Our Institute Director at IMI, Håvard Danielsen, is partner at the Norwegian Cancer Genomics Consortium.

Click this link to read the article featured on the Nature news website.

To read more about this software see “DNA ploidy in diagnostics”

IMI is dependant on external funding to improve our research activity. Funding applications were sent in september 2011, and we are happy to learn our efforts have been appreciated.

Håvard Danielsen has been granted funding for

• one PhD grant for the project “Chromosome organisation in cancer nuclei”
• one PostDoctor grant for the project “Large‐scale Genomic Instability: Biological and Prognostic Importance of DNA index, Binucleated cells and PLK1”

Fahri Saatcioglu has been granted

• one PhD grant for the project “STAMPs as biomarkers and therapeutic targets for prostate cancer”

The grants will facilitate further achievment of great results.

Link to norwegian text about the research grants.

Abstract:

All or almost all neoplasias subjected to systematic cytogenetic scrutiny have been found to harbor acquired chromosomal aberrations. The paradigm stemming from the study of hematopoietic malignancies and sarcomas is that cancers are of monoclonal origin (i.e., they have developed from a single transformed somatic progenitor) because all the neoplastic parenchyma cells share at least one primary chromosomal abnormality, with subsequent clonal evolution along the lines of Darwinian selection occurring among the various subclones carrying secondary aberrations. When carcinomas began to be studied more extensively by cytogenetic methods, however, sometimes many cytogenetically unrelated clones were found, in seeming contradiction to the monoclonal hypothesis. Also studies of multiple samples from the same patient led to a rethinking of what the cytogenetic evidence really revealed about tumor clonality, both in its early stages and during disease development. The observed cytogenetic heterogeneity in, for example, tumors of the breast and pancreas vastly surpasses that of leukemias, lymphomas, connective tissue tumors, or even most epithelial, including uroepithelial, tumors. Theoretical reasoning as well as the available experimental data we here review show that the clonal evolution of neoplastic cell populations follows either of four principal pathways: (1) initial monoclonality is retained throughout the entire course of the disease with no additional, secondary aberrations accrued as judged by karyotypic appearance; (2) tumorigenesis is monoclonal but additional aberrations develop with time leading to secondary clonal heterogeneity (clonal divergence); (3) polyclonal tumorigenesis exists from the beginning but is followed by an overall reduction in genomic complexity with time (clonal convergence) due to selection among cytogenetically unrelated clones during tumor progression, resulting in secondary oligo- or monoclonality; or (4) polyclonal tumorigenesis with early clonal convergence is followed by later clonal divergence due to the acquisition of additional cytogenetic changes by the clone(s) that survived during the middle phases of tumor progression. Further studies of individual tumor cells are necessary to elicit precise information about the cell-to-cell variability that exists in many, especially epithelial, neoplasms and which holds the key to a more profound understanding of the complex issue of tumor clonality during all stages of cancer development.

Copyright © 2011 Elsevier Inc. All rights reserved.

Background:

With the recent advances and availability of various high-throughput sequencing technologies, data on many molecular aspects, such as gene regulation, chromatin dynamics, and the three-dimensional organization of DNA, are rapidly being generated in an increasing number of laboratories. The variation in biological context, and the increasingly dispersed mode of data generation, imply a need for precise, interoperable and flexible representations of genomic features through formats that are easy to parse. A host of alternative formats are currently available and in use, complicating analysis and tool development. The issue of whether and how the multitude of formats reflects varying underlying characteristics of data has to our knowledge not previously been systematically treated.

Results:

We here identify intrinsic distinctions between genomic features, and argue that the distinctions imply that a certain variation in the representation of features as genomic tracks is warranted. Four core informational properties of tracks are discussed: gaps, lengths, values and interconnections. From this we delineate fifteen generic track types. Based on the track type distinctions, we characterize major existing representational formats and find that the track types are not adequately supported by any single format. We also find, in contrast to the XML formats, that none of the existing tabular formats are conveniently extendable to support all track types. We thus propose two unified formats for track data, an improved XML format, BioXSD 1.1, and a new tabular format, GTrack 1.0.

Conclusions:

The defined track types are shown to capture relevant distinctions between genomic annotation tracks, resulting in varying representational needs and analysis possibilities. The proposed formats, GTrack 1.0 and BioXSD 1.1, cater to the identified track distinctions and emphasize preciseness, flexibility and parsing convenience.

Background:

Angiogenesis plays a role in the biology of ovarian cancer. We examined the effect of bevacizumab, the vascular endothelial growth factor inhibitor, on survival in women with this disease.

Methods:

We randomly assigned women with ovarian cancer to carboplatin (area under the curve, 5 or 6) and paclitaxel (175 mg per square meter of body-surface area), given every 3 weeks for 6 cycles, or to this regimen plus bevacizumab (7.5 mg per kilogram of body weight), given concurrently every 3 weeks for 5 or 6 cycles and continued for 12 additional cycles or until progression of disease. Outcome measures included progression-free survival, first analyzed per protocol and then updated, and interim overall survival.

Results:

A total of 1528 women from 11 countries were randomly assigned to one of the two treatment regimens. Their median age was 57 years; 90% had epithelial ovarian cancer, 69% had a serous histologic type, 9% had high-risk early-stage disease, 30% were at high risk for progression, and 70% had stage IIIC or IV ovarian cancer. Progression-free survival (restricted mean) at 36 months was 20.3 months with standard therapy, as compared with 21.8 months with standard therapy plus bevacizumab (hazard ratio for progression or death with bevacizumab added, 0.81; 95% confidence interval, 0.70 to 0.94; P=0.004 by the log-rank test). Nonproportional hazards were detected (i.e., the treatment effect was not consistent over time on the hazard function scale) (P<0.001), with a maximum effect at 12 months, coinciding with the end of planned bevacizumab treatment and diminishing by 24 months. Bevacizumab was associated with more toxic effects (most often hypertension of grade 2 or higher) (18%, vs. 2% with chemotherapy alone). In the updated analyses, progression-free survival (restricted mean) at 42 months was 22.4 months without bevacizumab versus 24.1 months with bevacizumab (P=0.04 by log-rank test); in patients at high risk for progression, the benefit was greater with bevacizumab than without it, with progression-free survival (restricted mean) at 42 months of 14.5 months with standard therapy alone and 18.1 months with bevacizumab added, with respective median overall survival of 28.8 and 36.6 months.

Conclusions:

Bevacizumab improved progression-free survival in women with ovarian cancer. The benefits with respect to both progression-free and overall survival were greater among those at high risk for disease progression. (Funded by Roche and others; ICON7 Controlled-Trials.com number, ISRCTN91273375.).

Objective:

To compare the performance of different assays for measuring apoptosis in cytological specimens.

Methods:

Apoptosis was assessed in 27 specimens (22 effusions, five fine needle aspirates; 20 malignant, seven reactive) using flow cytometry, applying assays for the measurement of annexin V expression, caspase-3 and -8 cleavage and deoxynucleotidyl transferase deoxyuridine triphosphates (dUTP) incorporation. Results were studied for differences between reactive and malignant specimens, as well as performance across assays.

Results:

Wide variation in the degree of apoptosis was observed in both benign and malignant specimens using all assays. However, the percentage of annexin V-positive cells was higher compared with those showing caspase cleavage or dUTP incorporation in the majority of cases, irrespective of specimen type. Comparative analysis of benign and malignant specimens showed no significant differences in expression of any of the studied parameters. However, tumour cells and reactive mesothelial cells in pleural effusions had a significantly lower level of dUTP incorporation compared with their counterparts in peritoneal specimens (P = 0.001).

Conclusions:

The present data are in agreement with our previous observation in ovarian carcinoma effusions, that measurement of apoptosis by the annexin V assay provides higher expression values than those obtained by other assays, suggesting that this assay does not accurately reflect the degree of apoptosis in benign or malignant cells in effusions.

© 2010 Blackwell Publishing Ltd.

Abstract

Giant cell ependymoma, a rare ependymoma subtype, was recently recognized as a separate diagnostic entity with variations both in malignant potential and course of disease. We analyzed the first supratentorial giant cell ependymoma using G-band karyotyping, DNA ploidy analysis, and array comparative genomic hybridization. The tumor was hypodiploid, and the karyotype showed multiple monosomies. This novel cytogenetic pattern seems specific for giant cell ependymoma as the only previous cytogenetic analysis of a giant cell ependymoma found similar monosomies. We were also able to analyze cytogenetically the subsequent recurrent tumor, phenotypically an anaplastic ependymoma, allowing a first insight into the genetic events involved in disease progression.

Copyright © 2011 Elsevier Inc. All rights reserved.

Breast malignancy Overview

Close

Breast Overview

In comparison, the disease affected 1,235 women in 1970. Breast cancer affects first and foremost women over the age of 50. Only 5.6% of new cases occurred in women under 40 years in 2004. The disease constitutes 40% of all cancer in women between the ages of 30 to 54 years. The average age at diagnosis is 59. The risk increases with age, but isolated cases occur in women under 30 years of age.

Background

Breast cancer is by far the most common form of cancer in women. The disease is characterized by a varied course, from rapidly growing tumors with early distant metastasis, to slow growing tumors which remain in the breasts without metastasizing. Twenty-five to 35% of breast tumors are aggressive. The majority of breast tumors are carcinomas. Sarcoma tumors are rare, but are important to be aware of as they are treated differently from other breast carcinomas.

Survival after diagnosis and treatment has continually improved over many decades. This is in part due to increased use of mammography screening, which provides early detection of the disease, and improved treatment. Approximately 2/3 of patients are cured of the disease. Five year survival without a sign of relapse, all stages considered, is more than 80%. In 2004, 694 women and 3 men died of breast cancer in Norway. Of these, 423 were over 65 years. Breast cancer is the most important cause of lost years of life in women under 65 years and ranks before both heart/vascular diseases and accidents. At the end of 2005, there were 31,548 women with the diagnosis.

How to improve prognosis

Early diagnosis is, despite great differences in biology, the most important means of improving the prognosis. The prognosis is also strongly dependent on stage. Five year relative survival where the disease is limited to the breast is 94.1%, compared to 16.9%, if there is distant metastasis at the time of diagnosis.

Seventy to 80% of invasive breast carcinomas are histologically of the infiltrating ductal type. Ten to 20% are of the infiltrating lobular type, while other types constitute the rest.

Stages of Breast Cancer

Premalignant lesions are recognized microscopically by abnormal proliferative activity (cell growth) in the ductal system or in the glands (lobular), but where there are no signs that the epithelial cells have penetrated the basal membrane. The lesions can be classified according to proliferation, cellular atypia and tissue architecture as shown below:

• Lobular and ductal epithelial hyperplasia without atypia
• Lobular and ductal epithelial hyperplasia with atypia
• Lobular carcinoma in situ (LCIS)
• Ductal carcinoma in situ (DCIS) grade 1-3 (van Nuys grading) (2)

DCIS, also known as intraductal carcinoma, should not be confused with invasive carcinoma of the ductal type. Previously, DCIS was considered a rare condition and constituted only between 1.4 and 5.3% of all newly diagnosed breast cancer cases. After the introduction of mammography screening, more women are diagnosed with DCIS (10-30%).

In areas with established mammography screening programs, DCIS constitutes 25-30% of new breast cancer cases in the first screening round. In later screening rounds, the number is 10-20%. The main problem with DCIS is that the risk for local recurrence in the breast after resection alone is much greater than with other pre-malignant lesions in breast tissue. In addition,a large majority of DCIS will not develop into invasive carcinoma if left untreated. For this reason, there is a great need for dependable prognostic markers.

Prognostic markers

DNA ploidy by image analysis is established as a general diagnostic marker and as a prognostic/predictive marker for gynecological cancers and oral dysplasias. The potential as a prognostic marker is great, and multiple studies have evaluated the correlation between DNA ploidy and prognosis for breast cancer. The results from these studies are, however, sparse and many of the studies are too small or insufficient. Due to the lack of data, the American Society of Clinical Oncology has repeatedly recommended that DNA ploidy should not be used as a prognostic marker for breast cancer. Because of the inconsistent results from studies on correlation between DNA proliferation and prognosis, Bagwell et al. from Baylor College of Medicine developed a model which categorizes patients into different risk groups by adjusting the classification of ploidy histograms and S-phase fraction. The study was based on a cohort of 961 node-negative patients and gave promising and significant results. The model also gave similar improvements in prognostic value of DNA when used on Swedish and French breast cancer databases for 210 and 220 cases, respectively. Today, there are multiple groups using composite models to support breast cancer diagnosing.

Nucleotyping represents among other features an objective assessment of nuclear atypia, one of the most important features of histopathological diagnosis and prognosis. It a allows for a qualitative assessment of chromatin structure, and the method is also sensitive for larger chromosomal aberrations. Of even greater importance is the methods ability to map and quantify functional changes in DNA organization. Such changes are, to a large extent, sub-visual, and are therefore not detected by traditional microscopy. Nucleotyping might be described as interphase cytogenetics, or an interphase version of karyotyping, where organisational and functional domains of DNA are mapped and described. We will investigate the value of nucleotyping as a prognostic marker for breast cancer.

Breast Cancer Materials

Normal breast

This material consists of 43 normal breast specimens which can be used as control material. We have previously measured DNA ploidy for all cases.

Ductal carcinomas in situ

Ductal carcinoma in situ represents a special diagnostic challenge, since around 20% develop into invasive cancer and there is no clear maker for identification. We have a total of 121 patients separated into 75 patients from Nottingham (75 DCIS + 25 samples which later developed into invasive tumor) and 43 patients from Oslo University Hospital.

Breast cancer stage I/II

We have a total of 480 patients with a clear prognosis (good prognosis: disease free > 10 years after treatment, poor prognosis: recurrence or death within 5 years from the disease). This pilot study is for DNA ploidy and nucleotyping as a prognostic marker for breast cancer. The material can also be used for a comparative investigation of alternative methods for DNA ploidy determination. We have previously made TMA blocks for the project. The material has been used for a collaboration project with CCB (Kirsten Sandvig) where the purpose is to investigate the clinical significance of Flotillin 1 and 2, and the connection between expression levels of Flotillins and the known clinical biomarker ErbB2.