Ascertainment: An Overwiew of the Classical Segregation Analysis Model for Independent Sibships

Several different methodologies for parameter estimation under various ascertainment sampling schemes have been proposed in the past. In this article, some of the methodologies that have been proposed for independent sibships under the classical segregation analysis model are synthesized, and the general likelihoods derived for single, multiple and complete ascertainment. The issue of incorporating the sibship size distribution into the analysis is addressed, and the effect of conditioning the likelihood on the observed sibship sizes is discussed. It is shown that when the number of probands in a sibship is not specified, the corresponding likelihood can be used for a broader class of ascertainment schemes than is subsumed by the classical model.     

On Fisher's Method of Combining p-Values

The problem of combining p-values from independent experiments is discussed. It is shown that Fisher's solution to the problem can be derived from a “weight-free” method that has been suggested for the purpose of ranking vector observations (Biometrics 19: 85–97, 1963). The method implies that the value p = 0.37 is a critical one: p-values below 0.37 suggest that the null hypothesis is more likely to be false, whereas p-values above 0.37 suggest that it is more likely to be true.     

Evidence for colonization and destruction of hinge ligaments in cultured juvenile Pacific oysters (Crassostrea gigas) by cytophaga-like bacteria

Several strains of cytophaga-like gliding bacteria (CLB) were isolated as numerically dominant or codominant components of bacterial populations associated with proteinaceous hinge ligaments of cultured juvenile Pacific oysters, Crassostrea gigas. These bacteria were morphologically similar to long, flexible bacilli occurring within degenerative lesions in oyster hinge ligaments. Among bacteria isolated from hinge ligaments, only CLB strains were capable of sustained growth with hinge ligament matrix as the sole source of organic carbon and nitrogen. In vitro incubation of cuboidal portions of ligament resilium with ligament CLB resulted in bacterial proliferation on the surfaces and penetration deep into ligament matrices. Bacterial proliferation was accompanied by loss of resilium structural and mechanical integrity, including complete liquefaction, at incubation temperatures between 10 and 20 degrees C. The morphological, distributional, and degradative characteristics of CLB isolated from oyster hinge ligaments provide compelling, albeit indirect, evidence that CLB are the agents of a degenerative disease affecting juvenile cultured oysters. The motility, metabolic, and hydrolytic characteristics of hinge ligament CLB and the low moles percent G + C values (32.4 to 32.9) determined for three representative strains indicate that they are marine Cytophaga spp.     

Quantitative estimation of nuclear buds and micronuclei in bovine cells transformed by Rous sarcoma and SV 40 viruses

Summary A study of nuclear-budding and micronuclei formation has been performed on bovine fibroblastic cells in serial tissue culture. A comparison was made between control cells and cells morphologically transformed by Rous sarcoma virus and SV 40 virus. It was found that no obvious differences in the frequency of nuclear buds and micronuclei existed between RSV transformed and control cells whereas SV 40 transformed cells showed a high frequency of nuclear buds and micronuclei. There are indications that the frequency of nuclear buds and micronuclei is correlated to chromosomal abnormalities.Supported by grants from the Medical Faculty of the University of Uppsala.     

Some capabilities for model-based and model-free linkage analysis using the program package S.A.G.E. (Statistical Analysis for Genetic Epidemiology)

For both model-free and model-based linkage analysis the S.A.G.E. (Statistical Analysis for Genetic Epidemiology) program package has some unique capabilities in analyzing both continuous traits and binary traits with variable age of onset. Here we highlight model-based linkage analysis of a quantitative trait (plasma dopamine β hydroxylase) that is known to be largely determined by monogenic inheritance, using a prior segregation analysis to produce the best fitting model for the trait. For a binary trait with variable age of onset (schizophrenia), we illustrate how using age of onset information to obtain a quantitative susceptibility trait leads to more statistically significant linkage signals, suggesting better power.     

A Virtual Clinical Trial of FDG-PET Imaging of Breast Cancer: Effect of Variability on Response Assessment

INTRODUCTION: There is growing interest in using positron emission tomography (PET) standardized uptake values (SUVs) to assess tumor response to therapy. However, many error sources compromise the ability to detect SUV changes. We explore relationships between these errors and overall SUV variability. METHODS: We used simulations in a virtual clinical trial framework to study impacts of error sources from scanning and analysis effects on assessment of SUV changes. We varied tumor diameter, scan duration, pretherapy SUV, magnitude of change in SUV, image reconstruction filter, and SUV metric. Poisson noise was added to the raw data before image reconstruction. Variance from global sources of error, e.g., scanner calibration, was incorporated. Two thousand independent noisy sinograms per scenario were generated and reconstructed. We used SUVs to create receiver operating characteristic (ROC) curves to quantify ability to assess response. Integrating area under the ROC curve summarized ability to detect SUV changes. RESULTS: Scan duration and image reconstruction method had relatively little impact on ability to measure response. SUV_MAX is nearly as effective as SUV_MEAN, especially with increased image smoothing and despite size-matched region of interest placement. For an effective variability of 15%, we found the Positron Emission Tomography Response Criteria in Solid Tumors criteria for measuring response (±30%) similar to the European Organization for Research and Treatment of Cancer criteria (±25%). CONCLUSIONS: For typical PET variance levels, tumor response must be 30% to 40% to be reliably determined using SUVs. PET scan duration and image reconstruction method had relatively little effect.