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MCW Plans to Offer its WGS Service Externally in 2013; Aims to Build $60M Joint Facility

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The Medical College of Wisconsin is in the preliminary stages of planning a $60 million public/private partnership with the BloodCenter of Wisconsin and Froedtert Hospital in Milwaukee aimed at figuring out how to implement clinical sequencing within a mid-sized hospital system, Howard Jacob, director of MCW's Human and Molecular Genetics Center, told Clinical Sequencing News.

Additionally, it is planning to expand its whole-genome sequencing services, which it currently offers in conjunction with the Children's Hospital of Wisconsin for patients within its own hospital system, to external physicians and patients by the second quarter of 2013.

Jacob said that ever since the Nic Volker case where whole-exome sequencing was used to uncover the cause of the child's debilitating genetic disease and identify a life-saving treatment, the center has been working to put in place "a complete integrated clinic" including patient intake, data generation, data analysis, genetic counseling, data return, and clinical management (CSN 8/24/2011).

The partnership with the BloodCenter of Wisconsin and the Froedtert Hospital will aim to bring this type of care to mid-sized hospitals — "using our hospitals as a test bed and bringing in commercial partners to work with us to develop strategies, implementation, and tools," he said.

Jacob said it is important to figure out how to bring clinical sequencing into mid- and smaller-sized hospitals because over half of Americans are treated at such centers. So, part of the goal is to make sure sequencing technology and genomic medicine reaches more people.

Clinical sequencing within a smaller hospital would be different because these centers don't have the personnel or infrastructure of larger hospitals, Jacob said.

The aim is to do the bulk of the sequencing in-house, except in cases where there is not a sense of urgency, and then the center could partner with external sequencing providers.

Details as to how the center will be equipped with sequencing technology have not yet been worked out. Nor is there a time frame for when the center might be completed. "Basically, what we've done is talk about it and develop an initial business plan that is being assessed," he said.

Jacob also said that the diagnostic whole-genome sequencing program that is currently being offered by MCW and the Children's Hospital of Wisconsin only to their physicians will be expanded by the second quarter of 2013.

As part of that, the sequencing facility will be expanded, Jacob said, although he declined to provide details.

Currently, most of MCW's diagnostic sequencing is being done through Illumina's CLIA lab. But the center also has its own CLIA-certified and CAP-accredited laboratory, and when it upgrades its HiSeq 2000 to the 2500, which can sequence an entire genome in around 27 hours, Jacob said it would begin doing more of the sequencing in-house.

"If we have a very sick kid, we want to be able to do this in-house because the turnaround time is going to be faster," since samples and data won't have to be shipped back forth, he said.

Additionally, as it begins to offer the service externally, it will expand its program for conditions other than rare, undiagnosed genetic disease. Currently, whole-genome sequencing is available only as a last resort for children with rare diseases, for whom all other avenues have been explored and turned up negative.

Eventually, Jacob said he hopes to reach the point "where you sequence everyone first and ask questions later," but "I don't think it's at that point now."

Aside from children with rare genetic diseases, he said the service would be offered for "other phenotypes outside diagnostic odysseys" including some types of familial cancers or familial heart diseases.

The center is currently working with insurance companies to obtain reimbursement for the sequencing, and Jacob said that they have been successful in gaining approval and payment for about 50 percent of the cases.

He added that the current success rate for identifying the causal mutation is around 34 percent. One of the main challenges has been cases where an initial analysis of the sequence data does not turn up a definitive answer, but a list of variants of unknown significance.

It's hard at that point to say you're done, said Jacob, because the answer is likely one of those variants, but there is just enough evidence to make a definitive call.

"In some sense, you can say you're done. But, you're not really done because you're kind of waiting to see what comes," he said. "There could be more genomes sequenced, more publications, an animal study. So we end up starting to track all of that."

Already, he said, there have been cases where the initial analysis failed to provide an answer, but then a month or two later, a publication came out that enabled the team to make a diagnosis.

"We're trying to come up with a framework" for those cases, he said, where they can either be described as in a waiting mode, or still in active searching, or as having failed.

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