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Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper. Uppsala universitet, Science for Life Laboratory, SciLifeLab. (Cancer pharmacology and Computational medicine, Science for Life Laboratory)
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylär och morfologisk patologi.
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper. Uppsala universitet, Science for Life Laboratory, SciLifeLab. (Cancer pharmacology and Computatinal medicine, Science for Life Laboratory)
Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylär och morfologisk patologi.
Vise andre og tillknytning
2011 (engelsk)Inngår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 12, nr 10, s. R108-Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.

sted, utgiver, år, opplag, sider
2011. Vol. 12, nr 10, s. R108-
HSV kategori
Forskningsprogram
Bioinformatik
Identifikatorer
URN: urn:nbn:se:uu:diva-164141DOI: 10.1186/gb-2011-12-10-r108ISI: 000301176900011PubMedID: 22023820OAI: oai:DiVA.org:uu-164141DiVA, id: diva2:466656
Tilgjengelig fra: 2011-12-16 Laget: 2011-12-16 Sist oppdatert: 2018-02-01bibliografisk kontrollert
Inngår i avhandling
1. Copy Number Analysis of Cancer
Åpne denne publikasjonen i ny fane eller vindu >>Copy Number Analysis of Cancer
2015 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

By accurately describing cancer genomes, we may link genomic mutations to phenotypic effects and eventually treat cancer patients based on the molecular cause of their disease, rather than generalizing treatment based on cell morphology or tissue of origin.

Alteration of DNA copy number is a driving mutational process in the formation and progression of cancer. Deletions and amplifications of specific chromosomal regions are important for cancer diagnosis and prognosis, and copy number analysis has become standard practice for many clinicians and researchers. In this thesis we describe the development of two computational methods, TAPS and Patchwork, for analysis of genome-wide absolute allele-specific copy number per cell in tumour samples. TAPS is used with SNP microarray data and Patchwork with whole genome sequencing data. Both are suitable for unknown average ploidy of the tumour cells, are robust to admixture of genetically normal cells, and may be used to detect genetic heterogeneity in the tumour cell population. We also present two studies where TAPS was used to find copy number alterations associated with risk of recurrence after surgery, in ovarian cancer and colon cancer. We discuss the potential of such prognostic markers and the use of allele-specific copy number analysis in research and diagnostics.

sted, utgiver, år, opplag, sider
Uppsala: Acta Universitatis Upsaliensis, 2015. s. 42
Serie
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1072
Emneord
chromosomes, oncology, bioinformatics
HSV kategori
Forskningsprogram
Bioinformatik; Onkologi; Klinisk genetik
Identifikatorer
urn:nbn:se:uu:diva-244361 (URN)978-91-554-9175-8 (ISBN)
Disputas
2015-04-17, BMC E10:1307-1309, BMC, Husargatan 3, Uppsala, 13:00 (engelsk)
Opponent
Veileder
Tilgjengelig fra: 2015-03-26 Laget: 2015-02-16 Sist oppdatert: 2018-01-11

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