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Candidate Markers (candidate + marker)
Selected AbstractsP38 mitogen-activated protein kinase signal transduction in the diagnosis and follow up of immunotherapy of wasp venom allergy,CYTOMETRY, Issue 5 2010Marjoke M. Verweij Abstract Background: P38 mitogen-activated protein kinase (MAPK) is known to govern IgE-mediated basophil activation. Intracellular phosphorylated p38 MAPK (Pp38 MAPK) in IgE-activated basophils can be quantified flow cytometrically. Objectives: To study whether Pp38 MAPK constitutes a potential novel read-out for flow-assisted diagnosis of hymenoptera venom allergy and to investigate whether this marker allows follow-up of successful venom immunotherapy (VIT). Methods: Fifty-two patients with documented wasp venom allergy and seven wasp-stung asymptomatic control individuals were enrolled. Wasp venom-induced basophil activation was analyzed flow cytometrically with anti-IgE, anti-CD63, and anti-Pp38 MAPK to assess their activation status before starting immunotherapy. To assess whether p38 MAPK constitutes a candidate marker for monitoring VIT, we repeated the basophil activation test (BAT) in 25 patients on the fifth day of a build-up immunotherapy. In addition, we investigated whether the Pp38 MAPK-based BAT could contribute in the decision of discontinuing VIT in a cross-sectional analysis in 13 patients receiving treatment for 3 years and 14 patients receiving treatment for 5 years. Results: Patients exhibited a dose-dependent basophil activation with phosphorylation of p38 MAPK and upregulation of downstream CD63. In contrast, stung controls demonstrated a dose-dependent but "abrogated" signal transduction in basophils with less and shorter duration of the phosphorylation of p38 MAPK and without subsequent upregulation of CD63. When repeated after 5 days of VIT and when investigated cross-sectionally after 3 years or 5 years of maintenance therapy, no effect of VIT on the phosphorylation of p38 MAPK was demonstrable. Conclusions: This study discloses that not only basophils from patients, but also from the stung control individuals, respond to wasp venom stimulation with phosphorylation of p38 MAPK, although to a lesser extend. No clear effect of VIT on the phosphorylation of p38 MAPK was shown. Thus, although p38 MAPK provides an additional tool in the diagnosis of wasp venom allergy, it does not contribute to the decision whether to stop successful VIT. © 2010 International Clinical Cytometry Society [source] A randomized controlled trial of transcatheter arterial chemoembolization with lipiodol, doxorubicin and cisplatin versus intravenous doxorubicin for patients with unresectable hepatocellular carcinomaEUROPEAN JOURNAL OF CANCER CARE, Issue 5 2009M. MABED md, professor Hepatocellular carcinoma (HCC) is a major and often therapeutically frustrating oncological problem. A total of 100 patients with unresectable HCC were recruited and randomized to be treated with either transcatheter arterial chemoembolization (TACE) or systemic chemotherapy. Fifty patients were treated with TACE using lipiodol, doxorubicin and cisplatin, while 50 patients were treated with systemic doxorubicin alone. Patients treated with TACE achieved a significantly higher response rate, with partial response achieved in 16 patients (32%) versus five patients (10%) in the chemotherapy arm (P = 0.007). A significantly more favourable tumour response to chemoembolization was found in patients with single lesions (P = 0.02), Child class A (P = 0.007), Okuda stage 1 (P = 0.005) and ,-feto protein less than 400 ng/mL (P < 0.001). The probability of tumour progression was significantly lower in cases treated with TACE where the median progression free survival was 32 weeks (range, 16,70 weeks) versus 26 weeks (range, 14,54 weeks) for patients treated with systemic chemotherapy (P = 0.03). However, the median overall survival did not differ significantly in cases treated with TACE (38 weeks) compared with those treated with chemotherapy (32 weeks) (P = 0.08), except for patients with serum albumin >3.3 g/dL (60 vs. 36 weeks; P = 0.003). Multivariate Cox regression analysis showed that a rise of serum albumin by 1 g/dL is associated with a decrease in the risk of death by 33% (95% confidence interval: 0.12,0.94, P = 0.038). Mortality in the chemoembolization arm was due to tumour progression in 18 patients (53%), liver failure in 11 patients (32%) and gastro intestinal tract (GIT) bleeding in 5 patients (15%). Mortality in the chemotherapy arm was due to tumour progression in 23 patients (64%), liver failure in 9 patients (25%) and GIT bleeding in 4 patients (11%). Treatment-related mortality was 4% in the TACE arm versus 0% in the chemotherapy arm. In conclusion, the overall survival benefits of TACE and systemic doxorubicin are similar for patients with unresectable HCC amenable to either treatment. It is crucial to optimize the benefit,risk ratio of TACE. In this setting, serum albumin level is a candidate marker for selection of cases who may benefit from this procedure. [source] Heightened Expression of the Cytotoxicity Receptor NKG2D Correlates with Acute and Chronic Nephropathy After Kidney TransplantationAMERICAN JOURNAL OF TRANSPLANTATION, Issue 2 2007M. Seiler The activating cytotoxicity receptor NKG2D binds to stress-regulated molecules encoded by the major histocompatibility complex class I chain-related (MIC) and UL-16-binding protein (ULBP)/retinoic acid early transcript (RAET) gene family. To assess whether acute allograft rejection leads to an induction of these inducible ligands and their receptor NKG2D, we examined the mRNA profiles in kidney transplant biopsies. Expression levels were correlated with the incidence of acute rejection (aRx) episodes and chronic allograft nephropathy (CAN) proven by histology. Whereas MICA, ULBP1/3 and RAET1-E did not display heightened gene expression, elevated levels of NKG2D mRNA could be associated with aRx (p < 0.001). Immunohistology of kidney biopsies diagnosed with aRx revealed NKG2D+ cells in tubulointerstitial areas positive for CD8+ cells. Most importantly, elevated levels of NKG2D mRNA were associated with restricted long-term graft function assessed by the glomerular filtration rate at 6, 12 and 18 months posttransplantation. Induced NKG2D mRNA expression was still observable in biopsies diagnosed with CAN (p < 0.001), demonstrating a higher sensitivity and specificity compared to CD3, granzyme B and granulysin mRNA measurement. Significant elevated levels of NKG2D mRNA could be further detected in urine sediment prior to aRx, suggesting this receptor as a new candidate marker for the diagnosis of acute and chronic allograft rejection. [source] Muscle Nogo-a expression is a prognostic marker in lower motor neuron syndromesANNALS OF NEUROLOGY, Issue 1 2007Pierre-François Pradat MD Objective A proportion of patients with pure lower motor neuron syndrome (LMNS) progress to amyotrophic lateral sclerosis (ALS). Early detection of this progression is impossible, which delays the patient's access to treatment. Muscle expression of Nogo-A is a new candidate marker of ALS. We tested whether detection of Nogo-A in a muscle biopsy from patients with LMNS predicts progression to ALS. Methods Thirty-three patients who had undergone a muscle biopsy during the diagnostic workup of spinal LMNS were observed for 12 months. Nogo-A expression was measured by Western blot in muscle biopsy samples and compared with the final diagnosis. Results Nogo-A expression was detected in 17 patients and was absent in 16 patients. The detection of Nogo-A in muscle biopsy samples from LMNS patients correctly identified patients who further progressed to ALS with 91% accuracy, 94% sensitivity, and 88% specificity. In patients who later developed typical ALS, Nogo-A may be detected as early as 3 months after the onset of symptoms. Interpretation Nogo-A test is able to identify ALS early in the course of the disease when diagnosis is difficult, requiring further progression. Use of the test in clinical practice may shorten the delay before introduction of neuroprotective drugs or inclusion in clinical trials. Ann Neurol 2007 [source] Reg IV is an independent prognostic factor for relapse in patients with clinically localized prostate cancerCANCER SCIENCE, Issue 8 2008Shinya Ohara Regenerating islet-derived family, member 4 (REG4, which encodes Reg IV) is a candidate marker for cancer and inflammatory bowel disease. We investigated the potential prognostic role of Reg IV immunostaining in clinically localized prostate cancer (PCa) after radical prostatectomy. Immunohistochemical staining of Reg IV was performed in 98 clinically localized PCa tumors obtained during curative radical prostatectomy. Intestinal and neuroendocrine differentiation was investigated by MUC2 and chromogranin A immunostaining, respectively. The prognostic significance of immunohistochemical staining for these factors on prostate-specific antigen (PSA)-associated recurrence was assessed by Kaplan,Meier analysis and a Cox regression model. Phosphorylation of the epidermal growth factor receptor (EGFR) by Reg IV was analyzed by Western blot. In total, 14 (14%) of the 98 PCa cases were positive for Reg IV staining. Reg IV positivity was observed frequently in association with MUC2 (P = 0.0182) and chromogranin A positivity (P = 0.0012). Univariate analysis revealed that Reg IV staining (P = 0.0004), chromogranin A staining (P = 0.0494), Gleason score (P < 0.0001) and preoperative PSA concentration (P = 0.0167) were significant prognostic factors for relapse-free survival. Multivariate analysis indicated that Reg IV staining (P = 0.0312), Gleason score (P = 0.0014) and preoperative PSA concentration (P = 0.0357) were independent predictors of relapse-free survival. In the LNCaP cell line, EGFR phosphorylation was induced by the addition of Reg IV-conditioned medium. These results suggest that Reg IV expression is an independent prognostic indicator of relapse after radical prostatectomy. (Cancer Sci 2008; 99: 1570,1577) [source] The strength of anticipatory spatial biasing predicts target discrimination at attended locations: a high-density EEG studyEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 11 2009Simon P. Kelly Abstract Cueing relevant spatial locations in advance of a visual target results in modulated processing of that target as a consequence of anticipatory attentional deployment, the neural signatures of which remain to be fully elucidated. A set of electrophysiological processes has been established as candidate markers of the invocation and maintenance of attentional bias in humans. These include spatially-selective event-related potential (ERP) components over the lateral parietal (around 200,300 ms post-cue), frontal (300,500 ms) and ventral visual (> 500 ms) cortex, as well as oscillatory amplitude changes in the alpha band (8,14 Hz). Here, we interrogated the roles played by these anticipatory processes in attentional orienting by testing for links with subsequent behavioral performance. We found that both target discriminability (d') and reaction times were significantly predicted on a trial-by-trial basis by lateralization of alpha-band amplitude in the 500 ms preceding the target, with improved speed and accuracy resulting from a greater relative decrease in alpha over the contralateral visual cortex. Reaction time was also predicted by a late posterior contralateral positivity in the broad-band ERP in the same time period, but this did not influence d'. In a further analysis we sought to identify the control signals involved in generating the anticipatory bias, by testing earlier broad-band ERP amplitude for covariation with alpha lateralization. We found that stronger alpha biasing was associated with a greater bilateral frontal positivity at ,390 ms but not with differential amplitude across hemispheres in any time period. Thus, during the establishment of an anticipatory spatial bias, while the expected target location is strongly encoded in lateralized activity in parietal and frontal areas, a distinct non-spatial control process seems to regulate the strength of the bias. [source] Microarray analysis yields candidate markers for rotation resistance in the western corn rootworm beetle, Diabrotica virgifera virgiferaEVOLUTIONARY APPLICATIONS (ELECTRONIC), Issue 1 2010Lisa M. Knolhoff Abstract As pest species may evolve resistance to chemical controls, they may also evolve resistance to cultural control methods. Yearly rotation of corn (Zea mays) with another crop interrupts the life cycle of the western corn rootworm beetle (Diabrotica virgifera virgifera, Coleoptera: Chrysomelidae), but behavioral resistance to crop rotation is now a major problem in the Midwest of the USA. Resistant adult females exhibit reduced fidelity to corn as a host and lay their eggs in the soil of both corn and soybean (Glycine max) fields. Behavioral assays suggest that the adaptation is related to increased locomotor activity, but finding molecular markers has been difficult. We used microarray analysis to search for gene expression differences between resistant and wild-type beetles. Candidates validated with real-time polymerase chain reaction exhibit predicted patterns from the microarray in independent samples across time and space. Many genes more highly expressed in the rotation-resistant females have no matches to known proteins, and most genes that were more lowly expressed are involved in antimicrobial defense. [source] Tumor microenvironment in head and neck squamous cell carcinomas: Predictive value and clinical relevance of hypoxic markers.HEAD & NECK: JOURNAL FOR THE SCIENCES & SPECIALTIES OF THE HEAD AND NECK, Issue 6 2007A review Abstract Background. Hypoxia and tumor cell proliferation are important factors determining the treatment response of squamous cell carcinomas of the head and neck. Successful approaches have been developed to counteract these resistance mechanisms although usually at the cost of increased short- and long-term side effects. To provide the best attainable quality of life for individual patients and the head and neck cancer patient population as a whole, it is of increasing importance that tools be developed that allow a better selection of patients for these intensified treatments. Methods. A literature review was performed with special focus on the predictive value and clinical relevance of endogenous hypoxia-related markers. Results. New methods for qualitative and quantitative assessment of functional microenvironmental parameters such as hypoxia, proliferation, and vasculature have identified several candidate markers for future use in predictive assays. Hypoxia-related markers include hypoxia inducible factor (HIF)-1,, carbonic anhydrase IX, glucose transporters, erythropoietin receptor, osteopontin, and others. Although several of these markers and combinations of markers are associated with treatment outcome, their clinical value as predictive factors remains to be established. Conclusions: A number of markers and marker profiles have emerged that may have potential as a predictive assay. Validation of these candidate assays requires testing in prospective trials comparing standard treatment against experimental treatments targeting the related microregional constituent. © 2007 Wiley Periodicals, Inc. Head Neck, 2007 [source] Cancer-associated molecular signature in the tissue samples of patients with cirrhosis,HEPATOLOGY, Issue 2 2004Jin Woo Kim Several types of aggressive cancers, including hepatocellular carcinoma (HCC), often arise as a multifocal primary tumor. This suggests a high rate of premalignant changes in noncancerous tissue before the formation of a solitary tumor. Examination of the messenger RNA expression profiles of tissue samples derived from patients with cirrhosis of various etiologies by complementary DNA (cDNA) microarray indicated that they can be grossly separated into two main groups. One group included hepatitis B and C virus infections, hemochromatosis, and Wilson's disease. The other group contained mainly alcoholic liver disease, autoimmune hepatitis, and primary biliary cirrhosis. Analysis of these two groups by the cross-validated leave-one-out machine-learning algorithms revealed a molecular signature containing 556 discriminative genes (P < .001). It is noteworthy that 273 genes in this signature (49%) were also significantly altered in HCC (P < .001). Many genes were previously known to be related to HCC. The 273-gene signature was validated as cancer-associated genes by matching this set to additional independent tumor tissue samples from 163 patients with HCC, 56 patients with lung carcinoma, and 38 patients with breast carcinoma. From this signature, 30 genes were altered most significantly in tissue samples from high-risk individuals with cirrhosis and from patients with HCC. Among them, 12 genes encoded secretory proteins found in sera. In conclusion, we identified a unique gene signature in the tissue samples of patients with cirrhosis, which may be used as candidate markers for diagnosing the early onset of HCC in high-risk populations and may guide new strategies for chemoprevention. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html). (HEPATOLOGY 2004;39:518,527.) [source] Classification of cancer types by measuring variants of host response proteins using SELDI serum assaysINTERNATIONAL JOURNAL OF CANCER, Issue 5 2005Eric T. Fung Abstract Protein expression profiling has been increasingly used to discover and characterize biomarkers that can be used for diagnostic, prognostic or therapeutic purposes. Most proteomic studies published to date have identified relatively abundant host response proteins as candidate biomarkers, which are often dismissed because of an apparent lack of specificity. We demonstrate that 2 host response proteins previously identified as candidate markers for early stage ovarian cancer, transthyretin and inter-alpha trypsin inhibitor heavy chain 4 (ITIH4), are posttranslationally modified. These modifications include proteolytic truncation, cysteinylation and glutathionylation. Assays using Surface Enhanced Laser Desorption/Ionization Time of Flight Mass Spectrometry (SELDI-TOF-MS) may provide a means to confer specificity to these proteins because of their ability to detect and quantitate multiple posttranslationally modified forms of these proteins in a single assay. Quantitative measurements of these modifications using chromatographic and antibody-based ProteinChip® array assays reveal that these posttranslational modifications occur to different extents in different cancers and that multivariate analysis permits the derivation of algorithms to improve the classification of these cancers. We have termed this process host response protein amplification cascade (HRPAC), since the process of synthesis, posttranslational modification and metabolism of host response proteins amplifies the signal of potentially low-abundant biologically active disease markers such as enzymes. © 2005 Wiley-Liss, Inc. [source] Expression profiling reveals alternative macrophage activation and impaired osteogenesis in periprosthetic osteolysisJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 1 2008Panagiotis Koulouvaris Abstract Interactions between periprosthetic cells and prosthetic wear debris have been recognized as an important event in the development of osteolysis and aseptic loosening. Although the ability of wear debris to activate pro-inflammatory macrophage signaling has been documented, the full repertoire of macrophage responses to wear particles has not been established. Here, we examined the involvement of alternative macrophage activation and defective osteogenic signaling in osteolysis. Using real-time RT-PCR analysis of periprosthetic soft tissue from osteolysis patients, we detected elevated levels of expression of alternative macrophage activation markers (CHIT1, CCL18), chemokines (IL8, MIP1 ,) and markers of osteoclast precursor cell differentiation and multinucleation (Cathepsin K, TRAP, DC-STAMP) relative to osteoarthritis controls. The presence of cathepsin K positive multinuclear cells was confirmed by immunohistochemistry. Reduced expression levels of the osteogenic signaling components BMP4 and FGF18 were detected. Expression levels of TNF-,, IL-6, and RANKL were unchanged, while the anti-osteoclastogenic cytokine OPG was reduced in osteolysis patients, resulting in elevated RANKL:OPG ratios. In vitro studies confirmed the role of particulate debris in alternative macrophage activation and inhibition of osteogenic signaling. Taken together, these results suggest involvement in osteolysis of alternative macrophage activation, accompanied by elevated levels of various chemokines. Increased recruitment and maturation of osteoclast precursors is also observed, as is reduced osteogenesis. These findings provide new insights into the molecular pathogenesis of osteolysis, and identify new potential candidate markers for disease progression and therapeutic targeting. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 26:106,116, 2008 [source] Proteomic profiling of hepatocellular carcinoma in Chinese cohort reveals heat-shock proteins (Hsp27, Hsp70, GRP78) up-regulation and their associated prognostic valuesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 3 2006John M. Luk Dr. Abstract To facilitate the identification of candidate molecular biomarkers that are linked to the pathogenesis of hepatocellular carcinoma (HCC), we investigated protein-expression profiles of 146 tissue specimens including 67 pairs of tumors and adjacent non-tumors resected from HCC patients as well as 12 normal livers by 2-DE. Among the 1800 spots displayed in the liver proteome, a total of 90 protein species were found to be significantly different between the three groups (P,<,0.05). Three of the top candidate markers up-regulated in HCC, with high receiver operating characteristic (ROC) curves, were identified by MS/MS analysis and belonged to the chaperone members: heat-shock protein (Hsp)27, Hsp70 and glucose-regulated protein (GRP)78. Over-expression of these chaperone proteins in HCC tissues was confirmed by Western blotting and immunohistochemistry. In correlation with clinico-pathological parameters, expression of Hsp27 was linked to ,-fetoprotein level (P,=,0.007) whereas up-regulation of GRP78 was associated with tumor venous infiltration (P,=,0.035). No significant association of Hsp70 with any pathologic features was observed. The present HCC proteome analysis revealed that in response to the stressful cancerous microenvironment, tumor cells strived to increase the expression of chaperone proteins for cyto-protective function and to enhance tumor growth and metastasis. [source] Ovarian cancer proteomics: Many technologies one goalPROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2008Kothandaraman Narasimhan Abstract The last decade has seen major changes in the technologies used to identify markers for diagnosing cancer. This review focuses on recent developments on the evolving field of biomarker discovery, and validation techniques using proteomics platforms for ovarian cancer. It is possible now to diagnose various disease conditions using microliter quantities of body fluids. Currently the major developments were made in three distinct areas: (i) protein profiling, (ii) high-throughput validation techniques, and (iii) solid and liquid phase protein microarray platforms for analyzing candidate markers across subclasses and stages of cancers. The recent addition to the long list of technologies is metabolomics using metabolite profiling and informatics-based filtering of information for biomarker discovery of ovarian cancer. Emerging technologies need to address ways to eliminate the limitations posed by the complex dynamic nature of body fluids as well as ways to enrich low-abundance tumor markers if they were to become a successful biomarker discovery tool. These new technologies hold significant promise in identifying more robust markers for ovarian cancer. Since the prevalence of this disease in the population is low, the test must have a high specificity. [source] Mechanisms of lymphatic metastasis in human colorectal adenocarcinoma,THE JOURNAL OF PATHOLOGY, Issue 5 2009Daniel Royston Abstract The invasion of lymphatic vessels by colorectal cancer (CRC) and its subsequent spread to draining lymph nodes is a key determinant of prognosis in this common and frequently fatal malignancy. Although tumoural lymphangiogenesis is assumed to contribute to this process, review of the current literature fails to support any notion of a simple correlation between lymphatic vessel density and CRC metastasis. Furthermore, attempts to correlate the expression of various lymphangiogenic growth factors, most notably VEGF-C and VEGF-D, with the lymphatic metastasis of CRC have provided contradictory results. Recent evidence from animal and human models of tumour metastasis suggests that complex functional and biochemical interactions between the microvasculature of tumours and other cell types within the tumour microenvironment may play a pivotal role in the behaviour of commonly metastasizing tumours. Indeed, previous insights into tumoural blood vessels have provided candidate markers of tumoural angiogenesis that are currently the subject of intense investigation as future therapeutic targets. In this review article we survey the current evidence relating lymphangiogenesis and lymphangiogenic growth factor production to metastasis by CRC, and attempt to provide some insight into the apparent discrepancies within the literature. In particular, we also discuss some new and provocative insights into the properties of tumoural lymphatics suggesting that they have specific expression profiles distinct from those of normal lymphatic vessels and that appear to promote metastasis. These findings raise the exciting prospect of future biomarkers of lymphatic metastasis and identify potential targets for new generation anti-tumour therapies. Copyright © 2009 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Radiotherapy in laryngeal carcinoma: Can a panel of 13 markers predict response?,,THE LARYNGOSCOPE, Issue 2 2009Maarten A. M. Wildeman MD Abstract Objectives/Hypothesis: To find biomarkers associated with response to radiotherapy in laryngeal cancer that can be used together with clinical parameters to improve outcome prediction. Methods: In this study, 26 patients irradiated for laryngeal carcinomas with a local recurrence within two years (cases) and 33 patients without recurrence (controls) were included. All pretreatment biopsies were arrayed onto a tissue array. Immunohistochemistry was performed for 13 biomarkers that were selected from the literature as potential predictors for radioresponse in head and neck (HN) cancer: Bcl-2, Bcl-xL, p16, p21, p27, p53, cyclin D1, HIF-1,, CA9, COX-2, EGFR, ki-67, and pRB. Results: Univariate logistic regression models showed borderline statistically significant increased relative risks, with positivity for CA9, COX-2, and p53. Goeman's global testing revealed an overall association between outcome and the 13 markers together with clinical variables. The most important markers were CA9 and COX-2. Conclusions: In laryngeal carcinoma, hypoxia and COX-2 overexpression provide a stronger contribution to an increased risk of local recurrence after radiotherapy compared with the well-known candidate markers p53, Bcl-2, and cyclin D1. However, no robust expression profile for the prediction of radioresistance was found. Laryngoscope, 2009 [source] Development of novel SNP system for individual and pedigree control in a Japanese Black cattle population using whole-genome genotyping assayANIMAL SCIENCE JOURNAL, Issue 4 2010Kazuhiro HARA ABSTRACT Individual identification and parentage analysis using DNA markers are essential for assuring food identity and managing livestock population. The objective of this study was to develop a single nucleotide polymorphism (SNP) panel system for individual effective identification and parentage testing in a Japanese Black cattle population using BovineSNP50 BeadChip. On the basis of SNP frequencies, 60 unlinked informative SNPs were finally selected as candidate markers. The allelic frequencies for each SNP were estimated using additional individuals by PCR-RFLP (restriction fragment length polymorphism). A total of 87 SNP markers added in conjunction with previously developed 27 SNPs were evaluated to assess the utility of the test. The estimated identity power was 2.01 × 10,34. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.99999997 and 0.99998010, respectively. This developed SNP panel was quite powerful and could successfully exclude false sires with a probability of >0.9999 even if the dam's genotype information was not obtained. The SNP system would contribute to management of the beef industry in Japan. [source] Development of SNP markers for individual identification and parentage test in a Japanese Black cattle populationANIMAL SCIENCE JOURNAL, Issue 2 2010Kazuhiro HARA ABSTRACT This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR-RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 × 10,12. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan. [source] A Bayesian Spatial Multimarker Genetic Random-Effect Model for Fine-Scale MappingANNALS OF HUMAN GENETICS, Issue 5 2008M.-Y. Tsai Summary Multiple markers in linkage disequilibrium (LD) are usually used to localize the disease gene location. These markers may contribute to the disease etiology simultaneously. In contrast to the single-locus tests, we propose a genetic random effects model that accounts for the dependence between loci via their spatial structures. In this model, the locus-specific random effects measure not only the genetic disease risk, but also the correlations between markers. In other words, the model incorporates this relation in both mean and covariance structures, and the variance components play important roles. We consider two different settings for the spatial relations. The first is our proposal, relative distance function (RDF), which is intuitive in the sense that markers nearby are likely to correlate with each other. The second setting is a common exponential decay function (EDF). Under each setting, the inference of the genetic parameters is fully Bayesian with Markov chain Monte Carlo (MCMC) sampling. We demonstrate the validity and the utility of the proposed approach with two real datasets and simulation studies. The analyses show that the proposed model with either one of two spatial correlations performs better as compared with the single locus analysis. In addition, under the RDF model, a more precise estimate for the disease locus can be obtained even when the candidate markers are fairly dense. In all simulations, the inference under the true model provides unbiased estimates of the genetic parameters, and the model with the spatial correlation structure does lead to greater confidence interval coverage probabilities. [source] Analysis of the Repressor Element-1 Silencing Transcription Factor/Neuron-Restrictive Silencer Factor Occupancy of Non-Neuronal Genes in Peripheral Lymphocytes from Patients with Huntington's DiseaseBRAIN PATHOLOGY, Issue 1 2010Manuela Marullo Abstract We have previously demonstrated that the transcription of neuronal repressor element-1/neuron-restrictive silencer element (RE1/NRSE)-regulated genes is reduced in the brain of subjects with Huntington's disease (HD) as a result of increased binding of the repressor element-1 silencing transcription factor/neuron-restrictive silencer factor (REST/NRSF) to its RE1/NRSE targets. As specific non-neuronal REST/NRSF-regulated genes have been identified in the human genome, we exploited the possibility that the binding of REST/NRSF to its target RE1/NRSE sites may also be altered in the peripheral tissues of HD patients. Our results show that REST/NRSF occupancy is increased in lymphocytes from HD subjects, thus indicating for the first time that the activity of the RE1/NRSE sites is dysfunctional in vivo. Chromatin immunoprecipitation (ChIP) of the RE1/NRSE sites in lymphocytes may therefore be a reproducible, sensitive and specific means of searching for candidate markers of HD onset and progression. [source] Newer risk markers and surrogate endpoints in atherosclerosis managementCLINICAL CARDIOLOGY, Issue S3 2001Christie M. Ballantyne M.D. Abstract Summary: Risk markers that allow improved and individualized assessment of atherosclerotic disease risk and response to treatment are needed. Current candidate markers include cell adhesion molecules, such as intercellular adhesion molecule-1 and E-selectin, and inflammatory markers, such as C-reactive protein; advances in genomics and proteomics will suggest additional candidate markers. Noninvasive imaging procedures such as electron-beam computed tomography and magnetic resonance imaging also show considerable promise for monitoring disease status and response to treatment, and ultimately could provide surrogate endpoints for clinical trials of therapeutic interventions. [source] | |||||||||||||||||||||||||