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Following Internal Pilot Program, MCW Launches Clinical Whole-Genome, Exome Testing for External Users


The Medical College of Wisconsin's Human and Molecular Genetics Center recently started offering clinical whole-genome and whole-exome sequencing tests to external physicians, after piloting diagnostic genome sequencing in house for several years.

According to David Dimmock, one of the directors of the center's CLIA-certified sequencing laboratory, theirs is the first service in the US to offer whole-genome sequencing and clinical interpretation to outside physicians. "We have a lot of experience with returning the results internally, so we now feel very comfortable offering this to external clients," he told Clinical Sequencing News.

In collaboration with the Children's Hospital of Wisconsin, the center has been providing whole-genome sequencing testing to its own patients for several years (CSN 11/1/2012).

In mid-February, the new laboratory, called Developmental and Neurogenetics Laboratory-Sequencing, or DNL-SEQ for short, started offering the WGS test externally, and the WES test two weeks later.

A distinguishing feature of the lab is that all its directors, and those signing the lab reports, are practicing physicians, Dimmock said, which helps in answering questions from ordering physicians and in providing the most relevant clinical results.

The lab decided to add the exome test after seeing "huge demand from our internal clients for a less expensive genome-wide sequencing test," he said, and most physicians currently order that test.

While he still considers whole-genome sequencing "the best test," the additional cost might not always be justified on a routine basis. "We've been surprised at how the cost of sequencing has not fallen as quickly in the last couple of years," he said.

The clinical exome is about a third of the price of the clinical whole-genome test, and a clinical exome trio is about half the price of a genome. Both tests include DNA sequencing, data analysis, data storage, variant confirmation by Sanger sequencing, and a clinical report.

Dimmock declined to provide pricing information for the tests but said his lab is "definitely cheaper than everyone else" providing clinical exome testing.

Ambry Genetics, for example, offers a clinical diagnostic exome, which includes sequencing and analysis of a trio, for about $15,000, and a first-tier exome, which includes exome sequencing of a patient and analysis of 4,000 clinically relevant genes, for $5,800.

The DNL-SEQ offers to bill insurance directly, and it expects the tests to be reimbursed similarly to other molecular tests. "We see no difference in reimbursement rates for exome or genome than we do for our standard sequencing-based tests," Dimmock said.

The lab accepts samples from within and outside the US, "from anyone who can legally send it to us," which excludes certain states, such as New York.

Physicians can order the test for any disease indication. "Anyone a physician thinks is appropriate to test we would be happy to test," Dimmock said.

The testing includes genes involved in hereditary cancer, several of which Myriad Genetics claims IP rights to (CSN 5/15/2013). Dimmock said MCW has been providing clinical whole-genome sequencing for three years now, including individuals "with questions about cancer," and Myriad has not yet told it to stop.

Right now, the majority of cases submitted are children with inherited disorders, because "pediatricians are much more willing to adopt newer technologies faster," he said, but the lab has also analyzed, and successfully diagnosed, adults.

Customers can specify the results they want returned. For example, on the ordering form, physicians can submit a list of genes they want to be analyzed exclusively, but the lab can also look at the entire exome or genome.

The lab report always includes primary results, defined as variants that are likely responsible for the patient's disorder, as well as secondary results, or incidental findings, of variants that cause childhood onset disorders where medical intervention "can prevent or decrease the effect of a disease," according to the consent form.

In addition, physicians and their patients can choose which other incidental findings they want to receive, if any. The choices are untreatable childhood disorders, such as Tay-Sachs disease; treatable adulthood disorders, for example, hereditary colon cancer; untreatable adulthood disorders, such as Alzheimer's disease; and disease carrier status.

This is a departure from guidelines issued by the American College of Medical Genetics and Genomics earlier this year, which recommended returning pathogenic variants in 57 genes related to 24 disorders, including several with onset in adulthood. The recommendations have been somewhat controversial, and several other labs have said they will not adopt them in full (see other article, this issue).

"We remain of the opinion that the patient or the parents are in the best position, after counseling, to decide what results they want back," Dimmock said. "We don't believe that the education that is required to make those decisions is excessively burdensome."

Speaking from his own clinical experience, he said that many parents of pediatric patients only want to receive results for childhood-onset but not for adult-onset treatable conditions, even if those could be important for the health of the parents.

In addition to the report, which includes primary results and secondary findings as specified, the lab provides original data electronically to physicians who request it, including information about how well specific genomic regions were covered.

The lab does not routinely fill in regions of the exome or genome that were not covered sufficiently to call variants but "we would be happy to do that if customers wanted it," Dimmock said.

So far, the diagnostic rate for both the genome and the exome test has been comparable to that of other institutions, about 20 to 25 percent, Dimmock said. However, that number represents an average of many patient groups, including those who had tested negative in other tests. In the future, he said, the lab expects subgroups of patients to have much higher diagnostic rates – for example patients with cardiomyopathy – while other groups, such as patients with unspecified neurological symptoms, will have much lower rates.

For the last several years, MCW used Illumina's CLIA laboratory for whole-genome sequencing, but the DNL-SEQ now performs all sequencing in house.

At the moment, the lab is equipped with an Illumina HiSeq 2000, a HiSeq 2500, and a MiSeq, and uses the HiSeq 2000 for both the WGS and the WES tests. To capture the exome, it uses the Agilent SureSelect XT V4 All Exon kit, and it validates pathogenic variants by Sanger sequencing on an ABI 3730.

The lab uses CarpeNovo software to annotate variants, and GapMine to identify unsequenced genome regions, both developed in house.

Its current capacity would allow it to run up to several hundred samples a month, Dimmock said.

While the center also has a Pacific Biosciences PacBio RS and a Roche 454 sequencer, it does not use these in the clinical lab right now. However, according to an internal newsletter, it is has started to optimize the PacBio system for variant confirmation and for the diagnosis of diseases that are "too difficult or complex to sequence on the short-read sequencers," including trinucleotide repeat disorders and structural variants.

The lab guarantees a 90-day turnaround time for both the WGS and the WES tests, which Dimmock said is "extremely competitive," and often provides results faster.

It also offers a priority service with a turnaround time of just over two weeks for urgent cases, which also runs on the HiSeq 2000. That turnaround time is not guaranteed, though, in case of problems with instruments or reagents.

According to Catherine Brownstein, a project manager for next-gen sequencing at Boston Children's Hospital, the DNL-SEQ is "extremely responsive" and quoted an "incredibly fast turnaround time" when she approached it about sequencing for a case that seemed urgent. She did not use the service in the end because the sample was not available, but said that "it is great knowing that there is an option for 'emergency sequencing'."

While MCW does not use the HiSeq 2500 routinely in the clinical space yet, researchers from the center said earlier this year that they are working on an ultra-fast test for critically ill patients in the neonatal intensive care unit that will run on that platform and have a turnaround time of about 40 hours (CSN 3/6/2013).

Besides offering clinical testing to external physicians, since late 2012, the DNL-SEQ has also been providing clinical sequencing and analysis services for Transgenomic's 448-gene NuclearMitome. It also conducts exome testing for an undisclosed testing firm, Dimmock said, and it provides exome and genome sequencing for research purposes.