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Marker Panels (marker + panel)

Distribution by Scientific Domains

Medical Sciences	50%

Selected Abstracts

Primary colorectal carcinomas and their intrapulmonary metastases: Clinical, glyco-, immuno- and lectin histochemical, nuclear and syntactic structure analysis with emphasis on correlation with period of occurrence of metastases and survival

APMIS, Issue 6 2002
Klaus Kayser
Background. The aim of the study was to correlate clinical factors (disease-free interval/survival) with growth pattern in terms of structural entropy of patients with primary colorectal carcinomas and secondary lung lesions. Methods. Proliferation and apoptosis markers as well as determinants involved in information transfer by protein-carbohydrate interactions were monitored. The clinical history, surgical and histopathological reports, tumor load, survival of the patients with a maximum follow-up of 14 years, and sections of paraffin blocks of 60 colorectal carcinoma specimens and their pulmonary metastases were examined. Measurements of the staining intensities after processing sections of primary and secondary carcinomas with the marker panel and calculations of syntactic structure and stereological parameters were performed. Results. The majority of primary tumors (80%, 49/60) were surgically treated at advanced tumor stages (pT3/pT4), with detectable lymph node involvement (34/60). Lung metastases were resected after a median disease-free interval of 30.5 months, an average of 3.0 metastases adding up to a mean intrapulmonary tumor load of 9.98 ccm. The median survival was calculated to be 82 months after resection of the colon/rectal carcinomas and 40 months after that of intrapulmonary metastases. It was correlated with certain structural and vascular features such as vascular circumference. The proliferation index and several textural features were strongly associated with vascularization in primary and secondary tumors. Conclusions. Despite intra- and interindividual variations, vascularization properties and features such as bcl-2 positivity and CEA- and galectin-3-associated structural entropy in primary tumors or metastases are described as independent prognostic features. Absence of lymph node involvement or limited tumor stages of colon/rectal carcinomas should not exclude patients from thorough postsurgical scrutiny to detect lung metastases. [source]

Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3

GENETIC EPIDEMIOLOGY, Issue S1 2005
Marsha A. Wilcox
Abstract The papers in presentation groups 1,3 of Genetic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was ,1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use. Genet. Epidemiol. 29:(Suppl. 1): S7,S28, 2005. © 2005 Wiley-Liss, Inc. [source]

Genotyping errors, pedigree errors, and missing data

GENETIC EPIDEMIOLOGY, Issue S1 2005
Anthony L. Hinrichs
Abstract Our group studied the effects of genotyping errors, pedigree errors, and missing data on a wide range of techniques, with a focus on the role of single-nucleotide polymorphisms (SNPs). Half of our group used simulated data, and half of our group used data from the Collaborative Study on the Genetics of Alcoholism (COGA). The simulated data had no missing genotypes and no genotyping errors, so our group, as a whole, removed data and introduced artificial errors to study the robustness of various techniques. Our teams showed that genotyping errors are less detectable and may have a greater impact on SNPs than on microsatellites, but recently developed methods that account for genotyping errors help reduce false positives, and the assumptions of these methods appear to be supported by observations from repeated genotyping. The ability to detect linkage disequilibrium (LD) was also substantially reduced by missing data; this in turn could affect tagging SNPs chosen to generate haplotypes. In the COGA sample, genotyping measurements were repeated in three ways. First, full-genome screens were performed on three sets of markers: 328 microsatellites, 11,560 SNPs from the Affymetrix GeneChip Mapping 10,K Array marker set, and 4,720 SNPs from the Illumina Linkage III panel. Second, the entire Affymetrix marker set was typed on the same 184 individuals by two different laboratories. Finally, the Affymetrix and Illumina marker panels had 94 SNPs in common. Our teams showed that both SNPs and microsatellites can be readily used to identify pedigree errors, and that SNPs have fewer genotyping errors and a low inconsistency rate. However, a fairly high rate of no-calls, especially for the Affymetrix platform, suggests that the inconsistency rate may be higher than observed. Genet. Epidemiol. 29(Suppl. 1):S120,S124, 2005. © 2005 Wiley-Liss, Inc. [source]

Assessment of fibrosis in chronic liver diseases

JOURNAL OF DIGESTIVE DISEASES, Issue 1 2009
Kun ZHOU
The assessment of liver fibrosis provides useful information not only for diagnosis but also for therapeutic decisions. Although liver biopsy is the current gold standard for fibrosis assessment, it has some risks and limitations, including intra-observer and inter-observer variation, sampling error and variability. In recent years, many studies and great interest have been dedicated to the development of non-invasive tests to substitute a liver biopsy for fibrosis assessment and follow up. Advances in serological and radiological tests such as serum marker panels, transient elastography and their combinations can assess fibrosis accurately and reduce the need for a liver biopsy. But at present, all have failed to completely replace a liver biopsy because of their respective limitations and an imperfect gold standard used in current researches. The searching for an ideal surrogate is still in progress. [source]