Help & Documentation

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1. Overview

The Indian Breast Cancer Genome Atlas (IBCGA) is a national initiative to create a comprehensive genomics resource for breast cancer in India. It aims to improve clinical research, diagnosis, and treatment by providing high-quality WGS and WTS datasets representing the Indian population.

2. Datasets Available

Raw Data (FASTQ files):
- WGS FASTQ (tumor, normal, normal-like, post-treated)
- WTS FASTQ files

Processed Data:
- Copy Number Variation (CNV – WGS)
- Mutation Data (SNV – WGS)
- Structural Variants (SV – WGS)
- Raw gene counts (WTS)
- FPKM (WTS)
- TPM (WTS)
- Metadata and Batch information

3. How to Download the Datasets

Raw Data:
- Fill the Raw Data Access Form under Dataset → Raw Data
- Submit required institutional declarations (PI & student signature)
- DAC Committee reviews request (7–10 days)
- After approval, raw FASTQ downloads are enabled

Processed Data:
- Login → Dataset → Processed Data
- Read & accept the declaration
- Download all processed datasets instantly

4. Patient ID / Nomenclature Schema

Patient IDs: IBCGA-0001, IBCGA-0045, ...

WTS format: IBCGA-0001-002-01A
- 002 → Batch number
- 01/02/03 → Hospital codes
- A/B → Sequencing institute

5. Batch Information

Batch metadata includes hospital, institute, sequencing run, and batch IDs. Batch effects must be corrected during WTS differential expression analysis.

6. Data Access Policy

Please refer to the Data Access Policy PDF on the website. Users must:
- Cite IBCGA appropriately
- Not redistribute data
- Not host data externally without permission
- Not re-identify individuals
- Follow DPDP Act 2023 and Biotech-PRIDE guidelines