South American Genographic research center) work together on a new IBM laptop.
Today, the group got a quick introduction to these amazing little (in size) barcode printers and the scanners that they will be carrying in the field to label and scan their work. IBM also arranged to give them new laptops with a sufficient number of available USB ports so they can plug these devices right into the computer.
Photograph by Matt Kaplan.A scanner used to read the barcodes on the DNA samples.
And just like the barcodes that we use to identify samples, our DNA has its own unique barcode pattern too. DNA has distinct patterns of base repeats called STR (short tandem repeats). STRs are repeating segments of your genome that have a high mutation rate. We test all DNA samples for these patterns of repeats at specific locations to determine which haplogroup a person's DNA belongs to.
Below is the graphical representation of my STR profile shown as a barcode (12 22 15 10 7 16 11 12 11 13 14 16) which is common for Haplogroup L. It is amazing how we have this innate genetic barcode built into us that we pass on from one generation to the next.
No introduction to technology is complete without training, warnings and caveats. Kumar from IBM did all of that and more. Armed with their new laptops, the scientists got a quick refresher course on Genographic's central database and how the new features that Kumar and IBM created will improve their research methods in the field! Coupled with the new tools and technologies, the journey of the samples from field to the lab and into a decoded form is now even more effective than it was before.
Tomorrow we dive into analysis tools!
-Nirav Merchant, Human Origins Genotyping Laboratory Arizona Research Labs
