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The $1000 genome, what does it mean for patients?


HiSeq X

The HiSeq X Ten is capable of sequencing five human genomes a day, Illumina claims

The ability to sequence a human genome for just $1,000 has arrived, a US genetics company has announced.

San Diego-based Illumina says it is to release a new sequencing machine that can deliver five genomes in a day.

The race to unlock a human’s genetic blueprint for $1,000 has been underway for more than a decade.

The Archon X Prize had offered $10m to the first team that hit this target or came closest, until the contest was cancelled in August 2013.

The term was thought up as a symbolic landmark that would, in theory, light the fires of a long-anticipated revolution in personalised medicine.

Understanding how genes influence disease could lead to better treatments for patients.

The HiSeq X Ten high throughput genetic sequencing machine was announced at the annual JP Morgan Healthcare Conference in San Francisco this week.

In his presentation at the meeting, Illumina’s chief executive Jay Flatley said the HiSeq X Ten would improve on the scanning speed of its predecessor by a factor of six. This would offer the ability to sequence five whole human genomes in a single day, Bio-IT World reported.

He said the $1m sequencers (sold in a minimum of 10 units) would be able to deliver a genome for just under $1,000 (£610; 735 euros), consistent with calculations the National Human Genome Research Institute uses to estimate sequencing costs.

In his presentation, Mr Flatley said the world was “entering the supersonic age of genomics”.

Eric Lander, founding director of the Broad Institute, announced as one of the first customers, described this development as “tremendously exciting” and heralded it as “an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine”.

“The HiSeq X Ten should give us the ability to analyse complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”

On his blog, Mick Watson, a computational biologist at the University of Edinburgh, checked the maths behind Illumina’s claims for the HiSeq X Ten.

“I think they might be right in claiming the $1000 genome – if you do 18,000 human genomes per year for four years on each X Ten system. That’s a lot of human genomes though,” he wrote.

The term “$1,000 genome” was coined in 2001 at a closed scientific meeting to discuss the future of biomedical research. A year later, it became the subject of a symposium in Boston hosted by entrepreneur and genome pioneer Dr Craig Venter.

In the last few years, the decline in the cost of genome sequencing had outpaced the famous Moore’s Law, which describes how computer processors double in complexity every two years. Nevertheless, the target proved difficult to reach, even with large sums of money on offer.

Dr Venter’s foundation offered $500,000 to the first team able to realise $1,000 genome sequencing.

This sum was subsequently rolled into the Archon X Prize competition which was to have awarded $10m to successful scientists. However, this contest was cancelled in August 2013 because the effort had, in the words of X Prize co-founder Peter Diamandis, been “outpaced by innovation”.

“What we realised is that genome sequencing technology is plummeting in cost and increasing in speed independent of our competition,” he explained in a column for the Huffington Post.

However, this breakthrough is, as scientists would say, ‘necessary but not sufficient’ to deliver the health benefits of genomics. As Illumina Director of Scientific Research Sean Humphray observes on the company blog, making genomes really useful requires ‘annotation, leveraging public databases using tools’ – that is, analysis to identify the individual sequence variants within that sequence and their potential scientific relevance.

Turning a genome sequence into a clinically useful diagnostic report requires even further interpretation, selecting from the many millions of individual variants only those of most probable and significant relevance to that person’s health, and delivering this information in a meaningful format for normal clinicians to understand and use. Illumina themselves have provided a potential vision of the future in the form of their personal genome sequence interface, MyGenome – delivered in glorious technicolour on an  individual iPad – although a more utilitarian product would no doubt fit the bill for many health services.

Many more innovations and developments are still needed, not least in computing and bioinformatics, in order to move us from $1,000 genome to $1,000 clinical genome – but there’s little doubt that we can get there eventually.

Download Public Health Genomics briefing note for more information on the steps involved in whole genome analysis and clinical interpretation.

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ASCO Issues New Recommendations for Family History Taking in Oncology Setting


In new recommendations published in the Journal of Clinical Oncology, ASCO stated that family history of cancer in first- and second-degree relatives is critical to assessing for familial risk in patients with cancer. ASCO’s recommendations are the first to focus on family history taking specifically in oncology to help determine patients’ personal genetic risk for cancer.

Although the current standard in medical genetics, genetic counseling and research settings is a comprehensive recording of three generations, following a review of all available evidence, ASCO concluded that reported family history is most accurate in close relatives and loses accuracy in more distant relatives.

“Genetic factors are a key component of precision medicine because they can unlock important information that can help an oncologist determine the best course of individualized treatment, “ said ASCO President Clifford A. Hudis, MD, FACP. “An adequate family history is key to identifying those patients whose cancer may be associated with inherited genetic factors.”

For each relative with cancer, ASCO recommends recording type of primary cancer(s), age at diagnosis, lineage (maternal and/or paternal), ethnicity and results of any cancer genetic testing in any relative. Family history information should be recorded at a patient’s initial visit to the oncology provider, and be reassessed if new information about family members diagnosed with cancer becomes available.

Addressing Barriers to Implementation

In a separate analysis of data from ASCO’s Quality Oncology Practice Initiative QOPI®, results showed that of breast and colorectal patients with a first degree family history of cancer, 79.8 percent were documented in their chart and for those with a second degree family history of cancer, 64.6 percent were documented. These results document a greater opportunity for oncologists to maximize the potential of family history taking, and set a baseline for further quality improvement efforts.

To address barriers to implementation, ASCO recommends increasing patient education and awareness on the importance of a family history and the significance of a cancer risk assessment for patients and their family. Cancer.Net, ASCO’s patient website, will offer an article and infographic, as well as a cancer family questionnaire patients can download.

ASCO also notes that the increasing use of electronic health records (EHRs) can help providers overcome challenges to adopting these new recommendations.

ASCO will be providing a comprehensive update of cancer genetics including family history assessment at its annual meeting. For more information about ASCO’s prevention and genetics work, please click here.

 

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