Copy Number Variations in Genomic Disorders
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ABSTRACT:
PROVIDER: PRJNA75521 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Detection of genomic copy number variations induced by multiple DNA breaks
| PRJNA354382 | ENA
Project description:Analysis of copy number variations among Chinese cattle breeds
| PRJNA203535 | ENA
Project description:Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age-of-onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP do not recommend for routine genetic testing. Given numerous reports of etiologic copy number variations (CNVs) in other neurodevelopmental disorders, we used microarrays to genotype a population-based prospective cohort of children with CP and their parents. Here we identify de novo CNVs in 8/115 (7.0%) CP patients (~1% rate in controls). In four children, large chromosomal abnormalities deemed pathogenic were found, and they were significantly more likely to have severe neuro-motor impairments than those CP subjects without such alterations. Overall the CNV data would have impacted our diagnosis or classification of CP in 11/115 (9.6%) families. Dr. Maryam Oskoui* , Mr. Matthew Gazzellone* , Ms. Bhooma Thiruvahindrapuram , Dr. Mehdi Zarrei , Dr. John Andersen , Dr. John Wei , Dr. Zhouzhi Wang , Dr. Richard Wintle , Dr. Christian Marshall , Dr. Ronald Cohn , Dr. Rosanna Weksberg , Dr. James Stavropoulos , Dr. Darcy Fehlings , Dr. Michael Shevell, Dr. Stephen Scherer. Clinically Relevant Copy Number Variations Detected in Cerebral Palsy. Nature Communications, 2015. Following our rigorous quality control procedure, we successfully genotyped 147 proband samples from individuals with cerebral palsy (81 males and 66 females) and 282 samples obtained from parents (134 males and 148 females). This facilitated the identification of de novo and rare inherited copy number variations of clinical interest.
2015-07-28 | E-GEOD-70374 | biostudies-arrayexpress
Project description:aCGH for 15 rat strains for detection of copy number variations
2008-04-01 | E-MEXP-1514 | biostudies-arrayexpress
Project description:Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age-of-onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP do not recommend for routine genetic testing. Given numerous reports of etiologic copy number variations (CNVs) in other neurodevelopmental disorders, we used microarrays to genotype a population-based prospective cohort of children with CP and their parents. Here we identify de novo CNVs in 8/115 (7.0%) CP patients (~1% rate in controls). In four children, large chromosomal abnormalities deemed pathogenic were found, and they were significantly more likely to have severe neuro-motor impairments than those CP subjects without such alterations. Overall the CNV data would have impacted our diagnosis or classification of CP in 11/115 (9.6%) families. Dr. Maryam Oskoui* , Mr. Matthew Gazzellone* , Ms. Bhooma Thiruvahindrapuram , Dr. Mehdi Zarrei , Dr. John Andersen , Dr. John Wei , Dr. Zhouzhi Wang , Dr. Richard Wintle , Dr. Christian Marshall , Dr. Ronald Cohn , Dr. Rosanna Weksberg , Dr. James Stavropoulos , Dr. Darcy Fehlings , Dr. Michael Shevell, Dr. Stephen Scherer. Clinically Relevant Copy Number Variations Detected in Cerebral Palsy. Nature Communications, 2015.
2015-07-28 | GSE70374 | GEO
Project description:Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations
| PRJNA490196 | ENA
Project description:Segmental copy number variations (CNVs) in the human genome are associated with developmental disorders and susceptibility to human diseases. More importantly, these variations may represent a major genetic component of our phenotypic diversity. In this study, using a whole genome array CGH assay, we identified 3,654 autosomal segmental CNVs, of which 800 appeared at a frequency of at least 3%. 77% of these frequent CNVs are novel. In the 95 individuals analyzed, the most diverse genomes differed by at least 9 Mb in size or varied by at least 266 loci in content. Approximately 68% of the 800 polymorphic regions overlap with genes, reflecting human diversity in senses (smell, hearing, taste, and sight), Rhesus phenotype, metabolism, and disease susceptibility. Intriguingly, 14 polymorphic regions harbor 21 of the known human microRNAs, raising the possibility of microRNAs’ contribution to phenotypic diversity in humans. This in depth survey of CNVs across the human genome provides a valuable baseline for studies involving human genetics. Keywords: array CGH, segmental copy number variations (CNVs)
2006-12-06 | GSE5442 | GEO
Project description:Genomic copy number number characterisation of glioblastoma (GBM) cell lines.
| PRJNA489666 | ENA
Project description:Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genome-wide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intra-provenance cross (north-north cross, 58th parallel) and an inter-provenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a wide-spread North American forest tree. Results: A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar’s 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the inter-provenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar’s distribution, and higher photosynthetic assimilation rates and water-use efficiency at high-latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs, may in fact represent efficient adaptive variations against fast-evolving pathogens.
2018-09-11 | GSE119764 | GEO
Project description:Copy Number Variations (CNVs) were identified performing Comparative Genomic Hybridization (CGH) on 225 patients after whole-genome amplification, using Agilent SurePrint G3 4x180K microarrays. CNVs were further integrated with gene expression (Affymetrix U133+2 arrays) and mutations (targeted DNA resequencing). Complete description of the methods, array quality checks and called segments are available as supplemental material in the corresponding publication.
2019-10-24 | GSE136962 | GEO