DNA Sequencer Bubble Sensors

Many recent Illumina instruments have bubble sensors, this includes the HiSeq X which I tore-down a while ago. I decided to take a quick look at this sensor and rig it up on the bench.

The Fluid sensor is basically a very simple photointerrupter. There’s an LED and a photodiode. I powered the LED with a bench supply and used a transimpedance amplifier (TIA) I put together for another project to amplify the current from the photodiode:

This all worked well, and I could as I sucked liquid through the tube I could see it register on the scope:

Illumina seem to detect bubbles using this basic mechanism, which they discussed in a short conference paper on the topic:

Unfortunately there’s not a lot you can do about bubbles in an Illumina sequencer, but they suggest you can pump more reagents through the system or just completely abort the run:

As we’ve seen from log files previously, this information is also logged, and I guess can be helpful when getting field support to sort out instrument issues.