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Transcription profiling of breast cancer tissue in a large population-based cohort of Swedish patients

ABSTRACT: Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996. Material was frozen immediatley on dry ice or in liquid nitrogen and stored in -70Â°C freezers. This series contains expression data for n=159 tumors from which RNA could be collected in sufficient amounts and quality for analysis. Experiment Overall Design: All tumor specimens were assessed on U133 A and B arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Ploner

PROVIDER: E-GEOD-1456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts.

Pawitan Yudi Y Bjöhle Judith J Amler Lukas L Borg Anna-Lena AL Egyhazi Suzanne S Hall Per P Han Xia X Holmberg Lars L Huang Fei F Klaar Sigrid S Liu Edison T ET Miller Lance L Nordgren Hans H Ploner Alexander A Sandelin Kerstin K Shaw Peter M PM Smeds Johanna J Skoog Lambert L Wedrén Sara S Bergh Jonas J

Breast cancer research : BCR 20051003 6

<h4>Introduction</h4>Adjuvant breast cancer therapy significantly improves survival, but overtreatment and undertreatment are major problems. Breast cancer expression profiling has so far mainly been used to identify women with a poor prognosis as candidates for adjuvant therapy but without demonstrated value for therapy prediction.<h4>Methods</h4>We obtained the gene expression profiles of 159 population-derived breast cancer patients, and used hierarchical clustering to identify the signature ...[more]

PMID: 16280042

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Gene expression of breast cancer tissue in a large population-based cohort of Swedish patients

Project description:Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996. Material was frozen immediatley on dry ice or in liquid nitrogen and stored in -70°C freezers. This series contains expression data for n=159 tumors from which RNA could be collected in sufficient amounts and quality for analysis. Keywords: breast cancer, expression profiling, predictive gene signature, molecular classification of cancecr

2006-05-31 | GSE1456 | GEO

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Expression data from human sarcoma patient samples treated with either vehicle control or Nutlin-3a

Project description:This study has examined the molecular mechanisms underlying sensitivity of sarcomas to Nutlin-3a, a non-genotoxic activator of the p53 pathway. Human patient material was collected immediately following surgical resection, dissected into small pieces and ex planted onto gelatin sponges immersed in media containing either vehicle control or Nutlin-3a (10uM and/or 50uM) for 48 hours. Nutlin-3a represents a novel targeted therapy for the treatment of sarcomas. We have examined expression profiles of genes upregulated in sarcoma patient derived tissues following nutlin-3a treatment ex vivo 16 samples ((Vehicle control and Nutlin-3a (10uM and 50uM) treated samples)) from 6 sarcoma patients

2014-03-10 | E-GEOD-48296 | biostudies-arrayexpress

OncoScan analysis of breast carcinomas from the Swedish haemangioma cohort

Project description:The Swedish haemangioma cohort consists of 17,200 women treated with radium-226 for skin haemangioma at an early age (<1.5 years of age) between 1920 and 1965. A total of 877 breast cancer cases were reported by December 2009, estimating an excess relative and absolute risk at the age of 50 years of 0.48 Gy^(−1) and 10.4 (10^4 PYR Gy)^(−1), respectively. We screened 31 primary breast carcinomas for genetic alterations using the OncoScan CNV Plus Assay to assess genomic instability.

2019-04-12 | GSE125700 | GEO

Gene expression in obese humans before and during treatment with rimonabant

Project description:Rimonabant was prescribed to eight patients, admitted to the Overweight Study Unit at the Department of Medicine, Karolinska University Hospital. All patients had a BMI > 35 kg/m2, were treated on clinical indications (metabolic and mechanical disability) and without mental disturbances. Blood samples were collected before treatment and at the first clinical control, when the patients had received rimonabant, 20 mg daily, for 4 weeks.

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Cohort profile: the Swedish Pancreatitis Cohort (SwePan).

Project description:PurposeThe Swedish Pancreatitis Cohort (SwePan) was designed to study long-term outcomes following an episode of acute pancreatitis. It can also be used to study various risk factors for developing acute pancreatitis.ParticipantsThe SwePan is a register-based nationwide matched cohort. It includes all Swedish cases of acute pancreatitis during 1990-2019. It contains 95 632 individuals with acute pancreatitis and 952 783 pancreatitis-free individuals matched on sex, age and municipality of residence. Follow-up was censored at death, emigration or end of study (31 December 2019). The dataset includes comprehensive information based on several registries, and includes diagnoses, prescribed medications and socioeconomic factors both prior to inclusion and during follow-up.Findings to dateDuring the study period, the number of cases of acute pancreatitis in Sweden has more than doubled from 1977 cases in 1990 to 4264 cases in 2019. The median age of first episode of acute pancreatitis has increased from 58 years (IQR 44-73 years) in 1990 to 64 years (IQR 49-76 years) in 2019. Cases with acute pancreatitis were generally less healthy compared with the pancreatitis-free individuals (Charlson Comorbidity Index of 0 in 59.2% and 71.4%, respectively).Future plansSwePan will be used to determine the incidence of acute pancreatitis in Sweden over time and assess long-term all-cause and cause-specific mortality after an episode of acute pancreatitis. Some examples of additional planned studies are (1) assessment of long-term risk of diabetes and (2) risk of malignancy in adjacent organs following acute pancreatitis and (3) assessment of risk factors for development of acute pancreatitis including various drugs.

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Homo sapiens

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| PRJNA126209 | ENA

Perceived employability trajectories: A Swedish cohort study.

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Transcription profiling of Xenopus epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate cells, either alone or along with FoxJ1

Project description:Analysis of epithelial explants injected with the intracellular domain of Notch (ICD) to block the formation of multi-ciliate cells, either alone or along with FoxJ1. FoxJ1 misexpression leads to the induction fo ectopic cilia in Xenopus laevis epithelia. Results show which genes are affected by FoxJ1 during the induction of ectopic cilia. Ciliated cells that produce a leftward fluid flow have been proposed to mediate left-right patterning in many vertebrate embryos. These cilia combine features of primary sensory and motile cilia, but how such cilia are specified is unknown. We address this issue by analyzing the Xenopus and Zebrafish homologs of FoxJ1, a forkhead transcription factor necessary for ciliogenesis in multi-ciliate cells of the mouse. We show that the cilia that underlie left-right patterning on the Xenopus gastrocoel roof plate (GRP) and Zebrafish Kupfferâs vesicle (KV) are severely shortened or fail to form in FoxJ1 morphants. We also show that misexpressing XFoxJ1 is sufficient to induce ectopic GRP-like cilia formation in frog embryos. Microarray analysis indicates that XFoxJ1 induces the formation of cilia by upregulating the expression of motile cilia genes. These results indicate that FoxJ1 is a critical determinant in specifying cilia used in left-right patterning. Experiment Overall Design: 2-cell stage Xenopus embryos were injected with synthetic mRNA encoding ICD alone or along with FoxJ1. At stage 9/10 the presumptive ectoderm was cut off the embryo and cultured on a fibronectin coated coverslip. At stage 22 RNA was harvested from explants and used as the starting material for arrays.

2008-10-25 | E-GEOD-12613 | biostudies-arrayexpress

Cohort profile: The Swedish Tattoo and Body Modifications Cohort (TABOO).

Project description:PurposeThe Swedish Tattoo and Body Modifications Cohort (TABOO) cohort was established to provide an infrastructure for epidemiological studies researching the role of tattoos and other body modifications as risk factors for adverse health outcomes. It is the first population-based cohort with detailed exposure assessment of decorative, cosmetic, and medical tattoos, piercing, scarification, henna tattoos, cosmetic laser treatments, hair dyeing, and sun habits. The level of detail in the exposure assessment of tattoos allows for investigation of crude dose-response relationships.ParticipantsThe TABOO cohort includes 13 049 individuals that participated in a questionnaire survey conducted in 2021 (response rate 49%). Outcome data are retrieved from the National Patient Register, the National Prescribed Drug Register and the National Cause of Death Register. Participation in the registers is regulated by Swedish law, which eliminates the risk of loss to follow-up and associated selection bias.Findings to dateThe tattoo prevalence in TABOO is 21%. The cohort is currently used to clarify the incidence of acute and long-lasting health complaints after tattooing based on self-reported data. Using register-based outcome data, we are investigating the role of tattoos as a risk factor for immune-mediated disease, including hypersensitisation, foreign body reactions and autoimmune conditions.Future plansThe register linkage will be renewed every third year to update the outcome data, and we have ethical approval to reapproach the responders with additional questionnaires.

| S-EPMC10163470 | biostudies-literature

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