In the wake of a diagnostic sequencing milestone that garnered national headlines, the Medical College of Wisconsin has implemented a comprehensive framework intended to guide future clinical sequencing projects within its own walls and beyond.
Late last year, a team of MCW researchers published a paper in Genetics in Medicine that described the use of exome sequencing to provide a diagnosis for a 6-year-old boy with an extreme form of inflammatory bowel disease that had stumped his doctors.
Whole-exome sequencing on the Roche 454 FLX revealed a mutation in the XIAP gene, which was not previously associated with bowel disease, but had been implicated in a severe blood disorder that is curable through bone marrow transplantation. Based in part on this information, the MCW team recommended the transplant, which was performed last July. The child, Nicholas Volker, responded well and there has been no return of the bowel disease.
The project — among the first to use sequencing to successfully determine the appropriate therapy for a patient — attracted a great deal of attention from the national press and established MCW as a pioneer in the field of genome-wide diagnostic sequencing. And, according to Howard Jacob, director of human and molecular genetics at MCW, the group has no intentions of being a "one hit wonder" when it comes to future applications of high-throughput sequencing in the clinical setting.
Spurred by the Volker project, Jacob and his colleagues have spent the last year and a half developing a broad program to cover the range of issues that surround diagnostic sequencing — from patient selection to analysis and interpretation, consent and data-sharing policies, and reimbursement.
The framework has come in handy, since the team is seeing quite a bit of interest from other doctors at the Children's Hospital of Wisconsin. Since the program was formally launched in October, Jacob and his colleagues have fielded between six and eight requests per month, for a total of more than 30 to date. Six of those projects have been approved and five patients have been sequenced. Diseases that the program has studied so far include severe combined immune deficiency, hypoplastic left heart syndrome, and primary immune deficiencies.
"We have not gone out and advertised this as a service," Jacob told Clinical Sequencing News. "This is all by word of mouth — physician-to-physician contact — which suggests that there is going to be a huge number of people who are going to be interested in this."
Jacob acknowledged that it is still early days for genome-wide diagnostic sequencing, and that there are many unanswered questions regarding the best model for high-throughput sequencing in the clinical setting. However, he said that MCW's philosophy is that these questions won't be answered without taking action.
"We can use some of this information to help us clinically today," he said. "Are there problems with the data and the reference genome? Yes. Do we need to be cautious about how we deploy this in the clinic? Yes. Do we need to be responsible about how we do this? Yes. But can we use this information in the clinic today as another laboratory value? Yes."
Jacob said that his team is planning on publishing the framework it has developed in order to share its experiences with the broader community. They are drafting a paper now with plans to submit it for publication in the next month or so.
"What we'd really like is to enable other people to be able to do this," he said. "If nothing else, it will enable people to get their head around the fact that it is doable. It's not fun, it's not easy, but it's doable."
Make it Actionable
Among the most important aspects of the MCW clinical sequencing infrastructure is the criteria it has put in place for deciding which patients should be sequenced.
Cases must be nominated by two physicians, and MCW has established a committee that determines which ones will be approved. The committee includes the hospital's chief medical officer, the chair of the hospital ethics committee, an ethicist, a geneticist, a genetic counselor, a genomics expert, and three physicians that are knowledgeable about the individual case or disease.
Jacob said that the primary consideration for any case is whether is the results are likely to be actionable. "The most important step is to ensure the test is clinically useful for the individual patient," he said in a talk outlining the framework at the Future of Genomic Medicine conference hosted by the Scripps Translational Science Institute earlier this month.
"The goal of the committee, then, is to take what the clinicians know — all the assays that they've tried, what they think it might be — and then challenge them to say, 'OK, if you had this piece of information, what would you do with it?'"
He explained in a follow-up interview with CSN that actionable information can range from information on a specific therapeutic strategy, to a more general understanding of the course of treatment for a child, to helping families decide whether to have additional children.
Cases can be approved or denied, but there is a third category, dubbed the "parking lot," for cases in which the committee and the physicians believe sequencing will be useful, but that are deemed to be lower priority than those that are approved.
Jacob noted that the program is currently limited to cases that are believed to be monogenic diseases "because that gives us an opportunity to actually do something with it."
In addition, he stressed that approved cases must lend themselves to medical decision-making — "not scientific interest or generalizable knowledge."
Finally, cases will only be approved if all other clinical testing options have been exhausted. Jacob stressed that MCW has adopted sequencing as a means to "assist and enhance" medical decision-making. "It is not to make the diagnosis," he said, "it is to help the clinician with the diagnosis. We don't make a decision on a variant in the sequence."
The ability of a patient to pay is not a consideration for selection in the MCW clinical sequencing program.
Jacob said that the hospital submits each approved case to an insurer, "and if it's not funded by the insurance company, it's paid for by the hospital."
In late February, an undisclosed insurer informed MCW that it would authorize payment for sequencing in situations where the cost of routine genetic testing would exceed the price of whole-genome sequencing.
Jacob said that MCW has to provide detailed cost evidence for all these cases, but noted that "it's not an unreasonable request."
As for the current costs of sequencing under the program, Jacob said that it can vary, depending on the amount of analysis time that is required.
"Generating the sequence, that doesn't change. But the analysis can have a big difference on what the cost is," he said.
'A Big Jump'
Following its success with exome sequencing on the 454 platform, MCW decided to move into whole-genome sequencing on an Illumina HiSeq for all future studies.
Both the 454 and Illumina sequencers have been CAP- and CLIA-certified — a process that Jacob described as "a nightmare." As an example, he noted in his talk at the Future of Genomic Medicine conference that just one step in the clinical sequencing pipeline — Sanger sequencing validation — requires 547 pages of documentation.
Jacob acknowledged that the data-analysis challenges of moving from exome sequencing to whole-genome sequencing are considerable, but told CSN that those challenges were exactly why his team decided to leap into the whole-genome arena sooner rather than later.
"When you go from 18,000 variants, like what you typically find in an exome, to 3 million [variants in a whole genome], that's a big jump. And therefore you need to be in a position to make that jump. And I think the only way to do that is to do it."
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The MCW team developed a CAP- and CLIA-certified software package for the 454 system, called Carpe Novo, that was specifically developed to help clinical geneticists analyze genome sequence data. Since bringing in the HiSeq, the researchers have developed a new version of the software, called Illumina Carpe Novo, which relies on clinicians' existing knowledge to filter through the list of potential variants.
For example, the physician may have a list of specific genes that would serve as a good starting point. If the causative variant isn't found in that list, then the analysis could extend to possible pathways that relate to the phenotype.
"You try to use a decision process to whittle down the number of variants that the clinician is investigating," Jacob said. "The physician has a series of queries that they can decide what they want to prioritize the gene list on. That's really one of the key features — having the ability to make choices with the data you want to look at, instead of just handing someone 3 million variants and saying, 'Have fun.'"
Much of the data that supports Carpe Novo is drawn from publicly available research databases that are subject to change. Jacob said that the MCW team imports this data and then "freezes" it for the validated system, which must undergo proficiency testing regularly under CLIA guidelines. MCW updates the system every six months with new data and revalidates it using several whole genomes with known variants.
"We know what the calls are," he said. "The first pass is to make sure we're finding everything that we found before" In addition, they "spike" the dataset with new gene variants that the physician doesn't know about in order to see if the software can identify them.
Jacob said that the turnaround time for analysis is approximately four weeks per genome, though he and his colleagues are working to reduce that. Ideally, he said, "what you'd like is to have somebody come in and get them sequenced, get the data turned around, and then inform the decision while they're in the clinic."
'A One-Way Street'
The MCW team has implemented a "template" that provides a step-by-step script for the consent process for each case. Patients are evaluated by an MD geneticist, a genetic counselor builds a pedigree out to four generations, and there are "multiple" consenting counseling sessions, Jacob said.
Jacob said that consent is currently an "iterative" process and that the template "will continue to evolve as we go forward with this process."
In addition, as part of the consenting process, parents are asked what data they want returned. "From the very beginning, we discuss this relative to their child and them and their families," Jacob said. As part of this process, parents are educated about the potential implications of certain types of variants as well as genetic concepts such as pleiotropy, in which a single gene can influence many different phenotypic traits.
"We really have to spend time making them understand that, recognizing full and well that the choice to have knowledge is a one-way street," Jacob said. "Once you provide knowledge, you can't go backwards from that."
Once parents sign an initial contract, they are able to change their minds up until the results of the sequencing are disclosed, he said.
So far, of the six cases that have been approved, "we have a wide range of interest — from wanting everything back to only [wanting information] related to [the particular] disease," said Jacob.
Returnable data includes incidental findings and secondary results identified during the sequencing, "with some exceptions," Jacob said.
Regardless of what data is shared with patients and families, MCW has decided that it will include in a patient's electronic medical record only confirmed variants that have been validated with a second methodology.
"Our institution has decided that sequence and variants are not part of the EMR," he said.
One reason for this is patient privacy. Some patients expressed concern that they didn't want insurance companies or other doctors to see the results. In addition, Jacob said, some doctors were concerned that they might be liable for interpreting genomic data included in the medical record that is not related to the initial diagnosis.
As for whether doctors can go back to a patient's genome in the future for additional analysis, "that's part of the process we're trying to sort through," Jacob said. "There are a lot of issues about how you make that choice."
Moving forward, Jacob said that he and his colleagues are interested in following up with patients and physicians who have participated in the sequencing program in order to assess how the data is being used and how people feel about the information they received.
"That whole social side is to us very important because that then helps us understand the other question, which is, 'What do you do down the road with the data?' In some sense, having these first groups go through is helping us determine how do people feel about this … That will then help inform where we're going with the process in the future."
In addition, Jacob said that his team is starting to get inquiries from doctors with adult patients and is currently extending the framework to meet that need. The program would likely remain focused on single-gene disorders for adults, though it's likely that it would also be of use in cancer because of the ability to compare the tumor and normal genomes.
As for the use of sequencing to diagnose more common diseases, "the complexity of having to make choices on those variants is quite difficult," he said.
However, he added, "I think that probably within the decade we'll start to see some application to common diseases."
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