By Julia Karow
Sistemas Genómicos of Spain has released a dozen sequencing-based diagnostic gene panels on the SOLiD platform to assess a range of cardiac conditions and is working on other diagnostic tests for familial cancers.
The clinical diagnostic and research service provider, based in the Valencia Technology Park in Paterna, joins a number of other companies and institutions that also provide diagnostic tests for inherited conditions on next-generation sequencing platforms, including GeneDx, Emory University, Ambry Genetics, and ARUP Laboratories.
The company was founded in 1998 as a research sequencing service provider and initially focused on applications in agriculture and food production. In 2003, it branched out into biomedicine and in 2005 acquired the Institut de Genética Mèdica i Molecular, a company specializing in medical genetics and prenatal diagnostics. A year later, Sistemas founded the Instituto Valenciano de Genética, an outpatient clinic focused on genetic diagnostics and genetic counseling.
Sistemas says it is the first company to offer diagnostic gene panels for cardiology on the SOLiD platform. Until recently, the firm offered the tests only to selected partners, but after presenting them at a meeting of cardiologists in Madrid last week, it is gearing up to promote them worldwide, except in the US.
According to the company, next-gen sequencing has reached the point where "it is feasible to resequence a large number of genes of a given patient" at a cost that is equivalent to sequencing two to three genes by Sanger sequencing. It also maintains that next-gen sequencing is superior to microarrays because the technique discovers both known and unknown mutations.
Sistemas currently offers cardiology gene panels for 12 conditions on SOLiD, including four types of cardiomyopathy, aortic aneurism-related conditions, Brugada syndrome, long and short QT syndrome, atrial fibrillation, catecholaminergic polymorphic ventricular tachycardia, familial arrhythmia, and risk of sudden death.
The number of genes assessed in each panel ranges from three for aortic aneurism-related conditions to 72 for sudden death risk, and the tests are priced between €2,900 ($4,000) and €3,500 ($4,800).
The turnaround time from sample acceptance to report delivery is currently 90 days. Though the firm can actually complete the tests in two months, it added another three weeks for collecting 10 samples, which it needs for each SOLiD run to make the tests cost-effective. As sample volumes go up in the next few months, the turnaround time will likely go down, according to Blas Marco, the company's CEO.
Marco said that the company decided to start with cardiology gene panels because there is a medical need in this area. In addition, the company is working on oncology panels that it plans to launch shortly. On its website, it mentions a test for familial breast cancer that sequences on the SOLiD a panel of 15 genes, including BRCA1 and BRCA2; a test for non-polyposic hereditary colorectal cancer that sequences seven genes; a test for Li Fraumeni syndrome that sequences two genes; and a test for diffuse gastric cancer that sequences two genes.
In addition, the company offers custom sequencing panels, as well as "affordable" exome sequencing, according to promotional material. In collaboration with a group of researchers, the company just identified a mutation underlying an undisclosed genetic disease by exome sequencing and plans to publish the results soon.
Sistemas is one of the earliest users of the SOLiD — it became a certified service provider for the platform in 2008 — and chose to develop and run the tests on that platform because it said it offers "the highest accuracy rate of the raw data ... among all next-generation sequencing platforms" and "nearly perfect" accuracy at 15-fold coverage. Nevertheless, the company currently still confirms all mutations by Sanger sequencing. "We expect that when more operational experience is acquired, confirmation of mutations may not be necessary anymore," said David García, the firm's alliance manager. "But for the time being, we prefer to be 100 percent sure."
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The company also offers single-gene diagnostic tests and small testing panels that use Sanger sequencing alone.
For the next-gen sequencing tests, Sistemas uses an undisclosed capture technology to enrich the DNA of the genes to be sequenced on SOLiD. The tests detect SNPs, small deletions of up to 11 nucleotides, and small insertions of up to 3 nucleotides. Doctors receive a report with a full biological and clinical interpretation of the results, "no different from those generated using conventional sequencing," according to the firm.
The company's lab already has several certifications in Europe and elsewhere but currently lacks CLIA certification, which it expects to obtain by the end of the year, according to Marco. That is the reason it currently offers its next-gen sequencing panels anywhere except the US, he said, though it is looking to partner with a US lab to introduce its panels in that market, as well.
Before the end of the year, Sistemas also plans to purchase two additional sequencers, in addition to its single SOLiD 4, but has not yet decided which platform. García said the company is also "very excited" about new sequencing platforms coming online that promise to reduce the turnaround time, such as the Life Tech Ion Torrent or the Illumina MiSeq. "We are actually very excited with all these kinds of technologies," he said. "Nowadays, there is fierce competition between many companies and many competing technologies. And of course, that benefits us end users, and it benefits the patients."
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