NEW YORK – Genomics data analysis firm Simplify Genomics emerged from stealth mode last month, launching an automated variant interpretation platform for clinical whole-genome analysis and reporting.
A spinoff of personalized health company Human Longevity (HLI), Simplify Genomics is currently focusing on the concierge medicine market by providing clinical whole-genome reports for disease prevention.
"The concierge and longevity [medicine] market is getting bigger and bigger and is ripe for disruption," said Travis Lacey, Simplify Genomics cofounder and CEO. "We are now commercializing our whole-genome clinical report into that market."
According to Lacey, who joined HLI in 2017 and previously served in senior executive roles at the company, Simplify Genomics spun off from HLI around the beginning of 2022 turning HLI's genomics reporting and research division into a standalone business.
One important asset the startup inherited from HLI is an automated whole-genomic analysis and reporting engine that can help turn raw sequencing data into clinical reports. "[I]nstead of just supporting [HLI’s] longevity clinic, there is so much broader application for that technology," Lacey said.
The firm stayed in development mode since the spinoff optimizing the analysis platform, he added, leading to the launch last month of what it now branded as the Smart Genome platform.
Simplify Genomics currently operates its whole-genome analysis platform within its CLIA-certified and CAP-accredited laboratory and offers clinical reports to clinicians as a service. Lacey noted that the company’s offering is physician-mediated and not direct to consumers.
After ordering a report, a clinician’s office receives a blood sample collection kit from the company. After a patient provides a sample, it is shipped to Simplify Genomics’ contract clinical lab for whole-genome sequencing. After sequencing, the raw data are transferred back to Simplify Genomics through a secure portal for analysis.
Currently, the firm's analysis platform is validated for data generated on the Illumina NovaSeq platform, but Lacey said the company can "easily validate" the pipeline for other sequencing technologies.
It charges $1,250 to $1,500 for the initial report, Lacey said, which includes a one-time sequencing cost for the clinical lab. After that, every follow-up report is priced at $300 to $500, he added.
While Simplify Genomics currently involves a contract lab for sequencing, Lacey said the company is "lab agnostic" and happy to work with any clinical lab that is CAP-accredited and CLIA-certified, if the client chooses to submit their own raw sequencing data for analysis.
Leveraging the automated analysis platform, which has been used to annotate over 1.5 million variants, the company produces a clinical whole-genome report for each customer that covers about 2,000 genes. It includes clinical insights about hereditary monogenic diseases, polygenic risk, and pharmacogenomics, as well as nutrition and wellness traits, he added.
In terms of variant types, Lacey said the platform is currently validated for SNPs and indels, but the company plans to further validate it this year for larger genomics aberrations such as structural variants and copy number variations.
In the end, Simplify Genomics’ clinical lab director will double-check and sign off the report, which is then returned to the ordering clinician. The company also has genetic counseling services available to physicians and their clients through a partner firm, Lacey noted.
Currently, the stated turnaround time for Simplify Genomics’ service, from sample to report, is around 30 days, he said. However, the time frame includes the wait time for batching at the clinical sequencing lab to help minimize production costs. Once the company receives the raw data, the analysis turnaround time is "a matter of days," Lacey noted.
Besides the report, the company also offers clinicians a user-friendly search engine to help explore relevant clinical phenotypes and other genomic information that does not make it into the report. According to Lacey, the search engine, which is linked to major public variant databases such as ClinVar and the Human Gene Mutation Database (HGMD), is another major asset the company received from HLI.
Also underpinning the company’s analysis platform and search engine is a database of 35,000 human genomes with associated clinical information, which the company obtained from HLI as part of the spinoff, Lacey said. Individuals contributing these data have been de-identified and were consented to have their data used, he said. They include genomes that HLI sequenced for its pharmaceutical contracts as well as healthy individuals it analyzed through the longevity clinic.
Simplify Genomics is not the only company in the market that aims to offer automated whole-genome reporting at scale. Fabric Genomics, for example, has developed its AI-driven GEM platform to help prioritize and rank variants based on their match to a patient's phenotype. The company has partnered with the Broad Institute, which has been offering a sample-to-report clinical whole-genome sequencing service for patients at $1,000 per sample.
Additionally, bioinformatics solutions firm Golden Helix is also offering a suite of automated analysis tools for next-generation sequencing data, including VaSeq, which promises to provide streamlined variant annotation for gene panels, exomes, and whole genomes.
Lacey said one competitive advantage of his firm's platform is that it is highly automated for variant calling. "If you have a variant scientist spend one to two hours per report, it is impossible to scale," he said. "We have automated the process so when it gets downstream to a variant scientist, they don't have to spend a lot of time with the report." Additionally, he said the company’s search engine is another differentiating factor.
Furthermore, while many companies are focusing on disease applications, Lacey said Simplify Genomics is "hyperfocused" on the concierge health market. The goal for the company is to continue to provide analysis services to clients, including HLI’s longevity clinic, in order to "get to cash flow positive as quickly as possible," he said.
At the time of its spinoff, Simplify Genomics received an investment of undisclosed size from HLI and some of its board members, according to Lacey. So far, the company has generated several million dollars in revenues, doing about 150 reports a month, he said, adding that it is also in the midst of "a small" financing round, though he did not disclose the anticipated amount.
The company, based in San Diego, currently has around 10 full-time employees, including business experts, bioinformaticians, software engineers, genomics scientists, and a lab director, Lacey noted.
As Simplify Genomics continues to evolve, it plans to deploy its platform as a software package, Lacey said.
"Ultimately, we want to put this technology and this end-to-end solution in the hands of other people," he said. "We would like to have [our platform] as a software package that someone can use to do their own reporting."