| 1. |
- Edvardsen, Hege, et al.
(författare)
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SNP in TXNRD2 Associated With Radiation-Induced Fibrosis : A Study of Genetic Variation in Reactive Oxygen Species Metabolism and Signaling.
- 2013
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Ingår i: International journal of radiation oncology, biology, physics. - : Elsevier BV. - 1879-355X .- 0360-3016. ; 86:4, s. 791-9
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: The aim of the study was to identify noninvasive markers of treatment-induced side effects. Reactive oxygen species (ROS) are generated after irradiation, and genetic variation in genes related to ROS metabolism might influence the level of radiation-induced adverse effects (AEs).METHODS AND MATERIALS: 92 breast cancer (BC) survivors previously treated with hypofractionated radiation therapy were assessed for the AEs subcutaneous atrophy and fibrosis, costal fractures, lung fibrosis, pleural thickening, and telangiectasias (median follow-up time 17.1 years). Single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed for association to AE grade. SNPs associated with subcutaneous fibrosis were validated in an independent BC survivor material (n=283). The influence of the studied genetic variation on messenger ribonucleic acid (mRNA) expression level of 18 genes previously associated with fibrosis was assessed in fibroblast cell lines from BC patients.RESULTS: Subcutaneous fibrosis and atrophy had the highest correlation (r=0.76) of all assessed AEs. The nonsynonymous SNP rs1139793 in TXNRD2 was associated with grade of subcutaneous fibrosis, the reference T-allele being more prevalent in the group experiencing severe levels of fibrosis. This was confirmed in another sample cohort of 283 BC survivors, and rs1139793 was found significantly associated with mRNA expression level of TXNRD2 in blood. Genetic variation in 24 ROS-related genes, including EGFR, CENPE, APEX1, and GSTP1, was associated with mRNA expression of 14 genes previously linked to fibrosis (P≤.005).CONCLUSION: Development of subcutaneous fibrosis can be associated with genetic variation in the mitochondrial enzyme TXNRD2, critically involved in removal of ROS, and maintenance of the intracellular redox balance.
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| 2. |
- Pedersen, Kristina, et al.
(författare)
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A simple way to evaluate self-designed probes for tumor specific Multiplex Ligation-dependent Probe Amplification (MLPA)
- 2010
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Ingår i: BMC Research Notes. - : BioMed Central Ltd. - 1756-0500. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:The Multiplex Ligation-dependent Probe Amplification (MLPA) is widely used for analysis of copy number variations (CNVs) in single or multiple loci. MLPA is a versatile methodology and important tool in cancer research; it provides precise information on increased or decreased copy number at specific loci as opposed to loss of heterozygosity (LOH) studies based upon microsatellite analysis. Pre-designed MLPA kits and software are commercially available to analyze multiple exons, genes, and genomic regions. However, an increasing demand for new gene specific assays makes it necessary to self-design new MLPA probes for which the available software may not be applicable. During evaluation of new self-designed reference probes, we encountered a number of problems, especially when applying the MLPA methodology to tumor samples.FINDINGS:DNA samples from 48 unaffected individuals and 145 breast cancer patients were used to evaluate 11 self-designed MLPA probes and determine the cut-off values for CNV, before applying the MLPA probes to normalize the target probes in a cohort of affected individuals. To test the calculation strategy, three probes were designed to cover regions in Regulator of G-protein Signaling 8 (RGS8), which we previously have identified as being affected by allelic imbalance by LOH analysis across RGS8 in the cohort comprising 145 breast tumors. Agreement between the LOH results and the results obtained by each of the three MLPA probes in RGS8 was found for 64%, 73%, and 91%, of the analyzed samples, respectively.CONCLUSION:Here, we present a straightforward method, based upon the normalization pattern in both unaffected and affected individuals, to evaluate self-designed reference probes and to calculate CNV for the MLPA assay with specific focus on the difficulties when analyzing tumor DNA.
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| 3. |
- Wiechec, Emilia, et al.
(författare)
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Chromosome 1q25.3 copy number alterations in primary breast cancers detected by multiplex ligation-dependent probe amplification and allelic imbalance assays and its comparison with fluorescent in situ hybridization assays
- 2013
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Ingår i: Cellular Oncology. - : Springer Netherlands. - 2211-3428 .- 2211-3436. ; 36:2, s. 113-120
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Tidskriftsartikel (refereegranskat)abstract
- Background: Breast cancer is characterized by a complex pattern of chromosomal alterations, which is in accordance with its heterogeneous character. Simultaneous gains of 1q and losses of 16q represent early events in breast tumourigenesis and have been related to clinical outcome. Here, we evaluated the accuracy of 1q25.3 copy number detection in conjunction with allelic imbalance (AI) detection in a series of primary breast tumours.METHODS:We compared previously obtained AI results from the 1q25.3 region in a series of 222 primary breast tumours with newly obtained MLPA and FISH results. To this end, a novel 1q25.3 MLPA probe set was designed and a commercially available 1q25.3/1p35.2 dual color FISH probe set was used.RESULTS:MLPA revealed 1q25.3 copy number gains and copy number losses in subsets of the tumour samples tested. Next, tumour samples were examined by FISH and scored for the level of 1q25.3 alterations. Non-tumourigenic nuclei from healthy individuals were used to establish cut-off levels for 1q25.3 copy numbers. By doing so, we found a 100 % concordance between the FISH results in breast tumour samples displaying similar 1q25.3 copy number alterations as determined by MLPA and, previously, AI. Furthermore, FISH was found to be instrumental in determining 1q25.3 copy number alterations in samples exhibiting discordances between AI and MLPA.CONCLUSIONS:This study shows that both AI and MLPA assays can be employed to map regions exhibiting copy number alterations in cancer genomes, and that the results obtained are in concordance with FISH assays.
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| 4. |
- Wiechec, Emilia, et al.
(författare)
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High-Resolution Melting Analysis for Mutation Screening of RGSL1, RGS16, and RGS8 in Breast Cancer
- 2011
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Ingår i: Cancer Epidemiology, Biomarkers and Prevention. - : American Association for Cancer Research. - 1055-9965 .- 1538-7755. ; 20:2, s. 397-407
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Tidskriftsartikel (refereegranskat)abstract
- Background: Identification of specific mutation targets in cancer may lead to discovery of the genes modulating cancer susceptibility and/or prognosis. The RGSL1, RGS16, and RGS8 genes within the 1q25.3 region belong to the novel family of regulators of G protein signaling (RGS) genes, which increase the GTPase activity of the G alpha subunit to attenuate signaling from the G protein-coupled receptor. We evaluated the use of high-resolution melting (HRM) to screen for mutations in the genes of interest and assess their clinical significance. Methods: The HRM analysis was used to screen 32 coding exons of RGSL1, RGS16, and RGS8 in tumors from 200 breast cancer patients. All sequence variants detected by HRM resulted in abnormal shape of the melting curves. The identified mutations and known single nucleotide polymorphisms (SNP) were subsequently confirmed by sequencing, and distribution of the SNP genotypes was determined by SNaPshot analysis. A case-control analysis of genotype frequencies was carried out. Results: We identified three tumor specific missense mutations in RGSL1 (ex6 c.664 G>A (Val222Ile), ex13 c.2262 C>G (Asp754Glu), and ex13 c.2316 C>T (Ser772Leu) in three different breast cancer patients. In addition, a total of seven known SNPs were identified in this study. Genotype distributions were not significantly different between breast cancer patients and controls. Conclusions and Impact: Identification of novel mutations within RGSL1 provides a new insight into the pathophysiology of breast cancer. Moreover, the HRM analysis represents a reliable and highly sensitive method for mutation scanning of multiple exons.
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