I’m Louise Aigrain and I’m part of the R&D, DNA pipelines team here at the Sanger Institute.
My job is to test and develop new methods to sequence DNA.
A DNA pipeline is the process of taking DNA samples
preparing them for sequencing and sequencing them, before releasing the data to the researcher.
Because we work with DNA samples and sometimes the samples have a very low amount of DNA
we need to make sure that we will never contaminate them with our own DNA
and that's why we wear lab coats and gloves all the time.
We receive the samples in 96 well plates and they’ve already been extracted and purified from cell tissue or blood,
when we receive those samples we need to check the quality of the DNA to check that is still very long strings of genomic DNA
- that's what we call the quality control or QC step.
We really don't want to waste a lot of the sample for quality control
that's why we are using the Mosquito robot for that step because it's able to pipette only nanolitres of DNA.
These nanolitres of DNA pipetted by the robot are then mixed with a solution containing a fluorescent dye.
These molecules of dye glow very, very bright only when they touch DNA
so we can relate the level of fluorescence with the actual concentration of DNA in the sample.
Then when we are sure that our DNA is of good quality and in good amounts, we start the library construction itself.
This takes place in our pre-PCR lab on the Bravo robots.
The Bravo robots will be able to pipette some solution, containing what we call adaptors.
These adaptors are very short fragments of DNA that get attached or ligated to the end of our DNA samples.
The adaptors have two goals - they allow the sample to attach at the surface of the flow cell
and they also contain a tag that will be part of our sequencing data and will allow us to always know
which fragment of DNA came from which sample.
Because we process such a high number of samples we need to make sure that we never exchange them or lose them
and that's why we use barcodes on each of our plates.
We have a process called LIMS - which stands for Laboratory Information Management System -
which allows us to scan all those barcodes and track the samples all along the library preparation process.
After attaching the adaptors to our DNA fragment, we take the samples off the robot deck onto a bench.
Because we are sharing those benches with a lot of people in the lab they need to remain very tidy and clean,
so we have divided the space with tape and labels so that we know exactly where things are.
The samples are now ready for PCR amplification and during this process we have to heat the sample to a high temperature.
To avoid evaporation we seal the plates with a very tight seal.
PCR amplification has to be done in a different lab to avoid cross contamination
and we pass the sample through a special hatch between those two labs.
Each lab has different colours of lab coats to make sure that we are not contaminating samples between the labs.
We then take the samples and put them in a PCR machine that is able to amplify the DNA.
The DNA samples are now ready for sequencing and in order to be loaded on the sequencer, we need to remove the seal.
Now that's quite a tricky step, despite the fact that it looks very simple and no robot can do it.
It has to be done by hand to avoid splashes between the samples, which would lead to cross contamination.
The samples are then put on a flow cell, loaded onto the sequencer and the sequencing run can start.
During a run we can check on the monitor of each sequencer, the quality of the data being created
and check that everything is working fine on the sequencer.
When a sequencing run is finished the data is transferred to a data centre,which is a huge cluster of computers.
The last stage for our pipelines team is to check that we have produced enough data and of good quality
and when that last check is done, the researchers that initially requested the sequencing are able to access the data in the cluster.
I really like working in the DNA pipelines because it uses a lot of different skills.
I studied chemistry and then I worked in a biophysics lab, so that's why I particularly like it.
It's always exciting and never boring.