Integrated GWAS, linkage, and transcriptome analysis to identify genetic loci and candidate genes for photoperiod sensitivity in maize.

Introduction: Maize photosensitivity and the control of flowering not only are important for reproduction, but also play pivotal roles in the processes of domestication and environmental adaptation, especially involving the utilization strategy of tropical maize in high-latitude regions. Methods: In this study, we used a linkage mapping population and an inbred association panel with the photoperiod sensitivity index (PSI) phenotyped under different environments and performed transcriptome analysis of T32 and QR273 between long-day and short-day conditions. Results: The results showed that PSIs of days to tasseling (DTT), days to pollen shedding (DTP), and days to silking (DTS) indicated efficacious interactions with photoperiod sensitivity for maize latitude adaptation. A total of 48 quantitative trait loci (QTLs) and 252 quantitative trait nucleotides (QTNs) were detected using the linkage population and the inbred association panel. Thirteen candidate genes were identified by combining the genome-wide association study (GWAS) approach, linkage analysis, and transcriptome analysis, wherein five critical candidate genes, MYB163, bif1, burp8, CADR3, and Zm00001d050238, were significantly associated with photoperiod sensitivity. Discussion: These results would provide much more abundant theoretical proofs to reveal the genetic basis of photoperiod sensitivity, which would be helpful to understand the genetic changes during domestication and improvement and contribute to reducing the barriers to use of tropical germplasm.

Joint genotype and ancestry analysis identify novel loci associated with atopic dermatitis in African American population.

Atopic dermatitis (AD) is a chronic itchy inflammatory disease of the skin. Genetic studies have identified multiple risk factors linked to the disease; however, most of the studies have been derived from European and East Asian populations. The admixed African American (AA) genome may provide an opportunity to discovery ancestry-specific loci involved in AD susceptibility. Herein, we present joint analysis of ancestry and genotype effects followed by validation using differential gene expression analysis on AD using 726 AD-affected individuals and 999 non-AD control individuals from the AA population, genotyped using Multi-Ethnic Global Array (MEGA) followed by imputation using the Consortium on Asthma among African Ancestry Populations in the Americas (CAAPA) reference panel. The joint analysis identified two novel AD-susceptibility loci, rs2195989 in gene ANGPT1 (8q23.1) and rs62538818 in the intergenic region between genes LURAP1L and MPDZ (9p23). Admixture mapping (AM) results showed potential genomic inflation, and we implemented genomic control and identified five ancestry-of-origin loci with European ancestry effects. The multi-omics functional prioritization of variants in AM signals prioritized the loci SLAIN2, RNF39, and FOXA2. Genome-wide association study (GWAS) identified variants significantly associated with AD in the AA population, including SGK1 (rs113357522, odds ratio [OR] = 2.81), EFR3A (rs16904552, OR = 1.725), and MMP14 (rs911912, OR = 1.791). GWAS variants were common in the AA but rare in the European population, which suggests an African-ancestry-specific risk of AD. Four genes (ANGPT1, LURAP1L, EFR3A, and SGK1) were further validated using qPCR from AD and healthy skin. This study highlighted the importance of genetic studies on admixed populations, as well as local ancestry and genotype-ancestry joint effects to identify risk loci for AD.

Multi-omics analysis to reveal the synergistic mechanism underlying the multiple ingredients of Stephania tetrandra extract on rheumatoid arthritis through the PI3K/Akt signaling pathway.

Background: Stephania tetrandra has been used for treating rheumatic diseases for thousands of years in rural areas of China. Several studies have found that tetrandrine and fangchinoline can inactivate the PI3K/Akt signaling pathway by reducing the expression and phosphorylation of AKT. However, the mechanism underlying the therapeutic actions of S. tetrandra on RA is not well known. Methods: In this study, we determined the molecular mechanism of the therapeutic effects of the multiple ingredients of S. tetrandra extract (STE) on collagen-induced arthritic (CIA) rats by integrating pharmacometabolomics, proteomics, and PTMomics. Results: In the multi-omics joint analysis, first, the expression signatures of proteins, PTMs, metabolites, and STE ingredients were profiled in CIA rats PBMCs that underwent STE treatment. Bioinformatics analysis were subsequently probed that STE mainly regulated tryptophan metabolism, inflammatory response, and cell adhesion pathways in CIA rats. The interrelated pathways were further constructed, and the findings revealed that STE attenuated the inflammatory response and proliferation of PBMCs in CIA rats by mediating the key targets of the PI3K/Akt pathway, including Hint1, ACP1, FGR, HSP90@157W + dioxidation, and Prkca@220N + 845.4540 Da. The rheumatic functions of Hint1 and ACP1 were further confirmed by applying a transcriptomic data of RA patients who clinically received abatacept therapy. Furthermore, a cross-ome correlation analysis was performed and major in vivo ingredients of STE, including coclaurine-N-glucuronide, Me,coclaurine-O-glc, N-gluA-schefferine, corydamine, corypamine, tetrandrine, and fangchiniline, were found to act on these targerts to inactivate the PI3K/Akt pathway. Conclusion: These results elucidated the molecular mechanism by which the ingredients of STE mediate the expression of the key targets in the PI3K/Akt pathway, leading to anti-rheumatic functions. The findings of this study provided new insights into the synergistic effect of STE against arthritis in rats.

Multi-omics integration for both single-cell and spatially resolved data based on dual-path graph attention auto-encoder.

Single-cell multi-omics integration enables joint analysis at the single-cell level of resolution to provide more accurate understanding of complex biological systems, while spatial multi-omics integration is benefit to the exploration of cell spatial heterogeneity to facilitate more comprehensive downstream analyses. Existing methods are mainly designed for single-cell multi-omics data with little consideration of spatial information and still have room for performance improvement. A reliable multi-omics integration method designed for both single-cell and spatially resolved data is necessary and significant. We propose a multi-omics integration method based on dual-path graph attention auto-encoder (SSGATE). It can construct the neighborhood graphs based on single-cell expression profiles or spatial coordinates, enabling it to process single-cell data and utilize spatial information from spatially resolved data. It can also perform self-supervised learning for integration through the graph attention auto-encoders from two paths. SSGATE is applied to integration of transcriptomics and proteomics, including single-cell and spatially resolved data of various tissues from different sequencing technologies. SSGATE shows better performance and stronger robustness than competitive methods and facilitates downstream analysis.

Whole genome joint analysis reveals ATM:C.1564_1565del variant segregating with Ataxia-Telangiectasia and breast cancer.

ATM gene is implicated in the development of breast cancer in the heterozygous state, and Ataxia-telangiectasia (A-T) in a homozygous or compound heterozygous state. Ataxia-telangiectasia (A-T) is a rare cerebellar ataxia syndrome presenting with progressive neurologic impairment, telangiectasia, and an increased risk of leukemia and lymphoma. Although the role of ATM, separately, in association with A-T and breast cancer is well documented, there is a limited number of studies investigating ATM variants when segregating with both phenotypes in the same family. Here, using joint analysis and whole genome sequencing, we investigated ATM c.1564_1565del in a family with one homozygous member presenting with A-T (OMIM # 208900) and three heterozygous members, of whom one had breast cancer (OMIM #114480). To our knowledge, this is the first study of ATM c.1564_1565del segregation with both A-T and breast cancer phenotypes within the same kindred. This study highlights the need for a comprehensive genomic approach in the appropriate cancer risk management of heterozygote carriers of ATM in families with A-T.

An interpretable ensemble trees method with joint analysis of static and dynamic features for myocardial infarction detection.

Objective.In recent years, artificial intelligence-based electrocardiogram (ECG) methods have been massively applied to myocardial infarction (MI). However, the joint analysis of static and dynamic features to achieve accurate and interpretable MI detection has not been comprehensively addressed.Approach.This paper proposes a simplified ensemble tree method with a joint analysis of static and dynamic features to solve this issue for MI detection. Initially, the dynamic features are extracted by modeling the intrinsic dynamics of ECG via dynamic learning in addition to extracting classical static features. Secondly, a two-stage feature selection strategy is designed to identify a few significant features, which substitute the original variables that are employed in constructing the ensemble tree. This approach enhances the discriminative ability by selecting significant static and dynamic features. Subsequently, this paper presents an interpretable classification method named StackTree by introducing a stacked ensemble scheme to modify the ensemble tree simplification algorithm. The representative rules of the raw ensemble trees are selected as the intermediate training data that is used to retrain a decision tree with performance close to that of the source ensemble model. Using this scheme, the significant precision and interpretability of MI detection are thus comprehensively addressed.Main results.The effectiveness of our method in detecting MI is evaluated using the Physikalisch-Technische Bundesanstalt (PTB) and clinical database. The findings suggest that our algorithm outperforms the traditional methods based on a single type of feature. Additionally, it is comparable to the conventional random forest, achieving 97.1% accuracy under the inter-patient framework on the PTB database. Furthermore, feature subsets trained on PTB are validated using the clinical database, resulting in an accuracy of 84.5%. The chosen important features demonstrate that both static and dynamic information have crucial roles in MI detection. Crucially, the proposed method provides clear internal workings in an easy-to-understand visual manner.

Hierarchical joint analysis of marginal summary statistics-Part II: High-dimensional instrumental analysis of omics data.

Instrumental variable (IV) analysis has been widely applied in epidemiology to infer causal relationships using observational data. Genetic variants can also be viewed as valid IVs in Mendelian randomization and transcriptome-wide association studies. However, most multivariate IV approaches cannot scale to high-throughput experimental data. Here, we leverage the flexibility of our previous work, a hierarchical model that jointly analyzes marginal summary statistics (hJAM), to a scalable framework (SHA-JAM) that can be applied to a large number of intermediates and a large number of correlated genetic variants-situations often encountered in modern experiments leveraging omic technologies. SHA-JAM aims to estimate the conditional effect for high-dimensional risk factors on an outcome by incorporating estimates from association analyses of single-nucleotide polymorphism (SNP)-intermediate or SNP-gene expression as prior information in a hierarchical model. Results from extensive simulation studies demonstrate that SHA-JAM yields a higher area under the receiver operating characteristics curve (AUC), a lower mean-squared error of the estimates, and a much faster computation speed, compared to an existing approach for similar analyses. In two applied examples for prostate cancer, we investigated metabolite and transcriptome associations, respectively, using summary statistics from a GWAS for prostate cancer with more than 140,000 men and high dimensional publicly available summary data for metabolites and transcriptomes.

Integrated transcriptomics and metabolomics study of embryonic breast muscle of Jiaji ducks.

Because number of matured muscle fibers in poultry does not increase after birth, the meat yield is mainly determined during embryogenesis. We previously indicated breast muscle grew rapidly from 18th day after hatching (E18) to E27, and almost stopped from E27 to E34 of Jiaji ducks, while the mechanism is unclear. This study utilized RNA-seq to explore the related genes of muscle development and their relationship with small molecule metabolites at E18, E27 and E34 of Jiaji ducks. Several thousand differentially expressed genes (DEGs) were detected among E18, E27 and E34. DEGs expression profiles included 8 trend maps, among which trend 1 was opposite to and trend 6 was consistent with breast muscle development trend of Jiaji ducks. Through joint analysis between trend 1 of DEGs and trend 1 of differential metabolites (DEMs), protein digestion and absorption pathway stood out. The decrease of COL8A2 gene expression will lead to the decrease of arginine content, which will inhibit the development of breast muscle in embryonic Jiaji duck. Similarly, joint analysis between trend 6 of DEGs and trend 6 of DEMs indicated the increase of GAMT gene expression will cause the increase of proline content, and then promote the development of breast muscle of Jiaji duck in embryonic period. These results will be helpful for further understanding the mechanism of muscle yields of Jiaji ducks.

A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer.

Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify susceptibility genes. However, existing splicing-TWASs test the association of individual excised introns in breast tissue only and thus have limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 women of European ancestry. Splicing-level prediction models were trained in GTEx (v.8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni-corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified nine additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs, and 17 genes in seven loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our splicing-TWASs with previous gene-expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci that are identified only by the splicing-TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show a significant impact on breast cancer risk, whereas splicing quantitative trait loci (sQTL) showed a strong impact through intron excision events.

Investigation and Prediction of Nano-Silver Line Quality upon Various Process Parameters in Inkjet Printing Process Based on an Experimental Method.

As an emerging additive manufacturing technology, inkjet printing has been increasingly applied in microelectronics field. However, due to the impacting and rebounding behaviors of conductive ink droplets impinging onto flat substrates, it is challenging to fabricate conductive lines with desired quality, such as suitable line width and line thickness, and matching resistance when it is used for interconnecting multifarious electronic components if there is not a proper configuration of operating parameters. To address this research gap, this article aims to investigate the effect of process parameters on the quality of conductive lines, including the platform temperature, printing speed, number of layers, and delay time (droplet interarrival time), are selected to conduct a full factorial experiment. First, the approximate parameter ranges for ensuring the continuity of conductive lines are determined. Second, this study analyzes the interactive effect among process parameters on line quality. Third, an artificial neural network (ANN) is constructed to predict the quality of printed lines. Results show that the line width does not increase with an increased number of layers, while the line thickness shows an increasing trend. The low resistance and high aspect ratio of printed line are achieved by printing 5 layers with the platform temperature of 70°C, the delay time of 12.2 ms, and the printing speed of 1139.39 mm/min. Moreover, the ANN model can be used to predict line width and line thickness with excellent performance, except for the resistance due to the irregular line edge. This study provides a useful guide for the selection of appropriate printing parameters to realize a diverse range of quality properties for 3D printed conductive lines in integrated circuits.

A layer discrete particle based soft contact model in corroded rebar monitoring using linear and nonlinear ultrasonic guided waves.

In offshore reinforced concrete (RC) structures, the phenomenon of rebar corrosion is widespread, seriously threatening the durability of the structures. However, the issue of rebar corrosion detection especially for the early corrosion situation is also challengeable. It is of great significance to use ultrasonic guided waves (UGWs) for monitoring the situation of the rebar corrosion entire process. In this paper, a mechanical model was used to establish the relationship between different rebar corrosion expansion states and layer-surface contact pressures in the layered RC components with radial cracks. Based on this model, a soft pressure-dependent contact 2D model in Abaqus was used to simulate the local corrosion layer. A linear and nonlinear signal joint analysis (LNSJA) method using PZT-based UGWs was proposed to monitor rebar corrosions, and an LNSJA-based rebar corrosion damage index (RCDI) for corroded RC components was proposed. The proposed method which can effectively detect both the micro- and macro-thickness as well as local area of rebar corrosion layer was validated by the relevant experiment and finite element analysis (FEA).

Impact of Ergonomics on Muscle Fatigue During Surgical Drilling Using Surface Electromyography.

OBJECTIVE: To investigate the relationship between ergonomic positions and electromyographic muscle activity during otologic drilling. STUDY DESIGN: Cross-over experimental trial. SETTING: Tertiary Academic Medical Center. METHODS: Surgeon participants were tasked with delicate eggshell drilling in 3 different seated positions: "neutral," "slouched," and "craned." Surface electromyography (sEMG) sensors recorded the amplitude and frequency of muscle activity. The joint analysis of spectrum and amplitude (JASA) method, which combines temporal trends in frequency and amplitude, was used to identify trials that exhibited patterns of fatigue. RESULTS: The sEMG amplitude and frequency responses demonstrated wide temporal changes. In a majority of experiments, amplitude increased over the course of the experiment, while frequency remained more stable. On analysis of variance testing, only the mean frequency of the deltoid differed significantly between postures (P = .02). Under the JASA framework, external carpi radialis and upper trapezius experienced fatigue in nearly half of the trials regardless of position (47% vs 49%). The upper trapezius demonstrated fatigue during 46% and 69% of the "craned" and "slouched" trials, respectively, compared to just 31% of the "neutral" trials. Fewer attendings demonstrated upper trapezius fatigue compared to trainees (33% vs 62%). Female surgeons experienced fatigue in more trials than male counterparts (73% vs 25%). CONCLUSION: This study highlights a first step in quantifying the relationship between operating postures and muscle fatigue. Results suggest that specific muscle groups are more susceptible to fatigue; gender and experience may also impact muscle activity.

Using encrypted genotypes and phenotypes for collaborative genomic analyses to maintain data confidentiality.

To adhere to and capitalize on the benefits of the FAIR (findable, accessible, interoperable, and reusable) principles in agricultural genome-to-phenome studies, it is crucial to address privacy and intellectual property issues that prevent sharing and reuse of data in research and industry. Direct sharing of genotype and phenotype data is often prohibited due to intellectual property and privacy concerns. Thus, there is a pressing need for encryption methods that obscure confidential aspects of the data, without affecting the outcomes of certain statistical analyses. A homomorphic encryption method for genotypes and phenotypes (HEGP) has been proposed for single-marker regression in genome-wide association studies (GWAS) using linear mixed models with Gaussian errors. This methodology permits frequentist likelihood-based parameter estimation and inference. In this paper, we extend HEGP to broader applications in genome-to-phenome analyses. We show that HEGP is suited to commonly used linear mixed models for genetic analyses of quantitative traits including genomic best linear unbiased prediction (GBLUP) and ridge-regression best linear unbiased prediction (RR-BLUP), as well as Bayesian variable selection methods (e.g. those in Bayesian Alphabet), for genetic parameter estimation, genomic prediction, and GWAS. By advancing the capabilities of HEGP, we offer researchers and industry professionals a secure and efficient approach for collaborative genomic analyses while preserving data confidentiality.

Smoother: a unified and modular framework for incorporating structural dependency in spatial omics data.

Spatial omics technologies can help identify spatially organized biological processes, but existing computational approaches often overlook structural dependencies in the data. Here, we introduce Smoother, a unified framework that integrates positional information into non-spatial models via modular priors and losses. In simulated and real datasets, Smoother enables accurate data imputation, cell-type deconvolution, and dimensionality reduction with remarkable efficiency. In colorectal cancer, Smoother-guided deconvolution reveals plasma cell and fibroblast subtype localizations linked to tumor microenvironment restructuring. Additionally, joint modeling of spatial and single-cell human prostate data with Smoother allows for spatial mapping of reference populations with significantly reduced ambiguity.

Framework of wind joint analysis for different lake regions and its effects on the water quality.

Water quality of Lake Taihu (LT) is paid wide attention, and the wind field makes wind-induced flow, significantly impacting the water quality. As a wide lake, the wind field suffers spatial and temporal changes. The correlated relationship among the wind fields for different lake regions has not been studied, and the joint effects of wind field on the water quality is still unknown. Hence, this paper proposed a framework of wind joint analysis for different lake regions and modelling its effects on the water quality, including joint analysis of wind field for different lake regions using Copula function, random time series generation of wind field using Monte-Carlo simulation, and hydrodynamic and water quality numerical simulation. Taking the Lake Taihu (LT) as study case, the joint relationships of wind field for four lake regions were analyzed, and the CODMN, TP and TN distributions under different wind fields were simulated. This paper showed the following: (1) The relationship between the wind speed and direction was weak, and the correlated relationships among the wind fields for four lake regions were significant (ρ > 0.5). (2) The water quality of LT was more influenced by the wind direction rather than the wind speed, with an impacting ratio of ∼4.5. (3) The discharged weighted angle of runoff outflow (DWARO) was a practical index to improve the water quality. When regulating the input/output runoff discharge, water diversion project and water intakes in practice, the administrations should make the DWARO less than or equal to the average wind direction, to decrease the average pollutant concentration and improve the water quality of lake and intake. The proposed framework and results of LT could be extended to other wide shallow lakes to support the environmental management and basin runoff regulation.

Joint analysis of GWAS and multi-omics QTL summary statistics reveals a large fraction of GWAS signals shared with molecular phenotypes.

Molecular quantitative trait loci (xQTLs) are often harnessed to prioritize genes or functional elements underpinning variant-trait associations identified from genome-wide association studies (GWASs). Here, we introduce OPERA, a method that jointly analyzes GWAS and multi-omics xQTL summary statistics to enhance the identification of molecular phenotypes associated with complex traits through shared causal variants. Applying OPERA to summary-level GWAS data for 50 complex traits (n = 20,833-766,345) and xQTL data from seven omics layers (n = 100-31,684) reveals that 50% of the GWAS signals are shared with at least one molecular phenotype. GWAS signals shared with multiple molecular phenotypes, such as those at the MSMB locus for prostate cancer, are particularly informative for understanding the genetic regulatory mechanisms underlying complex traits. Future studies with more molecular phenotypes, measured considering spatiotemporal effects in larger samples, are required to obtain a more saturated map linking molecular intermediates to GWAS signals.

A novel method for sorting and reassociating commingled human remains using deviation analysis.

This study provides an innovative and novel method for sorting commingled human remains at the sacroiliac joint using deviation analyses. Virtual models were created at the University of Tennessee-Knoxville Donated Skeletal Collection from 69 os coxae and 66 sacra using an EinScan-Pro 2× + Handheld Surface Scanner. The shape of the auricular surfaces was analyzed in Geomagic Wrap 2017, and the congruency of the two auricular surfaces was measured using a deviation analysis. ROC curves were performed on a reference sample composed of 200 commingled and non-commingled joint pairs to identify threshold values that could help sort the commingled remains. A validation sample of 225 pairs was subsequently analyzed to demonstrate the efficacy of this new method on a sample of unknown individuals. Statistical analyses demonstrated that the deviation analysis values from sacroiliac joints of commingled pairs were significantly larger than those from non-commingled individuals (p < 0.0001). Based on the selected threshold values, 98%-100% of pairs were correctly sorted and reassociated. This novel and objective technique improves upon previously subjective strategies for sorting commingled remains and, in the future, will be applied to additional joint surfaces.

[Evaluation of Muscle Fatigue in Spinal Surgery Instruments Based on sEMG-JASA].

Based on the joint analysis of EMG spectrum and amplitude method (JASA), a study on muscle fatigue assessment of spinal surgical instruments based on surface EMG signals was carried out, and a comparative evaluation of the operating comfort before and after the optimization of spinal surgical instruments was completed. A total of 17 subjects were recruited to collect the surface EMG signals of their brachioradialis and biceps. Five surgical instruments before and after optimization were selected for data comparison, and the operating fatigue time proportion of each group of instruments under the same task was calculated based on the RMS and MF eigenvalues. The results showed that when completing the same operation task, the operation fatigue time of the surgical instruments before optimization was significantly higher than that after optimization (P<0.05); there was no significant difference in the fatigue status of brachioradialis and biceps when operating the same instrument (P>0.05). These results provide objective data and reference for the ergonomic design of surgical instruments and fatigue damage protection.

Serum Metabolomics and Ionomics Analysis of Hoof-Deformed Cows Based on LC-MS/MS and ICP-OES/MS.

In order to explore the metabolic and ionic changes of hoof-deformed cows, the serum samples of 10 healthy cows (group C) and 10 hoof-deformed cows (group T) were analyzed by LC-MS/MS and ICP-OES/MS. The pathway enrichment of differential metabolites was analyzed by screening and identifying differential metabolites and ions and using a bioinformatics method. The integration of metabolomics and ionics was analyzed with ggplot2 software in R language, and verified by MRM target metabolomics. The results showed that 127 metabolites were screened by metabolomics, of which 81 were up-regulated (p < 0.05) and 46 were down-regulated (p < 0.05). The results of ICP-OES/MS showed that 13 kinds of ions such as K, Li, and Pb in serum of dairy cows were up-regulated, while 18 kinds of ions such as Al, Cu and Sb were down-regulated. The integrated analysis of metabolomics and ionics found that potassium ions were positively correlated with L-tyrosine, L-proline, thiamine and L-valine. Sodium ions were positively correlated with L-valine and negatively correlated with α-D-glucose. The results of high-throughput target metabolomics showed that the contents of L-proline, L-phenylalanine and L-tryptophan in serum of dairy cows increased significantly, which was consistent with the results of non-target metabolomics. In a word, the metabolism and ion changes in dairy cows with hoof deformation were revealed by metabolomics and ionics.

Using Trial and Observational Data to Assess Effectiveness: Trial Emulation, Transportability, Benchmarking, and Joint Analysis.

Comparisons between randomized trial analyses and observational analyses that attempt to address similar research questions have generated many controversies in epidemiology and the social sciences. There has been little consensus on when such comparisons are reasonable, what their implications are for the validity of observational analyses, or whether trial and observational analyses can be integrated to address effectiveness questions. Here, we consider methods for using observational analyses to complement trial analyses when assessing treatment effectiveness. First, we review the framework for designing observational analyses that emulate target trials and present an evidence map of its recent applications. We then review approaches for estimating the average treatment effect in the target population underlying the emulation: using observational analyses of the emulation data alone; and using transportability analyses to extend inferences from a trial to the target population. We explain how comparing treatment effect estimates from the emulation against those from the trial can provide evidence on whether observational analyses can be trusted to deliver valid estimates of effectiveness - a process we refer to as benchmarking - and, in some cases, allow the joint analysis of the trial and observational data. We illustrate different approaches using a simplified example of a pragmatic trial and its emulation in registry data. We conclude that synthesizing trial and observational data - in transportability, benchmarking, or joint analyses - can leverage their complementary strengths to enhance learning about comparative effectiveness, through a process combining quantitative methods and epidemiological judgements.