The diffusion of new genetic tests for predicting disease.

This paper examines the pathways by which new genetic tests will become available to the public. In view of the scarcity of genetic specialists, the pathway is likely to involve primary care physicians. Other pathways entail state-mandated testing, community-based programs, or testing by laboratories without much involvement of primary care physicians. When testing does become available the "destination" will be either family-centered testing or population-oriented screening. The deterrent to screening will not be the inability to detect disease-causing mutations but the costs and attitudes of providers and the public. When tests are provided primarily to provide information about risks to future children, some people will oppose screening on religious or moral grounds. When there are no inexpensive treatments, some will fear that insurance companies and employers will use tests to deny them health care coverage. Some may not want to know their risks for disorders about which little can be done. For common, multifactorial disorders, genetic tests will have low predictive value. Because of these problems, the decision to be tested, regardless of the destination, requires that "testees" be fully informed and consent to testing. When acceptance rates are low, screening is less likely to be cost-effective; family-centered testing becomes the default destination.     

Technical reproducibility of genotyping SNP arrays used in genome-wide association studies

During the last several years, high-density genotyping SNP arrays have facilitated genome-wide association studies (GWAS) that successfully identified common genetic variants associated with a variety of phenotypes. However, each of the identified genetic variants only explains a very small fraction of the underlying genetic contribution to the studied phenotypic trait. Moreover, discordance observed in results between independent GWAS indicates the potential for Type I and II errors. High reliability of genotyping technology is needed to have confidence in using SNP data and interpreting GWAS results. Therefore, reproducibility of two widely genotyping technology platforms from Affymetrix and Illumina was assessed by analyzing four technical replicates from each of the six individuals in five laboratories. Genotype concordance of 99.40% to 99.87% within a laboratory for the sample platform, 98.59% to 99.86% across laboratories for the same platform, and 98.80% across genotyping platforms was observed. Moreover, arrays with low quality data were detected when comparing genotyping data from technical replicates, but they could not be detected according to venders' quality control (QC) suggestions. Our results demonstrated the technical reliability of currently available genotyping platforms but also indicated the importance of incorporating some technical replicates for genotyping QC in order to improve the reliability of GWAS results. The impact of discordant genotypes on association analysis results was simulated and could explain, at least in part, the irreproducibility of some GWAS findings when the effect size (i.e. the odds ratio) and the minor allele frequencies are low.     

Genetic dissection methods: designs used for tests of gene-environment interaction

Given recent advances in the field of molecular genetics, many have recognized the need to exploit either study designs or analytical methods to test hypotheses with gene-by-environment (G x E) interactions. The partial-collection designs, including case-only, partial case-control, and case-parent trio designs, have been suggested as attractive alternatives to the complete case-control design both for increased statistical efficiency and reduced data needs. However, common problems in genetic epidemiology studies, such as, presence of G x E correlation in the population, population mixture, and genotyping error may reduce the validity of these designs. On the basis of previous simulation studies and empirical data and given the potential limitations and uncertainty of assumptions of partial-collection designs, the case-control design is the optimal choice versus partial-collection designs.     

Markers for predicting death as an outcome for mice used in infectious disease research

Our goal in this study was to identify objective criteria that could be used to predict an outcome of death in mice subjected to experimental inoculation with infectious organisms. We conducted a retrospective analysis of data collected from 4 independent studies that used several infectious agents (influenza virus strains A/HK/x31[H3N2] and A/Puerto Rico/8/34[H1N1], Streptococcus pneumoniae, and Candida albicans) and mouse strains (A/J, DBA/2J, C57BL/6J, BALB/cByJ). Postinoculation periods ranged from 5 to 21 d, with survival of 30% to 60% of the subjects. In all studies, mice were implanted with either a subcutaneous identification microchip or an intraabdominal radiofrequency transmitter to allow remote measurement of body temperature. After inoculation, mice were weighed and monitored regularly until death occurred or euthanasia was performed. Hypothermia was the most valuable characteristic for distinguishing mice that would survive or succumb to the infection. In addition, weight loss was useful in some of the models. In some cases, the derived measure of the product of temperature and body weight provided the best differentiation of mice in the 2 outcome categories. Therefore, the utility of these measures varied substantially depending on the specific model. This study demonstrates that specific endpoint markers are not uniformly applicable to different models. Rather, such markers should be developed and tested in the context of the model in which they will be used. The use of validated markers for eventual death can signal the need for preemptive euthanasia to alleviate terminal distress and permit timely collection of biologic samples.     

Analysis of the diluents used for rubella virus hemagglutination and hemagglutination-inhibition tests

[This corrects the article on p. 222 in vol. 18.].     

Evaluation of tests for predicting the viability of axial pattern skin flaps in the pig.

The viability of axial pattern skin flaps in pigs was assessed by the use of intravenous fluorescein, intradermal injection of 133Xe in saline, intravenous 51Cr tagged red cells, and angiography. The results were correlated with flap survival at 4 days postoperatively. Intravenous fluorescein provided the most accurate method for prediction of viable tissue at the time of operation. There was no evidence of vascular perfusion in the distal portions of these flaps. These axial pattern flaps differed in their viability from similar flaps in humans, and anastomoses between discrete vascular territories were infrequent in pigskin.     

Normalizing shoulder EMG: An optimal set of maximum isometric voluntary contraction tests considering reproducibility

Normalization of the electromyography (EMG) signal is often performed relatively to maximal voluntary activations (MVA) obtained during maximum isometric voluntary contraction (MVIC). The first aim was to provide an inter-session reproducible protocol to normalize the signal of eight shoulder muscles. The protocol should also lead to a level of activation >90% of MVA for >90% of the volunteers. The second aim was to evaluate the influence of the method used to extract the MVA from the EMG envelope on the normalized EMG signal. Thirteen volunteers performed 12 MVICs twice (one week interval). Several time constants (100 ms to 2 s) were compared when extracting the MVA from the EMG envelope. The EMG activity was also acquired during an arm elevation. Our results show that a combination of nine MVIC tests was required to meet our requirements including reproducibility. Both the number of MVIC tests and the size of the time constant influence the normalized EMG signal during the dynamic activity (variations up to 15%). A time constant of 1 s was a good compromise to extract the MVA. These findings are valuable to improve the reproducibility of EMG signal normalization.     

The role of aquatic toxicity tests in predicting and monitoring pollution effects

The complementary role of aquatic toxicity tests in relation to other forms of pollution assessment is discussed. These tests may be predictive and designed to estimate hazard, or used for monitoring waters to assess compliance with standards. The effects of pollutants are significantly modified by certain water quality characteristics and by a variety of biological factors. The latter, particularly those causing physiological stress, are discussed.     

Allelism tests of 15 dominant cataract mutations in mice.

Fifteen autosomal dominant mutations that cause cataract of lenses in mice were tested for allelism. The outcrosses of double mutants revealed three allelism groups, consisting of 5, 4 and 2 mutations as well as 4 mutations which segregated independently. The results indicated 7 different cataract loci in the sample of 15 mutations. The biomicroscopic examination of the eyes showed that phenotypically similar as well as very distinct cataract mutations can be alleles of the same gene. Conversely, phenotypically similar mutations were shown to be non-allelic.     

Potentially difficult smears of women with squamous cell carcinoma pose fewer problems when PAPNET is used for primary screening

The diagnosis of squamous cell carcinoma (SCC) on a cervical smear is often far from easy. This study reports the analysis of 40 true-positive SCC smears detected in primary PAPNET screening and eight false-negative (FN) conventionally screened smears. All FN cases contained sparse abnormal material (< 10% of the slide). In these potentially difficult cases the diagnosis on the PAPNET images was not hard. Statistical analysis of the quantitative data indicated that the PAPNET images of the FN cases and the true-positive cases differed in some aspects. PAPNET highlighted the importance of background information (old blood, fibrin and necrosis). In addition, all FN smears contained cancer cells in the PAPNET images, allowing a correct diagnosis.     

Applying geographic profiling used in the field of criminology for predicting the nest locations of bumble bees

We tested whether geographic profiling (GP) can predict multiple nest locations of bumble bees. GP was originally developed in the field of criminology for predicting the area where an offender most likely resides on the basis of the actual crime sites and the predefined probability of crime interaction. The predefined probability of crime interaction in the GP model depends on the distance of a site from an offender's residence. We applied GP for predicting nest locations, assuming that foraging and nest sites were the crime sites and the offenders’ residences, respectively. We identified the foraging and nest sites of the invasive species Bombus terrestris in 2004, 2005, and 2006. We fitted GP model coefficients to the field data of the foraging and nest sites, and used GP with the fitting coefficients. GP succeeded in predicting about 10-30% of actual nests. Sensitivity analysis showed that the predictability of the GP model mainly depended on the coefficient value of buffer zone, the distance at the mode of the foraging probability. GP will be able to predict the nest locations of bumble bees in other area by using the fitting coefficient values measured in this study. It will be possible to further improve the predictability of the GP model by considering food site preference and nest density.