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PubMed2026

Freely available genomic datasets for atrial fibrillation research: current resources and analytical pipeline.

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia, characterized by clinical and genetic heterogeneity. Increasing use of genomics and other omics approaches has driven reliance on publicly available AF datasets to advance biological discovery. Thus, this systematic review aimed to identify freely available genomic AF datasets through Mendeley Data and its interconnected repositories, and to characterize the most common analyses performed on these data. The search was conducted in adherence to the PRISMA 2020 guideline. Nineteen freely available genomic AF datasets were identified: Summary statistics for 'Biobank-driven genomic discovery yields new insight into atrial fibrillation biology', hum0014.v8.58qt.v1, AF GWAS in UK Biobank, UK Biobank (Publication 9659), GWAS summary statistics from a 2025 multi-ancestry AF meta-analysis, GSE115574, GSE128188, GSE14975, GSE2240, GSE238242, GSE254133, GSE261170, GSE271748, GSE271839, GSE293813, GSE294456, GSE31821, GSE41177, and GSE79768. The GEO datasets were further examined using differential gene expression, functional enrichment, protein-protein interaction networks, hub gene analysis, microRNA target prediction, and gene clustering, as well as, for the more recently deposited datasets, eQTL colocalization, single-cell/single-nucleus clustering, cell-cell communication analysis, and gene-dosage-dependent transcriptional and electrophysiological profiling. These analyses show some consistency but also considerable heterogeneity in initial conditions, data normalization, and analytical methodological settings. In conclusion, only a limited number of datasets are freely available, so additional, well-characterized and standardized datasets are needed to provide a complete picture of the AF pathology.

Mendeley Data↗

PubMed1998

Heart rate variability effects of an agonist or antagonists of the beta-adrenoceptor assessed with scatterplot and sequence analysis.

There is evidence that the processes regulating heart rate variations reflect non-linear complexity and show 'chaotic' determinism. Data analyses using non-linear methods may therefore reveal patterns not apparent with conventional statistical approaches. We have consequently investigated two non-linear methods, the Poincaré plot (scatterplot) and cardiac sequence (quadrant) analysis, and compared these with standard time-domain summary statistics, during a normal volunteer investigation of an agonist and antagonists of the cardiac beta-adrenoceptor. Under double-blind and randomized conditions (Latin square design), 12 normal volunteers received placebo, celiprolol (beta 1- and beta 2-adrenoceptor partial agonist), propranolol (beta 1- and beta 2-adrenoceptor antagonist), atenolol (beta 1-adrenoceptor antagonist) and combinations of these agents. Single oral doses of medication (at weekly intervals) were administered at 22:30 hours with sleeping heart rates recorded overnight. The long (SDNN, SDANN) and short-term (rmsSD) time-domain summary statistics were reduced by celiprolol--effects different from the unchanged or small increases after atenolol and propranolol alone. The Poincaré plot was constructed by plotting each RR interval against the preceding RR interval, but unlike previous descriptions of the method, an automated computer method, with a high level of reproducibility, was employed. Scatterplot length and area were reduced following celiprolol and different from the small increases after propranolol and atenolol. The geometric analysis of the scatterplots allowed width assessment (i.e. dispersion) at fixed RR intervals. Differences between the drugs were confined to the higher percentiles (i.e. 75% and 90% of scatterplot length: low heart rate). The long-term time-domain statistics (SDNN, SDANN) correlated best with scatterplot length and area whereas the short-term heart rate variability (HRV) indices (rmsSD), pNN50) correlated strongly with scatterplot width. Cardiac sequence analysis (differences between three adjacent beats; delta RR vs delta RRn+1) assessed the short-term patterns of cardiac acceleration and deceleration, four patterns are identified: +/+ (a lengthening sequencing), +/- or -/+ (balanced sequences), and finally -/- (a shortening sequence). A running count of events by quadrant, together with the average magnitude of the differences was computed. The beta-adrenoceptor partial agonist celiprolol increased acceleration sequences. The duration of beat-to-beat difference shortened after celiprolol; this contrasted with increased duration of beat-to-beat difference after propranolol and atenolol. These results demonstrated a shift towards sympathetic dominance after the beta-adrenoceptor partial agonist celiprolol contrasting in parasympathetic dominance after the beta-adrenoceptor antagonists propranolol and atenolol. These non-linear methods appear to be valuable tools to investigate HRV in health and in cardiovascular disease and to study the implications of alterations in autonomic control during therapeutic intervention.

Adrenergic beta-Agonists↗

PubMed1999

A note on issues in meta-analysis for behavioral genetic studies using categorical phenotypes.

Meta-analysis of behavioral genetic studies would provide (i) tighter confidence intervals around parameter estimates, (ii) clarification of apparently discrepant study findings, and (iii) a mechanism for analyzing systematic causes of between-study differences. We examined some key issues that arise in the meta-analysis of categorical phenotypes. Data were simulated under a multifactorial threshold model that assumed an underlying normal liability distribution, and summary statistics (probandwise concordance rate, recurrence risk ratio, odds ratio, kappa) compared for given values of the liability correlation between relatives and given population prevalence. Although the odds ratio and kappa statistic performed well at moderate to high values of the population prevalence (15-50%), at low values all of these statistics were sensitive to overall prevalence. In cases where the assumption of a multifactorial threshold model is reasonable, direct estimation of genetic and environmental parameters from the summary statistics from all studies appears to be a preferable strategy. For cases where data from non-randomly ascertained samples are used, the impact of misspecification of the model for ascertainment was examined. For some parameter values, such misspecifications led to quite serious biases to estimates of genetic and environmental parameters. These biases varied in complex ways as a function of research design and of the true causes of variation in the population, so that the same misspecification could lead to an overestimate of the importance of genetic influences in twin data but an underestimation in adoption data or to an overestimate of the importance of genetic effects from twin data if shared environmental as well as genetic influences were simulated but an underestimate of genetic effects if shared environmental effects were assumed unimportant. These complexities emphasize the importance of being sensitive to the effects of misspecifying ascertainment corrections in any meta-analysis of behavioral genetic data.

Confidence Intervals↗

PubMed2025

From aerial drone to quantitative trait locus: leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa.

In recent years, accurate and low-cost variant calling has enabled the genotyping of large diversity panels for genome-wide association studies. As a result, phenotyping rather than genotyping is now the rate-limiting step, especially in field experiments. This has created a strong need for high-throughput, accurate, and low-cost in-field phenotyping. Here, we present a genome-wide association study (GWAS) study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using a drone equipped with an RGB and multispectral (MSP) camera. Our high-throughput phenotyping approach integrates an RGB- and MSP camera to measure the color and height of lettuce in this large-scale field experiment. We used the mean and other summary statistics, such as median, quantiles, skewness, kurtosis, minimum, and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using these summary statistics as traits for GWAS, we confirm several previously described genetic associations, now under field conditions, and identify additional novel associations for color and height traits in lettuce.

Lactuca↗

PubMed1993

Size and power of two-sample tests of repeated measures data.

One method of using repeated measures data to compare treatment groups in a clinical trial is to summarize each subject's outcomes with a single summary statistic, and then perform a distribution-free comparison based on the resulting statistics. We examine extensions of this approach and conditions under which they retain proper size in the presence of missing data. The asymptotic relative efficiencies of several summary statistic tests are calculated to show which perform best in a variety of situations. The techniques are illustrated using data from an AIDS clinical trial.

Analysis of Variance↗

PubMed2006

The earnings of U.S. health economists.

This paper presents data from a 2005 survey of health economists who were U.S. members of the International Health Economics Association or the Health Economics Special Interest Group of Academy Health. We present summary statistics of health economist earnings by rank and type of employer, estimate log earnings models as a function of education, experience, type of employer, and research productivity, and provide summary statistics of starting salaries expected to be offered to new Ph.D. health economists by type of employer. Our findings are compared to those for economics departments, business schools, schools of public health, and for health services researchers.

Data Collection↗

PubMed2001

Robustness of conditional moments: an application to premium calculation of reinsurance treaties.

In this study, the tail probability of a class of distributions commonly used in assessing the severity of insurance losses was examined. Without specifying any particular distribution, the use of an algebraic functional form Cx(-alpha) to approximate the tail behavior of the distributions in the class was demonstrated. Norwegian fire insurance data were examined, and the algebraic functional form was applied to derive the expected loss of a reinsurance treaty that covers all losses exceeding a retention limit. It was shown that (1) the expected loss is insensitive to the parameter alpha for a high retention limit (e.g., a catastrophe treaty), and (2) with a low retention limit (e.g., a largest claim treaty), a reliable estimate of the parameter alpha and a sound judgment on the maximum potential loss of the treaty could provide useful and defensible summary statistics for pricing the treaty. Thus, when dealing with the losses of certain reinsurance treaties, it was concluded that knowledge of a specific probability distribution is not critical, and the summary statistics derived from the model are robust with respect to a large class of loss distributions.

Journal Article↗

PubMed1999

A diary form quality of life questionnaire for Japanese patients with lung cancer and summarization techniques for longitudinal assessment.

The aim of this study was to confirm the validity and reliability of a new diary-type quality of life (QOL) self-rating questionnaire tailored for use by Japanese inpatients with lung cancer receiving chemotherapy. Two kinds of summary statistics were tested in QOL analysis. The questionnaire has a four-scale structure; physical, psychological, daily activity and global scales. Fifty-three patients were enrolled to test the reliability and validity. Summary statistics were assessed using indices of the area under the curve (AUC) and the maximum fluctuations of QOL scores (Dif max) in patients receiving cisplatin or carboplatin. The questionnaire had satisfactory reliability and validity. The physical, psychological and global scales scores changed to the worst levels after treatment, continuing for 1 week in the cisplatin group, whereas those of the carboplatin group began to worsen from day 3, but returned to prechemotherapy levels by day 9. The cisplatin group showed significant decrease of QOL compared with the carboplatin group in the AUC of psychological and two global scales, in the Dif max of psychological and linear analogue global scales. These results suggested that this questionnaire reflects differences in the influence of chemotherapy, and that AUC and Dif max may be useful indices for the analysis of QOL as measures to assess multidimensional QOL.

Adult↗

PubMed2021

Genetic Relationship Between Endometriosis and Melanoma.

Epidemiological studies have observed that risk of endometriosis is associated with history of cutaneous melanoma and vice versa. Evidence for shared biological mechanisms between the two traits is limited. The aim of this study was to investigate the genetic correlation and causal relationship between endometriosis and melanoma. Summary statistics from genome-wide association meta-analyses (GWAS) for endometriosis and melanoma were used to estimate the genetic correlation between the traits and Mendelian randomization was used to test for a causal association. When using summary statistics from separate female and male melanoma cohorts we identified a significant positive genetic correlation between melanoma in females and endometriosis (r g = 0.144, se = 0.065, p = 0.025). However, we find no evidence of a correlation between endometriosis and melanoma in males or a combined melanoma dataset. Endometriosis was not genetically correlated with skin color, red hair, childhood sunburn occasions, ease of skin tanning, or nevus count suggesting that the correlation between endometriosis and melanoma in females is unlikely to be influenced by pigmentary traits. Mendelian Randomization analyses also provided evidence for a relationship between the genetic risk of melanoma in females and endometriosis. Colocalization analysis identified 27 genomic loci jointly associated with the two diseases regions that contain different causal variants influencing each trait independently. This study provides evidence of a small genetic correlation and relationship between the genetic risk of melanoma in females and endometriosis. Genetic risk does not equate to disease occurrence and differences in the pathogenesis and age of onset of both diseases means it is unlikely that occurrence of melanoma causes endometriosis. This study instead provides evidence that having an increased genetic risk for melanoma in females is related to increased risk of endometriosis. Larger GWAS studies with increased power will be required to further investigate these associations.

endometriosis↗

PubMed2003

Detection of prostate cancer by integration of line-scan diffusion, T2-mapping and T2-weighted magnetic resonance imaging; a multichannel statistical classifier.

A multichannel statistical classifier for detecting prostate cancer was developed and validated by combining information from three different magnetic resonance (MR) methodologies: T2-weighted, T2-mapping, and line scan diffusion imaging (LSDI). From these MR sequences, four different sets of image intensities were obtained: T2-weighted (T2W) from T2-weighted imaging, Apparent Diffusion Coefficient (ADC) from LSDI, and proton density (PD) and T2 (T2 Map) from T2-mapping imaging. Manually segmented tumor labels from a radiologist, which were validated by biopsy results, served as tumor "ground truth." Textural features were extracted from the images using co-occurrence matrix (CM) and discrete cosine transform (DCT). Anatomical location of voxels was described by a cylindrical coordinate system. A statistical jack-knife approach was used to evaluate our classifiers. Single-channel maximum likelihood (ML) classifiers were based on 1 of the 4 basic image intensities. Our multichannel classifiers: support vector machine (SVM) and Fisher linear discriminant (FLD), utilized five different sets of derived features. Each classifier generated a summary statistical map that indicated tumor likelihood in the peripheral zone (PZ) of the prostate gland. To assess classifier accuracy, the average areas under the receiver operator characteristic (ROC) curves over all subjects were compared. Our best FLD classifier achieved an average ROC area of 0.839(+/-0.064), and our best SVM classifier achieved an average ROC area of 0.761(+/-0.043). The T2W ML classifier, our best single-channel classifier, only achieved an average ROC area of 0.599(+/-0.146). Compared to the best single-channel ML classifier, our best multichannel FLD and SVM classifiers have statistically superior ROC performance (P=0.0003 and 0.0017, respectively) from pairwise two-sided t-test. By integrating the information from multiple images and capturing the textural and anatomical features in tumor areas, summary statistical maps can potentially aid in image-guided prostate biopsy and assist in guiding and controlling delivery of localized therapy under image guidance.

Algorithms↗

PubMedDate not supplied

Cross-sectional growth standards for captive baboons: I. Organ weight by chronological age.

We present the first cross-sectional organ weight reference standards for captive baboons (Papio hamadryas). Organ weight data were obtained from necropsy reports for 634 healthy, pedigreed, captive female and male baboons. From summary statistics we calculated and fit cross-sectional, sex-specific percentile curves for: adrenals, brain, eyes, heart, kidneys, liver plus gall bladder, lungs, pancreas, pituitary gland, spleen, and thyroid gland in two year age class intervals and summary statistics by sex for each organ in one year age classes.

Animals↗

PubMed2026

Myeloid Dendritic Cell Counts and Coronary Heart Disease: a Bidirectional Mendelian Randomization Study.

BACKGROUND: Coronary heart disease (CHD) remains a leading cause of morbidity and mortality worldwide, with immune and inflammatory mechanisms playing important roles in its pathogenesis. Dendritic cells (DCs) are key regulators of immune responses; however, the relationship between specific DC subsets and CHD risk remains incompletely understood. METHODS: This study conducted a bidirectional two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) summary statistics to investigate the potential associations between circulating dendritic cell traits and CHD. Genetic instruments for myeloid dendritic cells (Myeloid DCs) and plasmacytoid dendritic cells (Plasmacytoid DCs), including both absolute counts and relative proportions, were obtained from immune cell GWAS datasets. Summary statistics for CHD were derived from a large European-ancestry population. Multiple MR methods were applied, and sensitivity analyses were performed to assess the robustness of the findings and potential pleiotropic effects. RESULTS: Nominal associations between genetically predicted Myeloid DC counts and CHD risk were observed in the MR-Egger and weighted median analyses, whereas the inverse variance weighted analysis demonstrated no significant association. These nominal associations did not remain statistically significant after correction for multiple testing. No significant associations were observed for Plasmacytoid DC counts or for the relative proportions of either DC subset. Reverse MR analyses were inconclusive due to wide confidence intervals, precluding meaningful inference regarding a causal effect of CHD on DC-related traits. Sensitivity analyses revealed no substantial heterogeneity or horizontal pleiotropy. CONCLUSIONS: This bidirectional MR study explored the potential relationships between circulating dendritic cell traits and CHD risk. Although nominal associations involving Myeloid DC counts were observed in secondary MR analyses, no robust evidence supporting an association remained after correction for multiple testing. Further studies using larger datasets and functional approaches are warranted to clarify the role of dendritic cells in CHD.

Humans↗

PubMedDate not supplied

Cross-sectional growth standards for captive baboons: II. Organ weight by body weight.

We present the first cross-sectional organ weight by body weight reference standards for captive baboons (Papio hamadryas). Organ weight data were obtained from necropsy reports for 634 healthy, pedigreed, captive female and male baboons. From summary statistics we calculated and fit cross-sectional sex-specific percentile curves for: adrenals, brain, eyes, heart, kidneys, liver plus gall bladder, lungs, pancreas, pituitary gland, spleen, and thyroid gland in three kilogram body weight intervals and cross-sectional summary statistics by sex for each organ in one kilogram body weight intervals.

Animals↗

PubMed2026

Genetic Evidence Links Sex Hormone-binding Globulin to Total Body Bone Mineral Density at Age 45-60 Years: A Two-sample Mendelian Randomization Study.

The menopausal transition and early postmenopause represent important periods for women's skeletal health, but the genetic relevance of metabolic, behavioral, and hormone-related factors to bone mineral density during midlife remains incompletely understood. This study used publicly available genome-wide association study summary statistics to examine associations between body mass index, 25-hydroxyvitamin D, sex hormone-binding globulin, high-density lipoprotein cholesterol, smoking initiation, and alcohol intake frequency and total body bone mineral density at ages 45-60 years. Exposure genome-wide association study summary statistics were derived from large European-ancestry populations and were not restricted to midlife women, whereas the outcome genome-wide association study captured an age-stratified total body bone mineral density phenotype at age 45-60 years. This age range overlaps with the menopausal transition and early postmenopause in women. Univariable, reverse, and multivariable Mendelian randomization analyses were performed, with inverse-variance weighting as the primary method and complementary sensitivity analyses used to assess heterogeneity, pleiotropy, and result stability. Genetically predicted higher sex hormone-binding globulin was associated with lower total body bone mineral density (β = -0.111, 95% CI: -0.170 to -0.051; P = 0.0003). Reverse Mendelian randomization did not support reverse causation from bone mineral density to sex hormone-binding globulin. Multivariable analyses suggested that this association persisted after adjustment for selected metabolic biomarkers. The other examined exposures did not show consistent evidence of association. These findings provide genetic evidence linking sex hormone-binding globulin to total-body bone mineral density at ages 45-60 years. Further prospective and predictive studies are needed to evaluate its clinical relevance beyond established bone health assessment tools.

Humans↗

PubMed1998

Box and whisker plots for graphic presentation of audiometric results of conductive hearing loss treatment.

The Committee on Hearing and Equilibrium of the American Academy of Otolaryngology-Head and Neck Surgery has published guidelines for the reporting of audiometric results of middle ear interventions. It recommends the reporting of several audiometric variables by means of two summary parameters: means and standard deviation. This article advocates the use of other summary statistics, namely the median, quartiles, and extremes, because they do not require a normal distribution of the audiometric data and they are not sensitive to variations of the extreme values. On the basis of the exploratory data analysis, we propose a graphic method to present the Committee's variables in terms of their summary statistics. This "multiple box and whisker plot" offers a detailed and accurate overview of six variables in one graph.

Audiometry↗

PubMed1986

A review of methodological issues of the standardized mortality ratio (SMR) in occupational cohort studies.

This paper is a review and clarification of methodological issues related to the standardized mortality ratio (SMR), widely used in occupational epidemiology. Although the SMR seems to be a simple statistic, it can be misused and misinterpreted. The paper discusses SMRs in relation to age-specific mortality ratios, relative risk, life expectancy, and statistics derived from direct standardization. Inter-SMR comparisons and the effect of the choice of the comparison population on the SMR are also discussed. Mathematical and empirical review of SMR use has led to the development of a correction procedure which permits direct comparisons of two SMRs by adjusting for the age distributions of the two populations. The paper also proposes a method for testing the trend of age-specific mortality ratios (MRs). If MRs are homogeneous, this method can also be used to compare two SMRs. If MRs are not homogeneous, the relative risk between two sets of age-specific MRs can be tested for significance, but no summary index, including the SMR, can accurately describe the mortality experience over the entire age range. It is suggested that the summary statistics of a cohort mortality experience should include relative risk, attributable risk, and life expectancy. These statistics are complementary and can be derived or approximated from the data that generated the SMR. A valid risk assessment should weigh the evidence from all three summary statistics.

Adult↗

PubMed2005

A correlation study of organochlorine levels in serum, breast adipose tissue, and gluteal adipose tissue among breast cancer cases in India.

We used data from a breast cancer pilot study carried out in Kerala, India in 1997, for which organochlorine levels were measured in three biological media, blood serum, breast adipose tissue, and gluteal adipose tissue, of 37 fasting breast cancer cases (pretreatment). Our objective was to investigate the relationships between organochlorine concentrations in different biological media. Gas-liquid chromatography determined serum, breast adipose, and gluteal adipose tissue levels of dichlorodiphenyltricholorethane, dichlorodiphenyldichloroethane, beta-benzene hexachloride, and polychlorinated biphenyl (PCB) congeners, PCB-153 and PCB-180. Correlation plots were made and Spearman correlation coefficients (r) calculated for breast adipose tissue versus serum, gluteal adipose tissue versus serum, and breast adipose versus gluteal adipose tissue. We also examined paired ratios of all summary statistics. There were strong correlations among serum, breast adipose tissue, and gluteal adipose tissue concentrations for most organochlorines analyzed, one exception being gluteal versus serum for PCB-153. The correlations for all other comparisons ranged from r = 0.65 to 0.94. Serum (ng/g) versus adipose ratios approached 1:1 for most of the organochlorine pesticide comparisons and did not vary by summary statistic. To our knowledge, this is the first study to use three different media from fasting subjects and to comprehensively investigate the relationship between organochlorines measured across the three media for both organochlorine pesticides and PCBs. These data indicate that blood serum reflects the present body burden of a range of organochlorines to the same extent as adipose tissue, and they support the view that serum may be collected in lieu of adipose tissue to obtain similar information. However, such measurements are a combination of both recent exposures and past exposures, which have metabolized slowly and may still persist. Therefore, investigators should use caution when assigning a level as lifetime body burden.

Adipose Tissue↗

PubMed1998

A comparison of smoothing techniques for CD4 data measured with error in a time-dependent Cox proportional hazards model.

The use of CD4+ T-lymphocyte counts as a covariate presents some unique challenges in survivorship analyses due to the variability of this marker. If one does not account for the measurement error component of this variability in some manner, the estimate of the relative risk parameter in a time-dependent Cox model is biased towards zero, and coverage levels of confidence intervals may be seriously incorrect. We use a two-stage approach to reduce the variability in the observed CD4 counts in order to obtain a more accurate estimate of the relative risk parameter and more valid summary statistics. In the first stage, population based smoothing methods derived from a random-effects model plus a stochastic process or individual based smoothing methods are used to replace the observed longitudinal CD4 counts with less variable imputes at each failure time. In the second stage, we use the imputes in a time-dependent Cox model to estimate the risk parameter and its associated summary statistics. We compare the smoothing methods in simulation studies and find that the use of these smoothing methods results in a substantial reduction in bias for the true risk parameter estimate, better efficiency, and more accurate coverage rates in confidence intervals. We apply our two-stage smoothing methods to the marker CD4 in the ACTG-019 clinical trial part B.

AIDS-Related Complex↗