Profiling of copy-number variation between DNA isolation from different tissues of BN and ACI rats
Ontology highlight
ABSTRACT: We used Nimblegen HD aCGH to detect DNA recovery from different tissue samples Comparison of DNA isolated from different tissues of BN and ACI rats in dye-swap setup
Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and SHR rats Comparison of single BN against single SHR individual in a dye-swap experiment
Project description:We used Nimblegen HD aCGH to detect copy-number variants between genomes of BN and M520 rats Comparison of single BN against single M520 individual in a dye-swap experiment
Project description:We used Nimblegen HD aCGH to detect copy-number variants between tumor and ear control-DNA samples from heterozygous and homozygous Tp53C273X knockout rats Comparison of tumor DNA with ear control-DNA from the same animal
Project description:gDNA was obtained from 26 frozen ERMS tumors for aCGH and copy number analysis Tumors compared to nimblegen pooled male reference, using 2.1 Million probe Nimblegen array CGH Build 18 NCBI36 26 ERMS tumors compared to nimblegen pooled male reference
Project description:Assays in bile duct cancer patients showed 984 CNVs in 306 CNV regions (CNVR) distributed throughout all 22 chromosomes. Bile duct cancer patients had a mean of 21.8 gains and 19.2 losses of genes, with an average of 35.9 CNVRs per patient. Frequent sites of gains were at chromosomes 22q11.22, 2p11.2-p.11.1, 14q32.33 and 17q12, whereas frequent sites of losses were at 19q12-q13.43. Investigation of CNV in 24 bile duct cancer tissue samples
Project description:Genome instability is a characteristic of malignant cells, however, evidence for its contribution to tumorigenesis has been enigmatic. In this study we demonstrate that a complex containing the retinoblastoma protein, E2F1, and Condensin II localizes to major satellite repeats at pericentromeres. In the absence of this complex, this genomic region fails to properly replicate and H2AX phosphorylation at pericentromeric repeats is increased. Our data indicates that these lesions contribute to defective chromosome segregation in the ensuing mitosis. Surprisingly, loss of even one copy of the retinoblastoma gene was sufficient to reduce recruitment of Condensin II to pericentromeres and cause this phenotype. Furthermore, we determined that human RB1 mutation status in cancers of mesenchymal origin correlated with copy number variation, chromosomal gains and losses, as well as chromothriptic rearrangements. Importantly, the magnitude of these chromosomal abnormalities was indistinguishable between RB1+/- and RB1-/- genotypes. Lastly, using gene-targeted mice we determined that mutation of just one copy of the murine Rb1 gene causes sarcomas and lymphomas with increased chromosome copy number variation. Our study connects replication stress with a number of common chromosomal abnormalities in cancer through a dosage sensitive complex present at pericentromeric repeats. Copy number data of thymic lymphomas from 12 different RB1 Δ/+; Trp53-/- mice were analyzed. Tumor DNA was hybridized against same sex control samples (pooled DNA from 5 normal male or female mice). NimbleGen performed a control male vs control female hybridization. All hybridizations were done on a mouse whole genome array (design 2006-07-26-MM8-WG-CGH). Conclusions were drawn from 10X window avereaged, CGH-segMNT analysed data files.
Project description:We describe a more detailed survey undertaken to detect candidate CNVs in a panel of 20 Asian cultivated rice and the genome-wide characteristics of CNVs in subspecies and groups. These resources allowed us to analyze genetic structure as indicated by CNVs, to implicate the biological roles of CNVs, and to identify candidate CNVs that are likely to occur independently in groups and contribute to differences between the subspecies. a panel of 20 accessions
Project description:Spontaneously occurring canine mammary cancer (MC) represents an excellent model of human breast cancer, but is greatly understudied. We performed high density arrays on 12 canine MC cases, including 7 simple carcinomas and four complex carcinomas. Simple carcinomas, which histologically match human breast carcinomas, harbor extensive genomic aberrations, many faithfully recapitulating key features of human breast cancer. Complex carcinomas, with luminal and myoepithelial cells both proliferating (which is rare in human breast cancer), appear to lack genomic abnormalities. Comparison of CNAs from canine mammary simple carcinomas and complex carcinomas
Project description:Investigating genome-wide characteristics of CNVs in 6 horses representing 6 distinct breeds by using the aCGH method and performed GO and KEGG analysis for the CNVs genes.This result is an important complement to the mapping of horse whole-genome CNVs and helpful to study plateau horsesM-bM-^@M-^Y adaption to the plateauM-bM-^@M-^Ys environment. Comparison Mongolia horse , Abaga horse, Hequ horse, Kazakh horse, Debao pony, Thoroughbred with Thoroughbred
Project description:We investigated copy number alterations in melanomas from two cohorts of Braf mutant mice (UV exposed and no UV exposure) by comparing tumour DNA to germline DNA by array CGH There were 15 tumour samples in each cohort (UV exposed and no UV exposure)