Background on CGCI
CGCI investigators developed and applied advanced sequencing methods for examining genomes, exomes, and transcriptomes of tumors. From the resulting molecular data, they identified novel genetic abnormalities, which may contribute to cancer pathogenesis.
CGCI projects involved the following phases for the molecular characterization of cancers:
Phase 1: Project Initiation
- Develop protocols, standard operating procedures, and regulatory paperwork, such as patient consent and material transfer agreements
- Accrue tumor and matched normal tissue for the discovery cohort, verify tumor diagnosis by pathology review, and collect clinical data
Phase 2: Discovery
- Sequence the genomes and transcriptomes of the discovery cohort, analyze sequencing data, determine any changes associated with clinical variables
- Collect tumor and normal tissues for validation
Phase 3: Validation
- Determine the frequency of candidate alterations identified in discovery cohort by screening the validation cohort, confirm clinical outcome correlations, and identify biological pathways altered in tumor subtypes
Phase 4: Publication
- Publish findings in peer-reviewed journals, present at scientific meetings, release generated data to the research community ensuring patients’ privacy and confidentiality
CGCI Data
Data collected and processed by the CGCI program is available at the Genomic Data Commons (GDC).
Analysis files from publications can be found in the “Supplemental Data” section of GDC publication pages for CGCI.
CGCI Tumor & Data Types
| Tumor Type/Data Use Limitation | Data Types and Data Use Limitation |
|---|---|
| Burkitt lymphoma | Pediatric whole genome sequencing, RNA-seq, and miRNA-seq data Epstein-Barr Virus (EBV) sequences are available as BAM alignments General research use and data use limitations for some cases |
| Non-Hodgkin lymphoma | Open access (analyzed) and controlled access (upper-level files e.g., VCF or MAF) mRNA-seq data, whole exome, and whole genome sequencing data Controlled access aligned sequence reads (BAM files) from mRNA-seq, whole exome, and whole genome sequencing data Cancer research only |
| HIV+ associated cervical cancer | Controlled-access whole genome sequencing, RNA-seq, miRNA-seq, and targeted sequencing data Controlled-access ChIP-Seq data and open-access methylation array data General research use |
Contact for CGCI
For additional information about CGCI, please contact Dr. Liming Yang.
Past Projects
Burkitt Lymphoma Genome Sequencing Project (BLGSP)
The goal of the Burkitt Lymphoma Genome Sequencing Project (BLGSP) was to explore genetic changes in patients with Burkitt lymphoma and uncover knowledge that could lead to better prevention, detection, and treatment of this rare and aggressive cancer.
BLGSP involved a collaboration between NCI and the Foundation for Burkitt Lymphoma Research.
120 cases were characterized.
Through an integrative analysis of whole-genome and transcriptome data, this project revealed a genome-wide increase in aberrant somatic hypermutation in EBV-positive tumors and novel candidate Burkitt lymphoma genes.
HIV+ Tumor Molecular Characterization Project (HTMCP)
The HIV+ Tumor Molecular Characterization Project (HTMCP) aimed to gain insight into the genetic events driving HIV-associated cancers and to determine why certain cancers (but not others) have higher incidences in HIV-positive patients.
HTMCP studied the following cancers based on their high rates of incidence and mortality among HIV-positive patients:
- Cervical Cancer
- Diffuse Large B-Cell Lymphoma (DLBCL)
- Lung Cancer
211 cases were characterized.
By analyzing cervical carcinomas, this project identified human papillomavirus (HPV) clade-specific epigenome and transcriptome landscapes.