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Hurdles ahead for whole genome sequencing

17 March 2014
Appeared in BioNews 746

Genome sequencing technology struggles to capture the complete genome accurately and reliably, a small study has found.

Many obstacles need to be overcome before whole genome sequencing (WGS), a DNA-evaluating technique that detects genetic disease risks, can be used routinely in clinics, say the researchers.

'We need to be very honest about what we can and cannot do at this point in time', said Dr Euan Ashley, co-author of the research and associate professor of medicine at Stanford University, California. 'It's clear that if we sequence enough cases, we can change someone's life. But with this opportunity comes the responsibility to do this right'.

To observe how WGS technique works in a real-life clinical setting, the researchers analysed the whole genomes of 12 healthy volunteers, and noted of the accuracy of the sequencing, the time and cost it took to analyse the genome data manually, and the clinical action prompted by the findings.

Two genome sequencing service providers were used for the research: Illumina and Complete Genomics, both based in California. Researchers found that both providers failed to capture ten to 19 percent of genes associated with inherited diseases, making it easy to miss out harmful mutations. Both providers were not always consistent, with the tests disagreeing on around two-thirds of gene mutations involving the addition or deletion of DNA.

Nevertheless, the researchers found the cost of WGS to be lower than expected. Dr Ashley estimated the total cost of sequencing the genome of one patient to be at US $11,000, with follow-up testing costing less than $1,000.

The study also found that interpreting the full genome data requires a significant amount of manpower and is time-consuming. Researchers spent about one hour interpreting each genome variant found, bringing the total cost to $15,000 per patient.

The WGS technique, if successful, could potentially be used routinely to detect risks of unusual, rare genetic diseases, and predict how patients might respond to treatments. Companies now aim to offer WGS services for $1,000 (reported in BioNews 738), but this pilot research shows that more work needs to be done before it can be implemented in the clinic.

'Our hope is that the identification of specific hurdles will allow researchers in this field to focus their efforts on overcoming them to make this technique clinically useful', said Dr Ashley.

'There are many steps that have to be worked out to ensure that we gain the most health-care benefit', said Dr William Gregory Feero of Maine Dartmouth Family Medicine Residency in an editorial accompanying the research.

Challenges remain before docs use whole-genome sequencing
Reuters |  11 March 2014
Clinical Application of Whole-Genome Sequencing: Proceed With Care
Journal of the American Medical Association |  12 March 2014
Clinical Interpretation and Implications of Whole-Genome Sequencing
Journal of the American Medical Association |  12 March 2014
Genome sequencing stumbles towards the clinic
Nature News |  11 March 2014
Whole-Genome Growing Pains
The Scientist |  11 March 2014
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