Discovering Biology in a Digital World

If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)

You may be wondering, and rightly so: just what is a SNP?

Never fear, hopefully this post will answer some of those questions.

tags: DNA sequencing, DNA , SNPs, genetic testing

SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a sequence of bases, and other people will have a different base at that position. The two forms of SNP are called "alleles." (Usually there are only two forms.)

If we compared two DNA sequences, and they contain a SNP, we might see something like this:

If we look at a trace from a chromatogram, and we have a mixed sample of DNA (you have DNA from both your mom and dad, so your DNA is a mixture), a SNP looks like this:

Image made with FinchTV

Those of you who've taken genetics are probably looking at this and saying, uh sure, that's a substitution mutation right? What makes that so special?

SNPs are different because they are inherited.

Mutations can happen in any DNA molecule, in any cell, but they are only inherited if they occur in the DNA that's passed on to our offspring. For example, mutations probably occur in my skin cell DNA whenever I spend too much time in the sun, but my children won't have those mutations. They only got the mitochondrial DNA and the set of chromosomes that I contributed when my body made their eggs.

That SNPs are inherited is pretty cool. We can use SNPs to look at human migration patterns and see where people's ancestors have been. We can also use SNPs to identify medical conditions and evaluate someone's ability to metabolize drugs, like warfarin or caffeine.

Other fun facts about SNPs:

• SNPs occur about every 200-1000 bases.


• SNPs are usually binary. That is, I might find an A or G at a certain position, but I'm far less likely to find an A, G, or C.


• The process of doing a genetic test to identify which SNP you have, is called "genotyping."


• Craig Venter has 3,213,401 single nucleotide polymorphisms (SNPs) (1).

SNPs are not the only form of genetic variation. I'll cover some of the others (indels, inversions, etc.) later on.

References:
1. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The Diploid Genome Sequence of an Individual Human. PLoS Biol 5(10): e254 doi:10.1371/journal.pbio.0050254