Finnish genetic testing firm Negen has launched a pharmacogenomics panel designed to help guide
decisions in the treatment of patients with SARS-CoV-2. The Helsinki-based firm is making its panel available for free to people who have already been studied by consumer genomics services or biobanks.
CEO Kirsi Auro said the company decided to release its panel for people who have their own data because the nature of the coronavirus pandemic has led to a slowdown in the production of genotype data, and because the data provided by the company could be immediately actionable.
"We are living in quite peculiar times with the COVID-19 situation globally, and as information about the drugs used to treat infection accumulated, we realized that some of these drugs have quite significant pharmacogenomics and this information could be extremely relevant for patients, but also, of course, for hospitals, "said Auro.
"We chose to accept data that is already available because it takes time to produce new genotype data," he said. "With this data we can do the analysis quickly and the person can get the results within the day."
Some of the drugs currently being considered to treat the SARS-CoV-2 virus include chloroquine, hydroxychloroquine, a combination of lopinavir / ritonavir, and Anakinra. As Negen points out on his website, pharmacogenomic effects have been described for all of these therapies, particularly for the antimalarial drugs chloroquine and hydroxychloroquine, since those with G6PD deficiency are predisposed to hemolytic anemia.
In addition to targeting G6PD variants, the panel also targets SLCO1B1 variants, which may indicate a decreased tolerance to Lopinavir, a therapy used to treat patients with HIV, as well as an elevated risk of adverse effects. of the variants of interleukin 1 (IL1), which are associated with adverse effects in those who receive Anakinra, a drug used to treat rheumatoid arthritis.
It is unclear if any other company is offering a similar pharmacogenomics panel tailored to COVID-19 treatments in Europe at this time, although individual tests are available for different variants from a large number of players. Auro said the reason competitors might not have assembled similar panels is because it is early in the pandemic and producing new tests takes time and resources. "As a small company we are quite agile and we have the ability to direct our efforts towards something new quite quickly," said Auro. "This is what we have done."
CTO Kimmo Aro said there are smaller panels on the market for these specific variants - Invitae and 23andMe offer G6PD deficiency testing, for example - but Negen decided that given the health crisis it made sense to group them into a single panel.
"We think that as many people as possible should have this information," Aro said. "We decided to make it free for people who have their own data, as the cost to us of producing it is not great when we don't need to genotype these samples."
Negen was founded in 2016 to design genomic risk panels for the Finnish population. "We noted that the potential risk panels produced in the United States did not necessarily accurately match Finland or other populations," Auro said. The private company approach has been to start in Finland and then expand to other populations, taking this population-tailored approach.
"We wanted to be as scientific as possible to produce polygenic risk scores and combine them with unique clinical variants for different diseases and also contribute some environmental risk factors," Auro said. The company's first product was a coronary heart disease panel called Negen - Heart. It has also developed and launched a second panel for diabetes called Negen - Diabetes. A third offering, Negen - 360, combines both panels into a single product.
The company relies on custom Illumina genotype arrays to generate data about its patients. Its two stand-alone panels cost € 239 ($ 258) each, while Negen-360 sells for € 349. A panel for breast cancer is also being developed. Customers who currently do not have their data can also opt for genotyping for the new pharmacogenomics service from a saliva sample for € 179. However, given the current situation, Auro cautioned that laboratory processing has been delayed.
In terms of data submission, the company currently accepts data files from 23andMe, Ancestry, MyHeritage, and Family Tree DNA on its site. While not all chips used by these services contain the markers included in Negen's panel, they have more or less the same coverage backbone as Negen's own custom Illumina matrix. Therefore, Negen can impute the data needed to enrich it and then calculate its models. "This is something we can do outside of the COVID panel and this is part of our portfolio," Auro said.
Consumer genomics has not been unpopular in Finland, although it is dwarfed by uptake in the United States. Auro said that around 20,000 Finns have such information available out of a total population of around 6 million. People who have already studied their genotype or complete genome or sequencing of a complete exome by a biobank can also upload their data and receive results. Finland currently has a genotyping initiative through FinnGen, which aims to study the genotype of 500,000 Finns by 2023.
The company itself relies on data from the biobank to design its dashboards, so data acquisition is not a goal of the new offering, although if you intend to use customer data, you first get their permission and all the analyzed data is protected by Europeans. Genetic Data Protection Regulation, as well as national regulations.
"It has been of interest in Finland," Auro said of the new panel. "The first day it was available, we received several hundred requests [for analysis]," he said. While the company launched the Finnish trial earlier this month, it is now in the process of expanding to reach international users by making it available in English.
"We know that in Finland, the percentage that have their own whole genome data is limited," Auro said. "We wanted to expand and see how this test could be delivered to global markets." When asked if the service could help the company reach more customers with its other panels, Auro agreed. "We believe this will help us reach more international customers for our other tests," he said.