Clinical OMICS

MAY-JUN 2019

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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www.clinicalomics.com May/June 2019 Clinical OMICs 29 in having a singular focus to get the job done and then to look at the opportunity to grow it. Other countries might have a different structure depending on the fund- ing and the government structure and so on. Is there a strength in the U.K. for the companies and organizations that existed to help with the ramp up? Bentley: Certainly we have strong presence here [in Cambridge], and a lot of IIlumina investment in the U.K. has preceded the project and has continued to grow during the project. In that sense, the foundations for building the facility to sequence genomes had a strong history before i Fast forward to the actual establishment of the sequencing facility itself at Hinxton on the Genome Campus. Our Hinxton laboratory is still a small part of Illumina; it is a model for being able to build others in the future. It shows that an efficient and self-contained organization is able to establish sequencing, and the model absolutely can be replicated in other centers, whether by Illumina or a local organization. The level of investment that was already here was tre- mendous in integrating into the research and medical community in the U.K. for a number of years before we got to start this, so that certainly benefitted us all as we established the 100,000 Genomes Project. Is there plenty of room to scale in Hinxton? Bentley: If you extrapolate our capacity where we are at the moment, 6, 7, sometimes 8,000 genomes a month, that is close to the demand that the NHS has indicated going forward. On top of that of course, the transition for the HiSeq to the NovaSeq is a significant jump in capacity, so we have the opportunity to scale substan- tially to continue to meet NHS demands. What potential roadblocks might Genomics England or the NHS encounter? Bentley: I don't see any fundamental roadblocks. I think we've done enough to know—and it's not just from Genomics England and NHS—we have seen a number of other initiatives both national and regional, in multiple countries, that are enthusiastically embracing the concept of whole genome sequencing in medicine. We have also seen tangible measurement of the value of the data in terms of accelerating diagnoses and sav- ing costs in some areas where this has been evaluated. That work will continue to grow. In rare genetic disease, the evidence is more advanced than in cancer. Cancer is perhaps a more challenging condition in terms of the mutation spectra which actu- ally lead to the disease. Nevertheless, in cancer, there is mounting evidence that whole genomes can make a difference as well. So not roadblocks, but challenges. Challenges con- verting the early evidential basis into formal structured evidence that will be required to support reimburse- ment, whether it is the U.S. reimbursement system or the NHS adding these tests to their test directory. The NHS has not commissioned all types of cancer, they have commissioned the leukemias and pediatric can- cers and sarcomas —so for every new cancer there has to be a period of evaluation before commissioning. Another challenge is that the entire medical field has to learn how to use the information. Perhaps the third one is data management. It is a large dataset. It is not an unman- ageable dataset, but we need to learn how to manage it. It is also not a trivial matter? Bentley: It is not a trivial matter. The world is gearing up to much larger genomic datasets. Whole genome sequences are at the high end of some of those data- sets, but we are learning how to handle those data. The key thing is not that you suddenly have to look at a whole genome before you can make a diagnosis. The point is that the whole genome very likely contains the answer. You didn't pick a series of sequential tests, each asking a different question. Instead, the whole genome sequence gets everything tested in one go, which is actually cost-effective, given the technology advances we have brought to the field. As a result, you have a much greater certainty the answer is in there. Finding it involves the process of interpretation, which all of us are finding out a lot more about how to do. The challenge is bringing a "big data" approach to then economically and quickly sift through the candidate causal mutation(s) to find the one or sev- eral candidates that matter to that patient. If you extrapolate our capacity where we are at the moment, 6, 7, sometimes 8,000 genomes a month, that is close to the demand that the NHS has indicated going forward."

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