Genomic testing is very new for healthcare, medicine and pathology. It's become possible now to read the DNA sequence of the entire individual's genetic material.
Genetic and genomic testing is a type of pathology medical test, and all pathology tests in Australia have to be part of an accredited certification process which is done to international standards. Part of that is that genomic testing has to be analytically correct, evidence based, and it has to have clinical utility which means it has to be able to assist the doctor treat the patient.
Capturing genomic data
The first step in genomic testing is sequencing. That's capturing a person's DNA. And to do that you need state of the art equipment, you need skilled staff, it's a very complicated process and it needs to be automated so that we can get thousands of samples through the lab.
A sequencing machine is basically a high resolution microscope combined with some complicated chemistry that allows you to capture the linear order of bases within our DNA. Each of these machines can sequence a whole human genome within a few days, and that generates terabytes of data.
Processing genomic data
The data that comes off the sequencing machines can't be used as is, it needs to be analysed and processed and also annotated before it's useful for a genomicist or a clinician. The data is aligned and compared to a reference genome and that helps us to find variations in the genome. These variations are what makes us different, but they can also be disease causing. It's very important to follow international standards for these sort of processes, to make sure that the data is handled in a secure fashion.
Analysing genomic data
To be able to analyse a genome we have to take a very large data set of about 3 billion data points and narrow that down to maybe one or two. So it's a very big scale problem and we need a lot of specialist individuals along the way to be able to solve that. What's really important to us is to be able to link the patient's clinical symptoms to specific gene variants in their genome. My role is to take tens of thousands of variants and try to understand which one or two of those variants is important for an individual's health or diagnosis.
Reporting genomic information
My role as a pathologist is to supervise the laboratory, to make sure it carries out the testing in an appropriate way and to the appropriate standards. So we'll be taking the scientific evidence we have, we'll be looking at the genetic variants we find, and we'll be expressing that in a synoptic or summary report in terms that the doctor will be able to understand so that they can apply this result to help their patient. We have medical specialists, we have scientific specialists, and we have IT specialists and all of them contribute to the final medical report of a genomic analysis. We're only at the beginning of the explosion of scientific knowledge that is emerging about the relationship between genes and disease.
To make sense of the genomic data that’s already been captured, we have to be able to link the patient’s clinical information to the genetic variation in their genome.
We have to at the starting point have a good clinical referral, and then once the genome is sequenced, take a very large set of data and whittle it down to the one or two variants in that data set that are relevant for the individual who has had their genome sequenced.
For some individuals we can make a diagnosis where one hasn’t been made before, and for other individuals we’re actually just finding the genetic underpinning to their disease for a diagnosis that’s already known, and both of these have huge value in terms of understanding their disease better, what might happen to them in the future, what things their physician needs to look out for.
Many people are looking to get a copy of their genomic data. If we’re going to engage with people in a meaningful way, giving them back their genomic data is one way of doing that.
Once you’ve had your genome sequenced, it has lifelong use or utility in that you can go back to the genome that’s been sequenced, and analyse it through the course of a person’s life to understand if they might have an increased risk of developing certain genetic diseases, or if they should develop a disease, what is the disease they’ve got, does it have a genetic basis, and how is it best treated.