Tumor Type

China
Gastric Cancer - Intestinal- and diffuse-type
Funding Organizations
China: Chinese Cancer Genome Consortium
China: Ministry of Science and Technology
China: National High Technology Research and Development Program (“863”Program) of China
China: National Natural Science Foundation of China
Research Organizations
China: Beijing Cancer Hospital/Institute
China: BGI-Shenzhen
China: Chinese Cancer Genome Consortium
China: Peking University School of Oncology
Research Activities
Publication Policy
1:   ICGC Goals, Structure, Policies and Guidelines Section E.3 - Publication Policy HTML 
2:   Template Letters to Facilitate Communications HTML 
to ensure appropriate dialogue between data users and generators and for authors to contact ICGC members and editors
Clinic & Pathology
China: Beijing Cancer Hospital/Institute
Peking University School of Oncology

Primary gastric cancer samples were collected from tumor bank of Beijing Cancer Hospital/Insititute, as approved by the Research Ethics Board at the Hospital/Institute. Specimens were surgically resected, snap-frozen and stored at -80°C. Through estimation by H&E staining and pre-screening by two pathologists,tumor nuclei proportion in chosed tumor sample was > 60-80%.
Sequencing & Analysis
China: BGI-Shenzhen

We will do whole exome sequencing using next generation sequncing technology mainly in Illumina GA II. Data processing will be performed by independently developed software. We will call multi-type mutations and find their relationship with cancer biology.
Complementary Studies
China: BGI-Shenzhen

Study of copy number variation and structure variation by low depth whole genome sequencing, transcriptome analysis by RNA-seq, methylome analysis by MeDIP-seq and micro RNA analysis; all performed using Illumina GA II sequencing and complementary informatic work.
Data Storage, Analysis & Management
China: Beijing Cancer Hospital/Institute
BGI-Shenzhen
Chinese Cancer Genome Consortium
Peking University School of Oncology

We are using self-developed LIMS system and real-time quality control system , coordinating with the automated data processing pipeline on BLC (Bioinfomatic Linux Cluster) to deal with the basic data analyzing and managing. For advanced anlysis and specific scientific goals, we will design certain software or construct new database.
Project Summary

In view of its high prevalence in China and the existence of possible interacting environmental factors, China will focus on gastric cancer as a part of the International Cancer Genome Consortium activities. In particular, China will focus both on Intestinal-type and diffuse-type cancer. The major reasons for selection of gastric cancer are:
• It is the most common cancer with high incidence and poor prognosis in China, most of cancer patients to be diagnostic too later to cure.
• Intestinal- type and diffuse-type cancer is different in clinical pathological features and gene expression profiling.
• About 50-80% of cancers have the high risk of recurrence and metastasis following creative resection,.
• Precancerous lesion including intestinal metaplasia (IM) and dysplasia (Dys) has high incidence and have a high risk to be transformed to malignance.
• It is fundamental to analyze genomic changes for discovering biomarkers to detect gastric cancer early and to predict prognosis.

Working Plan

(A) Samples & Collection
(A.1) Tumor samples were defined using Lauren and WHO criteria.
(A.2) Tissues from gastric cancer patients, each (a) previously untreated, (b) 500mg of tumor and mached normal tissues collected based on NCI and ICGC guidelines, (c) >60-80% of collected tissue should have viable-appearing tumour cells on histological assessment and <5% necrotic cells.
(A.3) Systematical collection of clinical data and follow-up, the patient therapy based on NCCN, guidelines, (Clinical practice in oncology: gastric cancer/Chinese version).

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

(C) DNA/RNA Isolation and Sample Storage
(C.1) Isolate high-quality DNA
(C.2) Isolate high-quality RNA
(C.3) Freeze, using NCI guidelines for biorepositories (2006)

(D) Genomics Analyses
(D.1) SNP Array genotyping: To identify CNVs LOH, etc.
(D.2) Exon capture and DNA deep-resequencing

(E) Data Management
(E.1) Creation of a database of project-specific workflows
(E.2) Creation of an integrated data warehouse and server.
(E.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)

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

Principal Investigators

• Huanming Yang
• Youyong Lu

Lead Jurisdiction