Tumor Type

Oral Cancer - Gingivobuccal
Project Profile
Funding Organizations
Research Organizations
Research Activities
Publication Policy

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Clinic & Pathology

India: Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre
Sequencing & Analysis

India: National Institute of Biomedical Genomics
Complementary Studies

Data Storage, Analysis & Management

India: Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre
National Institute of Biomedical Genomics
Project Summary

In view of its high prevalence in India and the existence of possible interacting environmental factors, India will focus on oral cancer as a part of the International Cancer Genome Consortium activities. In particular, India will focus on gingivo-buccal cancer. The primary reasons for selection of gingivo-buccal cancer are:
• It is the most common cancer among men in India and has a very high age-adjusted risk
• The site distribution of oral cancer in India is very different from that found in western countries
• While over 70% of tongue cancers have the propensity to metastasize, less than 50% of ginvivo-buccal cancers are found to metastasize
• Leukoplakia and sub-mucous fibrosis are two types of pre-cancerous lesion that can help track temporal genomic changes in gingivo-buccal cancer.

Work Plan

(A) Samples & Collection
(A.1) Oral cancer samples – defined using WHO-ICD10-ICDO criteria.
(A.2) Tissues from oral cancer patients, each (a) previously untreated, (b) 200mg of tissue, collected using laser microdissection, (c) >80% of collected tissue should have viable-appearing tumour cells on histological assessment and <20% necrotic or normal or pre-malignant (dysplastic) cells.
(A.3) Patient-matched control samples: mononuclear cell fraction from peripheral blood (Purpose: to discern somatic from germline mutations).
(A.4) Site-matched tissue control samples; >200mg of tissue from each control (Purpose: for transcriptomic and epigenomic analyses).
(A.5) General Data: Date of birth, Gender, Date of diagnosis, Ethnicity, Geographical area of residence, Presence of Metastasis, etc.
(A.6) Optional follow-up data: Therapy used, Response to therapy, etc.

(B) Sample Characterization
Histopathology: (a) Optical images to be stored, (b) To be reviewed by >2 pathologists

(C) DNA/RNA Isolation and Sample Storage
(C.1) Isolate high-quality DNA
(C.2) Isolate high-quality RNA
(C.3) Freeze, using WHO/IARC (2007) protocol

(D) Cytogenetic Analyses
Identification of translocations and other chromosomal rearrangements

(E) DNA Analyses
(E.1) Array genotyping: To identify LOH, CNVs, breakpoints, etc.
(E.2) DNA deep-resequencing (flow-cell, single DNA molecule)
(E.2.1) All coding exons and other genomic regions of particular biological interest to be resequenced
(E.2.2) Splice sites and miRNAs to be resequenced
(E.2.3) Regulatory and conserved non-coding regions to be resequenced
(E.3) Paired-end reads to identify >80% of somatic genomic rearrangements down to the sequence level resolution

(F) Data Management
(F.1) Creation of a database of project-specific workflows
(F.2) Creation of an integrated data warehouse and server.
(F.3) Creation of a protocol for dispatch of data on a regular basis for upload to the ICGC Backend Server (as required under ICGC guidelines)

(G) Statistical Analysis
Development of protocols and methodologies for an integrative statistical analysis

Principal Investigators

• Partha P. Majumder
• Rajiv Sarin

Lead Jurisdiction