Situation
A research institute set out to investigate rare DNA elements, non-canonical DNA fragments that exist outside of standard chromosomal sequences. These structures are increasingly recognized for their potential roles in gene regulation, genome stability, and disease-related processes.
The study faced several hurdles. Data came from both short-read (Illumina) and long-read (Oxford Nanopore) sequencing platforms.* Samples spanned both human and model organisms. Integrating these diverse datasets, filtering out technical artifacts, and generating a framework for cross-condition comparison required computational expertise beyond what was available in-house. They turned to Bridge Informatics (BI) for help.
*Want to learn more about when to use Illumina short reads versus Oxford Nanopore long reads? Explore our deep dive into the strengths of each platform and how they complement each other in modern genomics research.
Approach
The central question was clear: How can rare DNA elements be reliably identified, annotated, and connected to functional outcomes such as transcriptional activity?
To address this, we designed a multi-stage analytical strategy:
Multi-platform Assembly
Illumina short-read and Nanopore long-read datasets were combined. Rigorous quality control was applied to minimize artifacts and ensure assemblies reflected true biological signals.
Annotation Pipelines
Rare DNA elements were annotated against known genomic features, including coding and non-coding regions. This step distinguished high-confidence elements from background noise.
Integration with RNA-seq
RNA-seq reads were aligned to the rare DNA assemblies. This allowed us to determine which elements were transcriptionally active and to identify sequence motifs enriched under specific experimental conditions.
Comparative Frameworks
Cross-sample analyses highlighted both conserved and condition-specific DNA elements. These comparisons provided insight into when and under what biological contexts these rare structures emerge.
All workflows were deployed in a reproducible, containerized computing environment. This ensured consistency across analyses and scalability to additional datasets.
Results
Within one month, the institute received:
High-confidence assemblies: Curated FASTA files representing rare DNA elements filtered for technical noise.
Functional associations: Annotation tables linking elements to overlapping coding regions or demonstrating transcriptional activity.
Motif enrichment: Identification of conserved sequence motifs, offering hypotheses for mechanisms of origin and regulation.
Visualization outputs: Heatmaps, motif plots, and pile-up tracks, enabling rapid exploration of the results and incorporation into ongoing research.
Conclusion
This project transformed raw and heterogeneous sequencing data into interpretable biological findings. The discovery of transcriptionally active rare DNA elements, along with conserved motifs, deepened the institute’s understanding of genome dynamics. These results also provided a foundation for future studies and a publication.
If your team is ready to extract meaningful signals from complex genomic datasets, Bridge Informatics can help. Let’s build the workflows that turn your next discovery into impact. Click here to schedule a free introductory call with a member of our team.