? 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 ? ?
| 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 |
| Thomas, Elizabeth E; Srebro, Nathan; Sebat, Jonathan et al. (2004) Distribution of short paired duplications in mammalian genomes. Proc Natl Acad Sci U S A 101:10349-54 |
| Sebat, Jonathan; Lakshmi, B; Troge, Jennifer et al. (2004) Large-scale copy number polymorphism in the human genome. Science 305:525-8 |
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