The future of genomic medicine has arrived in Australia
Media Release: 15 January 2014
The transformation of medicine by human genome sequencing has moved closer following the announcement today that Sydney’s Garvan Institute of Medical Research is one of the first in the world to acquire machines that can sequence a whole human genome at a base cost below $US1,0001.
This will accelerate medical research and provide widespread medical benefits, with significantly lower health costs, through early prevention and more targeted treatments.
Speaking at the JP Morgan 32nd Annual Healthcare Conference in San Francisco this morning, Illumina2 CEO Jay Flatley introduced the HiSeq X Ten Sequencing System that enables large-scale sequencing for population disease studies. (See the Illumina media release here.)
Added Flatley,”We approached the Garvan Institute due to its strength in the analysis and interpretation of genomic data, and its close affiliation with St Vincent’s Hospital3. The HiSeq X Ten is a dramatic technology advance that will enable researchers at the Garvan Institute to undertake studies of unprecedented scale.”
With the generous support of the Kinghorn Foundation4, Garvan has purchased the Illumina HiSeq X Ten Sequencing System, capable of sequencing around 350 genomes a week, or 18,000 a year. Garvan’s acquisition will allow a massive increase in human genome sequencing capacity in Australia.
“I believe we have reached a tipping point where genome sequencing has become achievable on a broad scale,” said Professor John Mattick, Executive Director of Garvan.
“Just over a decade ago it cost over a billion dollars to sequence the first human genome. Illumina’s new system makes it possible to address the pressing clinical needs of the thousands of people in Australia with genetic diseases and the tens of thousands diagnosed with cancer each year. We are delighted to work with Illumina to access the HiSeq X Ten which is the only platform to make this scale of sequencing a cost-effective reality.”
“We will start by using our new system for large-scale research projects and for problem-dependent diagnostic purposes, specifically the routine analysis of cancer biopsies and people with genetic disorders. We will also begin to analyse the genomes of people suffering from other conditions, such as diabetes and Parkinson’s disease,” said Professor Mattick.
“I anticipate Garvan will serve as a genomics hub for Australia and possibly the region. The initiative must be undertaken at a national level – and in collaboration with international partners, as it will need massive global databases to support interpretation of the data. We look forward to working with our partners in other states, as well as State and Federal governments, to develop a national alliance for delivering genomic medicine in Australia.”
“We recognise there are many issues yet to be addressed, and protocols to be developed, but it is widely expected that genomic information will progressively inform and ultimately transform medicine and health.”
“Community and clinical education will be a vital part of the process, and we’ll work closely with clinicians on how to commission, use and interpret data,” added Mattick.
“At the same time, outcomes of global research will populate databases, and the clinical interpretation will be done by analytical engines that synthesise vast amounts of information.”
Associate Professor Marcel Dinger, Head of Clinical Genomics at Garvan and leader of the bioinformatics team charged with interpreting and managing data, said “Generating DNA sequences will be less of an issue than analysing them in a way that is meaningful to clinicians, so we are putting a lot of effort into transforming the primary data into clinical grade reports.”
“It is an enormous task, one that can only be undertaken by a leading-edge research institute with a mission to bring research advances rapidly to patients. It will also enable us to partner with similar efforts internationally.”
“Establishing a genome analysis facility5 requires many dedicated resources including skilled technical and computational staff, sophisticated computing infrastructure and support, huge databases, and robotics.”
“The real power of sequencing comes from volume. It provides the interpretative power that comes from being able to compare each newly sequenced genome with tens of thousands of other genomes, and pinpoint the relevant variations,” said Dr Dinger.
Dinger had his own genome sequenced recently, alerting him to a real problem he can now avert, “In my case, whole genome sequencing revealed a likely sensitivity to a commonly used general anaesthetic. I would want that in my electronic health records, and if I were ever in hospital, it would be clear to the anaesthetist that they should use a different formulation.”
Professor Mattick expects that genomic sequencing will become widely available for personal health management in the near future.
“With the advice of their physician, people will be able to avoid adverse drug reactions, understand and reduce their risk of diabetes, stroke or other conditions, and generally optimise their health futures,” he said.
“As a result, we will see a revolution in individual and public health, as well as health economics, with enormous impact on national well-being and prosperity.”
1. The base cost for sequencing a whole human genome (roughly 6,000,000,000 units of information, or ‘base pairs’) with the Illumina HiSeq X Ten Sequencing System will be less than $US1000 when the system is working at capacity. This figure includes neither the cost of obtaining samples nor the analysis and interpretation of the data, which are still very labour-intensive.
2. Illumina, Inc. is an American company that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function.
3. Garvan and St Vincent’s Hospital jointly run The Kinghorn Cancer Centre. The centre combines the scientific and medical expertise of both partners to provide a personalised medicine approach to the treatment and care of patients. The Garvan Institute and Kinghorn Cancer Centre form part of the St Vincent’s Research Precinct, the largest medical research precinct in the state of New South Wales.
4. The Kinghorn Foundation was established by John and Jill Kinghorn in 2005 with an initial donation of $5 million. This was augmented by a further donation of $295 million in 2007 from the sale of Mr Kinghorn’s interests in RAMS Home Loans to bring the capital base of the Foundation to $300 million. The Foundation distributes approximately $15 million each year to Australian registered charities. Its policy is to distribute not less than 5 per cent of its capital base each year.
5. In 2012, with the support of The Kinghorn Foundation, Garvan established the Kinghorn Centre for Clinical Genomics, Australia’s first purpose-built facility for undertaking clinical grade genomic sequencing and large-scale research projects. The centre is in the process of seeking NATA-accreditation, which will allow clinicians to sequence genomes for diagnostic and therapeutic purposes.
What is a genome?
A genome is the complete set of genetic information we inherit from our parents, contained in a DNA molecule that is roughly 2 metres long and located in every cell of our body.
What is the difference between genetics and genomics?
Genetics focuses on specific genes, or sections of DNA, while genomics (and genome sequencing) looks at the structure of the whole genome, including the DNA sequence.
What are clinical genomics and genomic medicine?
Clinical genomics is the use of genome sequencing to inform patient diagnosis and care.
Genomic medicine is patient diagnosis and treatment based on information about a person’s entire DNA sequence.
What is DNA sequencing?
DNA sequencing is a laboratory technique used to determine the sequence of units or bases (A, C, G, and T) in a DNA molecule. Sequencing methods have changed over time; Illumina’s machines use complex chemistry and high-resolution optics to determine the sequence.
The DNA sequence is a series of letters – As, Cs, Gs, and Ts – that represent the order of base pairs in a person’s DNA. The sequence of a human genome is around 3,000 million letters. As each person inherits one copy of their chromosomes from their mother and another from their father, there are technically 6,000 million letters to read and interpret.
In a sequencing laboratory, machines break the DNA up into manageable segments and read the order of the DNA bases or letters. Computers are then used to compare the DNA sequence with other sequences to locate the differences or variants.
Some useful information can be found here:
Who will have their genomes sequenced by Garvan?
The Kinghorn Centre for Clinical Genomics (KCCG) will sequence large cohorts of people for research purposes, as well as referred patients for clinical diagnostic purposes. The most immediate demand for the clinical use of this facility is expected to be diagnosis of monogenic disease and ‘stratification’ of cancer and other complex diseases - such as diabetes - to provide informed advice and to identify the most effective treatment options.
All human research studies undertaken at KCCG will be overseen by a Human Research Ethics Committee (HREC). HRECs review research proposals involving human participants to ensure that they are ethically acceptable and in accordance with relevant standards and guidelines.
KCCG is seeking NATA (National Association of Testing Authorities) accreditation to sequence genomes in a medical context, for specific applications requested by and reported to a registered health professional. One of the requirements of this accreditation is that the laboratory cannot offer genome sequencing directly to consumers.
Garvan will collaborate with other research institutes, clinicians, hospitals and health networks on population-scale genomics research in Australia and the Asia-Pacific region. Today, knowledge of the human genome is far from complete, and large numbers of genomes are required to identify the range of genetic variants that contribute to disease and disease susceptibility