SNPs, SNPs, and more SNPs...Wait....What in the World Are They???
Among Dr. Ashley Allison-Koch’s many studies, I am in her Healthy Pregnancy, Healthy Baby Study (HPS for short). The overall goal of this study is to look at various SNPs (single nucelotide polymorphisms) in specific strands of DNA that encompass specific genes thought to affect low birth weight, preterm births, high maternal blood pressure, and preeclampsia. One of the reasons Dr. Allison Ashley-Koch first wanted to research this topic was because of its interdisciplinary nature. There are many racial disparities within the four effects in pregnancy being studied. The study was designed to look at possible affects to low birth weight, preeclampsia, etc from genetic, social, and environmental perspectives.
The specific part I play in this large study is in the genetic region. I am currently looking at thirty SNPs within inflammatory response genes on four chromosomes (1, 3, 4, and 5) and at eight different loci. The way I test the 30 SNPs are to go through a very tedious process in quite a repetitive manner. However, it never seems to get old. Everyday brings with it new challenges and a different schedule of events. The only part of the whole process I really don’t like is the analysis bit at the end. Well, now that I have told you this, you might be wondering what the whole process actually entails. So, here goes….
I start by getting out three Taqman plates, each with 384 wells with DNA at the bottom. I then make a mixture that includes distilled water, master mix, and a specific assay, which is customized for whichever SNP I am running at the time. Next, I use an electronic multi-channel pipetter to transfer the slightly lavender mixture into each of the total of 768 wells. This process is quite difficult because the wells are small and made of clear plastic while the pipetter is finicky and temperamental. However, once the pipetting is finished and a seal is placed on each plate, the plates are centifuged and placed in PCR blocks which control the polymerase chain reaction that amplifies the DNA.
Once the reaction is complete (which takes about two hours to run with an annealing temperature 60 for 50 cycles), the plates are centrifuged again and then placed on a scanner that reads the fluorescent dye that is found in each well. This part of the process can be very frustrating because the scanner machine also doubles as a Real-time PCR machine, which is used by many other labs and takes hours to perform. However, once the scanning is complete, the analysis must take place. The analysis part is up to my discretion alone and can be quite tedious when there are many plotted points that might or might not fit into an exact group on the plot. Once the analysis is complete, the worst part is over. The only remaining step is to submit the data to the database, so that it can be accessed at a late time by the statistician.
Well, that is the basis of my whole summer at the Center for Human Genetics. As complicated as it may sound, I am actually having a lot of fun, and I really like the work I am doing. One of my favorite parts is the fact that I can clearly relate all of my extremely detailed lab work with the bigger picture of how it affects the greater population and future knowledge.
~~~Helen
