Approaching the Genome

Back in school after the Easter break and what a difference in the 6th form students. They were utterly spent at the end of last term, pale, shattered and weary of school. But now, well rested and with study leave less than 3 weeks away (for the Year 12s) and 5 weeks away (for the Year 13s), they’re positively bouncy, focussed, enthusiastic, energetic and raring to go.

The Year 13s are covering genome sequencing – how it’s done and why it’s interesting. This astonishing image

genome lollipops

shows all the currently identified risk factors for 17 types of trait at specific locations on each chromosome. It’s an attention grabbing start to the topic. Quite apart from anything else, how on earth would you set about finding all that out? What information do you need? The idea of sampling and comparing the alleles and other variants of more than 500,000 loci for thousands of people, some sick, some healthy, and looking for significant associations, is a bit of contrast to Chi2. It’s also clear why super-computers are vital for crunching the data and processing the stats….

We discuss the possible applications of this amazingly powerful information. One particular base sequence on chromosome 16 can contribute 3 to 4 extra kg of body mass. Then there’s Angelina Jolie and what she did with her knowledge of the BRCA genes. And just why are there so many conditions associated with Chromosome 6…? (where the MHC genes reside).

Then it’s time to figure out the technique, as stipulated by OCR. This resource The Enigma Code generally goes down well, though one girl did mutter this year, as her partner said brightly, “I wonder what the secret message is?” – “oh, it’ll be some lame joke.” How well they know me. This follow up, looking at the use of overlap, is also helpful Return of the Gene Sequencer.

But one of the things I really enjoy about working in Oxford, is that you get a real sense of how quickly Biology is changing and advancing. One girl, handing in her poster summarising automated Sanger sequencing http://www.dnalc.org/resources/animations/cycseq.html , reports, “my dad says that no-one does it like this anymore,” which provides the obvious response, “Don’t they? Right! Let’s find out what they do do…” though subsequently trying to get our collective heads around Nanopore sequencing was of limited success. Nowhere else does the specification lag so far behind developments in the real world!

Another girl reports that her father is associated with a company called 23andme and, joy of the information age, we can instantly access it in the lesson. https://www.23andme.com/en-gb/ Wow. This looks amazing! I’m wondering if I can wangle some dept. money to have a demonstration report on, say, me… for educational purposes, obviously. I already know I’m not a carrier for cystic fibrosis, but given my high consumption of espresso, it would be interesting to assess my ability to metabolise caffeine…

At £125 a pop, we obviously can’t do all the A-level students but they’re pretty happy to amplify part of their PTC receptor gene to identify their genotype and see how it links to their phenotype (this resource from Carolina Biological is superb http://www.carolina.com/human-genetics/using-a-single-nucleotide-polymorphism-snp-to-predict-bitter-tasting-ability-kit/FAM_211376.pr?catId=10141&mCat=10101&sCat=10138&ssCat=&trail=7002:10421&question= ). I’ve invested heavily in all kinds of genetic kit in recent years and it’s been worth every penny. What could be more exciting than not only extracting your own DNA, but then amplifying and analysing it? They love the equipment – using a micro-pipette never gets stale – and are fascinated by the procedure. All good stuff.

Back to PSA marking and invigilating. Next week I’ll report on how the Year 10s got on with fruit fly breeding and whether they managed to figure out the Mendelian laws of inheritance from first principle…

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