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Functionally Active Copy Number Variants Associated with Prostate Cancer Risk

ABSTRACT: Functionally Active Copy Number Variants Associated with Prostate Cancer Risk

PROVIDER: PRJNA157931 | ENA |

REPOSITORIES: ENA

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Functionally Active Copy Number Variants Associated with Prostate Cancer Risk

Project description:<p>Prostate cancer is a leading cause of cancer death in males throughout the world and has the largest estimated effect of heritability among the most common tumor types. Copy Number Variants (CNVs) are a recently recognized class of human germline polymorphisms (Iafrate AJ, et al. (2004) Nat Genet 36, 949-951; Sebat J, et al. (2004) Science 305, 525-528.) and are associated with a variety of human diseases, including cancer. This study characterized 1,903 individuals from the Tyrol Early Prostate Cancer Detection Program (Bartsch G, et al. (2008) BJU Int 101, 809-816) using a computational framework (Banerjee S, et al. (2011) PLoS One 29;6(3)). The study results establish non-coding and coding germline CNVs as significant risk factors for prostate cancer susceptibility and implicate their role in disease development and progression. The study "Identification of functionally active, low frequency copy number variants at 15q21.3 and 12q21.31 associated with prostate cancer risk," Demichelis F, Setlur SR, Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6686-91.</p>

| phs000487.v1.p1 | EGA

Functionally Active Copy Number Variants Associated with Prostate Cancer Risk

| phs000487 | dbGaP

Identification of Copy Number Variants in Dogs

Project description:Identification of Copy Number Variants in Dogs

| PRJNA153385 | ENA

Copy number variants in autism spectrum disorders

Project description:Copy number variants in autism spectrum disorders

| PRJNA1125015 | ENA

Copy number profiling of 556 high-risk neuroblastoma patients using aCGH or SNP arrays

Project description:Purpose: Neuroblastoma is characterized by substantial clinical heterogeneity. Despite intensive treatment, the survival rates of high-risk neuroblastoma patients are still disappointingly low. Somatic chromosomal copy number aberrations have been shown to be associated with patient outcome, particularly in low- and intermediate-risk neuroblastoma patients. To improve outcome prediction in high-risk neuroblastoma, we aimed to design a prognostic classification method based on copy number aberrations. Methods: In an international collaboration, normalized high-resolution DNA copy number data (arrayCGH and SNP arrays) from 556 high-risk neuroblastomas obtained at diagnosis were collected from nine collaborative groups and segmented using the same method. We applied logistic and Cox proportional hazard regression to identify genomic aberrations associated with poor outcome. Results: In this study, we identified two types of copy number aberrations that are associated with extremely poor outcome. (i) Distal 6q losses were detected in 5.9% of patients and were associated with a ten-year survival probability of only 3.4%. (ii) Amplifications of regions not encompassing the MYCN locus were detected in 18% of patients and were associated with a ten-year survival probability of only 5.8%. Conclusion: Using a unique large copy number dataset of high-risk neuroblastoma cases, we identified a small subset of high-risk neuroblastoma patients with extremely low survival probability that might be eligible for inclusion in clinical trials of new therapeutics. The amplicons may also nominate alternative treatments that target the amplified genes.

2018-03-13 | GSE103123 | GEO

Great Ape Copy Number Variation

Project description:Great Ape Copy Number Variation

| PRJNA144461 | ENA

Identification of copy number variants in horses

Project description:Custom exon aCGH analysis of copy number across the genomes of 16 horse breeds

2011-10-08 | GSE32702 | GEO

Identification of Copy Number Variants in Dogs

Project description:Custom exome aCGH analysis of copy number across the genomes of 16 canine breeds

2012-03-08 | GSE36333 | GEO

Progression risk of gland-forming gastric neoplasms assessed by DNA copy-number profiling

Project description:Progression risk of gland-forming gastric neoplasms assessed by DNA copy-number profiling