# Novel Technologies to Isolate and Analyze Extrachromosomal DNAs for Diagnostic Applications

> **NIH NIH R44** · PHINOMICS INC. · 2023 · $331,563

## Abstract

SUMMARY/ABSTRACT
Extrachromosomal circular DNA (eccDNA) elements are physically and topologically distinct components of
eukaryotic genomes that can contribute to intercellular copy-number variation, environmental adaptations, and
functional genomic diversity. Recently, high-throughput sequencing has made extensive genomic mapping of
eccDNA sequences possible. Notwithstanding this major advance, information regarding biogenesis of these
circular DNAs and causal connections between these DNA elements and human pathologies, remains extremely
limited. The sequences, structure, and biological properties of eccDNA molecules constitute a major knowledge
gap, information about which can lead to strategies targeting disease-specific eccDNA structure and function.
eccDNAs represent a large range of molecules (~100 bp to >1 Mbp) and coexist with eccDNAs found in normal
somatic cells; isolating and characterizing different classes of eccDNA comes with their own host of unique
challenges. To address these knowledge gaps, methods that can directly interrogate all circular DNA species in
the cell are critically needed.
In this FastTrack SBIR proposal, Phinomics, Inc. is developing is developing an innovative urine-based test that
will isolate eccDNA molecules in an intact state suitable for next-generation sequencing and epigenetic
characterization, and is complemented by a suite of biophysical and novel bioinformatic methods to identify and
define these molecules. In Phase I, Phinomics will 1) Demonstrate the capability of Phinomics’ proprietary
technology to isolate comprehensive/unbiased eccDNA repertoires (circulomes) from human cell lines; and 2)
Demonstrate the capability of Phinomics’ technology to robustly sequence, map, assemble, and informatically
profile the isolated circulome. Upon meeting Phase I Go/No-Go milestones, in Phase II Phinomics will 3) Validate
Phinomics’ technology as a molecular platform for bladder cancer diagnostic applications; 4) Extend the
application of Phinomics’ technologies to biological fluid samples; and 5) Develop a PCR test to detect circular
DNA species in non-muscle invasive bladder cancer to enable CLIA certification.
Preliminary data has begun to illuminate the circulome in normal somatic cell lines and tissues, glioblastoma
tumor samples, and plasma, potentiating the use of eccDNA as a valuable biomarker in both solid- and liquid-
biopsy applications. Surveillance based on eccDNA biomarkers is aimed at a minimally invasive strategy to
determine the immune response to therapies, predict recurrence likelihood, and monitor residual disease.

## Key facts

- **NIH application ID:** 10759774
- **Project number:** 1R44GM151907-01
- **Recipient organization:** PHINOMICS INC.
- **Principal Investigator:** Massa Shoura
- **Activity code:** R44 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $331,563
- **Award type:** 1
- **Project period:** 2023-08-01 → 2024-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10759774

## Citation

> US National Institutes of Health, RePORTER application 10759774, Novel Technologies to Isolate and Analyze Extrachromosomal DNAs for Diagnostic Applications (1R44GM151907-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10759774. Licensed CC0.

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