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Normal DNA (normal + dna)
Selected AbstractsHigh-resolution copy number arrays in cancer and the problem of normal genome copy number variationGENES, CHROMOSOMES AND CANCER, Issue 11 2008Kylie L. Gorringe High-resolution techniques for analysis of genome copy number (CN) enable the analysis of complex cancer somatic genetics. However, the analysis of these data is difficult, and failure to consider a number of issues in depth may result in false leads or unnecessary rejection of true positives. First, segmental duplications may falsely generate CN breakpoints in aneuploid samples. Second, even when tumor data were each normalized to matching lymphocyte DNA, we still observed copy number polymorphisms masquerading as somatic alterations due to allelic imbalance. We investigated a number of different solutions and determined that evaluating matching normal DNA, or at least using locally derived normal baseline data, were preferable to relying on current online databases because of poor cross-platform compatibility and the likelihood of excluding genuine small somatic alterations. © 2008 Wiley-Liss, Inc. [source] Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysisINTERNATIONAL JOURNAL OF CANCER, Issue 8 2008Yanlei Guan Abstract Mapping loss of heterozygosity (LOH) regions in the genomes of tumor tissues is a practical approach for identifying genes whose loss is related to tumorigenesis. Conventional LOH analyses using microsatellite or single nucleotide polymorphism (SNP) markers require the simultaneous examination of tumor- and matched normal-DNA. Here, we improved the previously developed SNP-based LOH assay using single strand conformation polymorphism (SSCP) analysis, so that LOH in tumor samples heavily contaminated with normal DNA can now be precisely estimated, even when matched normal DNA is not available. We demonstrate the reliability of the improved SSCP-based LOH detection method, called the LOH estimation by quantitative SSCP analysis using averaged control (LOQUS-AC), by comparing the results with those of the previous "LOH estimated by quantitative SSCP assay" (LOQUS) method. Using the LOQUS-AC assay, LOH was detected at a high consistency (98.1%) with the previous LOQUS method. We then applied this new method to characterize LOH profiles in 130 meningiomas, using 68 SNPs (i.e., a mean inter-SNP interval of 441 kbp) that are evenly distributed throughout chromosome 1p36. Benign, atypical and anaplastic meningiomas exhibited 1p36 LOH at frequencies of 48.39, 84.62 and 100.00%, respectively, using LOQUS-AC. Subsequently, we detected a candidate common LOH region on 1p36.11 that might harbor tumor suppressor genes related to malignant progression of meningioma. © 2007 Wiley-Liss, Inc. [source] Evidence for heritable predisposition to epigenetic silencing of MLH1INTERNATIONAL JOURNAL OF CANCER, Issue 8 2007Huiping Chen Abstract Epigenetic silencing of MLH1 is the most common cause of defective DNA mismatch repair in endometrial and colorectal cancers. We hypothesized that variation in the MLH1 gene might contribute to the risk for MLH1 methylation and epigenetic silencing. We undertook a case-control study to test for the association between MLH1 variants and abnormal MLH1 methylation. Eight MLH1 SNPs were typed in the normal DNA from women with endometrial carcinoma. For these studies, the cases were women whose cancers exhibited MLH1 methylation (N = 98) and the controls were women whose cancers had no MLH1 methylation (N = 219). One MLH1 SNP, rs1800734, located in the MLH1 CpG island at ,93 from the translation start site, was significantly associated with MLH1 methylation as were age at diagnosis and patient body mass index. In validation experiments, a similar-sized cohort of colorectal carcinoma patients (N = 387) showed a similar degree of association with the ,93 SNP; a smaller cohort of endometrial carcinomas (N = 181) showed no association. Combining all 3 cohorts showed an odds ratio of 1.61 (95% CI: 1.20,2.16) for the AA or AG vs. GG genotype at the ,93 SNP. Identification of risk alleles for MLH1 methylation could shed light on mechanisms of epigenetic silencing and may ultimately lead to new approaches to the prevention or treatment of malignancies associated with MLH1 inactivation. © 2007 Wiley-Liss, Inc. [source] Studies on BrdU labeling of hematopoietic cells: Stem cells and cell linesJOURNAL OF CELLULAR PHYSIOLOGY, Issue 2 2003Lizhen Pang Studies using chronic in vivo BrdU exposure, isolating primitive stem cells, and determining BrdU labeling, indicate that stem cells cycle. BrdU is also incorporated into DNA during damage/repair. DNA, which has incorporated BrdU due to cycle transit is heavier than normal, while the density of DNA with damage/repair incorporation is intermediate. DNA density of purified lineage,rhodamine low (rholow) Hoechst low (Holow) stem cells or FDC-P1 cell line cells,was assessed in vitro, after exposure to cytokines and BrdU (cycling model) or cytokines and BrdU with bleomycin to induce strand breaks and hydroxyurea to halt cycle progression (damage/repair model). We determined DNA density using cesium chloride (CsCl) gradients and either fluorometry or dot blot chemiluminesence. DNA from BrdU labeled cycling Lin-rholoHolo or FDC-P1 cells was heavier than normal DNA, while damage repair DNA had an intermediate density. We then assessed BrdU labeling of Lin-rholoHolo cells in vivo. We found that 70.9% of lin-rholoHolo cells labeled at 5 weeks. DNA density of these cells was low, in the damage/repair range, but similar results were obtained with stem cells, which had proliferated in vivo. Dilution of BrdU in in vitro culture of proliferating FDC-P1 cells also resulted in damage/repair density. We conclude that in vitro BrdU labeling models can distinguish between proliferation and damage/repair, but that we cannot obtain high enough in vivo levels to address this issue. All together, while we cannot absolutely exclude damage/repair as contributing to stem cell BrdU labeling, the data indicate that primitive bone marrow stem cells are probably a cycling population. J. Cell. Physiol. 197: 251,260, 2003© 2003 Wiley-Liss, Inc. [source] First Evidence of Genetic Imbalances in AngiofibromasTHE LARYNGOSCOPE, Issue 2 2002Bernhard Schick MD Abstract Objective/Hypothesis Angiofibromas are clinically well characterized by their origin at the posterior lateral nasal wall close to the sphenopalatine foramen, their occurrence in male adolescent patients, and the histological findings of a benign fibrovascular neoplasm with irregular, endothelium-lined vascular spaces in a fibrous stroma. However, their etiology and genetic causes remain unknown. The present study addresses genetic imbalances in angiofibromas. Study Design The present pilot study compared genomic hybridization in three angiofibromas to search for chromosomal abnormalities in this rare tumor. Methods Fluorescence-marked normal DNA and angiofibroma DNA were compared using genomic hybridization screening to detect chromosomal abnormalities. Their binding ratio to metaphase chromosomes were analyzed by special digital image analysis. Results Chromosomal gains and losses showing a high level of agreement were detected in all three angiofibromas. Specifically, DNA gains were observed on chromosomes 3q, 4q, 5q, 6q, 7q, 8q, 12p, 12q, 13q, 14q, 18q, 21q, and X, and DNA losses were screened on chromosomes 17, 19p, 22q, and Y. Finding chromosomal abnormalities at the sex chromosomes X and Y of this rare tumor is remarkable. Concurrent chromosomal gain on 8q12q22 was noted in all three tumor specimens. Conclusions Comparative genomic hybridization is suitable for screening angiofibromas on a genetic level. The results on these screens indicate that further genetic investigations of this rare benign tumor may provide more details about the tumor's genetic abnormalities and perhaps clarify the etiology of angiofibromas. [source] Control of ,-catenin/Tcf-directed transcription in medulloblastomaACTA PAEDIATRICA, Issue 2004C Raffel The ,-catenin, glycogen synthase kinase 3, (GSK-3,), and adenomatous polyposis coli (APC) gene products interact to form a network that influences the rate of cell proliferation. Medulloblastoma occurs as part of Turcot's syndrome and patients with Turcot's syndrome, who develop medulloblastomas, have been shown to harbor germline APC mutations. While APC mutations have been investigated and not identified in sporadic medulloblastomas, the status of the ,-catenin and GSK-3, genes has not been evaluated in this tumor. This study shows that 3 of 67 medulloblastomas harbor ,-catenin mutations, each of which converts a GSK-3, phosphorylation site from serine to cysteine. The ,-catenin mutation seen in the tumors was not present in matched constitutional DNA in the 2 cases where matched normal DNA was available. A loss of heterozygosity (LOH) analysis of 32 medulloblastomas with paired normal DNA samples was performed with 4 microsatellite markers flanking the GSK-3, locus; LOH with at least one marker was identified in 7 tumors. Sequencing of the remaining GSK-3, allele in these cases failed to identify any mutations. Taken together, these data suggest that activating mutations in the ,-catenin gene may be involved in the development of a subset of medulloblastomas. The GSK-3, gene does not appear to be a target for inactivation in this tumor. [source] | ||||||||||