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PubMed2002

Stochastic processes defining sensitivity and variability of internally calibrated quantitative NASBA-based viral load assays.

For quantitative assessment of virus particles in patient plasma samples various assays are commercially available. Typical performance characteristics for such assays are sensitivity, precision and the range of linearity. In order to assess these properties it is common practice to divide the range of inputs into subranges in order to apply different statistical models to evaluate these properties separately. We developed a general statistical model for internally calibrated amplification based viral load assays that combines these statistical properties in one powerful analysis. Based on the model an unambiguous definition of the lower limit of the linear range can be given. The proposed method of analysis was illustrated by a successful application to data generated by the NucliSens EasyQ HIV-1 assay.

HIV-1↗
PubMed2006

Good enough: a primer on the analysis and interpretation of noninferiority trials.

Active-control noninferiority trials are being performed with increasing frequency when standard placebo-controlled trials are considered unethical. Three attributes are optimally required to establish noninferiority: 1) The treatment under consideration exhibits therapeutic noninferiority to the active control; 2) the treatment would exhibit therapeutic efficacy in a placebo-controlled trial if such a trial were to be performed; and 3) the treatment offers ancillary advantages in safety, tolerability, cost, or convenience. Trials designed to show noninferiority require an appropriate reference population, a proven active control and dose, a high level of adherence to treatment, and adequate statistical power. However, the formal analysis of such trials is founded on several assumptions that cannot be validated explicitly. These assumptions are evaluated in the context of 8 recently published noninferiority trials. The analyses in this paper confirm the establishment of noninferiority in only 4 of the 8 trials. The authors conclude that if noninferiority trials are to be applied to clinical and regulatory decisions about the marketing and use of new treatments, these assumptions must be made explicit and their influence on the resultant conclusions assessed rigorously.

Cardiovascular Agents↗
PubMed2006

Goulphar: rapid access and expertise for standard two-color microarray normalization methods.

BACKGROUND: Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packages but it is often difficult to identify the most appropriate method. Furthermore, the use of R commands for functions and graphics can introduce mistakes that are difficult to trace. We present here a script written in R that provides a flexible means of access to and monitoring of data normalization for two-color microarrays. This script combines the power of BioConductor and R analysis functions and reduces the amount of R programming required. RESULTS: Goulphar was developed in and runs using the R language and environment. It combines and extends functions found in BioConductor packages (limma and marray) to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters for excluding incorrect signals during the pre-processing step. It displays informative output plots, enabling the user to monitor the normalization process, and helps adapt the normalization method appropriately to the data. All these analyses and graphical outputs are presented in a single PDF report. CONCLUSION: Goulphar provides simple, rapid access to the power of the R/BioConductor statistical analysis packages, with precise control and visualization of the results obtained. Complete documentation, examples and online forms for setting script parameters are available from http://transcriptome.ens.fr/goulphar/.

Algorithms↗
PubMed2000

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.

We describe a novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 microm diameter microbeads. After constructing a microbead library of DNA templates by in vitro cloning, we assembled a planar array of a million template-containing microbeads in a flow cell at a density greater than 3x10(6) microbeads/cm2. Sequences of the free ends of the cloned templates on each microbead were then simultaneously analyzed using a fluorescence-based signature sequencing method that does not require DNA fragment separation. Signature sequences of 16-20 bases were obtained by repeated cycles of enzymatic cleavage with a type IIs restriction endonuclease, adaptor ligation, and sequence interrogation by encoded hybridization probes. The approach was validated by sequencing over 269,000 signatures from two cDNA libraries constructed from a fully sequenced strain of Saccharomyces cerevisiae, and by measuring gene expression levels in the human cell line THP-1. The approach provides an unprecedented depth of analysis permitting application of powerful statistical techniques for discovery of functional relationships among genes, whether known or unknown beforehand, or whether expressed at high or very low levels.

Cell Line↗
PubMed2005

Genome scan meta-analysis of rheumatoid arthritis.

OBJECTIVE: Genome scans for rheumatoid arthritis (RA) have yielded inconsistent results. The absence of replication of linkage might be due to lack of power of individual studies. We performed a genome scan meta-analysis of published data to increase statistical power and to assess evidence for linkage of RA across genome scan studies. METHODS: Four RA whole-genome scans containing 767 families with 964 sibling pairs were included for the genome scan meta-analysis (GSMA). The GSMA method was applied to pool the results obtained from four genome scans. For each study, 120 genomic bins of approximately 30 centimorgans were defined and ranked according to maximum evidence for linkage within each bin. Bin ranks were weighted and summed across all studies. The summed rank for each bin was assessed empirically for significance using permutation methods. RESULTS: A total of nine bins lay above the 95% confidence level (P=0.05) and four bins were above the 99% confidence level (P=0.01) in the RA GSMA, suggesting that these bins contain RA-linked loci: bins 6.2, 6.4, 8.1, 18.3, 12.3, 12.2, 1.5, 6.3 and 16.2. The strongest evidence for linkage occurred on chromosome 6p22.3-6p21.1 (bin 6.2), containing the HLA region (P(sumrnk)=0.0000008). CONCLUSION: This RA GSMA confirmed the evidence for HLA loci as the greatest susceptibility factor to RA and showed evidence for linkage at non-HLA loci, such as chromosomes 1p, 6, 8p, 12, 16 and 18q, across studies. These data may provide a basis to carry out targeted linkage and candidate gene studies, particularly in the regions.

Arthritis, Rheumatoid↗
PubMed1999

Sequence analysis of alleles at a microsatellite locus D14S299 (wg1c5) and population genetic comparisons.

In order to increase the discriminating power of DNA analysis in personal identification, we evaluated the forensic utility of the microsatellite locus D14S299 (wg1c5) in the Japanese population and also in the Chinese and Caucasian populations. Twelve different alleles were identified in length by gel electrophoresis with silver staining. The major alleles in Japanese were sequenced and designated as the numbers of the variable repeats (GGAT or GGAA). There were five variable regions and extensive homoplasy was found. However, the allele fragment lengths were in 4 bp increments and no "interalleles" were found. The estimated heterozygosity and the polymorphism information content (PIC) were 0.726 and 0.689, respectively in Japanese. Those in Chinese (0.743 and 0.704) were similar to those in Japanese, while those in Caucasians (0.812 and 0.781) were much higher. After adjacent alleles were combined to yield at least five entries, statistical analysis was performed. The power of discrimination (PD) was 0.887 in Japanese, 0.895 in Chinese and 0.935 in Caucasians and no significant deviations from the Hardy-Weinberg equilibrium were found in the three populations. We retyped all apparently homozygous samples using an alternative pair of flanking primers and found them to be true homozygotes. D14S299 appears to be a useful STR locus for forensic practice.

Asian People↗
PubMed2005

High-resolution serum proteomic profiling of Alzheimer disease samples reveals disease-specific, carrier-protein-bound mass signatures.

BACKGROUND: Researchers typically search for disease markers using a "targeted" approach in which a hypothesis about the disease mechanism is tested and experimental results either confirm or disprove the involvement of a particular gene or protein in the disease. Recently, there has been interest in developing disease diagnostics based on unbiased quantification of differences in global patterns of protein and peptide masses, typically in blood from individuals with and without disease. We combined a suite of methods and technologies, including novel sample preparation based on carrier-protein capture and biomarker enrichment, high-resolution mass spectrometry, a unique cohort of well-characterized persons with and without Alzheimer disease (AD), and powerful bioinformatic analysis, that add statistical and procedural robustness to biomarker discovery from blood. METHODS: Carrier-protein-bound peptides were isolated from serum samples by affinity chromatography, and peptide mass spectra were acquired by a matrix-assisted laser desorption/ionization (MALDI) orthogonal time-of-flight (O-TOF) mass spectrometer capable of collecting data over a broad mass range (100 to >300,000 Da) in a single acquisition. Discriminatory analysis of mass spectra was used to process and analyze the raw mass spectral data. RESULTS: Coupled with the biomarker enrichment protocol, the high-resolution MALDI O-TOF mass spectra provided informative, reproducible peptide signatures. The raw mass spectra were analyzed and used to build discriminant disease models that were challenged with blinded samples for classification. CONCLUSIONS: Carrier-protein enrichment of disease biomarkers coupled with high-resolution mass spectrometry and discriminant pattern analysis is a powerful technology for diagnostics and population screening. The mass fingerprint model successfully classified blinded AD patient and control samples with high sensitivity and specificity.

Alzheimer Disease↗
PubMed2002

Determination of minimum sample size and discriminatory expression patterns in microarray data.

MOTIVATION: Transcriptional profiling using microarrays can reveal important information about cellular and tissue expression phenotypes, but these measurements are costly and time consuming. Additionally, tissue sample availability poses further constraints on the number of arrays that can be analyzed in connection with a particular disease or state of interest. It is therefore important to provide a method for the determination of the minimum number of microarrays required to separate, with statistical reliability, distinct disease states or other physiological differences. RESULTS: Power analysis was applied to estimate the minimum sample size required for two-class and multi-class discrimination. The power analysis algorithm calculates the appropriate sample size for discrimination of phenotypic subtypes in a reduced dimensional space obtained by Fisher discriminant analysis (FDA). This approach was tested by applying the algorithm to existing data sets for estimation of the minimum sample size required for drawing certain conclusions on multi-class distinction with statistical reliability. It was confirmed that when the minimum number of samples estimated from power analysis is used, group means in the FDA discrimination space are statistically different. CONTACT: gregstep@mit.edu

Acute Disease↗
PubMed1999

The effect of medroxyprogesterone acetate on angiogenesis in complex endometrial hyperplasia.

OBJECTIVE: To evaluate the effect of orally administered medroxyprogesterone acetate upon angiogenesis in the myometrium of patients with complex endometrial hyperplasia. METHODS: Microvessel counts in the myometrium of consecutive patients with complex endometrial hyperplasia, treated with oral medroxyprogesterone acetate prior to hysterectomy (n = 12), were compared with microvessel counts of consecutive control patients with complex endometrial hyperplasia without prehysterectomy medroxyprogesterone acetate treatment (n = 15). All specimens were stained immunohistochemically for factor VIII-related antigen as a sensitive and specific marker for vascular endothelium. Areas with the highest angiogenic intensity, within the myometrium immediately underlying complex endometrial hyperplasia, were selected. Three fields (x400) were selected for each slide, and the mean microvessel count per high-power field was calculated. Statistical analysis included factorial analysis of variance/covariance, and multiple regression analysis with P < 0.05 considered significant throughout. RESULTS: Microvessel counts of uterine specimens of patients with complex endometrial hyperplasia treated with oral medroxyprogesterone acetate were significantly lower than microvessel counts of control patients with complex endometrial hyperplasia without medroxyprogesterone acetate therapy (median 20, range 11-37 versus median 38, range 20-130, respectively, P < 0.001). CONCLUSION: Orally administered medroxyprogesterone acetate has a significant antiangiogenic effect upon myometrium immediately underlying complex endometrial hyperplasia.

Administration, Oral↗
PubMedDate not supplied

Computed tomographic evaluation of patients with tardive dyskinesia.

X ray computed tomography has been used since its introduction to evaluate patients with tardive dyskinesia (TD). A critical review of the 18 reports which have appeared since 1976 suggests that TD may be associated with neuroanatomical abnormalities. In particular, a meta-analysis of the reports of ventricular brain ratio found a trend for patients with TD to have larger lateral ventricles than unaffected patients. The magnitude of the difference appears to be small, however, and several well conducted studies have reported negative results. A careful analysis revealed that low statistical power, concurrent neuroleptic treatment, insensitive measures of ventricular dilatation, and variable diagnostic criteria for TD may have led to negative findings in most of the investigations. The possible significance of these results and suggestions for further research are discussed.

Age Factors↗
PubMed2004

Measuring survival rates from sudden cardiac arrest: the elusive definition.

BACKGROUND: Measuring survival from sudden out-of-hospital cardiac arrest (OOH-CA) is often used as a benchmark of the quality of a community's emergency medical service (EMS) system. The definition of OOH-CA survival rates depends both upon the numerator (surviving cases) and the denominator (all cases). PURPOSE: The purpose of the public access defibrillation (PAD) trial was to measure the impact on survival of adding an automated external defibrillator (AED) to a volunteer response system trained in CPR. This paper reports the definition of OOH-CA developed by the PAD trial investigators, and it evaluates alternative statistical methods used to assess differences in reported "survival." METHODS: Case surveillance was limited to the prospectively determined geographic boundaries of the participating trial units. The numerator in calculating a survival rate should include only those patients who survived an event but who otherwise would have died except for the application of some facet of emergency medical care-in this trial a defibrillatory shock. Among denominators considered were: total population of the study unit, all deaths within the study unit, and documented ventricular fibrillation cardiac arrests. The PAD classification focused upon cases that might have benefited from the early use of an AED, in addition to the likely benefit from early recognition of OOH-CA, early access of EMS, and early cardiopulmonary resuscitation (CPR). Results of this classification system were used to evaluate the impact of the PAD definition on the distribution of cardiac arrest case types between CPR only and CPR + AED units. RESULTS: Potential OOH-CA episodes were classified into one of four groups: definite, probable, uncertain, or not an OOH-CA. About half of cardiac arrests in the PAD units were judged to be definite OOH-CA events and therefore potentially treatable with an AED. However, events that occurred in CPR-only units were less likely to be classified as definite or probable OOH-CA events than those in CPR + AED units (43% versus 55%, odds ratio 0.78, 95% confidence interval 0.57-1.07). The study retained sufficient power to permit a statistical analysis of the alternative hypothesis that the CPR + AED method results in twice as many survivors as a CPR-only approach. The result is critically dependent on the denominator used for calculating survival rates; but the analysis does not require a denominator as the numerators will have identical Poisson distributions (counts for rare events) under the null hypothesis since randomization distributes the risk of cardiac arrest evenly between the two arms. CONCLUSION: Reported OOH-CA rates and survival rates vary widely, depending upon the definitions applied to events. Rigorous assessment of treatments applied to improve survival can be obscured by inappropriate definitions. Large-scale randomized interventions designed to improve survival from OOH-CA can be evaluated based upon the absolute numbers of patients surviving, rather than a change in the proportion surviving.

Cardiopulmonary Resuscitation↗
PubMed1984

Prediction of mandibular rotation: an empirical test of clinician performance.

An experiment was conducted in an attempt to determine empirically how effective a number of expert clinicians were at differentiating "backward rotators" from "forward rotators" on the basis of head-film information which might reasonably have been available to them prior to instituting treatment for the correction of Class II malocclusion. As a result of a previously reported ongoing study, pre- and posttreatment head films were available for 188 patients treated in the mixed dentition for the correction of Class II malocclusion and for 50 untreated Class II subjects. These subjects were divided into 14 groups (average size of group, 17; range, 6 to 23) solely on the basis of type of treatment and the clinician from whose clinic the records had originated. From within each group, we selected the two or three subjects who had exhibited the most extreme backward rotation and the two or three subjects who had exhibited the most extreme forward rotation of the mandible during the interval between films. The sole criterion for classification was magnitude of change in the mandibular plane angle of Downs between the pre- and posttreatment films of each patient. The resulting sample contained 32 backward-rotator subjects and 32 forward-rotator subjects. Five expert judges (mean clinical experience, 28 years) were asked to identify the backward-rotator subjects by examination of the pretreatment films. The findings may be summarized as follows: (1) No judge performed significantly better than chance. (2) There was strong evidence that the judges used a shared, though relatively ineffective, set of rules in making their discriminations between forward and backward rotators. (3) Statistical analysis of the predictive power of a set of standard cephalometric measurements which had previously been made for this set of subjects indicated that the numerical data also failed to identify potential backward rotators at a rate significantly better than chance. We infer from these findings that the ability of clinicians to identify backward rotators on the basis of information available at the outset of treatment is poor. Hence, we believe that it is unlikely that such predictions play any consequential operational role in the planning of successful orthodontic therapy at the present state of the art.

Cephalometry↗
PubMed2002

Enhanced bio-manufacturing through advanced multivariate statistical technologies.

The paper describes the interrogation of data, from a reaction vessel producing an active pharmaceutical ingredient (API), using advanced multivariate statistical techniques. Due to the limited number of batches available, data augmentation was used to increase the number of batches thereby enabling the extraction of more subtle process behaviour from the data. A second methodology investigated was that of multi-group modelling. This allowed between cluster variability to be removed, thus allowing attention to focus on within process variability. The paper describes how the different approaches enabled the realisation of a better understanding of the factors causing the onset of an impurity formation to be obtained as well demonstrating the power of multivariate statistical data analysis techniques to provide an enhanced understanding of the process.

Artifacts↗
PubMedDate not supplied

Coenzyme Q10, exercise lactate and CTG trinucleotide expansion in myotonic dystrophy.

Steinert's myotonic dystrophy (DM) is a genetic autosomal dominant disease and the most frequent muscular dystrophy in adulthood. Although causative mutation is recognized as a CTG trinucleotide expansion on 19q13.3, pathogenic mechanisms of multisystem involvement of DM are still under debate. It has been suggested that mitochondrial abnormalities can occur in this disease and deficiency of coenzyme Q 10 (CoQ10) has been considered one possible cause for this. The aim of this investigation was to evaluate, in 35 DM patients, CoQ10 blood levels and relate them to the degree of CTG expansion as well as to the amount of lactate production in exercising muscle as indicator of mitochondrial dysfunction. CoQ10 concentrations appeared significantly reduced with respect to normal controls: 0.85 +/- 0.25 vs. 1.58 +/- 0.28 microg/ml (p < 0.05). Mean values of blood lactate were significantly higher in DM patients than controls (p < 0.05) both in resting conditions (2.9 +/- 0.55 vs. 1.44 +/- 1.11 mmol/L) and at the exercise peak (6.77 +/- 1.79 vs. 4.90 +/- 0.59 mmol/L), while exercise lactate threshold was anticipated (30-50% vs. 60-70% of the predicted normal maximal power output, p < 0.05). Statistical analysis showed that serum CoQ10 levels were significantly (p < 0.05) inversely correlated with both CTG expansion degree and lactate values at exercise lactate threshold level. Our data indicates the occurrence of reduced CoQ10 levels in DM, possibly related to disease pathogenic mechanisms associated with abnormal CTG trinucleotide amplification.

Adult↗
PubMed2001

What happens to the student? The neglected variable in educational outcome research.

Disputes about the superiority of teaching methods often remain unresolved. The essential question we continuously want to answer is: Which teaching methods yield the best knowledge and skills in students? Abundant literature, in medical education and in education in general, on research with educational methods as independent variables and measures of outcome (e.g., test scores) as the dependent variable often point at "no significant difference" or only small differences between methods. Many factors do influence the educational outcome in students and large statistical power (such as meta analysis) should be helpful to eliminate many sources of error. However, one source we cannot tackle this way. That is, students will usually adapt quantity and quality of studying to meet testing requirements. In doing so, they may compensate for teaching quality. Some teaching may generate more effort in students than other teaching. Since test scores reflect primarily student activities, it is their efforts that may bring differences in teaching methods close to equality in test scores. Therefore, knowledge and skills should not be considered the primary outcome of teaching but the outcome of learning activities. If we want to discriminate between teaching methods, we must at least consider what happens to students.

Clinical Competence↗
PubMed2004

An update of cancer mortality among the French cohort of uranium miners: extended follow-up and new source of data for causes of death.

The follow-up of the French cohort of uranium miners has been extended to 1994, and a new source of information for causes of death has been used. The paper presents the new results regarding the risk of death among the cohort, and analyses the impact of the methodological changes on these results. The extension of the follow-up results in a substantial increase in statistical power compared with previous analysis (+25% for person-years and +74% for the number of deaths). The use of the National Mortality Database as the principal source for causes of death allows to reduce the potential bias in the calculation of standardized mortality ratios (SMR). As a consequence, an excess risk of deaths from laryngeal cancer, suggested in the first analysis, is not confirmed. The analysis shows the existence of an excess risk of deaths from lung cancer among French uranium miners (85 observed deaths, SMR = 1.9, 95% confidence interval CI: 1.5-2.3), and an increase of this risk with cumulative exposure to radon (excess relative risk per 100 working level month = 0.6, 95% CI: 0.1-1.2). These results confirm the existence of a risk of death from lung cancer in a population chronically exposed to relatively low levels of radon.

Adult↗
PubMed2006

Identification of probable genotyping errors by consideration of haplotypes.

Undetected genotyping errors pose a problem in genetic epidemiological studies, as they may invalidate statistical analysis or reduce its power. Haplotype analysis requires an improved standard of the data, because a haplotype can be inferred correctly only if the genotypes of all its markers are correct. Here, we present a method that identifies probable genotyping errors in trio samples with the help of the estimated haplotype frequency distribution of the sample. If the likelihood of the most likely haplotype explanation depends strongly on just one genotype, in the sense that setting the genotype to be missing leads to a much more likely haplotype explanation, this genotype is considered as a potential genotyping error. We describe a method that systematically searches the whole data set for such potential errors. Based on the haplotype distribution of a real data set, we carry out a simulation study to estimate the sensitivity and specificity of the method. In addition, we apply our approach to the real data set itself. Potentially erroneous genotypes are re-determined via sequencing. The results of both the simulation study and of the application to the real data set show that a considerable proportion of true genotyping errors is detected and that the number of false-positive signals is acceptable. We conclude that it is indeed possible to identify probable genotyping errors by considering haplotypes. The method described here will be part of the next release of our FAMHAP software.

Computer Simulation↗
PubMed2003

The effect of three commercial coaching courses on Step One USMLE performance.

BACKGROUND: A substantial industry exists to provide formal review courses for Step 1 of the United States Medical Licensing Examination (USMLE). There are limited data on the usefulness of these courses. AIM: To determine whether or not student participation in a commercial coaching course improves performance on Step 1 of the USMLE. METHODS: Scores achieved by 468 students on the National Board of Medical Examiners (NBME) Comprehensive Basic Science Examination (CBSE) were used to predict a score on Step 1 of the USMLE. The NBME is the organisation that prepares and administers the USMLE. Predicted USMLE scores were then regressed against the actual scores achieved by the students on Step 1. The students were divided into 2 groups: those who took a 3-4-week live commercial coaching course and those who studied on their own. RESULTS: The regression lines for the 369 students who studied on their own and the 99 students who took a commercial coaching course were statistically indistinguishable. The analysis was powerful enough to have picked up a difference of 1% on average (P = 0.05) or 2 questions out of the 350 constituting Step 1 of the USMLE. Neither the students who performed above average nor those who performed below average on the CBSE improved their performance on Step 1 as a result of the coaching courses. CONCLUSIONS: Students who take a live, 3-4-week commercial coaching course to improve performance on Step 1 of the USMLE do not achieve higher scores than students who study on their own. Students should strongly consider whether or not a substantial investment in time and money for a commercial coaching course is justified in the light of such meagre returns.

Curriculum↗