Pediatric Gliomas Research Pipeline

Comprehensive genomic analysis pipeline for pediatric glioma research with interactive visualization and therapeutic target identification

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Interactive Teal Application Demonstrations

Watch these videos showcasing the key features and capabilities of the Teal application for pediatric glioma genomic analysis.

Teal Application Walkthrough

Tour of the genomic analysis interface showing data visualization, mutation profiling, and therapeutic analysis features in action.

Clinical Dashboard Exploration

Demonstration of filters and variables across dashboards for mutational profiling, therapy meta-analysis, and data integration using the Teal framework, applied to CDISC-compliant pediatric clinical data.

SRA Data Processing

Automated download, quality control, and FASTQ conversion from NCBI SRA database with comprehensive validation.

Variant Analysis

Complete variant calling pipeline including SNV, CNV, and Indel detection with clinical significance annotation.

Interactive Visualization

Sophisticated Teal-based Shiny application for exploratory data analysis and result interpretation.

Therapeutic Insights

Meta-analysis of treatment targets and precision medicine approaches with evidence-based recommendations.

Technical Architecture

The pipeline integrates multiple bioinformatics tools and frameworks to provide a comprehensive analysis workflow:

Python Components

SRA data processing, variant analysis, and mutational profiling with BioPython integration.

R Analytics

Advanced statistical analysis and interactive visualization using Teal framework and Shiny.

Nextflow Workflows

Scalable and reproducible pipeline execution with parallel processing capabilities.

Data Management

PostgreSQL integration for clinical data storage and meta-analysis management.

Featured in Seqera Blog

This project's innovative approach to SRA data automation was featured in Seqera's technical blog, highlighting the effective use of Nextflow for large-scale genomic data processing.

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Key Results & Impact

The pipeline has been successfully applied to pediatric glioma research with significant outcomes:

50+

Genomic Samples Analyzed

Key Genes Profiled

Analysis Modules

100%

Reproducible Results

Clinical Applications

This pipeline directly contributes to precision medicine in pediatric oncology and supports a CDISC-compliant clinical analytics workflow:

Biomarker Discovery: Identification of prognostic and predictive genetic markers.
Treatment Stratification: Patient classification based on molecular and clinical profiles.
Drug Target Identification: Novel therapeutic vulnerabilities in pediatric gliomas.
Clinical Trial Support: Companion diagnostics, patient matching, and evidence generation.
Regulatory-Grade Analytics: End-to-end data standardization from raw sources to submission-ready outputs.

Data Flow (Clinical + Genomics):

Sources: Raw CRF data (eCRF/EDC) and non-CRF data (EHR, LIMS, labs, imaging, omics: VCF/MAF, RNA-seq).
Standardization to SDTM: DM, AE, EX, LB, VS and QS with controlled terminology.
Analysis Datasets (ADaM): ADSL, ADAE, ADLB, ADQS, ADTTE.
Final Outputs: TLFs(Tables, Listing and Figures) and interactive Teal dashboards.