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More rivulets of blood along my pinky, my eyes tear up, and she squeezes my finger over the test tube.

Today, you can use an Oxford Nanopore ($1000 dollars) to sequence whatever DNA you want in less than 48 hours. Or so their marketing materials say.

Right now, if you want to sequence your own DNA, you have to send blood or a cheek swab to some shady third party that, for all I know, gives my DNA away on a USB stick with 10,000 other peoples’ DNA in a dark corner of Shenzhen.

Some friends and I became curious: How hard would it be for us to buy a Nanopore and sequence DNA, using makeshift equipment in our bedroom?

Before getting into the equipment, please allow me a quick technical digression into how DNA sequencing has changed over the years:

Add an electric current across a gel and the smaller bits will separate. You can then read the bands like a barcode.

‘Sequencing by synthesis’. instead of chopping up and separating each base pair through a gel lattice, we

Now we use electrical nanopores and read the individual charge of each base pair. Nothing needs to get chopped up, the processed DNA is unwound and passed through a tiny hole. each base pair like beads on a molecular string pulled through a hole

Blood itself has all this gunk in it – mostly red blood cells, which don’t even have DNA. You need to dissolve the white blood cell membranes and separate out this DNA. The Zymo kit gave us the right enzymes and a special test tube that acted as a filter when spun through a centrifuge. We followed the instructions using our thermal cycler which worked fine.

We then had to follow the Nanopore prep kit, which basically had us attach adapter molecules so the nanopore could tell what it was reading.

I wanted to look at my single nucleotide polymorphisms (eg lactose tolerance genes, breast cancer genes). To confidently call SNPs you want to sequence the same section multiple times. We had most spots sequenced zero or one times.

Another problem was our flow cell was malfunctioning from the start — only 623 out of 2048 pores were working.

Run the DNA through small electric holes so the Nanopore can read individual base pairs of each DNA fragment

Oxford Nanopore MinION starter kit ($1,000) – includes the USB sequencer, flow cell with tiny biological pores, and prep chemicals

Thermal cycler replacement: An electric kettle ($20) + bucket + styrofoam to float our sample tube on hot water (a new thermal cycler costs ~3k-5k).

“God… do you want me to do it for you?”“Sure, I guess”

Before I can say anything more, she stabs the needle into my finger again. And again. And again.

The cost of sequencing has fallen faster than Moore’s law. Source

The first human genome took $2.3 billion dollars and 13 years to sequence.

Then vs now (3730xl DNA Analyzer machines from Applied Biosystems vs Oxford Nanopore)

The goal is to get from 10ml of blood to a string of 3 billion A’s, C’s, G’s, and T’s.

A summary of the Three Ages of DNA Sequencing from this excellent paper.

This approach took 13 years and $2.3 bn to do the human genome (~3 billion bp).

So I have to acknowledge that the results were basically useless for analysis.

Still! We sequenced a meaningful fraction of my human genome for $1100.

Thank you to my dear friends Lenni, Cece, and S for conducting this experiment with me

Zymo DNA extraction kit (free sample from their website)

Mini centrifuge from Amazon ($50) – spins stuff fast

lab consumables: eppendorf tubes, lancets, pipette ($50)