High Density SNP Association Analysis of Melanoma: Case-Control and Outcomes Investigation
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ABSTRACT:
PROVIDER: PRJNA75477 | ENA |
REPOSITORIES: ENA
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Project description:<p>This research builds upon an extensive resource of melanoma cases and hospital based controls collected over several years at the U.T. M.D. Anderson Cancer Center. The goal of this research is to identify novel susceptibility and outcome-related genes for melanoma using a systematic genome-wide association-based approach. Our goal is to conduct high-density SNP association and outcome studies. This dbGaP study contains samples from 2000 European ancestry cases and 1000 European ancestry controls using the Illumina OMNI1-Quad SNP chip. As a part of an ongoing R01 project, we have epidemiological data together with candidate gene results for 1000 of the melanoma cases and the controls. With regard to the outcome aspect of our design, as part of our melanoma Specialized Program of Research Excellence (SPORE) grant, our MelCore database contains comprehensive, prospectively maintained clinical information from all melanoma patients included in the study cohort, including primary tumor histopathology and staging information, standard and investigational blood tumor markers, details of surgical and systemic therapies, and extensive follow-up information, including time to relapse or recurrence, pattern of recurrence and survival duration. Finally, we intend to collaborate with the GenoMEL collaboration so we can jointly evaluate each other's findings. The goal of our analysis will be to identify novel genetic factors predisposing the development of melanoma, as well as genetic factors controlling melanoma stage at presentation, recurrence and progression.</p> <p>This study is part of the Gene Environment Association Studies initiative (GENEVA, <a href="http://www.genevastudy.org" target="_blank">http://www.genevastudy.org</a>) funded by the trans-NIH Genes, Environment, and Health Initiative (GEI). The overarching goal is to identify novel genetic factors that contribute to melanoma through large-scale genome-wide association studies of 2000 European ancestry cases and 1000 European ancestry controls. Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data cleaning and harmonization were done at the GEI-funded GENEVA Coordinating Center at the University of Washington.</p>
| phs000187.v1.p1 | EGA
Project description:High Density SNP Association Analysis of Melanoma: Case-Control and Outcomes Investigation
| PRJNA75479 | ENA
Project description:The Illumina GoldenGate Genotyping Assay is a flexible, pre-optimized assay that uses a discriminatory DNA polymerase and ligase to interrogate 96 SNP loci simultaneously. This Assay utilizes the BeadArray Reader. Using this assay, we examined the distribution of the patients` genotypes to determine which genotype tends to have a better outcomes for cancer treatment.
2015-05-30 | GSE52072 | GEO
Project description:Development and validation of 58K SNP-array and high-density linkage map in Nile tilapia (O. niloticus)
| PRJEB28330 | ENA
Project description:The integration of genomic and epigenomic data is becoming increasingly popular as we try to gain better understanding of the complex mechanisms driving the development and progression of cancer. However, this results in increased cost and sample depletion, the latter being particularly important when considering intra-tumour heterogeneity. We therefore sought to investigate the possible utility of high-density DNA methylation arrays to assess both aberrant methylation as well as changes in gene copy number. Comparing CN (Copy Number) data derived from the Infinium Human Methylation 450K arrays with that generated on SNP arrays, we demonstrate the utility of the Infinium arrays to detect single copy alterations as well as homozygous deletions and high level amplification with the reliability of current gold standard platforms. Furthermore, we show that the gene centric design of the Infinium methylation arrays allows identification of small single gene alterations, which would not be detected using standard SNP array analysis. These results show that Infinium 450K methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. The ability to integrate such data from the same sample is critical for cancer research and will improve our understanding of how complex genomic and epigenomic interactions are driving the development and progression of a malignant phenotype.
2016-05-31 | GSE48941 | GEO
Project description:Whole Genome Association Study of Mammographic Density
| PRJNA292935 | ENA
Project description:High density genotyping of 7 affected and 3 unaffected family members was performed using the Illumina Omni2.5-8 v1.3 BeadChip SNP.
2021-12-31 | GSE191116 | GEO
Project description:The integration of genomic and epigenomic data is becoming increasingly popular as we try to gain better understanding of the complex mechanisms driving the development and progression of cancer. However, this results in increased cost and sample depletion, the latter being particularly important when considering intra-tumour heterogeneity. We therefore sought to investigate the possible utility of high-density DNA methylation arrays to assess both aberrant methylation as well as changes in gene copy number. Comparing CN (Copy Number) data derived from the Infinium Human Methylation 450K arrays with that generated on SNP arrays, we demonstrate the utility of the Infinium arrays to detect single copy alterations as well as homozygous deletions and high level amplification with the reliability of current gold standard platforms. Furthermore, we show that the gene centric design of the Infinium methylation arrays allows identification of small single gene alterations, which would not be detected using standard SNP array analysis. These results show that Infinium 450K methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. The ability to integrate such data from the same sample is critical for cancer research and will improve our understanding of how complex genomic and epigenomic interactions are driving the development and progression of a malignant phenotype. Extracted DNA from each sample was hybridised to Illumina CytoSNP12 v2.1 BeadChips.
2016-05-31 | E-GEOD-48941 | biostudies-arrayexpress
Project description:Acute promyelocytic leukemia (APL) is a hematopoietic malignant disease characterized by the chromosomal translocation t(15;17), resulting in the formation of the PML-RARA gene. Here, 47 t(15;17) APL samples were analyzed with high-density single-nucleotide polymorphism microarray (50K and 250K SNP-chips) using the new algorithm AsCNAR (allele-specific copy-number analysis using anonymous references). Copy-number-neutral loss of heterozygosity (CNN-LOH) was identified at chromosome 10q (3 cases), 11p (3 cases) and 19q (1 case). Twenty-eight samples (60%) did not have an obvious alteration (normal-copy-number [NC] group). Nineteen samples (40%) showed either one or more genomic abnormalities: 8 samples (17%) had trisomy 8 either with or without an additional duplication, deletion, or CNN-LOH (+8 group); and 11 samples (23%) had genomic abnormalities without trisomy 8 (other abnormalities group). These chromosomal abnormalities were acquired somatic mutations. Interestingly, FLT3-ITD mutations (11/47 cases) only occurred in the group with no genomic alteration (NC group). Taken together, these results suggest that the pathway of development of APL differs in each group: FLT3-ITD, trisomy 8, and other genomic changes. Here, we showed for the first time hidden abnormalities and novel disease-related genomic changes in t(15;17) APL. Keywords: SNP-chip To identify oncogenic lesions in APL, we performed a genome-wide analysis of primary APL samples using high-density SNP arrays (Affymetrix GeneChip).
2010-04-03 | E-GEOD-14016 | biostudies-arrayexpress