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Subgroup analyses in randomised controlled trials: quantifying the risks of false-positives and false-negatives.

BACKGROUND: Subgroup analyses are common in randomised controlled trials (RCTs). There are many easily accessible guidelines on the selection and analysis of subgroups but the key messages do not seem to be universally accepted and inappropriate analyses continue to appear in the literature. This has potentially serious implications because erroneous identification of differential subgroup effects may lead to inappropriate provision or withholding of treatment. OBJECTIVES: (1) To quantify the extent to which subgroup analyses may be misleading. (2) To compare the relative merits and weaknesses of the two most common approaches to subgroup analysis: separate (subgroup-specific) analyses of treatment effect and formal statistical tests of interaction. (3) To establish what factors affect the performance of the two approaches. (4) To provide estimates of the increase in sample size required to detect differential subgroup effects. (5) To provide recommendations on the analysis and interpretation of subgroup analyses. METHODS: The performances of subgroup-specific and formal interaction tests were assessed by simulating data with no differential subgroup effects and determining the extent to which the two approaches (incorrectly) identified such an effect, and simulating data with a differential subgroup effect and determining the extent to which the two approaches were able to (correctly) identify it. Initially, data were simulated to represent the 'simplest case' of two equal-sized treatment groups and two equal-sized subgroups. Data were first simulated with no differential subgroup effect and then with a range of types and magnitudes of subgroup effect with the sample size determined by the nominal power (50-95%) for the overall treatment effect. Additional simulations were conducted to explore the individual impact of the sample size, the magnitude of the overall treatment effect, the size and number of treatment groups and subgroups and, in the case of continuous data, the variability of the data. The simulated data covered the types of outcomes most commonly used in RCTs, namely continuous (Gaussian) variables, binary outcomes and survival times. All analyses were carried out using appropriate regression models, and subgroup effects were identified on the basis of statistical significance at the 5% level. RESULTS: While there was some variation for smaller sample sizes, the results for the three types of outcome were very similar for simulations with a total sample size of greater than or equal to 200. With simulated simplest case data with no differential subgroup effects, the formal tests of interaction were significant in 5% of cases as expected, while subgroup-specific tests were less reliable and identified effects in 7-66% of cases depending on whether there was an overall treatment effect. The most common type of subgroup effect identified in this way was where the treatment effect was seen to be significant in one subgroup only. When a simulated differential subgroup effect was included, the results were dependent on the nominal power of the simulated data and the type and magnitude of the subgroup effect. However, the performance of the formal interaction test was generally superior to that of the subgroup-specific analyses, with more differential effects correctly identified. In addition, the subgroup-specific analyses often suggested the wrong type of differential effect. The ability of formal interaction tests to (correctly) identify subgroup effects improved as the size of the interaction increased relative to the overall treatment effect. When the size of the interaction was twice the overall effect or greater, the interaction tests had at least the same power as the overall treatment effect. However, power was considerably reduced for smaller interactions, which are much more likely in practice. The inflation factor required to increase the sample size to enable detection of the interaction with the same power as the overall effect varied with the size of the interaction. For an interaction of the same magnitude as the overall effect, the inflation factor was 4, and this increased dramatically to of greater than or equal to 100 for more subtle interactions of < 20% of the overall effect. Formal interaction tests were generally robust to alterations in the number and size of the treatment and subgroups and, for continuous data, the variance in the treatment groups, with the only exception being a change in the variance in one of the subgroups. In contrast, the performance of the subgroup-specific tests was affected by almost all of these factors with only a change in the number of treatment groups having no impact at all. CONCLUSIONS: While it is generally recognised that subgroup analyses can produce spurious results, the extent of the problem is almost certainly under-estimated. This is particularly true when subgroup-specific analyses are used. In addition, the increase in sample size required to identify differential subgroup effects may be substantial and the commonly used 'rule of four' may not always be sufficient, especially when interactions are relatively subtle, as is often the case. CONCLUSIONS--RECOMMENDATIONS FOR SUBGROUP ANALYSES AND THEIR INTERPRETATION: (1) Subgroup analyses should, as far as possible, be restricted to those proposed before data collection. Any subgroups chosen after this time should be clearly identified. (2) Trials should ideally be powered with subgroup analyses in mind. However, for modest interactions, this may not be feasible. (3) Subgroup-specific analyses are particularly unreliable and are affected by many factors. Subgroup analyses should always be based on formal tests of interaction although even these should be interpreted with caution. (4) The results from any subgroup analyses should not be over-interpreted. Unless there is strong supporting evidence, they are best viewed as a hypothesis-generation exercise. In particular, one should be wary of evidence suggesting that treatment is effective in one subgroup only. (5) Any apparent lack of differential effect should be regarded with caution unless the study was specifically powered with interactions in mind. CONCLUSIONS--RECOMMENDATIONS FOR RESEARCH: (1) The implications of considering confidence intervals rather than p-values could be considered. (2) The same approach as in this study could be applied to contexts other than RCTs, such as observational studies and meta-analyses. (3) The scenarios used in this study could be examined more comprehensively using other statistical methods, incorporating clustering effects, considering other types of outcome variable and using other approaches, such as Bootstrapping or Bayesian methods.

Data Interpretation, Statistical↗

Reliability of cancer mortality statistics in Ontario: a comparison of incident and death diagnoses, 1979-1983.

We compared the underlying cause of cancer death listed on death certificates, to the registry diagnosis from the incident file in the Ontario Cancer Registry (OCR). For the 68,772 cancer deaths having both a registry diagnosis and a cancer cause of death, 79.3% agreed between the two sources at the third digit level of ICD-9; this rose to 85.8% when sites were aggregated into about 30-site groups (positive predictive value 85.8%, sensitivity 82.9%). The most common sites, accounting for greater than 80% of all cancer deaths, all had agreement rates above 80%. Sites of questionable reliability, comprising less than 10% of all cancer deaths, included liver and larynx, and most other ill-defined and unspecified sites. Recommendations to improve the quality of published cancer mortality statistics include combining colon and rectum, and the non-Hodgkin's lymphomas. Caution in the use and interpretation of statistics for cancers of the liver and larynx is suggested owing to poor reliability.

Cause of Death↗

Fast and sensitive probe selection for DNA chips using jumps in matching statistics.

The design of large scale DNA microarrays is a challenging problem. So far, probe selection algorithms must trade the ability to cope with large scale problems for a loss of accuracy in the estimation of probe quality. We present an approach based on jumps in matching statistics that combines the best of both worlds. This article consists of two parts. The first part is theoretical. We introduce the notion of jumps in matching statistics between two strings and derive their properties. We estimate the frequency of jumps for random strings in a non-uniform Bernoulli model and present a new heuristic argument to find the center of the length distribution of the longest substring that two random strings have in common. The results are generalized to near-perfect matches with a small number of mismatches. In the second part, we use the concept of jumps to improve the accuracy of the longest common factor approach for probe selection by moving from a string-based to an energy-based specificity measure, while only slightly more than doubling the selection time.

Algorithms↗

How to read, interpret, and understand evidence-based literature statistics.

To implement best practices through research utilization, nurses need to read, interpret, and understand literature formatted with evidence-based practice language and statistics. Hypothetical examples highlight 7 terms and their formulas. A scenario to personally calculate such evidence-based practice statistics can be used to enhance personal effectiveness and to teach others.

Comprehension↗

Evolutionarily conserved allosteric network in the Cys loop family of ligand-gated ion channels revealed by statistical covariance analyses.

The Cys loop family of ligand-gated ion channels mediate fast synaptic transmission for communication between neurons. They are allosteric proteins, in which binding of a neurotransmitter to its binding site in the extracellular amino-terminal domain triggers structural changes in distant transmembrane domains to open a channel for ion flow. Although the locations of binding site and channel gating machinery are well defined, the structural basis of the activation pathway coupling binding and channel opening remains to be determined. In this paper, by analyzing amino acid covariance in a multiple sequence alignment, we have identified an energetically interconnected network in the Cys loop family of ligand-gated ion channels. Statistical coupling and correlated mutational analyses along with clustering revealed a highly coupled cluster. Mapping the positions in the cluster onto a three-dimensional structural model demonstrated that these highly coupled positions form an interconnected network linking experimentally identified binding domains through the coupling region to the gating machinery. In addition, these highly coupled positions are also condensed in the transmembrane domains, which are a recent focus for the sites of action of many allosteric modulators. Thus, our results revealed a genetically interconnected network that potentially plays an important role in the allosteric activation and modulation of the Cys loop family of ligand-gated ion channels.

Allosteric Regulation↗

Assessing progress in systematics with continuous jackknife function analysis.

Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted against the accumulating number of characters. Continuous jackknife function (CJF) analysis is a new graphical method that portrays the extent to which available data converge on a specified phylogenetic hypothesis, the reference tree. The method removes characters with increasing probability, analyzes the rarefied data matrices phylogenetically, and scores the clades shared between each of the resulting trees and the reference tree. As more characters are removed, the number of shared clades must decrease, but the rate of decrease will depend on how decisively the data support the reference tree. Curves for stable phylogenies are clearly asymptotic with nearly 100% congruence for a substantial part of the curve. Less stable phylogenies lose congruent nodes quickly as characters are excluded, resulting in a more linear or even a sigmoidal relationship. Curves can be interpreted as predictors of whether the addition of new data of the same type is likely to alter the hypothesis under test. Continuous jackknife function analysis makes statistical assumptions about the collection of character data. To the extent that CJF curves are sensitive to violations of unbiased character collection, they will be misleading as predictors. Convergence of data on a reference tree does not guarantee historical accuracy, but it does predict that the accumulation of further data under the sampling model will not lead to rapid changes in the hypothesis.

Algorithms↗

Stability parameter estimation at ambient temperature from studies at elevated temperatures.

The determination of specific kinetic constants k(i) in pH-profile studies is often undertaken at ambient temperature. However, when dealing with a drug substance that is stable at ambient temperature, the pH-profile study is conducted at a chosen elevated temperature and the kinetic parameters are given at this particular elevated temperature. But in stability studies we generally need kinetic constants at ambient or storage temperature for practical reasons (information and storage conditions of formulation). To assess this ambient kinetic information from studies at elevated temperatures, cumulative sequential steps are usually employed with very few statistical concerns on the final estimates. The statistical problems on these final estimates in cumulative procedures are highlighted in many papers. Because these stability parameters are useful for drug formulation and storage conditions, good practical decisions have to be made on the basis of statistically unbiased identified parameters. We propose in this paper a nonlinear model that allows the direct determination of specific activation energies E(ai) that are linked to the specific kinetic constants k(i). Hence, a mathematical relationship between drug concentration C, pH, temperature T, and time t is obtained. Kinetic data from acetylsalicylic acid (ASA) hydrolysis (first-order kinetics) are used to validate the model. The results show that it is possible to obtain directly, by an extrapolation procedure, the kinetic parameters (specific kinetic constants k(i), specific activation energies E(ai), and dissociation constant pK(a)) at low temperature from data gathered at elevated temperatures using more meaningful statistics.

Data Interpretation, Statistical↗

A powerful method of combining measures of association and Hardy-Weinberg disequilibrium for fine-mapping in case-control studies.

We present a new method for fine-mapping a disease susceptibility locus using a case-control design. The new method, termed the 'weighted average (WA) statistic', averages the Cochran-Armitage (CA) trend test statistic and the difference between the Hardy Weinberg disequilibrium test statistics (the HWD trend) for cases and controls. The main features of the WA statistic are that it mitigates against the weaknesses, and maintains the strong points, of both the CA trend test and the HWD trend test. To allow for the extra variance induced by population structure and cryptic relatedness, the WA statistic can be adjusted for variance inflation. Based on the results of a simulation study, when there is no population structure the WA test statistic shows good performance under a variety of genetic disease models. When there is population structure, the adjusted WA statistic maintains the correct probability of type I error. Under all genetic disease models investigated, the adjusted WA statistic has better power than the adjusted CA trend test, the HWD trend test or the product of the adjusted CA trend test and the HWD trend test statistics.

Case-Control Studies↗

Spatial analysis of disease--applications.

The application of spatial statistical analysis to health data has reached adolescence. The theory and the software are both still maturing. We are drawing upon the experiences of the geostatisticians in modeling surfaces and the econometricians in modeling time series. "New and improved" computer algorithms are constantly being provided to implement the evolving theory or to improve the processing in terms of stability, reliability, and efficiency. We will come of age when we have the theory, the software, and the process to reliably produce "generalized spatio-temporal" models suitable for health data. In the meantime, biostatisticians need to acknowledge when their data is not independently distributed and to consider the spatial correlation in their analysis. This chapter provided examples using four available methods. The methods were spatial filtering, identifying clusters using the spatial scan statistic, hierarchical modeling, and conditional autoregression modeling.

Cluster Analysis↗

Is loss-free counting under statistical control?

A new formula for the statistical uncertainty of "loss-free counting" (LFC) is presented. Its validity is demonstrated by comparing with experimental data obtained with a HPGe gamma-ray spectrometer. Also, computer simulation data of nuclear counting with different types of count loss (pileup rejection, extending and nonextending dead time) are in agreement with the predicted counting uncertainty. The proposed formula for LFC uncertainty is applicable to spectrometers with a classical semi-Gaussian pulse-shaping amplifier as well as with a gated-integrator amplifier. Hence, achieving statistical control seems to be a feasible goal.

Computer Simulation↗

A parallel approach to post source decay MALDI-TOF analysis.

We present a novel enhancement to matrix-assisted laser desorption ionization (MALDI) post-source decay (PSD) analysis whereby fragment ions from multiple precursor ions are acquired into the same spectrum without employing a timed ion gate to preselect each parent ion. Fragment ions are matched to their corresponding precursor ions by comparing spectra acquired at slightly different reflectron electric fields. By measuring the difference in time-of-flight (TOF) between the two spectra for each fragment, it is possible to calculate the mass of the fragment ion and its parent. This new "parallel PSD" technique reduces analysis time and consumes less sample than conventional PSD, which requires an ion gate for serial preselection of precursor ions.

Algorithms↗

Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp.

Phylogenetic relationships among the nine spiral-horn antelope species of the African bovid tribe Tragelaphini are controversial. In particular, mitochondrial DNA sequencing studies are not congruent with previous morphological investigations. To test the utility of nuclear DNA intron markers at lower taxonomic levels and to provide additional data pertinent to tragelaphid evolution, we sequenced four nuclear DNA segments (MGF, PRKCI, SPTBN, and THY) and combined these data with mitochondrial DNA sequences from three genes (cytochrome b, 12S rRNA, and 16S rRNA). Our molecular supermatrix comprised 4682 characters which were analyzed independently and in combination. Parsimony and model based phylogenetic analyses of the combined nuclear DNA data are congruent with those derived from the analysis of mitochondrial gene sequences. The corroboration between nuclear and mtDNA gene trees reject the possibility that genetic processes such as lineage sorting, gene duplication/deletion and hybrid speciation account for the conflict evident in the previously published phylogenies. It suggests rather that the morphological characters used to delimit the Tragelaphid species are subject to convergent evolution. Divergence times among species, calculated using a relaxed Bayesian molecular clock, are consistent with hypotheses proposing that climatic oscillations and their impact on habitats were the major forces driving speciation in the tribe Tragelaphini.

Animals↗

Misleading statistical calculations in far-advanced glaucomatous visual field loss.

OBJECTIVE: In this study, the capability of statistical analysis indices to characterize static automated visual fields (VFs) accurately in cases of far-advanced glaucoma was assessed. DESIGN: Retrospective observational case series. PARTICIPANTS: Sixteen eyes of 15 patients with end-stage glaucoma and evidence of collapse of VF statistical analysis indices were included in the study. METHODS: End-stage glaucoma was defined as vertical cup-to-disc ratio of 0.9 or more, mean deviation less than -24 dB and with only a central or temporal island remaining in the VF gray scale. Collapse of statistical indices was defined as any of the following: pattern deviation probability plot without a single VF location showing P < 0.5%; corrected pattern standard deviation (CPSD) and pattern standard deviation (PSD) probability less than 5% or within normal limits (WNL); short-term fluctuation (SF) probability WNL; glaucoma hemifield test (GHT) not outside normal limits (ONL); or presence of a low patient reliability comment triggered by 40% or more false-negative (FN) responses. MAIN OUTCOME MEASURES: Visual field statistical indices. RESULTS: Of the 16 VFs showing misleading statistical calculations, 9 of 16 eyes had a normal pattern deviation probability plot. The PSD, SF, and CPSD parameters were normal or barely outside the normal range in 4 of 16, 10 of 16, and 5 of 16 eyes, respectively. The GHT was ONL in 7 of 13 eyes, borderline with generalized reduction of sensitivity (GRS) in three eyes, and only GRS in two additional eyes. Low patient reliability was triggered because of an FN score of 40% or more in 10 of 16 eyes. CONCLUSIONS: Statistical indices are crucial for the interpretation of automated static VFs. However, in end-stage glaucomatous VF loss, both summary statistical indices and reliability indices may not detect abnormality, thus misleading the casual observer.

Data Interpretation, Statistical↗

Statistical considerations for use of composite health-related quality-of-life scores in randomized trials.

BACKGROUND: Quality of life instruments are frequently used as outcomes in randomized trials. Instruments that consist of several subscales present researchers with a choice of whether to combine some or all scales into a single composite score. There may be several clinically and scientifically reasonable alternative combinations of subscales for the primary outcome measure. MAJOR FINDINGS: The statistical efficiency of different combinations of subscales depends on the relative effect size of the intervention on each subscale and the correlation between the subscales. Simple equations can be derived for determining the relative statistical efficiency of each clinically reasonable combination of subscales. Hypothetical scenarios show that the number of patients needed in a clinical trial can be twice as great for some combinations of subscales as for others. CONCLUSIONS: There are often compelling clinical or scientific reasons to use a particular subscale or composite in a randomized trial. In the case where a number of different alternatives would be reasonable, statistical efficiency can help guide the choice of endpoint.

Data Interpretation, Statistical↗

[Proper handling of correlated data in rehabilitation research].

Many study designs in rehabilitation science give rise to correlated data. For example, patients are followed over time, different responses are measured for each patient, or patients are observed in logical units. Standard statistical methods, however, are only valid for independent responses, and careless application of these methods for actually correlated observations might give erroneous results. By means of a simple example, we show how using methods for correlated data can indeed give a gain in statistical power. In the following, different approaches (Summary measures, Repeated Measurement ANOVA, MANOVA, and Mixed Models) to deal with correlated data are presented. We conclude that among these, the Mixed Models approach is the method of choice because it allows flexible modelling of correlation structure and is, meanwhile, also available in standard statistical software packages.

Analysis of Variance↗

Ecological inference.

Ecological inference is the process of drawing conclusions about individual-level behavior from aggregate-level data. Recent advances involve the combination of statistical and deterministic means to produce such inferences.

Behavior↗

How practitioners (and others) can make scientifically viable contributions to clinical-outcome research using the single-case time-series design.

Although clinicians typically possess considerable interest in research, especially about which interventions do and do not work, all too often they dismiss the notion that they themselves can make viable scientific contributions to the outcome literature. This derives from an unfortunate assumption that the only true experiment is a between-groups experiment. There is another form of true experiment that is perfectly compatible with real-world clinical practice: the single-case time-series design. Intensive and systematic tracking of one or a few patients over time can yield viable inferences about efficacy, effectiveness, and, under some circumstances, mechanism of change. This paper describes how clinicians working with hypnosis can carry out such research. The rationale and essential features of time-series studies are outlined; each design is illustrated with actual studies from the hypnosis literature; and new methods of statistical analysis, well within the statistical competence of practitioners, are described.

Data Interpretation, Statistical↗

Mathematics-assisted mapping in analysis of medical disease.

Genetic mapping in analysis of medical disease is performed under several assumptions and (experimental) conditions, which are made about the data in general and the disease in particular. Here we discuss these conditions, what they mean, and what kind of deleterious effects they might have on the analysis. We also illustrate how to proceed and what kind of possibilities the statistical analysis may provide to medical scientists.

Chromosome Mapping↗