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PubMed2004

Combined linkage and association tests in mx.

Statistical methods aimed at the detection of genes for quantitative traits suffer from two problems: (i) when a linkage approach is employed, relatively large sample sizes are usually required; and (ii) when an association approach is employed, effects of population stratification may blur genuine locus-trait associations. The variance components method proposed by Fulker et al. (1999) addressed both these problems; it is statistically powerful because it involves a combined analysis of linkage and association and can include information from multiplex families, which reduces the overall amount of necessary individual genotypes. In addition, it includes an explicit test for the presence of spurious association. After a brief illustration of the various ways in which population stratification may affect locus-trait associations, the implementation in Mx (Neale, 1997) of the method as proposed by Fulker et al. (1999) is discussed and illustrated. In addition, an extension to this method is proposed that allows the use of (variable) sibship sizes greater than two, the estimation of additive and dominance association effects, and the use of multiple alleles. These extensions can be implemented when parental genotypes are available or unavailable.

Alleles↗
PubMed2001

A prospective randomized comparison of laparoscopic appendectomy with open appendectomy: Clinical and economic analyses.

BACKGROUND: Previous randomized studies of laparoscopic appendectomy produced conflicting recommendations, and the adequacy of sample sizes is generally unknown. We compared clinical and economic outcomes after laparoscopic and open appendectomy in a sample of predetermined statistical power. METHODS: A pre-study power analysis suggested that 200 randomized patients would yield 80% power to show a mean decrease of 1.3 days' hospitalization. One hundred ninety-eight patients with a preoperative diagnosis of acute appendicitis were randomized prospectively to laparoscopic or open appendectomy. Economic analysis included billed charges, total costs, direct costs, and indirect costs associated with treatment. RESULTS: Laparoscopic appendectomy took longer to perform than open appendectomy (median, 107 vs 91 minutes; P <.01) and was associated with fewer days to return to a general diet (mean, 1.6 versus 2.3 days; P <.01), a shorter duration of parenteral analgesia (mean, 1.6 versus 2.2 days; P <.01), fewer morphine-equivalent milligrams of parenteral narcotic (median, 14 mg versus 34 mg; P =.001), a shorter postoperative hospital stay (mean, 2.6 versus 3.4 days; P <.01), and earlier return to full activity (median, 14 versus 21 days; P <.02). However, operative morbidity and time to return to work were comparable. Billed charges and direct costs were not significantly different in the 2 groups ($7711 versus $7146 and $5357 versus $4945, respectively), but total costs (including indirect costs) of laparoscopic appendectomy were, on average, nearly $2400 less, given the shorter length of stay and abbreviated recuperative period ($11,577 versus $13,965). Subgroup analyses suggested the benefit of a laparoscopic approach for uncomplicated appendicitis and for patients with active lifestyles. CONCLUSIONS: While laparoscopic appendectomy is associated with statistically significant but clinically questionable advantages over open appendectomy, a laparoscopic approach is relatively less expensive. The estimated difference in total costs of treatment (direct and indirect costs) was at least $2000 in more than 60% of the bootstrapped iterations. The economic significance and implications favoring a laparoscopic approach cannot be ignored.

Appendectomy↗
PubMed1992

Meta-analysis: the fashion of summing-up evidence. Part II: Interpretations and uses.

In this commentary, we use evidence produced by the Early Breast Cancer Trialists' Collaborative Group (EBCTCG) ten-year update of a meta-analysis of trials of adjuvant therapies for early breast cancer which started prior to 1985 to illustrate aspects of interpretations and uses of meta-analysis results. The following issues are discussed: i) The meta-analysis provides an average summary for the effect of a treatment. Greater statistical power is obtained by increasing the number of events contributing to the analysis. However, summing up the results of various trials necessitates the loss of individual information concerning the magnitude of treatment effects which depend on tumor- and patient-related factors. Subgroup analyses within the meta-analysis process allow some recovery of such features; ii) The absolute benefit obtained from an effective treatment depends not only on the relative benefit of the treatment but also on the prognosis of the individual patients; iii) The results are more immediately applicable if less reliance is placed on the arithmetic construct inherent in the overview, using instead unconfounded information about the value of treatments actually administered. This avoids the need to extrapolate the effect for one component of the therapy by assuming a lack of interaction with its other components; iv) Although indirect comparisons between different meta-analyses are regularly made to pick the "winner" from among tested treatment modalities, it is unlikely that the optimal therapeutic regimen can be defined via such indirect comparisons, though such comparisons may raise interesting, testable hypotheses.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed1995

Meta-analysis of the role of oral contraceptive agents in inflammatory bowel disease.

Numerous epidemiological studies have been performed to determine factors that might contribute to the development of inflammatory bowel disease. Although the role of oral contraceptive agents in Crohn's disease (CD) and ulcerative colitis (UC) have been assessed, most studies were of small sample size and characterised by low statistical precision. A meta-analysis was performed to increase the statistical power and to investigate the association between the use of oral contraceptives and the development of CD and UC. The study was based on a search of a Medline database from 1975 to October 1993 and a review of reference lists from published articles, reviews, symposia proceedings, and abstracts from major gastrointestinal meetings. All studies specifically designed to evaluate this association were selected. The combined results of nine studies--two cohort studies (30,379 unexposed and 30,673 exposed patients) and seven case-control studies (482 CD, 237 UC, and 3198 controls)--which satisfied our selection criteria were evaluated. The pooled relative risk (adjusted for smoking) associated with oral contraceptive use was 1.44 (1.12, 1.86) for CD and 1.29 (0.94, 1.77) for UC. These results suggest modest associations between the use of oral contraceptives and the development of CD and UC. As these associations are weak, non-causal explanations for the findings cannot be eliminated.

Case-Control Studies↗
PubMed1998

Chromosome analysis of lymphocytes from radiation workers in tritium-applying industry.

OBJECTIVES: The frequency of chromosomal aberrations (CA) and micronuclei (MN) in peripheral blood lymphocytes was compared in two groups of persons occupationally exposed to tritium either through the use of luminous paints or in the weapons industry, with the aim of finding a correlation between the CA and MN assays, the extent of radiation hazard, and the duration of occupational exposure to chemical forms of tritium and the ability of the latter to induce hazards in human lymphocytes. METHODS: CA analysis and the cytochalasin B micronucleus test were performed. Urinary tritium in both groups was measured using a liquid scintillation method. For purposes of comparison, 2 control groups (40 persons) were examined; 24 exposed individuals were matched to their controls according to age, sex, and smoking habits. RESULTS: Values recorded for the frequency of CA in the group of workers handling tritium in luminous dial painting were 0.015 +/- 0.014 dicentrics/cell, 0.023 +/- 0.017 total unstable CA/cell, and 0.035 +/- 0.019 MN/binucleated cell. Urinary levels of tritium in this group of employees ranged from 1.35 to 9.43 MBq/l. As compared with their matched controls, in these workers the differences in the yield of CA as well as in MN were statistically highly significant (P < 0.005 and P < 0.003, respectively). The same parameters analyzed in workers employed in the armament industry gave values of 0.001 +/- 0.003 dicentrics/cell, 0.010 +/- 0.008 total unstable CA/cell, and 0.021 +/- 0.029 MN/binucleated cell. No detectable concentration of urinary tritium was found. As compared with their matched controls, in these workers the differences were also statistically significant (P < 0.027 and P < 0.012, respectively). The yield of CA, particularly the yield of dicentrics, was significantly higher (P < 0.005) in the group of luminous dial painters as compared with the weapons industry workers. The difference found in the yield of MN between the two groups of workers was also statistically significant (P < 0.084). Intercontrol differences in the yields of spontaneous CA as well as in MN were insignificant (P < 0.683 and P < 0.735, respectively). The results are discussed with respect to individual variations in the response to low doses of ionizing radiation, disorders in the handling of radionuclides, the duration of occupational exposure, and the chemical properties of the radionuclides used. CONCLUSION: Tritium in the chemical form of luminous paint is a more powerful clastogenic agent than tritium gas. Statistical analysis demonstrated that lymphocyte effects are due to the concentration of tritium in urine rather than to the duration of occupational exposure. Since the radiation hazard measured by the MN assay did not differ from that determined by the CA assay, the MN test can be recommended as a rapid assay for screening purposes in cases of occupational exposure to low radiation doses.

Adult↗
PubMed2001

Stapled versus handsewn methods for colorectal anastomosis surgery.

BACKGROUND: Randomized controlled trials comparing stapled with handsewn colorectal anastomosis have not shown either technique to be superior, perhaps because individual studies lacked statistical power. A systematic review, with pooled analysis of results, might provide a more definitive answer. OBJECTIVES: To compare the safety and effectiveness of stapled and handsewn colorectal anastomosis. The following primary hypothesis was tested: the stapled technique is more effective because it decreases the level of complications. SEARCH STRATEGY: The RCT register of the Cochrane Review Group was searched for any trial or reference to a relevant trial (published, in-press, or in progress). All publications were sought through computerised searches of EMBASE, LILACS, MEDLINE, the Cochrane Controlled Clinical Trials Database, and through letters to industrial companies and authors. There were no limits upon language, date, or other criteria. SELECTION CRITERIA STUDIES: All randomized clinical trials (RCTs) in which stapled and handsewn colorectal anastomosis were compared. PARTICIPANTS: Adult patients submitted electively to colorectal anastomosis. INTERVENTIONS: Endoluminal circular stapler and handsewn colorectal anastomosis. OUTCOMES: a) Mortality b) Overall Anastomotic Dehiscence c) Clinical Anastomotic Dehiscence d) Radiological Anastomotic Dehiscence e) Stricture f) Anastomotic Haemorrhage g) Reoperation h) Wound Infection i) Anastomosis Duration j) Hospital Stay. DATA COLLECTION AND ANALYSIS: Data were independently extracted by the two reviewers (SASL, DM) and cross-checked. The methodological quality of each trial was assessed by the same two reviewers. Details of the randomization (generation and concealment), blinding, whether an intention-to-treat analysis was done, and the number of patients lost to follow-up were recorded. The results of each RCT were summarised on an intention-to-treat basis in 2 x 2 tables for each outcome. External validity was defined by characteristics of the participants, the interventions and the outcomes. The RCTs were stratified according to the level of colorectal anastomosis. The Risk Difference method (random effects model) and NNT for dichotomous outcomes measures and weighted mean difference for continuous outcomes measures, with the corresponding 95% confidence interval, were presented in this review. Statistical heterogeneity was evaluated by using funnel plot and chi-square testing. MAIN RESULTS: Of the 1233 patients enrolled ( in 9 trials), 622 were treated with stapled, and 611 with manual, suture. The following main results were obtained: a) Mortality: result based on 901 patients; Risk Difference - 0.6% Confidence Interval -2.8% to +1.6%. b) Overall Dehiscence: result based on 1233 patients; Risk Difference 0.2%, 95% Confidence Interval -5.0% to +5.3%. c) Clinical Anastomotic Dehiscence : result based on 1233 patients; Risk Difference -1.4%, 95% Confidence Interval -5.2 to +2.3%. d) Radiological Anastomotic Dehiscence : result based on 825 patients; Risk Difference 1.2%, 95% Confidence Interval -4.8% to +7.3%. e) Stricture: result based on 1042 patients; Risk Difference 4.6%, 95% Confidence Interval 1.2% to 8.1%. Number needed to treat 17, 95% confidence interval 12 to 31. f) Anastomotic Hemorrhage: result based on 662 patients; Risk Difference 2.7%, 95% Confidence Interval - 0.1% to +5.5%. g) Reoperation: result based on 544 patients; Risk Difference 3.9%, 95% Confidence Interval 0.3% to 7.4%. h) Wound Infection: result based on 567 patients; Risk Difference 1.0%, 95% Confidence Interval -2.2% to +4.3%. i) Anastomosis duration: result based on one study (159 patients); Weighted Mean Difference -7.6 minutes, 95% Confidence Interval -12.9 to -2.2 minutes. j) Hospital Stay: result based on one study (159 patients), Weighted Mean Difference 2.0 days, 95% Confidence Interval -3.27 to +7.2 days. REVIEWER'S CONCLUSIONS: The evidence found was insufficient to demonstrate any superiority of stapled over handsewn techniques in colorectal anastomosis, regardless of the level of anastomosis.

Adult↗
PubMed1983

Evaluating the medical literature. Part II: Statistical analysis.

We have attempted to provide sufficient information to enable the reader to verify that the investigator has used an appropriate statistical test for the evaluation of his study data. We have not discussed the actual calculation of the tests presented. With the wide availability of computers and programmable calculators, it is safe to assume that the investigator has performed the necessary mathematics accurately. Instead of assessing the accuracy of these calculations, the reader should verify that the correct statistical test was chosen in the first place. The astute reader may be surprised at how frequently an incorrect test is used. Merely achieving statistical significance does not characterize the author's data as clinically important. Neither does it, in and of itself, prove one agent superior to another nor prove a cause-and-effect relationship between two variables. When appropriately interpreted, however, statistical analysis can be a very useful and powerful tool in helping to arrive at the "truth."

Analysis of Variance↗
PubMed2003

Statistical and graphical methods for quality control determination of high-throughput screening data.

High-throughput screening (HTS) is used in modern drug discovery to screen hundreds of thousands to millions of compounds on selected protein targets. It is an industrial-scale process relying on sophisticated automation and state-of-the-art detection technologies. Quality control (QC) is an integral part of the process and is used to ensure good quality data and mini mize assay variability while maintaining assay sensitivity. The authors describe new QC methods and show numerous real examples from their biologist-friendly Stat Server HTS application, a custom-developed software tool built from the commercially available S-PLUS and Stat Server statistical analysis and server software. This system remotely processes HTS data using powerful and sophisticated statistical methodology but insulates users from the technical details by outputting results in a variety of readily interpretable graphs and tables. It allows users to visualize HTS data and examine assay performance during the HTS campaign to quickly react to or avoid quality problems.

Computer Graphics↗
PubMed2003

Improved statistical methods for hit selection in high-throughput screening.

High-throughput screening (HTS) plays a central role in modern drug discovery, allowing the rapid screening of large compound collections against a variety of putative drug targets. HTS is an industrial-scale process, relying on sophisticated automation, control, and state-of-the art detection technologies to organize, test, and measure hundreds of thousands to millions of compounds in nano- to microliter volumes. Despite this high technology, hit selection for HTS is still typically done using simple data analysis and basic statistical methods. The authors discuss in this article some shortcomings of these methods and present alternatives based on modern methods of statistical data analysis. Most important, they describe and show numerous real examples from the biologist-friendly Stat Server HTS application (SHS), a custom-developed software tool built on the commercially available S-PLUS and StatServer statistical analysis and server software. This system remotely processes HTS data using powerful and sophisticated statistical methodology but insulates users from the technical details by outputting results in a variety of readily interpretable graphs and tables.

Algorithms↗
PubMed2005

New approach to the statistical analysis of cardiovascular data.

Fourier-based approaches to analysis of variability of R-R intervals or blood pressure typically compute power in a given frequency band (e.g., 0.01-0.07 Hz) by aggregating the power at each constituent frequency within that band. This paper describes a new approach to the analysis of these data. We propose to partition the blood pressure variability spectrum into more narrow components by computing power in 0.01-Hz-wide bands. Therefore, instead of a single measure of variability in a specific frequency interval, we obtain several measurements. The approach generates a more complex data structure that requires a careful account of the nested repeated measures. We briefly describe a statistical methodology based on generalized estimating equations that suitably handles this more complex data structure. To illustrate the methods, we consider systolic blood pressure data collected during psychological and orthostatic challenge. We compare the results with those obtained using the conventional methods to compute blood pressure variability, and we show that our approach yields more efficient results and more powerful statistical tests. We conclude that this approach may allow a more thorough analysis of cardiovascular parameters that are measured under different experimental conditions, such as blood pressure or heart rate variability.

Algorithms↗
PubMed2004

Ordered subset linkage analysis supports a susceptibility locus for age-related macular degeneration on chromosome 16p12.

BACKGROUND: Age-related macular degeneration (AMD) is a complex disorder that is responsible for the majority of central vision loss in older adults living in developed countries. Phenotypic and genetic heterogeneity complicate the analysis of genome-wide scans for AMD susceptibility loci. The ordered subset analysis (OSA) method is an approach for reducing heterogeneity, increasing statistical power for detecting linkage, and helping to define the most informative data set for follow-up analysis. OSA assesses the linkage evidence in subsets of potentially more homogeneous families by rank-ordering family-specific lod scores with respect to trait-associated covariates or phenotypic features. Here, we present results of incorporating five continuous covariates into our genome-wide linkage analysis of 389 microsatellite markers in 62 multiplex families: Body mass index (BMI), systolic (SBP) and diastolic (DBP) blood pressure, intraocular pressure (IOP), and pack-years of cigarette smoking. Chromosome-wide significance of increases in nonparametric multipoint lod scores in covariate-defined subsets relative to the overall sample was assessed by permutation. RESULTS: Using a correction for testing multiple covariates, statistically significant lod score increases were observed for two chromosomal regions: 14q13 with a lod score of 3.2 in 28 families with average IOP </= 15.5 (p = 0.002), and 6q14 with a lod score of 1.6 in eight families with average BMI >/= 30.1 (p = 0.0004). On chromosome 16p12, nominally significant lod score increases (p </= 0.05), up to a lod score of 2.9 in 32 families, were observed with several covariate orderings. While less significant, this was the only region where linkage evidence was associated with multiple clinically meaningful covariates and the only nominally significant finding when analysis was restricted to advanced forms of AMD. Families with linkage to 16p12 had higher averages of SBP, IOP and BMI and were primarily affected with neovascular AMD. For all three regions, linkage signals at or very near the peak marker have previously been reported. CONCLUSION: Our results suggest that a susceptibility gene on chromosome 16p12 may predispose to AMD, particularly to the neovascular form, and that further research into the previously suggested association of neovascular AMD and systemic hypertension is warranted.

Aged↗
PubMed1989

Methodologic approaches to quality care evaluation.

A number of problems inherent to quality of care evaluation have been described above. Although issues such as limited resources and clinical staff resistance may not be specific to cancer care, they certainly impact on the evaluation of the quality of care offered to cancer patients. Other issues such as complexity of care and the time span over which care can occur are more applicable to the cancer patient population alone. In response to these issues, I have offered a number of solutions, such as reorganizations of tasks, the use of statistical techniques such as sampling and power analysis, and various feedback mechanisms which have been implemented at MSKCC. The data presented indicate that these mechanisms have been at least partially successful; however, given the absence of a controlled environment, drawing firm conclusions about the relationship between cause and effect is not possible. I hope that in the future these results may be replicated at other institutions who elect to implement any of the suggestions I have made.

Cancer Care Facilities↗
PubMed1987

Tests of linkage and heterogeneity in Mendelian diseases using identity by descent scores.

When linkage between a recessive Mendelian disease and specific candidate genes is investigated, identity by descent scores in affected sib pairs may be used for tests of linkage and heterogeneity. Statistical tests for performing this analysis are presented. The efficiency and statistical power of the method are also investigated using computer simulations.

Biometry↗
PubMed1989

Behavioral teratogenic effect of methylmercury and d-amphetamine: meta-analysis and power analysis of data from the Collaborative Behavioral Teratology Study of National Center for Toxicological Research.

The data of the Collaborative Behavioral Teratology Study (CBTS) were analyzed. Population-effect sizes were estimated, in terms of confidence intervals, by meta-analysis. A treatment effect of methylmercury was clearly observed and a dose-response effect was also observed. On the other hand, no clear treatment effect was observed in the d-amphetamine study. The effect of auditory startle habituation was very large, although it was limited to the high-dose group in the methylmercury study. The effects observed for physical landmarks were, as a whole, somewhat larger than those for behavioral measures. There is no clear evidence for sex-related differences except for activity measures. A curious treatment effect that was not referred to in the CBTS report was observed: eye-opening day and incisor-eruption day were hastened by the treatment of methylmercury. Power analysis results showed that obtaining a statistically significant effect for these compounds is very difficult, suggesting that even though published papers reported the significant effect of these compounds there might have been many unpublished experiments that obtained nonsignificant effects. If one uses these compounds as positive controls, a very large sample size will be needed. No highly sensitive test that is reproducible across compounds or dose-levels was observed among tests employed in the CBTS.

Amphetamine↗
PubMed2002

Multiple QTL mapping in related plant populations via a pedigree-analysis approach.

QTL mapping experiments in plant breeding may involve multiple populations or pedigrees that are related through their ancestors. These known relationships have often been ignored for the sake of statistical analysis, despite their potential increase in power of mapping. We describe here a Bayesian method for QTL mapping in complex plant populations and reported the results from its application to a (previously analysed) potato data set. This Bayesian method was originally developed for human genetics data, and we have proved that it is useful for complex plant populations as well, based on a sensitivity analysis that was performed here. The method accommodates robustness to complex structures in pedigree data, full flexibility in the estimation of the number of QTL across multiple chromosomes, thereby accounting for uncertainties in the transmission of QTL and marker alleles due to incomplete marker information, and the simultaneous inclusion of non-genetic factors affecting the quantitative trait.

Journal Article↗
PubMed2003

Coeliac disease patients carry conserved HLA-DR3-DQ2 haplotypes revealed by association of TNF alleles.

Certain HLA-DQ alleles are known to contribute to predisposition to coeliac disease (CD). The existence of additional independent risk-modifying loci in the HLA complex is still being debated. The DR3-DQ2 haplotype has been studied most, but the evidence is conflicting. The discrepancies may stem from the absence of such an effect, insufficient statistical power to detect an effect (i.e. small studies) and/or incomplete control of linkage disequilibrium (LD) to the neighbouring DQ-loci, known to elicit a strong effect. In the present study, we aimed to undertake a statistically high-powered family-based analysis, fully controlling effects of LD between the major DQ-risk haplotypes and neighbouring candidate loci. We investigated five markers on DR3-DQ2, DR5-DQ7 and DR7-DQ2 haplotypes in 327 Norwegian and Swedish families. Our primary finding was that TNF-308A ( TNF2) was significantly associated on the DR3-DQ2 haplotype [stratum specific odds ratio (OR) = 2.40 (1.25-4.48), Pc = 0.009, where P(c) = Pn and n = number of tests performed]. Furthermore, we confirmed earlier indications that LD between TNF2 and DQA1*05-DQB1*02 on the DR3 haplotype is more strongly maintained in family-based cases than family-based controls. In conclusion, we confirmed in this study, the largest of its kind, that additional CD risk factors independent of DQ2 alleles do exist on the DR3 haplotype.

Case-Control Studies↗
PubMed1989

Biomagnetic measurements in uterine leiomyomas using a superconducting quantum interference device (SQUID).

Using the biomagnetometer superconducting quantum interference device (SQUID), the magnetic signals relating to spontaneous uterine activity were measured for the first time in 25 women with uterine leiomyomas, and 12 women with normal, non-leiomyomatous, uteri. Magnetic radiation, in the range of low frequency (below 2 Hz), was of low amplitudes in normal uterine tissues and of high amplitudes in benign leiomyomas. The observed differences were confirmed by the corresponding power spectra obtained from the statistical Fourier analysis. It is suggested that biomagnetic measurements may facilitate the detection of uterine leiomyomas in equivocal cases.

Adult↗