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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 -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. Experiment Overall Design: All tumor specimens were assessed on U133 A and B arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Pawitan Y

PROVIDER: S-ECPF-GEOD-1456 | biostudies-other | 2005

REPOSITORIES: biostudies-other

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Transcription profiling 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 -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.

2008-06-12 | E-GEOD-1456 | biostudies-arrayexpress

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

Risk and predictors of psoriasis in patients with breast cancer: a Swedish population-based cohort study.

Project description:The risk of psoriasis in patients with breast cancer is largely unknown, as available evidence is limited to case findings. We systematically examined the incidence and risk factors of psoriasis in patients with breast cancer.A Swedish nationwide cohort of 56,235 breast cancer patients (2001-2012) was compared to 280,854 matched reference individuals from the general population to estimate the incidence and hazard ratio (HR) of new-onset psoriasis. We also calculated HRs for psoriasis according to treatment, genetic, and lifestyle factors in a regional cohort of 8987 patients.In the nationwide cohort, 599 patients with breast cancer were diagnosed with psoriasis during a median follow-up of 5.1 years compared to 2795 cases in the matched reference individuals. This corresponded to an incidence rate of 1.9/1000 person-years in breast cancer patients vs. 1.7/1000 person-years in matched reference individuals. Breast cancer patients were at an increased risk of psoriasis (HR = 1.17; 95% confidence interval (CI) = 1.07-1.28), especially its most common subtype (psoriasis vulgaris; HR = 1.33; 95% CI = 1.17-1.52). The risk of psoriasis vulgaris was highest shortly after diagnosis but remained increased up to 12 years. Treatment-specific analyses indicated a higher risk of psoriasis in patients treated with radiotherapy (HR = 2.44; 95% CI = 1.44-4.12) and mastectomy (HR = 1.54, 95% CI = 1.03-2.31). Apart from treatment-specific effects, we identified genetic predisposition, obesity, and smoking as independent risk factors for psoriasis in breast cancer patients.The incidence of psoriasis is slightly elevated among patients with breast cancer, with treatment, lifestyle, and genetic factors defining the individual risk profile.

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The Montreal Cognitive Assessment: Normative Data from a Large Swedish Population-Based Cohort.

Project description:The Montreal Cognitive Assessment (MoCA) has a high sensitivity for detecting cognitive dysfunction. Swedish normative data does not exist and international norms are often derived from populations where cognitive impairment has not been screened for and not been thoroughly assessed to exclude subjects with dementia or mild cognitive impairment.To establish norms for MoCA and develop a regression-based norm calculator based on a large, well-examined cohort.MoCA was administered on 860 randomly selected elderly people from a population-based cohort from the EPIC study. Cognitive dysfunction was screened for and further assessed at a memory clinic. After excluding cognitively impaired participants, normative data was derived from 758 people, aged 65-85.MoCA cut-offs (-1 to -2 standard deviations) for cognitive impairment ranged from <25 to <21 for the lowest educated and <26 to <24 for the highest educated, depending on age group. Significant predictors for MoCA score were age, sex and level of education.We present detailed normative MoCA data and cut-offs according to the DSM-5 criteria for cognitive impairment based on a large population-based cohort of elderly individuals, screened and thoroughly investigated to rule out cognitive impairment. Level of education, sex, and age should be taken in account when evaluating MoCA score, which is facilitated by our online regression-based calculator that provide percentile and z-score for a subject's MoCA score.

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Plasma lipid profiling in a large population-based cohort.

Project description:We have performed plasma lipid profiling using liquid chromatography electrospray ionization tandem mass spectrometry on a population cohort of more than 1,000 individuals. From 10 ?l of plasma we were able to acquire comparative measures of 312 lipids across 23 lipid classes and subclasses including sphingolipids, phospholipids, glycerolipids, and cholesterol esters (CEs) in 20 min. Using linear and logistic regression, we identified statistically significant associations of lipid classes, subclasses, and individual lipid species with anthropometric and physiological measures. In addition to the expected associations of CEs and triacylglycerol with age, sex, and body mass index (BMI), ceramide was significantly higher in males and was independently associated with age and BMI. Associations were also observed for sphingomyelin with age but this lipid subclass was lower in males. Lysophospholipids were associated with age and higher in males, but showed a strong negative association with BMI. Many of these lipids have previously been associated with chronic diseases including cardiovascular disease and may mediate the interactions of age, sex, and obesity with disease risk.

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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

Whole genome expression profiling based on paraffin embedded tissue of a large DLBCL cohort

Project description:Gene expression profiling was carried out for RNA extracted from Formalin-fixed, paraffin embedded (FFPE) biopsies for 1311 patients with diffuse large b-cell lymphoma (DLBCL) using the Illumina DASL platform.

2021-07-30 | GSE181063 | GEO

Transcription profiling of human breast epithelial tissue

Project description: Not available

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Transcription profiling of human breast tissue tumors vs. normal tissue

Project description:bulk breast tumor RNA from patient; Abstract: Sporadic basal-like cancers (BLC) are a distinct class of human breast cancers that are phenotypically similar to BRCA1-associated cancers. Like BRCA1-deficient tumors, most BLC lack markers of a normal inactive X chromosome (Xi). Duplication of the active X chromosome and loss of Xi characterized almost half of BLC cases tested. Others contained biparental but nonheterochromatinized X chromosomes or gains of X chromosomal DNA. These abnormalities did not lead to a global increase in X chromosome transcription but were associated with overexpression of a small subset of X chromosomal genes. Other, equally aneuploid, but non-BLC rarely displayed these X chromosome abnormalities. These results suggest that X chromosome abnormalities contribute to the pathogenesis of BLC, both inherited and sporadic. total 62 sample incudes 43 tumor, 7 normal breast and 12 normal organelle Experiment Overall Design: compare expression of tumor to normal breast tissue

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Population epigenomics of Swedish Arabidopsis

Project description:Plants display remarkable developmental and phenotypic plasticity in order to adapt to their environment. It has long been postulated that epigenetics plays a key role in these processes, but with one or two exceptions, solid evidence for the role of epigenetic variation in these processes is lacking. A key impediment to understanding these processes is the lack of information on the extent of epigenetic variation and how it relates to genetic and phenotypic variation in natural population, both over the lifecycle of an individual, and over evolutionary time. Here we show that genetic variants under selection in the north of Sweden appear to drive variation in DNA methylation, which in turn is highly correlated with local climate. Selective sweeps and genetic variants associated with adaptation to the local environment have previously been identified within the Swedish Arabidopsis population. Our finding that they harbour variants responsible for climate associated epigenetic variation strongly supports the role of epigenetic processes in local adaptation. These findings provide a basis for further dissecting the role of epigenetics in local adaptation at the molecular level

2015-03-28 | GSE65685 | GEO

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