Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Array-CGH screening of medulloblastoma

ABSTRACT: DNA copy-number profiling of 80 primary medulloblastomas of different histologies Keywords: Genetic modification Comparison of tumor DNA (medulloblastoma) versus control DNA (pool of lymphocyte DNA from 10 healthy donors). Whole-genome screening for DNA copy-number aberrations using array-based comparative genomic hybridization (aCGH). Tumor DNA labeled in Cy3 and control DNA labeled in Cy5.

ORGANISM(S): Homo sapiens

SUBMITTER: Stefan Pfister

PROVIDER: E-GEOD-8634 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci.

Pfister Stefan S Remke Marc M Benner Axel A Mendrzyk Frank F Toedt Grischa G Felsberg Jörg J Wittmann Andrea A Devens Frauke F Gerber Nicolas U NU Joos Stefan S Kulozik Andreas A Reifenberger Guido G Rutkowski Stefan S Wiestler Otmar D OD Radlwimmer Bernhard B Scheurlen Wolfram W Lichter Peter P Korshunov Andrey A

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20090302 10

<h4>Purpose</h4>Medulloblastoma is the most common malignant brain tumor in children. Current treatment decisions are based on clinical variables. Novel tumor-derived biomarkers may improve the risk stratification of medulloblastoma patients.<h4>Patients and methods</h4>A model for the molecular risk stratification was proposed from an array-based comparative genomic hybridization (array-CGH) screen (n = 80). Fluorescence in situ hybridization (FISH) analyses for chromosome arms 6q, 17p, and 17q ...[more]

PMID: 19255330

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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-BarrÃ© and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-BarrÃ© or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. The genomic diversity of 33 South African, 2 Mexican and 1 Canadian Campylobacter jejuni strains from humans were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two or three replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

Dataset Information

Array-CGH screening of medulloblastoma

Publications

Outcome prediction in pediatric medulloblastoma based on DNA copy-number aberrations of chromosomes 6q and 17q and the MYC and MYCN loci.

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