Genetic Variation I: What is a SNP?

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Sandra Porter

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

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

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 two forms, but that's not always true.) If we compared two DNA sequences, and they contain a SNP, we might see something like this:

A DNA sequence inherited from one parent, compared with the sequence inherited from the other parent.

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:

The height of the gray bar corresponds to the certainty of identifying a base.  If two bases are present, the quality is low because there's more than one base.

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 when I spend too much time in the sun.  Unlike a SNP though, my children won't have those mutations. They only get the mitochondrial DNA and the set of chromosomes that I contribute when my body makes their eggs.

That fact 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

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