Biomarker discovery with public data

Overview

Programme overview

Participants can translate a biomarker question into a documented public-data search, screen candidate studies, assess metadata fitness and produce a cautious evidence brief.

Audience

Who should attend

Researchers who want to locate, assess and reuse public functional-genomics studies to refine a biomarker question before commissioning new experiments.

Capability gained

Learning outcomes

• Define a searchable question using disease, tissue, organism, modality and study-design terms
• Locate relevant records in public functional-genomics repositories
• Distinguish study, sample, platform and processed-data records
• Assess metadata completeness, comparability, confounding and reuse constraints
• Create a reproducible study-screening table and inclusion rationale
• Conduct a bounded exploratory analysis on an approved public dataset
• Report evidence, limitations and next experiments without making a clinical claim

Structure

Curriculum

1. 01From biomarker question to search protocol
2. 02Repository structure: studies, samples, platforms and files
3. 03Search strategy, accession tracking and provenance
4. 04Metadata fitness, phenotype definitions and exclusion criteria
5. 05Downloading approved public processed data and recording transformations
6. 06Exploratory analysis and candidate-context visualisation
7. 07Evidence brief: support, limitations and next questions

Preparation

Prerequisites

Basic R or equivalent data-analysis experience. Exercises use public, non-sensitive datasets selected and frozen before delivery.