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High-resolution gene copy number and expression profiling of human chromosome 22 in ovarian carcinomas
Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
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2005 In: Gene, Chromosomes & Cancer, Vol. 42, no 3, 228-237 p.Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2005. Vol. 42, no 3, 228-237 p.
Identifiers
URN: urn:nbn:se:uu:diva-93931OAI: oai:DiVA.org:uu-93931DiVA: diva2:167576
Available from: 2006-03-22 Created: 2006-03-22Bibliographically approved
In thesis
1. Development and Application of Human Chromosome 22 Genomic Microarray: Chromosome 22-Associated Disorders Analyzed by Array-Based Comparative Genomic Hybridization
Open this publication in new window or tab >>Development and Application of Human Chromosome 22 Genomic Microarray: Chromosome 22-Associated Disorders Analyzed by Array-Based Comparative Genomic Hybridization
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The array-based form of comparative genomic hybridization (array-CGH) is a new methodology that has shown to be of significant importance. This thesis focuses on the development of array-CGH with the aim to define candidate regions/genes on chromosome 22 in a wide spectrum of cancer-related conditions. In paper I, we developed and applied the first comprehensive genomic microarray, representing human chromosome 22, for analysis of DNA copy number. Using this array-based approach, we identified gene copy number alterations, including heterozygous/homozygous deletions, amplifications, IGLV/IGLC locus instability and the breakpoints of imbalanced translocation, in several 22q-associated disorders. In paper II, we applied the same array to perform DNA copy number profiling of a series of ovarian carcinoma. cDNA arrays were also used in this study to correlate gene expression levels with DNA-copy number. In the course of this analysis, we determined a small 3.5 Mb candidate 22q telomeric region and suggested a number of specific candidate genes. Paper III described the comprehensive and high-resolution analysis of chromosome 22 in a large set of various stage breast cancers. Multiple distinct patterns of genetic aberrations were observed. The smallest identified candidate locus was 220 kb in size and mapped to a gene-rich region in the vicinity of telomere of 22q. Intriguing result of this study was the detection of high frequency (26.6%) of intra-tumoral clonal variation in gene copy number profiles, which should be viewed as a high number, considering that we study in detail only a single human chromosome. In paper IV, we profiled a series of 28 Wilms tumor samples using 22q-array in order to assess specific regions affected with DNA dosage-alterations. The distribution of aberrations defined a complex amplifier genotype and delimited two tumor suppressor/oncogene candidate loci. These results open up for several avenues for continued research of these tumor forms. These findings also demonstrate the power of array-CGH in the precise determination of minute DNA copy number alterations and strengthen the notion that further studies, preferentially in the context of the entire human genome, are needed.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2006. 56 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 99
Keyword
Molecular genetics, DNA copy number changes, chromosome 22, genomic microarray, array-CGH, schwannoma, neurofibromatosis type 2, ovarian carcinoma, breast cancer, Wilms tumor, Genetik
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-6272 (URN)91-554-6439-4 (ISBN)
Public defence
2006-03-17, Rudbecksalen, Department of Genetics and Pathology, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala, 09:15
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Available from: 2006-03-22 Created: 2006-03-22Bibliographically approved

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