By Monica Heger
This study was originally published Feb. 7.
In a step toward making personalized medicine available to UK citizens through the National Health Service, researchers at the University of Manchester have developed a next-generation sequencing-based test for inherited blindness.
The targeted sequencing-based assay sequences the exons of 105 genes and is available now to all NHS patients who have been referred to their local clinical genetics service. It can detect inherited forms of retinal degeneration including isolated progressive retinal degeneration, Leber congenital amaurosis, achromatopsia, Usher syndrome, and Bardet-Biedl syndrome.
"This is one of the first examples of a next-gen sequencing assay being offered by the NHS and certainly one of the first with such a large coverage of genes," Graeme Black, a professor genetics and opthamology at the University of Manchester, who led the team that developed the test, told Clinical Sequencing News.
While this is one of the first next-gen sequencing-based tests to be covered by the NHS, the UK government is also funding a project to bring targeted-sequencing based cancer tests to market as part of a broad personalized medicine initiative (CSN 6/21/2011).
The blindness test runs on Life Technologies' SOLiD 5500 platform, and the team is using Agilent's SureSelect capture array to target 1,874 exons from 105 genes. It will be offered through an accredited clinical laboratory at Central Manchester University Hospital's department of genetic medicine.
All clinically significant results will be confirmed with Sanger sequencing, and then a report will be generated for the patient's physician.
The test costs £897 ($1,418), which is more expensive than existing genetic tests for blindness, but it screens for more genes. For instance, a two-gene test for X-linked retinal pigmentosis costs between £700 and £750 ($1,100 to $1,186), while a test for dominant retinal pigmentosis is £450 ($712) for a set of genes that are most commonly associated with the disorder and another £400 ($633) for a second set of genes
Retinal dystrophy is a broad term for a "heterogeneous group of conditions" caused by defects in many different genes, said Black. The currently available tests are only relevant for about one-third of patients with retinal dystrophy and, of those, only about two-thirds receive a molecular diagnosis, he said.
Because the next-gen-based assay screens so many more genes, it should be applicable to nearly all patients with retinal dystrophy. Furthermore, Black said he expects that it could find the molecular cause of the disease in more than 60 percent of patients.
"That's an enormous step-change in our ability to find pathogenic variants and also in the NHS's ability to offer testing to many more patients and give them an answer back," he said.
In a pilot study involving 50 patients, the team used the test to identify pathogenic variants in around 45 percent of the subjects, but Black said he expects the performance to improve with future iterations of the test. For example, the assay tested in the pilot did not cover a portion of a gene on the X chromosome that harbors mutations responsible for X-linked retinitis pigmentosa.
That area, the RPGR gene, will likely remain difficult for calling variants because it is highly repetitive, but Black said that improvements to paired-end sequencing and bioinformatics will help and should "boost numbers significantly" so that the test can provide a diagnosis for around 60 percent of patients, Black said.
Black said that the two-thirds of retinal dystrophy patients for whom current tests are ineffective either have a recessive condition or sporadic disease with no family history. "While patients with no family history are likely to have recessive disease, it's possible that it is in fact X-linked or dominant. But, until now, we have not been able prove it."
For those patients in particular, the next-gen assay could help pinpoint a diagnosis that would affect patient management, he said.
Already, among the patients that have been tested, "we've found new dominant mutations and X-linked mutations," Black said. "So you're able to determine many more of the unexpected results and go beyond averages to more clear-cut approaches to diagnosis."
Even though there is no cure for retinal dystrophy, a molecular diagnosis can still affect patient management, said Black. For instance, he said, in the case of patients with a suspected recessive disorder, it is important to rule out an X-linked cause because that may impact a patient's decision about having children.
Additionally, the test may identify whether a patient is a carrier for other retinal dystrophies.
One recessive disorder, Bardet-Biedl syndrome, is associated not only with retinal dystrophy, but also polydactyly, developmental disorders, and obesity. Patients with that syndrome are also recommended to have annual screenings for kidney problems. Black said that among the patients that have been screened so far, some have been found to have variants in the same genes that are associated with Bardet-Biedl syndrome. While the consequences of those variants need to be more fully studied, it suggests "potentially, that screening for kidney problems in those patients may be worthwhile," said Black.
For another subtype of retinal dystrophy caused by mutations to the gene RPE65, gene therapy has demonstrated treatment potential. So, as specific gene therapy treatments become available, a molecular diagnosis will be important for "knowing whether that's relevant to you or not" and will inform whether a patient is "eligible for entering into a clinical trial," Black said.
Black anticipates that the test will identify three classes of patients: those in which a pathogenic variant is identified, those that have variants with uncertain pathogenicity, and those with no significant variants.
For those patients with variants of unknown pathogenicity, results will be returned to the physician with a report explaining that the variants have unknown significance, but these variants will not be verified by Sanger sequencing.
Patient data will also be stored, so as more research is done on those variants or as the bioinformatic tools improve, physicians can go back to the reports and re-analyze the results.
Going forward, Black said that the "test will not stay static." Genes are being discovered on a regular basis and "the assay will be updated in a step-wise progression," he said.
He said that the team is also aiming to develop sequencing-based tests for a range of other disorders, first with monogenic conditions, and then with more common diseases, and has a number of different sequencing platforms available.
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