Abstract

? We will continue developing and applying tools for the genomic analysis of cancer. Specifically, ? 1. We have developed a representational array based method for the measurement of gene copy levels in cells, and propose a high resolution analysis of tumor cell lines to develop a database of commonly amplified and deleted loci. ? 2. We will use this database to identify candidate tumor suppressor genes, that will be validated by the analysis of somatic mutations in tumors. ? 3. We will perform a functional analysis of lead candidates, utilizing [[among other tools]] microarray expression analysis and tumorigenicity experiments ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA078544-06
Application #
6731155
Study Section
Genome Study Section (GNM)
Program Officer
Couch, Jennifer A
Project Start
1998-07-15
Project End
2007-04-30
Budget Start
2004-05-01
Budget End
2005-04-30
Support Year
6
Fiscal Year
2004
Total Cost
$502,725
Indirect Cost

  Institution

Name
Cold Spring Harbor Laboratory
Department
Type
DUNS #
065968786
City
Cold Spring Harbor
State
NY
Country
United States
Zip Code
11724

  Publications

Navin, Nicholas E; Hicks, James (2010) Tracing the tumor lineage. Mol Oncol 4:267-83
Navin, Nicholas; Grubor, Vladimir; Hicks, Jim et al. (2006) PROBER: oligonucleotide FISH probe design software. Bioinformatics 22:2437-8
Zender, Lars; Spector, Mona S; Xue, Wen et al. (2006) Identification and validation of oncogenes in liver cancer using an integrative oncogenomic approach. Cell 125:1253-67
Pelham, Robert J; Rodgers, Linda; Hall, Ira et al. (2006) Identification of alterations in DNA copy number in host stromal cells during tumor progression. Proc Natl Acad Sci U S A 103:19848-53
Lakshmi, B; Hall, Ira M; Egan, Christopher et al. (2006) Mouse genomic representational oligonucleotide microarray analysis: detection of copy number variations in normal and tumor specimens. Proc Natl Acad Sci U S A 103:11234-9
Hicks, James; Krasnitz, Alexander; Lakshmi, B et al. (2006) Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 16:1465-79
Jobanputra, Vaidehi; Sebat, Jonathan; Troge, Jennifer et al. (2005) Application of ROMA (representational oligonucleotide microarray analysis) to patients with cytogenetic rearrangements. Genet Med 7:111-8
Hicks, J; Muthuswamy, L; Krasnitz, A et al. (2005) High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. Cold Spring Harb Symp Quant Biol 70:51-63
Sebat, Jonathan; Lakshmi, B; Troge, Jennifer et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305:525-8
Olshen, Adam B; Venkatraman, E S; Lucito, Robert et al. (2004) Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5:557-72

Showing the most recent 10 out of 16 publications