🧬 refCNV.org Overview & Use Cases (v2)¶

refCNV.org provides curated CNV (Copy Number Variation) profiles derived from reference samples, including analyses from multiple pipelines (e.g., DRAGEN-CNV, PennCNV, QuantiSNP). It supports exploratory analysis, visualization, and comparison of CNV data across tools and platforms.

🚧 Note: This platform is under development and should not be used for clinical or publication purposes at this stage.

🌐 Homepage Overview¶

Homepage

The homepage introduces the concept of regional CNV profiling using reference samples from large projects like the 1000 Genomes. It shows typical frequency plots (e.g., for DRAGEN-CNV) with summary visualizations of gains (orange) and losses (blue).

📊 Use Case 1: Compare CNV Profiles Across Pipelines¶

Explore how different CNV calling pipelines produce divergent results for the same sample set.

Pipeline UI

Select refCNV - germline reference CNVs
Choose pipelines: DRAGEN, EnsembleCNV, QuantiSNP, PennCNV, iPattern
Generate output in heatmap, histogram, or sparkline formats

Pipeline Heatplot

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📊 Use Case 2: Explore Pipeline-Specific Datasets¶

Use the "Analysis Pipelines" section to browse and visualize all samples processed by a specific CNV calling pipeline.

Pipeline Overview

Panel A: Select any listed pipeline (e.g., DRAGEN, EnsembleCNV)
Panel B: View CNV histogram for that pipeline and access download links for SVG and data files
Inspect sample counts, data origin, and direct search for specific entries

📊 Use Case 3: Platform-Based CNV Exploration¶

Use the “Array and Sequencing Platforms” panel to explore CNV patterns derived from specific microarray or sequencing technologies.

Platform View

Panel A: Choose a platform subset (e.g., Affymetrix, Illumina, BAC arrays)
Panel B: Generate CNV frequency histograms across selected platforms
Adjust settings like histogram height or line width before plotting

💡 Interpretation Tips¶

Pipelines differ in CNV calling sensitivity and precision
Platforms contribute inherent variability due to probe density and noise
Use comparative plots to benchmark tools and choose references

🛠️ Additional Use Cases¶

Single Sample CNV Track Viewer
Visualize one sample across all pipelines
Cohort CNV Signature Construction
Create merged profiles by disease or sample group
Batch Normalization Evaluation
Compare groups to detect CNV call shifts caused by preprocessing