Rapid RNA Sequencing for Precision Oncology

A precision oncology centre, needed a comprehensive genomic analysis solution to support real-time clinical decision-making for cancer patients. The organisation required a complete end-to-end workflow capable of processing NanoString nCounter data and generating physician-ready reports within minutes. The technical challenge involved analysing individual cancer samples without paired normal controls whilst maintaining statistical rigour, processing large datasets efficiently, and delivering actionable treatment recommendations to clinicians at the point of care.

• Develop a complete RNA sequencing analysis pipeline for NanoString nCounter data

• Enable single-sample differential expression analysis without paired controls

• Achieve sub-minute processing times for clinical datasets

• Create an integrated PDF report generation system for physician use

• Establish scalability for processing 1,500+ samples monthly

• Implement comprehensive quality control and normalisation modules

1. Data Architecture Analysis

• Evaluated NanoString nCounter data structure and specifications

• Curated publicly available PBMC reference datasets for comparative analysis

• Modified reference data to ensure kit version compatibility

• Established methodology for healthy blood-based sample comparisons

2. Technical Implementation

• Integrated NanoTube Bioconductor package for core analysis

• Developed innovative single-sample differential expression methodology

• Implemented comprehensive QC modules with RUV and nSolver backup methods

• Constructed multi-criteria gene ranking algorithm incorporating fold-change, p-value, abundance, and coefficient of variation

• Created modular architecture supporting future enhancements

• Developed automated installation script for all dependencies

3. Solution Delivery

• Built professional PDF report generation system with dynamic data integration

• Created visual analytics framework for gene expression significance

• Provided comprehensive template framework with structured patient data

• Delivered fully documented execution scripts with usage instructions

• Established version control structure via GitHub repository

Quantitative Outcomes

• Achieved sub-minute processing time for datasets exceeding 3,800 samples

• Validated scalability for 1,500+ monthly sample throughput

• Delivered complete solution ahead of original 4-week timeline

• Successfully processed actual client-provided datasets during validation

• Implemented comprehensive reference database with healthy population controls

Qualitative Benefits

• Enabled real-time clinical decision support at point of care

• Addressed fundamental challenge of analysing cancer samples without paired normal controls

• Provided physician-ready reports with actionable treatment insights

• Created flexible framework supporting future drug categorisation enhancements

• Established foundation for expanded reference population integration

"The pipeline delivered by Umbizo provides exactly what we needed - a complete, production-ready solution that processes our genomic data in real-time and delivers actionable insights to our physicians. The innovative approach to single-sample analysis was crucial for our clinical workflow, and the sub-minute processing time enables us to integrate genomic insights directly into patient consultations."

Client Clinical Team

• Requirements Analysis and Design: 3 days

• Core Pipeline Development and Integration: 1 week

• Report Generation System Development: 4 days

• Testing and Validation: 3 days

• Total Project Duration: Under 3 weeks (ahead of 4-week target)

Future enhancements will focus on expanding the drug treatment database with comprehensive cytotoxic versus immuno-stimulatory classifications. Additional reference populations will be incorporated to strengthen comparative analyses across diverse patient demographics.