# Presentation: 464546

## 	Cancer Genome Anatomy Project

- Lynette H. Grouse, Ph.D.
- National Cancer Institute

- Resource for the Research Community

## Cancer Genome Anatomy Project (CGAP)

- The overall goal of CGAP is to achieve a comprehensive molecular characterization of normal, precancerous, and cancerous cells.
- Facilitate the interface of genomics and cancer research through the establishment of platform information and technology infrastructures.
- All project resources accessible through public databases and resource centers.

## CGAP Library Collection

- Adipose
- Adrenal
- B cells
- Blood
- Bone
- Bone marrow
- Brain
- Breast
- Colon
- Germ cell
- Kidney

- Larynx
- Liver
- Lung
- Lymph
- Muscle
- Nasopharynx
- Neural
- Gingiva
- Head /Neck
- Squamous
- Ovary

- Pancreas
- Peripheral    Nerve
- Prostate
- Skin
- Stomach
- Thymus
- Thyroid
- Tongue
- Tonsil
- Uterus

## Expressed Sequence Tag (EST)

**5’ EST**

**3’ EST**

**cDNA**

- Produce cDNA libraries from normal and cancerous tissue.
- Sequence 3’ ends of each clone to evaluate library diversity.
- Sequence 5’ ends of clones.
- Sequence additional 5’ ends to complete clone insert.

**5’ EST**

- EST sequences are deposited into dbEST and
- clones are available from the IMAGE Consortium**.**

**Notes:**
This slide outlines the current strategy being used to generate and sequence full-ORF clones:

Once the cDNA libraries are produced, their quality is determined by EST sequencing and comparison to known protein sequences.  

5’ and 3’ EST sequencing will be performed on 768 clones or  2 X 384 well plates per library.  If sequence data suggests that the library is rich in full-length clones, i.e., presence of full-N and C-terminal coding regions - as compared to known genes - then an additional 10,000 clones are arrayed  and sequenced at the 5’ end only.  
Candidate full-ORF clones - containing putative N-terminal coding sequences are then sequenced to high quality and the sequences are submitted into GenBank.  

All EST sequences are submitted to dbEST and the clones are available through IMAGE.  Note that these ESTs are all being generated on capillary machines, so the identity of the clones should match the sequences at high frequency.

## NCBI Home Pagehttp://www.ncbi.nlm.nih.gov

## UniGene Database

- Partitions EST sequences into a non-redundant set of “clusters”.
- Each cluster represents a unique gene.
- CGAP analysis of expression data depends on the definition of a gene cluster within UniGene.

## CGAP Home Pagehttp:/cgap.nci.nih.gov

## Entry Portals to CGAP Data

## Entry Portals to CGAP Data

## Gene Finder
Nucleotide BLAST
List of Candidate,Validated, 	and Confirmed SNPs
SNP500Cancer
SNP Gene Viewer

- Nucleotide BLAST
- List of Candidate,Validated, 	and Confirmed SNPs
- SNP500Cancer
- SNP Gene Viewer

- Genes Analysis Tools

## Entry Portals to CGAP Data

## Library Finder
Gene Library Summarizer (GLS)
cDNA xProfiler
Differencial Gene Expression      	Displayer (DGED)
SAGEmap xProfiler 
SAGEmap vNorthern

- Gene Library Summarizer (GLS)
- cDNA xProfiler
- Differencial Gene Expression      	Displayer (DGED)
- SAGEmap xProfiler
- SAGEmap vNorthern

- Tissue Analysis Tools

## Library Finder
Gene Library Summarizer (GLS)
cDNA xProfiler
Differencial Gene Expression      	Displayer (DGED)
SAGEmap xProfiler 
SAGEmap vNorthern

- Gene Library Summarizer (GLS)
- cDNA xProfiler
- Differencial Gene Expression      	Displayer (DGED)
- SAGEmap xProfiler
- SAGEmap vNorthern

- Tissue Analysis Tools

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## Entry Portals to CGAP Data

## Mitelman Database of Chromosome Aberrations in Cancer
FISH-mapped BACs
Genetic and Physical SNP 	Maps

- FISH-mapped BACs
- Genetic and Physical SNP 	Maps

- Chromosome Analysis Tools

## Mitelman Database of Chromosome Aberrations in Cancer
FISH-mapped BACs
Genetic and Physical SNP 	Maps

- FISH-mapped BACs
- Genetic and Physical SNP 	Maps

- Chromosome Analysis Tools

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## Entry Portals to CGAP Data

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## SAGE Genie

- Collaboration with Duke University and the Ludwig Institute for Cancer Research, San Paulo, Brazil.
- Generated approximately 80-100 SAGE libraries.
- Tissues include:
- -Brain, kidney, pancreas, ovary, colon, lung
-   liver, stomach, muscle.

- ~

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## Mammalian Gene Collectionhttp:/mgc.nci.nih.gov

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## CGAP Home Pagehttp:/cgap.nci.nih.gov