A5061295465- Cancer Genomics and Diagnostics
- Genomic variations and chromosomal abnormalities
- Gene expression and cancer classification
- Lung Cancer Treatments and Mutations
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Epigenetics and DNA Methylation
- Molecular Biology Techniques and Applications
- Nutrition, Genetics, and Disease
- Single-cell and spatial transcriptomics
- Cancer and biochemical research
- Testicular diseases and treatments
- Bayesian Methods and Mixture Models
- Genetic factors in colorectal cancer
- Breast Cancer Treatment Studies
- Cancer Cells and Metastasis
- Science, Research, and Medicine
- Inorganic Chemistry and Materials
- Advanced Statistical Methods and Models
- Chromosomal and Genetic Variations
- Radiopharmaceutical Chemistry and Applications
- Statistical Methods and Applications
- Genomics and Phylogenetic Studies
- Ovarian cancer diagnosis and treatment
- Genetics and Neurodevelopmental Disorders
- Data Mining Algorithms and Applications
University of Oslo
2011-2021
Oslo University Hospital
2010
Abstract Background Cancer progression is associated with genomic instability and an accumulation of gains losses DNA. The growing variety tools for measuring copy numbers, including various types array-CGH, SNP arrays high-throughput sequencing, calls a coherent framework offering unified consistent handling single- multi-track segmentation problems. In addition, there demand highly computationally efficient algorithms, due to the emergence very high density scans number. Results A...
Homozygous deletions are rare in cancers and often target tumour suppressor genes. Here, we build a compendium of 2218 primary tumours across 12 human cancer types systematically screen for homozygous deletions, aiming to identify suppressors. Our analysis defines 96 genomic regions recurrently targeted by deletions. These recurrent occur either over suppressors or fragile sites, increased instability. We construct statistical model that separates sites from showing signatures positive...
Chromosomal instability is a well-defined hallmark of tumor aggressiveness and metastatic progression in colorectal cancer. The magnitude genetic heterogeneity among distinct liver metastases from the same patient at copy number level, as well its relationship with chemotherapy exposure outcome, remains unknown. We performed high-resolution DNA analyses 134 deposits 45 cancer patients to assess: (i) intra-patient inter-metastatic using score based on pair-wise distances deposits; (ii)...
The presence of disseminated tumor cells (DTCs) in bone marrow (BM) identifies breast cancer patients with less favorable outcome. Furthermore, molecular characterization is required to investigate the malignant potential these cells. This study presents a single-cell array comparative genomic hybridization (SCaCGH) method providing analysis immunomorphologically detected DTCs. resolution limit was estimated using cell line SK-BR-3 on 44 and 244k arrays. technique further tested 28...
Genomics studies frequently involve clustering of molecular data to identify groups, but common methods such as K-means and hierarchical do not determine the number clusters. Methods for estimating clusters typically focus on identifying global structure in data, however discovery substructures within may also be great biological interest. We propose a novel method, Partitioning Algorithm based Recursive Thresholding (PART), that recursively uncovers distinct subgroups groups already...
Abstract Somatic copy number alterations are a frequent sign of genome instability in cancer. A precise characterization the architecture would reveal underlying mechanisms and provide an instrument for outcome prediction treatment guidance. Here we show that local spatial behavior profiles conveys important information about this architecture. Six filters were defined to characterize regional traits profiles, resulting Copy Aberration Regional Mapping Analysis (CARMA) algorithm was applied...
Abstract Background Genetic alterations are common in non-small cell lung cancer (NSCLC), and DNA mutations translocations targets for therapy. Copy number aberrations occur frequently NSCLC tumors may influence gene expression further alter signaling pathways. In this study we aimed to characterize the genomic architecture of identify differences between stratified by histology mutation status. Furthermore, sought integrate copy data with mRNA find genes putatively regulated oncogenic...
Testicular germ cell tumours (TGCTs) appear as different histological subtypes or mixtures of these. They show similar, multiple DNA copy number changes, where gain 12p is pathognomonic. However, few high-resolution analyses have been performed and focal changes with corresponding candidate target genes remain poorly described for individual subtypes. We present the first aberration (CNA) analysis on subtype embryonal carcinomas (ECs), including 13 primary ECs 5 EC lines. identified...
555 Background: Almost 50% of patients with colorectal cancer (CRC) develop liver metastases, often as multiple simultaneous metastatic deposits. Up to 25% the are eligible for partial resection, but 70% will relapse after surgery and there currently no good criteria select who benefit from treatment. Genetic heterogeneity among deposits has great potential impact on disease progression, not been well described. Methods: Totally 134 were collected 45 undergoing resection CRC according a...
Abstract Tumor evolution is dependent on and constrained by the genotypes emerging from genome instability. We hypothesized that non-site-specific copy number motifs would correlate with underlying replication defects also tumor patient fate. Six feature detectors were defined to characterize score local spatial behaviour of a profile. By accumulating scores across genomic regions, low-dimensional representation was obtained. The proposed Copy Aberration Regional Mapping Analysis (CARMA)...
Abstract Background: Genetic alterations are common in non-small cell lung cancer (NSCLC), and DNA mutations translocations targets for therapy. Copy number aberrations occur frequently NSCLC tumors may influence gene expression further alter signaling pathways. In this study we aimed to characterize the genomic architecture of identify differences between stratified by histology mutation status. Furthermore, sought integrate copy data with mRNA find genes putatively regulated oncogenic...