GenomeWeb - June 2023

NEW YORK – Almaden Genomics, a company with roots in an IBM Research laboratory in Silicon Valley, launched last October with functional software, a lot of engineers, but not much of a sales and marketing apparatus. Now, it is catching up on the sales and marketing side.

Dallas-based Almaden brought in Ellen Gordon as VP and head of business development last month. "My first focus is on the sales team, figuring out what we're doing, what's working, and where we need to make changes," Gordon said. Then, she will turn more of her attention to partnership opportunities.

CEO David Gascoigne has been on board since January. "My focus in the first [few] months has really been the commercial side, building brand awareness, building a sales organization, focusing on the product and the budget strategy and commercial strategy," he said at last month's Bio-IT World Conference & Expo in Boston. "From a technology perspective, we're probably way ahead of other startups."

Almaden is backed by Catalyze Dallas, a firm that purchases technology assets from Fortune 100 companies to accelerate commercialization. Catalyze Dallas, which is funded by wealthy individuals looking for new investments, bought the intellectual property that became Almaden from IBM last September, its first investment in life sciences. Terms were not disclosed.

Accompanying the launch of Almaden was the introduction of g.nome®, a cloud-based software platform meant to improve genomic research and discovery by simplifying the process of building and managing bioinformatics workflows.

Though g.nome was developed for the IBM Cloud environment, Almaden migrated the software to Amazon Web Services earlier this year since that is what a majority of the fledgling company's users prefer, according to Almaden CSO Mark Kunitomi. He said that g.nome can still run on the IBM Cloud, and Gascoigne described the technology as "cloud-agnostic," so it would not be too difficult to add support for the Google Cloud Platform or Microsoft's Azure.

Almaden is initially focusing its sales efforts in the US, though UK native Gascoigne said that he was at the LSX World Congress in London last month "exploring avenues in Europe." He said that g.nome should be available in Europe before the end of the year once the company makes sure it complies with the General Data Protection Regulation (GDPR) and other EU and UK requirements.

Gascoigne wants the sales team to collect feedback from current and prospective customers about g.nome to inform future product development. "I'm building something for the future over the next three to five years, so the feedback we're getting from [sales] is vitally important in terms of future-state investments," he said.

Gascoigne talked about four pillars of Almaden's development strategy in that time frame: building use cases to demonstrate the efficacy of the software, optimizing user workflows with g.nome, managing vast quantities of data, and producing insights derived from analytics.

Last month, Almaden Genomics announced that it was partnering with OmicsEdge on a service to analyze patient genomic data in clinical trials. OmicsEdge, a part of personalized health software company SelfDecode that offers algorithms for polygenic risk scoring, genetic imputation, and genome compression, will incorporate g.nome into its drug discovery service.

Kunitomi said that the company is trying to differentiate itself in a crowded marketplace with its tools that allow users to build and modify workflows with minimal programming. g.nome is a "low-code" or "no-code" platform aimed at scientists and clinicians who lack bioinformatics expertise. 

No-code development is a philosophy in the world of web development that allows people without specific programming knowledge to build software via graphical user interfaces. Startups LatchBio and Watershed Informatics are among those following this approach.

The field got more crowded in May when Google introduced Google Cloud Multiomics Suite and a companion product for drug discovery called Target and Lead Identification Suite. Shortly thereafter, AWS debuted a collection of "pre-built" workflows, support for graphical processing units (GPUs), direct data uploads through an application programming interface (API), and streamlined variant querying and analysis for its nascent Amazon Omics service.

Kunitomi said that g.nome has the same kind of prepackaged workflows but is designed to be easier to modify.

The firm also recently introduced integration with Jupyter notebooks. "In addition to that, we're … creating templated Jupyter notebooks that assist people in their ability to analyze their data and build meaningful and interpretable visualizations," Kunitomi said.

Kunitomi called prepackaged workflows "a fantastic first start" to get users up and running quickly. But such technology needs to be easily customizable.

"It's that combination of ease of use with that flexibility," he said. "Our system allows you to change any given tool within a workflow and replace it."

The g.nome platform is built to be expandable as new bioinformatics tools and new scientific knowledge come out, according to Kunitomi. While not quite drag-and-drop, g.nome can be updated by pointing to applications in Docker containers and then adding some minimal documentation before the system walks the user through a series of questions to set parameters for invoking the app, he explained.

Gascoigne said that artificial intelligence is on the company's roadmap for future development.

Analytics in g.nome now tend to be case-specific, according to Kunitomi. "One thing that we're doing a lot of work towards is single-cell analytics, but that's not something that's mature enough for the marketplace at this point," he said.

Something the company will have to decide is whether to self-develop analytics technology or add through partnerships. Gascoigne said that "it would not be sensible" for Almaden to become a data provider, so the firm is in discussions with potential suppliers of genomic data.

"Those are the types of things that we're working through, where to invest directly and where to partner," he said.

Last month, Almaden created an advisory board. Inaugural members include Samir Courdy, senior VP for informatics at City of Hope Cancer Center; Rayna Herman, chief commercial officer of Eversana; Graham Hughes, a former executive at SAS Analytics and GE Healthcare; Adrian Lee, director of the Institute of Precision Medicine at the University of Pittsburgh and UPMC; and David Miller, operating partner of private equity firm GHO Capital and a former senior VP of global market access at Biogen.

Gascoigne said that the firm has a few paying customers now, ahead of the initial timetable for commercializing the technology, as Almaden is still running and learning from pilots.

Some pilots were conducted when the technology was still under IBM Research, but Kunitomi said that the spinoff allowed the firm to scale up its programs much faster. "It's a lot easier when you're an independent company to be able to make agreements and be flexible and agile," he said.

Some of the pilots and partnerships are meant to create "application-specific" but customizable workflows for common use cases, particularly in oncology, according to Kunitomi.

One pilot is being run by David Corey, a computational professor of biochemistry and pharmacology at University of Texas Southwestern Medical Center in Dallas. He spoke at Bio-IT World about how g.nome helped with research in molecular biology in a lab that does not have computational biologists.

"Things should be drag-and-drop and everything should be transparent, intuitive, and above anything, a pipeline needs to enable independent use by us," he said.

Corey noted that there are no approved microRNA therapeutics in the US. Some of that has to do with the fact that so many of the thousands of papers on miRNA and cancer published each year lack proper controls and provide little insight into binding mechanisms, he said.

"We need an efficient workflow to analyze the effect of increasing cell density on gene expression. We need to know how that increasing cell density affects splicing. And it's essential that we prioritize genes accurately before time-consuming experimental bench science," Corey explained.

Speaking just two months after first meeting Almaden and displaying observations no more than three weeks old at the time, Corey discussed how a g.nome pipeline had helped him whittle the list of potential miRNA binding sites to about 200 candidates. He will soon be looking to isolate chromatin.

g.nome helps make experiments reproducible, he said.

Since g.nome is a low-code/no-code software platform, Almaden is targeting smaller biotech and biopharmaceutical companies that are short on informatics expertise. "It's companies where speed, ease, [and] getting to insights faster is a greater focus," Gascoigne said.

Kunitomi said that g.nome can also make bioinformaticians more efficient by automating some of their work, thus enabling them to serve more biologists. "Bioinformaticians are always overwhelmed," he said.

Gascoigne said that the company has enough working capital for at least the rest of this year. "I'd say we're good in the short term," he said. "We will do a more significant fundraise at some stage," though he did not elaborate on the timing, citing the need to make some strategic decisions.


Originally published on genomeweb.com