NEW YORK (GenomeWeb) – Molecular diagnostics firm Genomed has developed a prophylactic whole-genome sequencing test for consumers that it is currently beta testing in the Polish market. The company, based in Warsaw, offers a variety of sequencing-based tests and genetic counseling services for inherited diseases, including BGI's NIFTY noninvasive prenatal screening test, as well as a number of research services.
The whole-genome analysis has been available to beta customers since early 2015 and currently costs PLN 11,500 ($2,900). It includes a detailed report on variants in 240 genes that have been associated with genetic diseases prevalent in the Polish and European population, including a proband's carrier status; pathogenic or likely pathogenic variants with an allele frequency of less than 5 percent in the Human Gene Mutation Database (HGMD); pharmacogenomic variants with treatment implications; and nutrigenomic variants with nutritional recommendations. Â Â
Consumers interested in ordering the whole-genome analysis must meet with a medical geneticist from Genomed for a pre-test counseling session and sign a consent form, including an agreement for the reporting of secondary findings recommended by the American Society of Medical Genetics and Genomics. They also meet with a doctor to receive their results, and have the opportunity to meet again after a number of weeks to discuss follow-up questions. Customers also receive a written report that uses easy-to-understand language.
To protect customers' privacy, Genomed stores their personal data and sequencing data separately and moves the sequence and variant files off its server after completing the analysis, storing them on discs in a safety deposit box. Customers also receive a copy of their data, including the sequencing files, on a disc or memory chip.
Genomed offers a reanalysis of the data free of charge after one year. Additional re-analyses are available for $300, and the company plans to offer this as a subscription service.
Genomed is currently working on improving the test, for example, by adding copy number variant analysis, and plans to make it more widely available in early 2017. In addition, it is working on a less expensive exome sequencing version of the test.
Marek Zagulski, Genomed's COO and one of its cofounders, told GenomeWeb this week that wanting to offer personal genomics services was the main reason he and several colleagues, all molecular biologists, founded the company in 2007.
Zagulski has been involved in genome sequencing since 1994, initially focusing on yeast genomics while working at the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences in Warsaw. In 2000, he started an academic core facility that offered Sanger sequencing and oligonucleotide synthesis services, which he said was the first such service in Poland and rapidly grew in size.
After visiting several genome sequencing centers in the US in 2007, "I convinced my colleagues from our core facility that it was time to start a company" that would focus on human genome sequencing services, including genetic disease diagnostics. He and his cofounders provided €80,000 ($90,000) in initial capital to get Genomed — which has no affiliation with companies in several other countries that bear the same name — off the ground.
In 2008, Genomed received a €450,000 investment from the MCI.BioVentures fund of MCI Capital, a Polish private equity group, allowing the company to purchase Sanger sequencing and other equipment.
Three years later, Genomed raised €700,000 in a private offering on the NewConnect stock exchange, which is owned by the Warsaw Stock Exchange and caters to small firms, mostly in biotechnology and informatics. "This helped us to further develop the company, especially the diagnostic part that became the most important part for us," said Anna Boguszewska-Chachulska, the company's CEO and cofounder, who heads the Genomed Healthcare Center, a lab which the firm founded in 2009 to offer diagnostic services, including genetic counseling services.
Today, about 70 percent of the company's business comes from clinical diagnostic and screening tests, which include more than 130 single-gene tests, gene panels for rare diseases and hereditary cancer, exome sequencing, whole-genome analysis, and NIPT. The remaining 30 percent comes from research services, including Sanger sequencing, oligo synthesis, and NGS bioinformatics. Last year, the company had €2.27 million in service revenues and made a small profit.
Prices for Genomed's tests, which are often ordered by physicians but can also be ordered directly by patients after consulting with a doctor, range from about €50 for targeted mutation analyses, €200 to €700 for Sanger single-gene tests, €500 for the NIFTY test, and €650 to €840 for NGS panels to €1,300 for clinical exome sequencing. Most of the firm's tests are paid for by patients and customers out of pocket. While the more focused tests currently provide the firm's bread and butter, "we really focus our activity now on clinical and prophylactic exome and whole-genome analysis," Boguszewska-Chachulska said.
The company, which has grown to nearly 50 employees, operates two laboratories in Warsaw: One is part of the Genomed Healthcare Center, while the other lab, which opened last year, focuses on running BGI's NIFTY test.
After initially offering the NIFTY test as a distributor, with the test being conducted in BGI's Hong Kong laboratory, Genomed transferred the test technology in house a year ago, one of a handful of European labs to do so.
What factored into the decision to adopt BGI's technology was the fact that the NIFTY test had been well validated, with more than a million tests run by BGI so far. "The NIFTY test is not very well known in the US but very popular and common around the world," Zagulski said.
Genomed currently has a "dominant position" for NIPT in Poland, he added, and is considering expanding its NIPT services to Central and Eastern European countries.
Besides Sanger sequencers, the firm operates an Illumina MiSeq and has two Thermo Fisher Scientific Ion Protons installed in its NIFTY lab. However, it decided to outsource larger sequencing projects to BGI, Macrogen, or other commercial service providers.
The firm also is in the process of applying for ISO15189 certification for its main laboratory, which Boguszewska-Chachulska said is a lengthy process. The lab is already part of the Reference Laboratories Network of the Polish Society of Human Genetics, and is registered by the Polish National Chamber of Laboratory Diagnosticians. It also has been participating for several years in quality assessment schemes by the European Molecular Quality Network and the Cystic Fibrosis Network.
In addition to its service work, Genomed has been involved in several research projects that were funded by the European Union, including the recently completed Polish Reference Genome for Genomic Diagnostics and Personalized Medicine project. For this study, which resulted in the commercially available Polish Reference Genome Database, Genomed and its collaborators sequenced the genomes of 126 healthy Polish individuals at least 90 years of age and analyzed the sequence data in conjunction with phenotypic and lifestyle data.
Variants detected in this project, which include several million novel variants, will inform Genomed's whole-genome analysis and other services going forward, helping to classify variants. "We really needed this type of database as a control population," Boguszewska-Chachulska said.
Besides developing new NGS-based tests, the company is working on projects that focus on the treatment of genetic diseases, she added.