Using big data to manage big genetics
At the Melbourne healthXL day, held at the Royal Children’s Hospital on the 22nd February 2018, the second session was titled Precision Medicine and Genomics – how can we improve population health using personal genomics?
The guest speakers came from the four main areas that are needed to to bring precision medicine and genomics to the hospital bedside:
- International research
- Clinical practice
- Big data and AI
They were Andrew Sinclair, Marcel Dinger, Cameron Bean and John Pearson.
The massive amount of data created by genetics study
The world’s largest public catalogue of human variation and genotype data is the 1000 Genomes Project, an international project that ran between 2008 and 2015.
Key findings from the 1000 Genomes Project
- Scientists found double the amount of human genetic variation than expected. This includes structural variants, where one or more copies of a gene were deleted, inserted, duplicated or inverted. They found more than 200 genes, any of which can be entirely missing in any one individual. In many instances there are ‘hotspots’ in the human genome that are prone to structural changes.
- Scientists estimate that each person’s genome contains between three and four million genomic variants, which are specific changes in DNA sequence.
- So much big data was generated by the research that it has now reached 200 terabytes. As few researchers have the computing power to use it, the 1000 genomes project is currently hosted on Amazon Web Servers cloud.
The information uncovered by this large international project is slowly being transformed into more accurate diagnosis and treatments for patients. Sick children will be a major beneficiary of this big data.
A study published in 2004 on admissions to a pediatric hospital in Cleveland, Ohio…” revealed that an underlying disorder with a significant genetic component was found in 71% of the admitted children.”
Tranforming this data into clinical treatments
Professor Andrew Sinclair is a scientist with training in human molecular genetics and genomics. He also executive Director of Victorian Clinical Genetics Services at the Royal Children’s Hospital, where he works on a project helping to uncover genetic diseases in sick children.
Andrew points out the need to use the genetic data in a practical way. He believes scientists need to focus on people who actually present with a disease, not just doing academic research.
‘ I think most of the projects around the world have been driven really by the technology itself. What we are looking to do is to drive it from a clinician and patient perspective.’ Putting genes into healthcare
‘ …it’s really by doing things, getting hands-on experience themselves for clinicians, not just clinical geneticists but cardiologists, neurologists, oncologists, actually understanding the sequence and how it relates to real patients in front of them.’ Putting genes into
Andrew is involved with a project with Melbourne Genomics, that has been recruiting patients for genomic tests at the same times as they are undergoing standard medical treatments at the Royal Children’s Hospital.
Five main areas of study are:
- Developmental childhood conditions
- Peripheral neuropathies
- Acute myeloid leukaemia
- Bowel cancer
He points out that many children were presenting to hospital with a broad range of symptoms and no clear diagnosis could be given.
‘A lot of these kids were a mystery’.
Genetic testing has led to a massive increase in diagnosis, from 20% to 50%. This translates into far more accurate treatments and clearer information given to parents.
However Andrew warned that the jump between academic research and clinical practice is a huge one.
Stepping into the gap is a myriad of private companies, bringing genetic testing into the lives of everyday people.
Australian companies providing affordable solutions
Marcel Dinger is a serial entrepreneur, with a PhD in biochemistry and molecular biology.
He has previously established and developed three highly profitable businesses, a software company that produced DNA sequence analysis software, an information company that licensed databases and a web hosting company.
He is currently the Chief Executive Officer of Genome.One. The company launched in July 2006.
This company offers Australians their first opportunity will be able to have their whole genome sequenced. People are able to screen all 20,000 genes at once and detect a genetic predisposition for a wide range of cancers, heart conditions and other diseases.
The cost is $6400, not refundable by Medicare.
People have a physical health assessment from a GP, with blood, urine and saliva samples taken. The testing takes about 12 weeks to complete and include consultations with a genetic counsellor.
They would also be seen by a genetic counsellor who outlines the patient’s potential risks of 31 cancers, 13 heart conditions and five other inherited conditions.
They will also get details of potential responses to more than 200 medications such as antidepressants, painkillers and anaesthetics.
Children with high risk cancer are also able to receive genetic sequencing, thanks to a $3.2 million fund established by the Lions Club.
“Genetic information provides an entirely new dimension to understand your health, but its value is best realised in the context of other health data.”
Roughly five to ten percent of people tested will discover they carried a genetic variation that put them at increased risk of one of the conditions the service tests for.
However this does not necessarily mean that they will develop the condition. It means they have a higher risk than the average person. They will be given information on how to reduce their risks.
The genome sequencing technology was developed by the Garvan Institute. It took four years to translate into a commercial venture.
Since launching, Dr Dinger said the biggest challenge had been educating Doctors, the health bureaucracy and the public about such new technology.
“You’re dealing with a lot of guidelines made to fit a different technological environment to the one we have today…”
Genome.One is a wholly owned subsidiary of the Garvan Institute of Medical Research. The company partners with organisations across Australia and the world with a focus in personal health genomics and big data sets for governments and hospitals.
All this data requires very special software to sort, catalogue, analyze and make sense of it.
Cameron Bean also attended the panel. He works at Max Kelsen, a Queensland company that specialises in analytics and software engineering.
“GenomiQa have the ability to benchmark different sequencing providers against each other. The result is more information and better choices.”
Cameron points to a dramatic drop in the cost of the genomic sequencing, and the need to ensure that quality is retained, as this technology becomes more commoditised.
Companies they work with include QIMR Berghofer, the former Queensland Institute of Medical Research and IBM’s medical research group Watson.
The big data industry has a symbiotic relationship with genomics. The only way to make sense of the vast amount of data coming from massive data sets like the 1000 Genomes Project, is using artificial intelligence and machine learning.
Max Kelsen also has a partnership with GenomiQa. GenomiQa is a start-up company originating from QIMR Berghofer Medical Research Institute’s SEEDBox® initiative (Scientific Exploitation and Entrepreneurial Development). GenomiQa will offer hospitals, clinicians and companies high-quality analysis of data from whole genome sequencing.
John Pearson is an engineer, computer scientist and co-founder of GenomiQa.
It’s a long journey, from the genetic testing of 2,504 individuals across 26 populations, to terabytes of data and trillions of DNA base pairs, analyzed by artificial intelligence and machine learning, assessed by international research projects, translated into hundreds of commercial ventures and finally, more accurate medical diagnosis and treatments.
But that’s what it takes to bring the power of genetics to the hospital bedside.
The Burden of Genetic Disease on Inpatient Care in a Children’s Hospital – Am J Hum Genet.
© Wikihospitals April 2018