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- Study Description
Recently, significant progress has been made in characterizing and sequencing the genomic alterations in statistically robust numbers of samples from several types of cancer. For example, The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC) and other similar efforts are identifying genomic alterations associated with specific cancers (e.g., copy number aberrations, rearrangements, point mutations, epigenomic changes, etc.) The availability of these multi-dimensional data to the scientific community sets the stage for the development of new molecularly targeted cancer interventions. Understanding the comprehensive functional changes in cancer proteomes arising from genomic alterations and other factors is the next logical step in the development of high-value candidate protein biomarkers. Hence, proteomics can greatly advance the understanding of molecular mechanisms of disease pathology via the analysis of changes in protein expression, their modifications and variations, as well as protein=protein interaction, signaling pathways and networks responsible for cellular functions such as apoptosis and oncogenesis. Realizing this great potential, the NCI launched the third phase of the CPTC initiative in September 2016. As the Clinical Proteomic Tumor Analysis Consortium, CPTAC continues to define cancer proteomes on genomically-characterized biospecimens. The purpose of this integrative approach was to provide the broad scientific community with knowledge that links genotype to proteotype and ultimately phenotype. In this third phase of CPTAC, the program aims to expand on CPTAC II and genomically and proteomically characterize over 2000 samples from 10 cancer types (Lung Adenocarcinoma, Pancreatic Ductal Adenocarcinoma, Glioblastoma Multiforme, Acute Myeloid Leukemia, Clear cell renal Carcinoma, Head and Neck Squamous Cell Carcinoma, Cutaneous Melanoma, Sarcoma, Lung Squamous Cell Carcinoma, Uterine Corpus Endometrial Carcinoma) .Germline DNA is obtained from blood and Normal control samples for proteomics varied by organ site. All cancer samples were derived from primary and untreated tumor.
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- Study Inclusion/Exclusion Criteria
- Newly diagnosed, untreated patients undergoing primary cytoreductive surgery for a cancer meeting study diagnostic requirements, or evaluation for AML.
- Tumor from appropriate anatomic site only (other anatomic sites not acceptable, except as noted).
- Informed consent provided for the provision of biospecimens and data.
- Donor meets age of majority for institution/state/country.
- Prior history of other malignancies within the past 12 months, except basal cell carcinoma of the skin.
- Prior systemic chemotherapy, radiation therapy or biological therapy for any cancer at a different site within 10 years of the date of consent except as noted below.
- Lack of informed consent.
- Molecular Data
Type Source Platform Number of Oligos/SNPs SNP Batch Id Comment Whole Genome Sequencing Illumina HiSeq X N/A N/A Whole Exome Sequencing Illumina TruSeq Custom Amplicon N/A N/A Transcriptome Sequencing Illumina HiSeq 4000 N/A N/A Small RNA (miRNA) sequencing Illumina TruSeq Small RNA Sample Prep Kit N/A N/A Whole Genome Methylation Sequencing Illumina TruSeq N/A N/A Methylation Array Illumina Infinium HumanMethylation450 BeadChip N/A N/A
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