(originally posted Feb 1, 2015 on the Nature blog “SciLogs”)
I am delighted to be writing my first blog for SciLogs. I thought for my initial post I should do a bit of an introduction in case you were wondering “Who is this girl with the Nerdy Mind?”
I spend my days at the USC Keck School of Medicine doing genetic based cancer research. (I often spend my spare time writing, watching movies and listening to my English Bulldog snore, but I think you’re here for the science.)
When I started out about 11 years ago, our big new technology was Applied Biosystems Taqman Genotyper. It allowed us to look at one particular SNP of interest in however many subjects as we wanted. A SNP (Single Nucleotide Polymorphism) is a change in a single nucleotide (A, C, G, or T) of the DNA sequence. Ahh, those were the days. High Throughput Genotyping has changed rapidly in a decade. Now pretty much exclusively, we use Genome Wide Association Scans (GWAS). We look at tens of thousands of people and so far as many as 1 million SNPs at a time.
Genotyping is important in the research of genes and gene variants associated with disease and it is how we determine differences in the genetic make-up of an individual. We look at their DNA sequence and compare it to another’s DNA sequence. We analyze known SNPs in the human genome and determine which alleles correlate to an increased risk of cancer. An allele is which version of the genotype you have. So, how does that correlate to disease? If you think of your genome as a book, we humans all have a copy of the same book. Genotyping would compare some chapters of that book to determine which words are spelled differently. Those differences in spellings of the same word would be the alleles. Take for instance the sentence “The sky is not gray”. Change one letter (spell gray with at E or an A) to “The sky is not grey”, the sentence has the same meaning, people are still planning their day at the beach. The “A” allele or the “E” allele, it doesn’t really change anything. We wouldn’t be too interested in that SNP, we would call that a silent mutation.
On the other hand change the word “not” from a T to a W and you have “The sky is now gray” That changes everything! We’ve canceled beach day and are grabbing our umbrellas. It could be that the W allele correlates to an increased risk of cancer.
Think of BRCA1, with over a dozen or so SNPs which are associated with an increased risk of breast cancer, and have a medical test for them. You can be tested to see if you carry those mutations giving you the chance to change your lifestyle to decrease risk and/or have prophylactic surgery to reduce the risk even more.
On the other hand mutations aren’t all bad. Sometimes they can be linked with a decreased risk: such as rs140068132 which is associated with lower risk of breast cancer in Latino women. FYI – Eventually all SNPs are given an rs#. It’s much easier to refer to a mutation as rs#12345678 than to say “That SNP that changed from a T to a C on chromosome 9 at position 3901666”.
Now you know a bit more about me and how I spend my work days.
I hope you will enjoy my eclectic science posts in the future. I look forward to writing them and spreading the science. Thank you for reading.