NSCCG_CRC_GWAS
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002184 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Genotype data from 7,281 individuals with colorectal cancer. Genotyped on the Illumina OncoArray. Data has not been quality controlled. Data provided in plink format
| EGAS00001005412 | EGA
Project description:Genotype data of 1,950 individuals from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).
| EGAD00010002186 | EGA
Project description:<p>Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE) was one of five projects funded in 2010 as part of the NCI's Genetic Associations and Mechanisms in Oncology (GAME-ON) initiative (<a href="http://epi.grants.cancer.gov/gameon/">http://epi.grants.cancer.gov/gameon/</a>). GAME-ON's overall goal was to foster an intra-disciplinary and collaborative approach to the translation of promising research leads deriving from the initial wave of cancer GWAS. Specific goals included replication of previous GWAS findings and identification of new susceptibility loci through meta analyses of existing GWAS data and fine mapping of identified loci to better pinpoint causal variants; and identify germline variants that are associated with risk of multiple cancers. The other four funded GAME-ON projects were: the ColoRectal TransdisciplinaryStudy (CORECT), Elucidating Loci Involved in Prostate Cancer Susceptibility (ELLIPSE), Follow-up of Ovarian Cancer Genetic Association and Interaction Study (FOCI), and Transdisciplinary Research in Cancer of the Lung (TRICL).</p> <p>To identify additional cancer risk loci, improve the precision of fine-mapping, and facilitate cross-cancer analyses, the GAME-ON projects and other consortia formed the OncoArray network (<a href="http://epi.grants.cancer.gov/oncoarray/">http://epi.grants.cancer.gov/oncoarray/</a>), which developed and genotyped a new custom genotyping array (the "OncoArray") in large numbers of cancer cases and controls (over 400,000 samples). The OncoArray is a custom array manufactured by Illumina. The array includes a backbone of approximately 260,000 SNPs that provide genome-wide coverage of most common variants, together with markers of interest for each of the five GAME-ON cancers identified through genome-wide association studies (GWAS), fine-mapping of known susceptibility regions, sequencing studies, and other approaches. The array also includes loci of interest identified through studies of other cancer types, and other loci of interest to multiple cancer types (including loci associated with cancer related phenotypes, drug metabolism and radiation response). Additionally, SNPs relating to quantitative phenotypes such as body mass index (BMI), height, and breast density that correlate with common cancer risks are also included.</p> <p>The DRIVE data included under this dbGAP submission include OncoArray data from 60,015 breast cancer cases and controls genotyped at the Center for Inherited Disease Research (CIDR), University of Cambridge, National Cancer Institute, University of Copenhagen, University of Southern California and Mayo Clinic. Details on an additional approx. 80,000 breast cancer cases and controls genotyped at other centers can be found at <a href="http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/">http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/</a>. </p>
| phs001265 | dbGaP
Project description:Genotype data from the COIN and COIN-B trials of advanced/metastatic colorectal cancer. Data provided in plink format, and has been quality controlled. Control data used was from the WTCCC2 project National Blood Donors (NBS) Cohort (EGAD00000000024).
| EGAS00001005421 | EGA
Project description:Crosslinking mass spectrometry (CXMS) is a powerful technique to study protein structures and interactions. However, software tools for CXMS data analysis suffer from poor speed and credibility, especially at a proteome scale. Here, we introduce pLink 2, a search engine with higher speed and credibility for proteome-scale identification of crosslinked peptides. With a novel two-stage open search strategy facilitated by fragment indexing, pLink 2 is ~40 times faster than pLink 1 and 3~10 times faster than Kojak. Furthermore, four new analysis methods, using simulated datasets, synthetic datasets, 15N metabolically labeled datasets, and entrapment databases, were designed to evaluate the credibility of ten state-of-the-art search engines, this systematic evaluation showed that pLink 2 achieved the highest precision and sensitivity. Finally, four whole-cell lysate datasets, previously analysed by pLink 1 in months, were reanalysed by pLink 2 only in days, with up to 27.4% more crosslinks identified. The new search engine pLink 2 and the new evaluation methods are well positioned to become new benchmarks in the CXMS research field.
2019-07-26 | PXD012109 | Pride
Project description:<p>The Clinical Sequencing Exploratory Research (CSER) program supports multi-disciplinary projects that bring together clinicians, bioinformaticians, and ethicists to research the challenges of utilizing genomic sequence data in the clinic in the routine practice of medicine. The challenges are many and not disease-specific. Important aims of the research include: development of technical specifications and standards for sequencing in a clinical setting, investigation of methods to transmit genome-scale data to physicians in a fashion and timescale that fits the normal clinical workflow, exploration of regulatory requirements for applying genomic sequence data to patient care, study of physician and patient preferences regarding presentation of genomic information, and study of the ethical implications of returning unanticipated findings. More information about CSER and the investigators and institutions who comprise the CSER consortium can be found at <a href="http://www.genome.gov/27546194" target="_blank">http://www.genome.gov/27546194</a>.</p> <p>The NEXT (New Exome Technology) Medicine Study utilizes a randomized controlled trial (RCT) structure to compare usual care (UC) practice in Medical Genetics Clinics with the introduction of a powerful research tool of whole exome sequencing plus UC practices for Colorectal Cancer and Polyposis (CRCP) in adults. In doing so, the study aims to explore the practical, economic, and ethical implications of identifying and returning incidental findings ("extra" whole exome genetic risk results not associated with CRCP that includes pharmacogenetic variants) to patients. The study will also attempt to identify novel causal genes for CRCP by studying relatives of selected research subjects.</p>
| phs000999 | dbGaP
Project description:Colorectal cancer organoids (CCOs) recapitulate the gene expression signatures of their respective primary tumors. These CCOs provide valuable model for studying the primary cancers.
2021-07-20 | GSE171681 | GEO
Project description:Colorectal cancer organoids (CCOs) recapitulate the gene expression signatures of their respective primary tumors. These CCOs provide valuable model for studying the primary cancers.
2021-07-20 | GSE171680 | GEO