We will operate a Cancer Genome Characterization Center in which we will systematically analyze the genome and transcriptome of human cancers as provided under the TCGA pilot project. We will use Molecular Inversion probes to measure allele specific copy numbers in at least 500 tumors and 500 normal samples per year for the duration of the TCGA pilot project. We will also assay exon-specific transcriptional profiles for the same tumor and normal samples. Together, data from these assays will allow us to identify genes that are likely to harbor somatic mutations in cancers. We will release all data in rapid manner while continually striving to increase data quality, decrease cost, and increase sample throughput. The TCGA pilot project is a preliminary effort to systematically understand the genetic changes that occur and cause cancers. We will participate in this effort by providing the identification of genes that are likely to show mutations in cancers, termed somatic mutations. Our effort will involve identify genes whose intermediary form (mRNA) are aberrantly produced in cancers using a """"""""gene chip"""""""" that can detect the production of abnormal mRNAs. Cancers are known to fracture their genetic material (chromosomes) resulting in extra copies of some genes and missing copies of others. These aberrations are critical for the development of many cancers and identifying the regions of the genome that become preferentially amplified or deleted is extremely helpful for identifying those genes that are responsible for cancer.
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| Cancer Genome Atlas Research Network (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature 511:543-50 |
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| Brennan, Cameron W; Verhaak, Roel G W; McKenna, Aaron et al. (2013) The somatic genomic landscape of glioblastoma. Cell 155:462-77 |
| Daemen, Anneleen; Griffith, Obi L; Heiser, Laura M et al. (2013) Modeling precision treatment of breast cancer. Genome Biol 14:R110 |
| Drake, Penelope M; Schilling, Birgit; Niles, Richard K et al. (2012) Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J Proteome Res 11:2508-20 |
| Ortiz-Estevez, Maria; Aramburu, Ander; Bengtsson, Henrik et al. (2012) CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation. Bioinformatics 28:1793-4 |
| Gagnon-Bartsch, Johann A; Speed, Terence P (2012) Using control genes to correct for unwanted variation in microarray data. Biostatistics 13:539-52 |
| Collisson, Eric A; Trejo, Christy L; Silva, Jillian M et al. (2012) A central role for RAF?MEK?ERK signaling in the genesis of pancreatic ductal adenocarcinoma. Cancer Discov 2:685-93 |
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