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PubMed2002

Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans.

Epistasis, the interaction between genes, is a topic of current interest in molecular and quantitative genetics. A large amount of research has been devoted to the detection and investigation of epistatic interactions. However, there has been much confusion in the literature over definitions and interpretations of epistasis. In this review, we provide a historical background to the study of epistatic interaction effects and point out the differences between a number of commonly used definitions of epistasis. A brief survey of some methods for detecting epistasis in humans is given. We note that the degree to which statistical tests of epistasis can elucidate underlying biological interactions may be more limited than previously assumed.

Data Interpretation, Statistical↗
PubMed2002

An introduction to biostatistics.

This introduction to biostatistics and measurement is the first in a series of articles designed to provide Radiology readers with a basic understanding of statistical concepts. Although most readers of the radiology literature know that application of study results to their practice requires an understanding of statistical issues, many may not be fully conversant with how to interpret statistics. The goal of this series is to enhance the ability of radiologists to evaluate the literature competently and critically, not make them into statisticians.

Biometry↗
PubMed2004

Phylogenomics of eukaryotes: impact of missing data on large alignments.

Resolving the relationships between Metazoa and other eukaryotic groups as well as between metazoan phyla is central to the understanding of the origin and evolution of animals. The current view is based on limited data sets, either a single gene with many species (e.g., ribosomal RNA) or many genes but with only a few species. Because a reliable phylogenetic inference simultaneously requires numerous genes and numerous species, we assembled a very large data set containing 129 orthologous proteins ( approximately 30,000 aligned amino acid positions) for 36 eukaryotic species. Included in the alignments are data from the choanoflagellate Monosiga ovata, obtained through the sequencing of about 1,000 cDNAs. We provide conclusive support for choanoflagellates as the closest relative of animals and for fungi as the second closest. The monophyly of Plantae and chromalveolates was recovered but without strong statistical support. Within animals, in contrast to the monophyly of Coelomata observed in several recent large-scale analyses, we recovered a paraphyletic Coelamata, with nematodes and platyhelminths nested within. To include a diverse sample of organisms, data from EST projects were used for several species, resulting in a large amount of missing data in our alignment (about 25%). By using different approaches, we verify that the inferred phylogeny is not sensitive to these missing data. Therefore, this large data set provides a reliable phylogenetic framework for studying eukaryotic and animal evolution and will be easily extendable when large amounts of sequence information become available from a broader taxonomic range.

Animals↗
PubMed1994

A geometric approach to the analysis of physiological flow data.

Physiological flow data are common in various medical fields. Examples include urinary, blood and expiratory flows. They are widely used in assessing functions in the urinary, circulatory, or pulmonary systems, respectively. Current statistical methods for analysing these flow data in clinical trials are either univariate analyses, which do not utilize all the information together, or some conventional multivariate methods (such as regression analyses) which yield results that do not render clear medical interpretations. This paper presents a new approach to analysing the flow data, using urinary flow as the primary focus. The basic idea and technical steps are applicable to other flow data as well. The proposed method aims to transform the flow measurements back to the shape of the flow graphs. Since the whole geometric pattern of the flow graph provides more information about the patient's flow condition than any individual flow parameter alone, the method is a meaningful way of combining and analysing the flow data in both statistical and clinical senses. The method is a three-stage procedure. Patients are classified into three classes in the first stage and then ranked in sequence in the second stage, according to the geometry of the shape pattern and some clinical criteria. The classification procedure is shown to be very reliable when compared with the clinician's visual evaluation, and hence can be implemented by computer programming to aid clinical trials involving many patients. The whole ranking score is then readily analysed at the third stage for comparing treatment effects by the analysis of covariance method based on ranks, with the post-treatment score as the response variable and the baseline score as the covariate. An example of a urinary flow data set is provided to illustrate the use of the procedure.

Analysis of Variance↗
PubMedDate not supplied

Benchmarking in healthcare: evaluating data and transforming it into action.

After the benchmarking team has accumulated data for the development of comparisons, it must be validated for completeness and consistency. Various factors can skew the analysis and should be watched: Subjective interpretations of survey questions. Lack of common definitions. Composition of input data. External factors and extraordinary events. After verifying consistency of data gathered from benchmarking partners, calculate appropriate statistics for the performance metric. Typical data tabulations are: mean, median, ratio, minimum and maximum value, normal operating range, standard deviation and correlation coefficient. Statistics derived from the data produce the benchmark against which you will measure your institution's performance. Gap analysis establishes the difference between your internal operation's performance and that of the benchmark. Information developed from properly collected data will help you determine reasons for the gap between your performance and the benchmark and project future trends. The next step is to develop an action plan based on what has been learned from benchmarking and targeted to improving performance in areas that further the strategic goals of the institution. In addition to determining performance goals, you must analyze the decision-making process involved in making changes that will move you toward those goals. Since the goal of benchmarking is to improve the organization, the team must present its analysis to those members of management who can approve an action plan. Changes resulting from benchmarking can range from incremental improvement of existing practices all the way to reenginering. Action plans are designed to effect change at levels that will vary according to the goals that have been set. The more incremental the change, the easier the implementation. The more radical the change, the greater the reward.

Data Display↗
PubMed2006

A phyloproteomic characterization of in vitro autophosphorylation in calcium-dependent protein kinases.

Calcium-dependent protein kinases (CDPKs) are a novel class of signaling molecules that have been broadly implicated in relaying specific calcium-mediated responses to biotic and abiotic stress as well as developmental cues in both plants and protists. Calcium-dependent autophosphorylation has been observed in almost all CDPKs examined, but a physiological role for autophosphorylation has not been demonstrated. To date, only a handful of autophosphorylation sites have been mapped to specific residues within CDPK amino acid sequences. In an attempt to gain further insight into this phenomenon, we have mapped autophosphorylation sites and compared these phosphorylation patterns among multiple CDPK isoforms. From eight CDPKs and two CDPK-related kinases from Arabidopsis thaliana and Plasmodium falciparum, 31 new autophosphorylation sites were characterized, which in addition to the previously described sites, allowed the identification of five conserved loci. Of the 35 total sites analyzed approximately one-half were observed in the N-terminal variable domain. Homology models were generated for the protein kinase and calmodulin-like domains, each containing two of the five conserved sites, to allow intelligent speculation regarding subsequent lines of investigation.

Amino Acid Motifs↗
PubMed1999

Multilevel daily process designs for consulting and clinical psychology: a preface for the perplexed.

The next 3 articles in this issue use multilevel statistical procedures to analyze data collected in daily process studies of (a) stress and coping, (b) binge eating, and (c) chronic pain experience. Important differences in the methods and procedures of these studies illustrate the many options available to investigators and data analysts. This article serves as a preface to help readers who are new to these studies' methodology appreciate their novel contributions to the literature in consulting and clinical psychology. Four frequently asked questions are addressed concerning the design of daily process studies, the distinctive meaning of a within-person finding, the possibility that self-monitoring studies are measurement reactive, and complexities in the use of multilevel statistical procedures for analyzing person-day data sets.

Data Interpretation, Statistical↗
PubMed1997

Expression of transforming growth factors beta-1, beta 2 and beta 3 in human bladder carcinomas.

We previously detected elevated transforming growth factor beta-1 (TGF-beta1) serum levels in patients with invasive bladder carcinomas. In this study, we therefore investigated whether elevated serum levels correlate with enhanced TGF-beta expression in human bladder tumours. mRNA levels of TGF-beta1, -beta2 and -beta3 were reduced in bladder tumour tissue to 86%, 68% and 56%, respectively, of the levels in normal urothelium. On the other hand, TGF-beta1 protein levels were found to be higher in superficial tumours (Ta-T1) (mean level of 0.153 ng mg(-1)) and in invasive T2/T3 tumours (mean level of 0.104 ng mg(-1)) compared with normal urothelium (mean level of 0.065 ng mg(-1)). Invasive T4 tumours, however, contained only low amounts of TGF-beta1 (mean level of 0.02 ng mg(-1)). Neither in mean nor in individual patients were serum and tissue TGF-beta levels correlated with each other. Cell culture experiments on primary bladder cells revealed a 57% decrease in TGF-beta1 mRNA levels in tumour compared with normal epithelial cells. Tumour epithelial cells contained about two times higher levels of TGF-beta2 and TGF-beta3 mRNA than normal epithelial cells. Fibroblasts expressed about the same amount of TGF-beta1 or TGF-beta2 as epithelial cells. Yet, fibroblasts released only 19% and 13% of the amount secreted by tumour epithelial cells into the supernatant. TGF-beta3, on the other hand, was expressed by fibroblasts with higher levels than by epithelial cells. TGF-beta1 was the predominent isoform in bladder tissue and cells at protein as well as on mRNA levels indicating that TGFs-beta2 and -beta3 are of minor importance in bladder cancer. In summary, there is a lack of correlation between TGF-beta serum levels and TGF-beta expression in tumour tissue in bladder cancer.

Base Sequence↗
PubMed1998

Perturbation of CD4+ and CD8+ T-cell repertoires during progression to AIDS and regulation of the CD4+ repertoire during antiviral therapy.

The T-cell antigen receptor (TCR) repertoire was studied longitudinally by analyzing the varying lengths of the beta chain CDR3 hypervariable region during the course of HIV-1 infection and following combination antiretroviral therapy. Drastic restrictions in CD8+ T-cell repertoire usage were found at all stages of natural progression and persisted during the first six months of treatment. In contrast, significant CD4+ T-cell repertoire perturbations were not found in early stages of infection but correlated with progression to AIDS. Out of ten patients presenting with pretreatment perturbations, normalization of the CD4+ repertoire was observed in eight good responders, but not in two cases of unsuccessful therapy. These results indicate that, besides CD4+ cell count rise, an efficient control of HIV replication may allow qualitative modifications of the CD4+ repertoire balance.

Acquired Immunodeficiency Syndrome↗
PubMed2001

Algorithms for identifying protein cross-links via tandem mass spectrometry.

Cross-linking technology combined with tandem mass spectrometry (MS-MS) is a powerful method that provides a rapid solution to the discovery of protein-protein interactions and protein structures. We studied the problem of detecting cross-linked peptides and cross-linked amino acids from tandem mass spectral data. Our method consists of two steps: the first step finds two protein subsequences whose mass sum equals a given mass measured from the mass spectrometry; and the second step finds the best cross-linked amino acids in these two peptide sequences that are optimally correlated to a given tandem mass spectrum. We designed fast and space-efficient algorithms for these two steps and implemented and tested them on experimental data of cross-linked hemoglobin proteins. An interchain cross-link between two beta subunits was found in two tandem mass spectra. The length of the cross-linker (7.7 A) is very close to the actual distance (8.18 A) obtained from the molecular structure in PDB.

Algorithms↗
PubMed2005

How to assess the reliability of measurements in rehabilitation.

To evaluate the effects of rehabilitation interventions, we need reliable measurements. The measurements should also be sufficiently sensitive to enable the detection of clinically important changes. In recent years, the assessment of reliability in clinical practice and medical research has developed from the use of correlation coefficients to a comprehensive set of statistical methods. In this review, we present methods that can be used to assess reliability and describe how data from reliability analyses can aid the interpretation of results from rehabilitation interventions.

Data Interpretation, Statistical↗
PubMed1998

A software system for data analysis in automated DNA sequencing.

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing, analysis, and base-calling. BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilation. Powerful scripting capabilities combined with modularity and multilane handling allow the user to customize BaseFinder to virtually any type of trace processing. We have developed an extensive set of data processing and analysis modules for use with the program in fluorescence-based sequencing. GelImager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently allowing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapsody. Work is ongoing to deploy the software on additional platforms, including Solaris, Linux, and MacOS. This software has been thoroughly tested and debugged in the analysis of >2 million bp of raw sequence data from human chromosome 19 region q13. Overall sequencing accuracy was measured using a significant subset of these data, consisting of approximately 600 sequences, by comparing the individual shotgun sequences against the final assembled contigs. Also, results are reported from experiments that analyzed the accuracy of the software and two other well-known base-calling programs for sequencing the M13mp18 vector sequence. [The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF025422]

Algorithms↗
PubMed1996

Angiotensin I-converting enzyme genotypes and angiotensin II receptors. Response to therapy.

In the present study, we studied angiotensin II type 1 (AT1) and type 2 (AT2) receptor messengers by quantitative reverse transcriptase-polymerase chain reaction. We examined peripheral blood mononuclear cells from 30 healthy subjects and 50 subjects with primary hypertension, in whom angiotensin I-converting enzyme genotype was determined, before and after 15 days of treatment with different antihypertensive drugs. The medication included a calcium channel antagonist, an angiotensin I-converting enzyme inhibitor, and a beta 1-blocker. We also studied the relationship between AT1 receptor gene expression and biochemical parameters of the renin-angiotensin system. AT1 receptor messenger levels were positively correlated with plasma renin activity in both normotensive and untreated hypertensive subjects. Increases of this messenger and plasma angiotensin II levels were correlated with the D allele in the same individuals. AT1 receptor messenger levels decreased significantly with angiotensin I-converting enzyme inhibitor treatment in subjects with the DD genotype, and a significant decrease was observed in subjects with the II and ID genotypes treated with a calcium antagonist. No changes were observed in mRNA with the beta 1-blocker. We conclude that the AT2 receptor is not expressed in peripheral leukocytes and that AT1 receptor messenger levels vary in relation to angiotensin I-converting enzyme genotype and pharmacological treatment. These results suggest that angiotensin I-converting enzyme genotype may be an important factor when deciding on antihypertensive therapy in individuals with primary hypertension.

Adrenergic beta-Antagonists↗
PubMed1995

Human T cell responses to autoantibody variable region peptides.

The origins and regulation of autoantibodies in SLE may involve idiotypic cell interactions. The purpose of this study was to determine if SLE patients have T cells reactive with the idiotopes of autoantibodies. Sequences of the variable regions of two DNA-binding autoantibodies (V lambda of antibody B3 and VH of 9G4) were selected according to the predicted location of their idiotypes defined previously by anti-idiotypic antibodies. The sequences were prepared as synthetic 16mer peptides (idiopeptides). Peripheral blood mononuclear cells were prepared from SLE patients (n = 28) and controls (n = 13) and put into multiple microcultures with idiopeptide for 6 days. The frequency of responding cultures was determined as those incorporating thymidine at levels above the mean plus three standard deviations of the control cultures lacking peptide. Of the 28 lupus patients, six responded to B3 idiopeptide and five to the 9G4 idiopeptide. Some patients responded to other idiopeptides, but only one normal individual responded to each reference peptide. The difference between the patient and control responses to all idiopeptides was significant by chi 2 analysis (P = 0.025). We conclude that patients with SLE show evidence of sensitisation of T cells to idiotopes of autoantibodies. Such anti-idiotypic T cells could either provide idiotype-specific help or suppression for autoantibody responses in SLE.

Adult↗
PubMed2005

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

BACKGROUND: We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is superior to Needleman-Wunsch-based multi-alignment programs on locally related sequence sets. However, it is often outperformed by these methods on data sets with global but weak similarity at the primary-sequence level. RESULTS: In the present paper, we discuss strengths and weaknesses of DIALIGN in view of the underlying objective function. Based on these results, we propose several heuristics to improve the segment-based alignment approach. For pairwise alignment, we implemented a fragment-chaining algorithm that favours chains of low-scoring local alignments over isolated high-scoring fragments. For multiple alignment, we use an improved greedy procedure that is less sensitive to spurious local sequence similarities. To evaluate our method on globally related protein families, we used the well-known database BAliBASE. For benchmarking tests on locally related sequences, we created a new reference database called IRMBASE which consists of simulated conserved motifs implanted into non-related random sequences. CONCLUSION: On BAliBASE, our new program performs significantly better than the previous version of DIALIGN and is comparable to the standard global aligner CLUSTAL W, though it is outperformed by some newly developed programs that focus on global alignment. On the locally related test sets in IRMBASE, our method outperforms all other programs that we evaluated.

Algorithms↗