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PubMed1994

Evaluation of 13 short tandem repeat loci for use in personal identification applications.

Personal identification by using DNA typing methodologies has been an issue in the popular and scientific press for several years. We present a PCR-based DNA-typing method using 13 unlinked short tandem repeat (STR) loci. Validation of the loci and methodology has been performed to meet standards set by the forensic community and the accrediting organization for parentage testing. Extensive statistical analysis has addressed the issues surrounding the presentation of "match" statistics. We have found STR loci to provide a rapid, sensitive, and reliable method of DNA typing for parentage testing, forensic identification, and medical diagnostics. Valid statistical analysis is generally simpler than similar analysis of RFLP-VNTR results and provides powerful statistical evidence of the low frequency of random multilocus genotype matching.

Alleles↗
PubMed2004

Macrolide therapy for Chlamydia pneumoniae in the secondary prevention of coronary artery disease: a meta-analysis of randomized controlled trials.

STUDY OBJECTIVE: As recent studies have shown that antibiotic therapy to eradicate Chlamydia pneumoniae may be beneficial in the secondary prevention of coronary artery disease, and studies to date may have lacked statistical power, we conducted a meta-analysis of randomized controlled trials to determine the role of antibiotic therapy in this patient population. DESIGN: Systematic review and meta-analysis of randomized controlled trials. PATIENTS: A total of 12,032 patients from nine studies. MEASUREMENTS AND MAIN RESULTS: We searched MEDLINE, EMBASE, the Cochrane Controlled Trials Register, and abstracts of conference proceedings to identify pertinent studies. The random effects model was used to estimate a pooled relative risk. Heterogeneity was assessed using the bootstrap version of the Q statistic with 1000 replications. In total, we reviewed nine randomized controlled trials enrolling 12,032 patients; six enrolled patients with acute coronary syndrome, two enrolled patients with stable coronary artery disease, and one enrolled a mixed population. Compared with placebo, macrolide therapy was not associated with a significant reduction in any coronary event (relative risk [RR] 0.98, 95% confidence interval [CI] 0.88-1.08), myocardial infarction or angina (RR 0.89, 95% CI 0.68-1.16), or overall mortality (RR 0.95, 95% CI 0.81-1.12). CONCLUSION: Our results do not support routine use of antichlamydial therapy for secondary prevention of coronary events.

Antibiotic Prophylaxis↗
PubMed2000

Postprandial response of gastric slow waves: correlation of serosal recordings with the electrogastrogram.

Controversial interpretations have been given to the postprandial increase in the dominant power (amplitude) of the electrogastrogram (EGG). The aim of this study was to find an appropriate interpretation of the postprandial EGG power changes. Simultaneous serosal and cutaneous recordings of gastric myoelectrical activity were made in 11 patients with gastroparesis in the fasting state and after the ingestion of 8 oz of water. The dominant frequency and corresponding power of the recording before and after water were computed using the power spectral analysis method. It was found that the dominant frequency of the EGG was the same as that of the serosal recording in 10 patients. One patient showed a substantial amount of dysrhythmia and no obvious dominant frequency was noted. A decrease in the dominant frequency was found in these 10 patients after the ingestion of water. Tachygastria of higher than 4 cycles/min was observed in one of 11 patients both in the prewater and postwater states. Consistent changes in amplitude after a drink of water were noted in both serosal recording and EGG. Statistical analysis demonstrated that the dominant power change after water computed from the EGG was correlated with that observed in the serosal recording (r = 0.757, P = 0.007). In conclusion, exogenous stimulation, such as ingestion of water, may change the amplitude of the gastric slow wave and this change is reflected in the EGG, suggesting that the change of the slow-wave amplitude is an important contributing factor to the postprandial change in the EGG dominant power.

Adult↗
PubMed2006

No contribution of angiotensin-converting enzyme (ACE) gene variants to severe obesity: a model for comprehensive case/control and quantitative cladistic analysis of ACE in human diseases.

Candidate gene analyses are often inconclusive owing to genetic or phenotypic heterogeneity, low statistical power, selection of nonfunctional SNPs, and inadequate statistical analysis of the genetic architecture. Angiotensin-converting enzyme (ACE) is involved in adipocyte growth and function and the ACE-processed angiotensin II inhibits adipocyte differentiation. Associations between body mass index (BMI) and ACE polymorphisms have been reported in general populations, but the contribution to severe obesity of this gene, which is located under an obesity genome-scan linkage peak on 17q23, is unknown. ACE is one of the most studied genes and markers responsible for variation in circulating ACE enzyme levels have been extensively characterised. Eight of these variants were genotyped in 1054 severely obese cases and 918 nonobese controls, as well as 116 nuclear families from the genome scan (n=447), enabling the known clades to be inferred. Qualitative analysis of individual single-nucleotide polymorphisms (SNPs), haplotypes, clades, and diploclades demonstrated no significant associations (P<0.05) after minimal correction for multiple testing. Quantitative analysis of clades and diploclades for BMI, waist-to-hip ratio, or ZBMI in children were also not significant. This rigorous, large-scale study of common, well-defined, severe polygenic obesity provides strong evidence that functionally relevant sequence variation in ACE, whether it is defined at the level of SNPs, haplotypes, or clades, is not associated with severe obesity in French Caucasians. Such a study design exemplifies the strategy needed to clearly define the contribution of the ACE gene to the plethora of complex genetic diseases where weak associations have been previously reported.

Case-Control Studies↗
PubMedDate not supplied

Planning research studies: an alternative to power analysis.

Hypothesis testing is a cumbersome method of statistical analysis and sometimes leads to misinterpretation of results. Whenever possible, it is preferable to design studies and analyze data using estimation procedures. For ANOVA, correlation analysis, regression, and other standard statistical methods, it is possible, and no more difficult, to use estimation procedures.

Analysis of Variance↗
PubMed2005

Clinical trials in ALS: a review of the role of clinical and neurophysiological measurements.

We have reviewed all the published clinical trials of ALS and, from those considered sufficiently large, and containing a control group, we have evaluated their methodology with regard to statistical power. This implies a critical analysis of the endpoint measurements. We have concluded that clinical endpoints used in clinical trials of ALS have frequently been insufficiently sensitive, non-linear, or even not intuitively highly relevant to the disease. We suggest that the ALS-FRS, perhaps also MUNE and the Neurophysiological Index, may be the best measures currently available. These techniques have complementary characteristics that allow them to be used to address different aspects of the disease and its treatment in various trials designs. In the past some trials may have failed to demonstrate a treatment effect because the chosen endpoint measures and the trial design were inappropriate.

Amyotrophic Lateral Sclerosis↗
PubMed2005

Space radiation does not induce a significant increase of intrachromosomal exchanges in astronauts' lymphocytes.

Chromosome aberration analysis in astronauts has been used to provide direct, biologically motivated estimates of equivalent doses and risk associated to cosmic radiation exposure during space flight. However, the past studies concentrated on measurements of dicentrics and translocations, while chromosome intrachanges (inversions) have never been measured in astronauts' samples. Recent data reported in the literature suggest that densely ionizing radiation can induce a large fraction of intrachanges, thus leading to the suspicion that interchanges grossly underestimate the cosmic radiation-induced cytogenetic damage in astronauts. We have analyzed peripheral blood lymphocytes from 11 astronauts involved in short- or long-term space flights in low-Earth orbit using high-resolution multicolor banding to assess the frequency of intrachromosomal exchanges in both pre- and post-flight samples. We did not detect any inversions in chromosome 5 from a total of 2800 cells in astronauts' blood. In addition, no complex type exchanges were found in a total of 3590 astronauts' lymphocytes analyzed by multifluor fluorescence in situ hybridisation. We conclude that, within the statistical power of this study, the analysis of interchanges for biological dosimetry in astronauts does not significantly underestimate the space radiation-induced cytogenetic damage, and complex-type exchanges or intrachanges have limited practical use for biodosimetry at very low doses.

Astronauts↗
PubMed2002

Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays.

The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at http://genome-www.stanford.edu/TMA/explore.shtml.

Cluster Analysis↗
PubMed2004

Time-dependent surgical outcomes following cauda equina syndrome diagnosis: comments on a meta-analysis.

STUDY DESIGN: In this Journal Club review, we critically examine the methodology and results of a recently published meta-analysis describing the time dependency of surgical outcomes associated with cauda equina syndrome (CES) diagnosis. OBJECTIVES: Our objectives are to clarify the strengths, weaknesses, and appropriate use of statistics regarding the findings of the previous publication. SUMMARY OF BACKGROUND DATA: Surgical outcomes from published reports are related to both preoperative conditions and the time between surgery and diagnosis of CES. METHODS: We reexamined many of the papers that were used to create the surgical outcomes data set, including the publications that supplied quantitative information for logistic regression. Of special focus were studies that contributed to the "less than 24 hours from diagnosis" data. The use of statistical parameters such as probabilities and odds ratios to infer possible future outcomes is also addressed to clarify the papers' interpretations. To support the overall limitations of their generalized findings, we conducted a power analysis, which highlights the lack of statistical strength in the resulting conclusions. RESULTS: The results of the initial work state that an advantage exists in treating patients within 48 hours in comparison to treating them during a period greater than 48 hours after the onset of CES symptoms. However, the authors also state that no difference exists between the effects of an early surgery (less than 24 hours) compared with a subsequent period between 24 and 48 hours after CES onset. Key elements of logistic regression and meta-analysis are used to refute specific aspects of their methodology as well as their clinical interpretation regarding acute intervention. CONCLUSIONS: We conclude that a flawed methodology and misinterpretation of results are reported, understating the value of early surgical intervention.

Humans↗
PubMed2006

Longitudinal analysis of T-cell receptor variable beta chain repertoire in patients with acute graft-versus-host disease after allogeneic stem cell transplantation.

T-cell receptor variable beta chain (TCRBV) repertoire spectratyping involves the estimation of CDR3 length distributions for monitoring T-cell receptor diversity and has proven useful for analyses of immune reconstitution and T-cell clonal expansions in graft-versus-host disease (GVHD) and graft-versus-leukemia after allogeneic stem cell transplantation. We performed a longitudinal spectratype analysis of 23 TCRBV families in 28 patients who underwent allogeneic T cell-depleted peripheral blood stem cell transplantation. Sixteen patients subsequently developed acute GVHD. We recently developed statistical methods that bring increased power and flexibility to spectratype analysis and allow us to analyze TCRBV repertoire development under appropriately complex statistical models. Applying these methods, we found that patients with acute GVHD demonstrated TCRBV repertoire development statistically distinct from that repertoire development in patients without GVHD. Specifically, GVHD patients showed spectratypes indicative of lower diversity and greater deviation from the spectratypes expected in healthy individuals at intermediate times. Most individual TCRBV subfamilies had spectratypes statistically distinguishable between GVHD and non-GVHD patients at 6 months after transplantation. These results suggest that the T-cell receptor repertoire perturbations associated with acute GVHD are widely spread throughout the TCRBV families.

Acute Disease↗
PubMed2003

Responsivity: the value of providing intensive services to high-risk offenders.

Tests of the importance of service matching have had varying results, yet little attention has been given to testing the hypotheses about outcomes for clients based on differing risks to recidivate. We set out to test the risk and responsivity principles using a sample of clients from one site of a four-site randomized block experimental design study examining the effectiveness of a seamless system approach vs. traditional criminal justice supervision. Findings from our preliminary examination of official and self-report data from this site suggest the importance of the risk and responsivity concepts in providing substance abuse treatment, particularly for high-risk clients. Because of the relatively low statistical power of the tests employed in this exploratory analysis, many observed relationships were not statistically significant. Nonetheless, findings offer important implications for the delivery of substance abuse treatment. Future analyses are also recommended to further explore the impact of different service delivery systems.

Adult↗
PubMed1989

Autism is not associated with the fragile X syndrome.

We provided a controlled test of the hypothesis that individuals with the Martin-Bell or Fragile X [fra(x)] syndrome are more autistic than mentally retarded control individuals. A sample of fra(x) individuals was obtained from the register of a clinical genetics unit and compared with mentally retarded control individuals selected from an assessment centre who were individually matched for age, sex, and IQ. A comparison of 45 pairs of fra(x) cases and control individuals on the DSM-III (R) criteria for autism and two standardized "instruments" for the assessment of autism (ABC and ADC) failed to find a higher prevalence of autism among fra(x) individuals. There was no statistically significant difference between fra(x) individuals and control individuals, and the mean differences on both the ABC and ADC scales were in the direction contrary to the hypothesis. An analysis of the study's statistical power suggested that it is unlikely the investigation failed to detect a large to medium difference between fra(x) individuals and control individuals in autistic behaviour. Subsidiary analyses of case-control differences showed that two autistic-like behaviours occurred at a higher rate among fra(x) individuals than other mentally retarded children, namely, gaze avoidance and hand flapping. These abnormalities may have misled clinicians into thinking that autism and fra(x) are associated.

Adolescent↗
PubMed2006

A prospective study of breast size and premenopausal breast cancer incidence.

Studies of the association between breast size, as a proxy for mammary gland mass, and breast cancer risk have given equivocal results. Most have been case-control studies with limited statistical power. We conducted a prospective analysis of the relation between breast size as measured by self-reported bra cup size and breast cancer risk among premenopausal women enrolled in the Nurses' Health Study II. Bra cup size at age 20 was assessed among 89,268 premenopausal women aged 29-47 in 1993. Subsequent incident cases of invasive breast cancer were assessed until 2001. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated with a Cox proportional hazards model adjusting for potential confounders and risk factors for breast cancer. During 622,732 person-years of follow-up, 803 premenopausal women were newly diagnosed with invasive breast cancer. For women with a BMI below 25 kg/m2, those with a bra cup size of "D or larger" had a significantly higher incidence of breast cancer than women who reported "A or smaller" (covariate adjusted HR=1.80; 95% CI 1.13-2.88; ptrend=0.01). There was no significant association among women with a BMI of 25 kg/m2 or higher. Stratifying by BMI at age 18 at a cutoff point of 21 kg/m2 gave similar results. Larger bra cup size at a young age is associated with a higher incidence of premenopausal breast cancer, though this association is limited to leaner women.

Adult↗
PubMed2001

Prognostic parameters in endometrial stromal sarcoma: a clinicopathologic study in 31 patients.

OBJECTIVE: The aim of this study was to evaluate the behavior of endometrial stromal sarcomas (ESS) in relation to their clinical and pathologic features and to identify possible prognostic factors. METHODS: Thirty-one patients with histologically proven ESS were included in the analysis. Endometrial stromal sarcoma is characterized by proliferations composed of cells with endometrial stromal cell differentiation. A breakpoint of 10 mitoses per 10 high-power fields was used in the statistical analysis to distinguish between low-grade and high-grade endometrial stromal sarcoma and to evaluate the prognostic value of mitotic count in patients with ESS. RESULTS: The median follow-up time was 72 months (range 34-110). The median overall survival of the 31 patients was 127 months, resulting in a 5-year overall survival rate of 62%. Adjuvant therapy was administered to 25 patients; among those, 20 patients received postoperative radiotherapy and 5 patients received chemotherapy. Ten of the irradiated patients and 3 patients undergoing chemotherapy developed disease recurrence. Concerning the response rate to adjuvant chemotherapy, 1 patient showed a complete response, 1 patient a partial response, 1 patient stable disease, and 2 patients progressive disease. Altogether, 14 patients developed recurrent disease with a median disease-free survival of 11 months (range 5-60). Twelve patients died of the disease. A univariate model revealed that early tumor stage (P < 0.0007), low myometrial invasion (P < 0.008), and low mitotic count (P < 0.005) were associated with a lengthened overall survival in patients with endometrial stromal sarcoma. Age and adjuvant therapy did not influence overall survival of patients with ESS. CONCLUSION: Early tumor stage, low myometrial invasion, and low mitotic count are associated with a lengthened overall survival in patients with ESS.

Adult↗
PubMed1991

Hyperactivity and the fragile X syndrome.

Workers who have claimed an association between Fragile X [fra(x)] Syndrome and Hyperactivity and aggressive behavior have done so despite the lack of controlled studies using standard diagnostic criteria. Accordingly, we provided a controlled test of the hypothesis that individuals with the fra(x) Syndrome are more hyperactive and have more symptoms of aggression than other mentally retarded individuals. The test formed part of a study to assess autistic behavior in fra(x) individuals. A sample of fra(x) individuals was obtained from the register of a clinical genetics unit and individually matched for age, sex, and IQ with mentally retarded individuals selected from assessment centres. Forty-five pairs of fra(x) cases and control individuals were compared on criteria which reflected DSM-III concepts of hyperactivity and on criteria reflecting aggressive behavior. The comparison failed to find a higher prevalence of these symptoms in the fra(x) group. An analysis of the study's statistical power suggested that it is unlikely that the investigation failed to detect a large to medium difference between fra(x) individuals and control individuals in the symptoms investigated.

Adolescent↗
PubMed1987

Characteristic views of prokaryotic 50S ribosomal subunits.

Multivariate statistical analysis and classification techniques are powerful tools in sorting noisy electron micrographs of single particles according to their principal features, enabling one to form average images with an enhanced signal-to-noise ratio and a better reproducible resolution. We apply this methodology here to determining the characteristic views of the large (50S) ribosomal subunits from the eubacterium Escherichia coli and the archaebacteria Methanococcus vannielii, Sulfolobus solfataricus, and Halobacterium marismortui. Average images were obtained of the subunit in the common crown and kidney projections, but views of the particle in orientations intermediate between these two extremes were also elucidated for all species. These averages show reproducible detail of up to 2.0 nm resolution, thus enabling the visualization and interspecies comparison of many structural features as a first step toward comparing the actual three-dimensional structures. Our results disprove evolutionary lineages recently postulated on the basis of electron microscopical images of ribosomal subunits.

Archaea↗
PubMed2006

IR microspectroscopy: potential applications in cervical cancer screening.

Screening exfoliative cytology for early dysplastic cells reduces incidence and mortality from squamous carcinoma of the cervix. In the developed world, screening programmes have adopted a 3-5 years recall system. In its absence, cervical cancer would be the second most common female cancer in these regions; instead, it is currently eleventh. However, there exist a number of limitations to the smear test even given the removal of contaminants using liquid-based cytology. It is prohibitively expensive, labour-intensive and subject to inaccuracies that give rise to significant numbers of false negatives. There remains a need for novel approaches to allow efficient and objective interrogation of exfoliative cytology. Methods that variously exploit infrared (IR) microspectroscopy are one possibility. Using IR microspectroscopy, an integrated 'biochemical-cell fingerprint' of the lipid, protein and carbohydrate composition of a biomolecular entity may be derived in the form of a spectrum via vibrational transitions of individual chemical bonds. Powerful statistical approaches (e.g. principal component analysis) now facilitate the interrogation of large amounts of spectroscopic data to allow the extraction of what may be small but extremely significant biomarker differences between disease-free and pre-malignant or malignant samples. An increasing wealth of literature points to the ability of IR microspectroscopy to allow the segregation of cells based on their disease status. We review the current evidence supporting its diagnostic potential in cancer biology.

Female↗