Who are you comparing me to, anyway?

Researchers around the world carry out genetic and genomic studies comparing the genetic makeup of a person, or a group of people, to a “reference” human genome.

This has paved the way for some integral discoveries: genes underlying bipolar disorder, Crohn’s disease, diabetes, and many types of cancer have been identified using this wealth of information. We can now look at the genome holistically with Genome-Wide Association Studies, or GWAS. GWAS data are appropriately visualised using a Manhattan Plot, where the Empire State Building and One World Trade Center (and, perhaps, 432 Park these days) represent the strongest associations between single nucleotide polymorphisms (SNPs) in that position and the disease or trait in question.

A Manhattan Plot from Petukhova et al. 2010 (doi:10.1038/nature09114)

Ultimately, though, we are left with a question, one that researchers and discerning members of the public should be concerned with: Who is this model human, and why are we using his or her genome as the baseline for all other genomes?

Genome Sequencing and the Lowly Undergrad

It’s not every day you get to sequence a genome (unless you run a genomics facility for a living, in which case you probably sequence more genomes in a day than you think is appropriate).

More specifically, it’s not every day an undergrad gets to sequence a genome. Undergrads are relegated to cartoon demonstrations of Illumina sequencing, on a 10 foot tall projection in front of a lecture hall full of half-asleep third year bio majors. They get the incredibly fun job of remembering which “Next” of Next Next Next Next Generation Sequencing we’re on. Not interesting. No wonder people find biology class boring. But it’s a different story when you get to go into the lab and do it.

My genomics class at the University of Edinburgh made it possible for ~150 undergraduates to sequence Clostridium difficile genomes that had never been sequenced before.

Real science. Oh, the thrill of finding out things that have never been found out before! It makes the practical report that much more interesting.

And I’m not even kidding.