By Monica Heger
This story was originally published Jan. 9.
Researchers at the Medical College of Wisconsin are developing a sequencing-based pharmacogenomics panel on the Ion Torrent PGM, Clinical Sequencing News has learned.
The panel will sequence 35 genes known to predict response to a range of drugs. The MCW team is currently validating the panel and plans to offer it from its CLIA-certified and CAP-accredited laboratory by the summer.
While there are around 100 genes known to affect drug response, Ulrich Broeckel, a professor of pediatrics at MCW, said the team decided to begin with a smaller subset of genes that are associated with a broad range of drugs.
"We looked at those genes that are key to a broad set of drugs … and whether there are genetic markers that are relevant that we already offer testing for," he said. Broeckel and his colleagues currently offer a pharmacogenetic test based on SNP arrays and PCR.
Genes in the sequencing panel include CYP2D6, which affects response to tamoxifen, many antidepressants, and opiates; CYP2C19, which is relevant for antidepressants, antiepileptics, and some drugs for coronary heart disease; and VKORC1, which affects warfarin response.
The team is using Agilent SureSelect for sequence capture and has been using the PGM 316 chip but recently began testing the 318 chip. It is sequencing the entire length of each gene as well as two to three kilobases upstream and downstream. In total, the panel targets 1.4 megabase pairs and sequences to between 60- and 100-fold coverage.
Currently, Broeckel and his team are in the midst of validating the panel on clinical samples as well as samples that have been sequenced as part of the 1000 Genomes Project.
So far, the MCW researchers have tested the panel on two sets of 1000 Genomes trios and around 10 clinical samples for which they had both Illumina sequence data and array data.
In an analysis of three clinical samples, the team found 1,300 variants, including "all the major, relevant SNPs," and the results were 99.5 percent concordant with Illumina sequencing and array data, Broeckel said.
The analysis also found, however, that sequencing depth and the software used for analysis can affect call quality.
The researchers also found several areas that were problematic for all three platforms. For example, the genes included in the panel have a "high presence of pseudogenes," which is challenging for all the platforms, Broeckel said. Additionally, areas of high sequence similarity and copy number variations are trickier to call than SNPs, regardless of the platform used.
For example, there is a pseudogene immediately adjacent to CYP2D6 and in some cases there are duplications that involve fusions between CYP2D6 and the pseudogene.
"For clinical purposes, this needs very careful evaluation," he said. "We're just in the process of evaluating how this will actually look in a sequence capture."
While validating the sequencing assay for CNVs, pseudo-genes, and other tricky areas has proven to be challenging, Broeckel said that sequencing technology would ultimately prove to be more effective in these areas than other approaches, such as arrays and qPCR. "Being able to sequence the full gene, we'll have a better possibility of finding functional variants," he said.
The group currently provides PGx testing for St. Jude's Hospital, which is in the midst of implementing a program to incorporate that genetic information into patients' electronic medical records.
Broeckel said that once the sequencing-based panel is validated, he plans to migrate St. Jude's PGx testing to the new platform. He added that he would also be open to similar collaborations with other groups.
"There's already a lot of infrastructure, knowledge, and clinical reporting from the SNP [array] data," he said, which will make the transition to sequencing relatively easy.
The main challenge in converting from arrays to sequencing will be "dealing with the additional variants that can be identified," he said.
The team has not yet set a price for the panel and Broeckel said it will depend somewhat on the volume of tests that are ordered. He noted that the panel would almost certainly be less expensive for cases where multiple single-gene tests would otherwise be necessary.
"A lot of patients, particularly at St. Jude's, get a variety of drugs, so would need more than just one [single-gene] test," he said.
Additionally, because insurance companies already reimburse for many of these single-gene tests, it should become "pretty clear" for payors that reimbursing for a multi-gene panel is more cost-effective than multiple single-gene tests, said Broeckel.
Have topics you'd like to see covered by Clinical Sequencing News? Contact the editor at mheger [at] genomeweb [.] com.