It was only one week to the day after Francisco Marchi, Ph.D., ’25, completed his doctoral degree from the University of Florida College of Pharmacy that he launched Alma Genomics, a cloud-based platform that provides timely, state-of-the-art analysis of blood cancer-related tumors using precision medicine and machine-learning techniques.
The former trainee in the lab of Jatinder Lamba, Ph.D., associate dean for research and graduate education and a professor of pharmacotherapy and translational research in the UF College of Pharmacy, wasted no time embarking on this business venture, his swiftness matched only by the urgency of the disease he aims to tackle.
According to the National Foundation for Cancer Research, every three minutes, one American is diagnosed with blood cancer, and more than 55,000 Americans die each year from blood cancers like leukemia and myeloma. Marchi said these deaths can result from the misdiagnosis and incorrect profiling of aggressive tumors, which require immediate treatment.
“Imagine yourself or your loved one in a hospital waiting room, waiting to learn the diagnosis of a tumor. Every minute that passes is horrendous and full of suffering and uncertainty,” Marchi said. “Our technology at Alma Genomics uses genomic and epigenomic sequencing data to give blood cancer patients their correct diagnoses. It’s a race against time, so we want to do this fast and accurately.”
The need for speed
During Marchi’s training at the UF College of Pharmacy, he and Lamba spearheaded the development of the Acute Leukemia Methylome Atlas, or ALMA, a tool that can match patients to 27 leukemia subtypes as defined by the World Health Organization by mapping specific tags in DNA known as methylation patterns across 3,300 leukemia samples.
Lamba has been working on DNA methylation patterns in leukemia for several years through a National Cancer Institute-funded grant award. By extracting and sequencing a patient’s DNA, the tool accelerates the time that patients wait for a tumor diagnosis from about a week to within a business day. Marchi likens the ALMA to the sorting hat from the Harry Potter children’s book series, which sorted students into different schoolhouses based on their characteristics.
“When a patient presents with a new tumor, its characteristics are analyzed against hundreds of thousands of data points representing other patients’ tumors. The ALMA identifies matches and similarities, providing an accurate diagnosis, and quickly. It also has the capacity for therapy prediction, so the clinician has treatment plan suggestions, as well as the evidence to enroll that patient in clinical trials,” Marchi explained. “This allows the clinician to focus on making patients feel heard and understood, which is the goal.”
Galvanized by the prospect of using machine learning to accelerate the diagnosis of blood cancers, 16 institutes around the world have joined Lamba in moving this research forward under the umbrella of the American Consortium of Epigenomics in Leukemia and Lymphoma. With a patent currently in the nationalization phase, the ALMA stands to evolve the standard of care for patients with acute leukemia and other blood cancers, and it’s already being utilized within a molecular pathology lab at UF.
Lamba said ALMA’s translation from a research tool into a clinical diagnostic service was accelerated thanks to a $220,000 gift from the Harry T. Mangurian, Jr. Foundation via the UF Health Cancer Institute. This assistance equipped the molecular pathology lab to accelerate the clinical implementation of ALMAseq-based diagnostics as a laboratory developed test. Utilizing a standardized workflow combining sample preparation, sequencing, computational analysis, quality control and clinical interpretation, ALMAseq is designed to provide comprehensive diagnostic information within 48-60 hours, helping clinicians select the best treatments sooner.
“Every day matters when treating acute leukemia,” Lamba said. “With ALMA, our goal is to replace a multi-step diagnostic process that takes weeks with a rapid, DNA methylation–based approach that can accurately identify leukemia subtypes and provide clinicians with actionable information sooner. By shortening the time from diagnosis to the right treatment, we hope to reduce complications, improve outcomes and ease the burden on patients, families and healthcare systems.”
Currently, Vivek Shastri, Ph.D., a research assistant professor, and Elizabeth Do, a postbaccalaureate student in Lamba’s research group, are working closely with the UF Health Molecular Pathology Lab and Marchi on refining and applying the rapid diagnosis pipeline in real-time for patients across several leukemia subtypes, including the rare ones.
In a heartbeat
Lamba serves as founding scientific advisor for Alma Genomics, a vehicle she said will allow the ALMA and its related research to experience a wider application across hospitals and healthcare institutes.
“In collaboration with institutions across the United States and internationally, we are working to standardize the methodology and clinical application of DNA methylation classification,” Lamba said. “By combining this technology with adaptive sampling to enhance genomic detection — and ultimately integrating the test into patients’ electronic health records — we aim to enable rapid, accurate leukemia diagnosis and facilitate its transition into the standard of care.”
Alma Genomics is a live, research use-only, HIPAA-compliant tool that can be accessed by anyone with an institutional email account. After completing clinical trials over the next year or two, Marchi intends the tool to be available for clinical use. When it comes to Marchi’s motivation for this work, he credits his own experiences in the clinic — from the points of view of both a provider and a patient.
“To be very honest, what drives me is the feeling of an emotional debt. All the young people I’ve met who did nothing to deserve an aggressive tumor, and ultimately lost their lives to it, have given me a duty to try to do something about it and act with the urgency this disease demands,” Marchi said.
“When I was 19, during my first semester at Gainesville’s Santa Fe College, I developed an aggressive blood cancer lymphoma. The great people in Unit 42 of the pediatric hematology/oncology wing of UF Health Shands Hospital cured me, so that’s why I turned my career into this,” he said. “Alma Genomics stands to stop blood cancer-related deaths and reduce extreme suffering by way of accurate, fast and accessible diagnosis and treatment plans using genomics, epigenomics and the latest technologies for machine learning and sequencing.”