The ICGA Data Visualization Platform
The ICGA offers a cutting-edge platform that provides a detailed, integrative view of the genetic, molecular, and clinical profiles of cancer in India. Our data visualization platform, powered by cBioPortal, enables researchers to explore and analyze genomic data, starting with a focused study on Indian breast cancer patients.
Study Title: ICGA Breast Cancer Cohort
The ICGA Breast Cancer Cohort represents a significant initiative aimed at understanding the molecular landscape of breast cancer among Indian patients. This study includes tumor tissue, adjacent normal tissue as control, and associated clinical data from patients across India. All participants were treatment-naive, aged between 18 and 75 years, and underwent whole-genome sequencing at a depth of 70X [+/-5], along with RNA sequencing and proteomics analysis. Control samples from breast-adjacent normal tissues are included for each patient.
Metadata of the ICGA’s cohort on breast cancer patients
S. NO | ICGA ID | Diagnosis | Consent | Gender | LN Status | Pathological staging | Estrogen receptor status | Progesterone receptor status | Chemotherapy |
1 | ICGA_BC_01 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N1a | POSITIVE | POSITIVE | YES |
2 | ICGA_BC_02 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT3N2a | POSITIVE | POSITIVE | YES |
3 | ICGA_BC_03 | CA BREAST | CONSENTED | FEMALE | NEGATIVE | Pt2n0 | POSITIVE | POSITIVE | YES |
4 | ICGA_BC_04 | CA BREAST | CONSENTED | FEMALE | NEGATIVE | pT2N0 | POSITIVE | POSITIVE | YES |
5 | ICGA_BC_05 | CA BREAST | CONSENTED | FEMALE | POSITIVE | Pt2n3 | POSITIVE | POSITIVE | YES |
6 | ICGA_BC_06 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT3N2a | POSITIVE | POSITIVE | YES |
7 | ICGA_BC_07 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N1(mi) | POSITIVE | POSITIVE | YES |
8 | ICGA_BC_08 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N2a | POSITIVE | POSITIVE | YES |
9 | ICGA_BC_09 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N2a | POSITIVE | POSITIVE | YES |
10 | ICGA_BC_10 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT3N3a | POSITIVE | POSITIVE | YES |
11 | ICGA_BC_11 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N3a | POSITIVE | POSITIVE | YES |
12 | ICGS_BC_12 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N2a | POSITIVE | POSITIVE | YES |
13 | 1CGA_BC_13 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N3a | POSITIVE | POSITIVE | NO |
14 | 1CGA_BC_14 | CA BREAST | CONSENTED | FEMALE | Negative | NA | POSITIVE | POSITIVE | Yes |
15 | 1CGA_BC_15 | CA BREAST | CONSENTED | FEMALE | Negative | pT2N0M0 | POSITIVE | POSITIVE | Yes |
16 | 1CGA_BC_16 | CA BREAST | CONSENTED | FEMALE | Positive | pT3N2aM0 | POSITIVE | POSITIVE | Yes |
17 | 1CGA_BC_17 | CA BREAST | CONSENTED | FEMALE | Positive | pT2N2aM0 | POSITIVE | POSITIVE | Yes |
18 | 1CGA_BC_18 | CA BREAST | CONSENTED | FEMALE | Positive | pT1cN1aM0 | POSITIVE | POSITIVE | Yes |
19 | 1CGA_BC_19 | CA BREAST | CONSENTED | FEMALE | Positive | pT4bN1aM0 | POSITIVE | POSITIVE | Adviced Adjuvant chemo.Patient not taken chemo |
20 | 1CGA_BC_20 | CA BREAST | CONSENTED | FEMALE | Positive | pT3N3cM0 | POSITIVE | POSITIVE | Yes |
21 | 1CGA_BC_21 | CA BREAST | CONSENTED | FEMALE | Positive | pT2N1M0 | POSITIVE | POSITIVE | Yes |
22 | 1CGA_BC_22 | CA BREAST | CONSENTED | FEMALE | Positive | pT2N1M0 | POSITIVE | POSITIVE | No |
23 | 1CGA_BC_23 | CA BREAST | CONSENTED | FEMALE | Negative | pT2N0M0 | POSITIVE | POSITIVE | Yes |
24 | 1CGA_BC_24 | CA BREAST | CONSENTED | FEMALE | Positive | pT2N3M0 | POSITIVE | POSITIVE | Yes |
25 | 1CGA_BC_25 | CA BREAST | CONSENTED | FEMALE | Positive | pT1cN1M0 | POSITIVE | POSITIVE | Adviced Adjuvant chemo.Patient not taken chemo |
26 | 1CGA_BC_26 | CA BREAST | CONSENTED | FEMALE | Positive | pT2N0M0 | POSITIVE | POSITIVE | Yes |
27 | 1CGA_BC_27 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N2a | POSITIVE | POSITIVE | YES |
28 | 1CGA_BC_28 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N1a | POSITIVE | POSITIVE | YES |
29 | 1CGA_BC_29 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT2N1a | POSITIVE | POSITIVE | YES |
30 | 1CGA_BC_30 | CA BREAST | CONSENTED | FEMALE | POSITIVE | pT3N2a | POSITIVE | POSITIVE | YES |
31 | 1CGA_BC_31 | CA BREAST | CONSENTED | FEMALE | 11 | 2 | 70-80% | 0 | NA |
32 | 1CGA_BC_32 | CA BREAST | CONSENTED | FEMALE | 14 | 2 | 7 | 1+ | AC + TAXOL |
33 | 1CGA_BC_33 | CA BREAST | CONSENTED | FEMALE | 22 | 2 | 80% | 0 | NA |
34 | 1CGA_BC_34 | CA BREAST | CONSENTED | FEMALE | 19 | 2A | 95% | 0 | NA |
35 | 1CGA_BC_35 | CA BREAST | CONSENTED | FEMALE | 26 | 3 | NA | NA | AC + TAXOL |
36 | 1CGA_BC_36 | CA BREAST | CONSENTED | FEMALE | 16 | 3 | NA | NA | AC + TAXOL |
37 | 1CGA_BC_37 | CA BREAST | CONSENTED | FEMALE | 9 | 3 | NA | NA | CMF |
38 | 1CGA_BC_38 | CA BREAST | CONSENTED | FEMALE | 17 | 2 | NA | NA | AC + TAXOL |
39 | 1CGA_BC_39 | CA BREAST | CONSENTED | FEMALE | 0 | pT2N0 | Neg | Neg | Inj adriamycin, & cyclophophamide, paclitaxeland carcoplatin |
40 | 1CGA_BC_40 | CA BREAST | CONSENTED | FEMALE | 3 | pT3N1a | Positive | Positive | Inj adriamycin, & cyclophophamide |
41 | 1CGA_BC_41 | CA BREAST | CONSENTED | FEMALE | 1 | pT2N1a | Positive | Positive | Not started yet |
42 | 1CGA_BC_42 | CA BREAST | CONSENTED | FEMALE | 17 | pT3N3a | Positive | Positive | Inj adriamycin, & cyclophophamide |
43 | 1CGA_BC_43 | CA BREAST | CONSENTED | FEMALE | 0 | pT2N0 | Neg | Neg | Not started yet |
44 | 1CGA_BC_44 | CA BREAST | CONSENTED | FEMALE | 26 | pT3N3a | POSITIVE | POSITIVE | YES |
45 | 1CGA_BC_45 | CA BREAST | CONSENTED | FEMALE | 1 | pT2N1a | POSITIVE | POSITIVE | NO |
46 | 1CGA_BC_46 | CA BREAST | CONSENTED | FEMALE | 0 | Pt2n0 | POSITIVE | POSITIVE | NO |
47 | IBCGA_BC_47 | CA BREAST | CONSENTED | FEMALE | 1 | pT2N1a | POSITIVE | POSITIVE | YES |
About the ICGA Portal
The ICGA platform is your gateway to exploring comprehensive genomic data. Built on the robust cBioPortal framework, the platform provides researchers with access to processed data essential for genomic and molecular analysis.
Data Availability and Ethical Compliance
The ICGA is committed to adhering to ethical data-sharing practices. The datasets available through the ICGA portal are limited to somatic mutations only. This restriction is a result of ethical approvals that ensure patient privacy and compliance with responsible data-use guidelines.
To uphold these standards, ICGA has utilized analysis pipelines that specifically focus on somatic mutations, avoiding the analysis of germline mutations. This ensures that inherited genetic data, which could potentially impact patient privacy, is not included in the research.
Data Access
Please refer to ICGA Data Policy and DBT PRIDE guidelines to understand terms and conditions of access. Researchers interested in accessing the ICGA data should follow the given instructions. The submitted applications will be reviewed by the ICGA Data Access Committee (DAC). Incomplete applications will not be considered.
To request access to ICGA data, please follow the two-step process outlined below:
Step 1: Stage 1 Form
At this stage, you are expected to provide:
- A scientific research proposal,
- Study investigators and research team with clear roles and responsibilities.
- A data safety and management plan with funding information,
- Conflict of interest,
- Timelines, and
- Plans for ethical approvals.
Step 2: Stage 2 Submission
If your proposal is provisionally approved by ICGA’s Data Access Committee, you will be asked to submit following:
- A Revised and detailed proposal,
- Institutional ethical approvals, undertakings, etc.
- Training of investigators (for example, any certifications), etc.
Full and final approval will be followed by the signing of a data sharing agreement with ICGA.
Stage 1 Form for data access request is available here.
ICGA Data, Resources, and Materials
ICGA is dedicated to advancing cancer research through an extensive process that involves:
- Collecting diverse biospecimen and clinical metadata
- Generating molecular analytes for detailed characterization
- Applying advanced sequencing and molecular characterization methods
- Providing accessible data for the research community
Requests for Biological Samples and Materials
Due to legal and ethical considerations, the ICGA is unable to accommodate requests for biological samples, analytes, or tissue materials. All cases within the ICGA program have been consented exclusively for ICGA use, and the redistribution of materials to outside parties is prohibited. Additionally, the majority of tissue samples have been depleted due to the multiple assays performed for ICGA research.
Citing ICGA in Your Work
Researchers utilizing ICGA data in their studies should acknowledge the ICGA Network. A citation example:
“The results [published or shown] here are in whole or in part based upon data generated by the ICGA Network: https://icga.in, https://icga.net.in.”