Mendelian randomization: causal inference leveraging genetic data.

Mendelian randomization (MR) leverages genetic information to examine the causal relationship between phenotypes allowing for the presence of unmeasured confounders. MR has been widely applied to unresolved questions in epidemiology, making use of summary statistics from genome-wide association studies on an increasing number of human traits. However, an understanding of essential concepts is necessary for the appropriate application and interpretation of MR. This review aims to provide a non-technical overview of MR and demonstrate its relevance to psychiatric research. We begin with the origins of MR and the reasons for its recent expansion, followed by an overview of its statistical methodology. We then describe the limitations of MR, and how these are being addressed by recent methodological advances. We showcase the practical use of MR in psychiatry through three illustrative examples - the connection between cannabis use and psychosis, the link between intelligence and schizophrenia, and the search for modifiable risk factors for depression. The review concludes with a discussion of the prospects of MR, focusing on the integration of multi-omics data and its extension to delineating complex causal networks.

Bidirectional two-sample Mendelian randomization study of differential white blood cell counts and schizophrenia.

BACKGROUND: Schizophrenia and white blood cell counts (WBC) are both complex and polygenic traits. Previous evidence suggests that increased WBC are associated with higher all-cause mortality, and other studies have found elevated WBC in first-episode psychosis and chronic schizophrenia. However, these observational findings may be confounded by antipsychotic exposures and their effects on WBC. Mendelian randomization (MR) is a useful method for examining the directions of genetically-predicted relationships between schizophrenia and WBC. METHODS: We performed a two-sample MR using summary statistics from genome-wide association studies (GWAS) conducted by the Psychiatric Genomics Consortium Schizophrenia Workgroup (N = 130,644) and the Blood Cell Consortium (N = 563,946). The MR methods included inverse variance weighted (IVW), MR Egger, weighted median, MR-PRESSO, contamination mixture, and a novel approach called mixture model reciprocal causal inference (MRCI). False discovery rate was employed to correct for multiple testing. RESULTS: Multiple MR methods supported bidirectional genetically-predicted relationships between lymphocyte count and schizophrenia: IVW (b = 0.026; FDR p-value = 0.008), MR Egger (b = 0.026; FDR p-value = 0.008), weighted median (b = 0.013; FDR p-value = 0.049), and MR-PRESSO (b = 0.014; FDR p-value = 0.010) in the forward direction, and IVW (OR = 1.100; FDR p-value = 0.021), MR Egger (OR = 1.231; FDR p-value < 0.001), weighted median (OR = 1.136; FDR p-value = 0.006) and MRCI (OR = 1.260; FDR p-value = 0.026) in the reverse direction. MR Egger (OR = 1.171; FDR p-value < 0.001) and MRCI (OR = 1.154; FDR p-value = 0.026) both suggested genetically-predicted eosinophil count is associated with schizophrenia, but MR Egger (b = 0.060; FDR p-value = 0.010) and contamination mixture (b = -0.013; FDR p-value = 0.045) gave ambiguous results on whether genetically predicted liability to schizophrenia would be associated with eosinophil count. MR Egger (b = 0.044; FDR p-value = 0.010) and MR-PRESSO (b = 0.009; FDR p-value = 0.045) supported genetically predicted liability to schizophrenia is associated with elevated monocyte count, and the opposite direction was also indicated by MR Egger (OR = 1.231; FDR p-value = 0.045). Lastly, unidirectional genetic liability from schizophrenia to neutrophil count were proposed by MR-PRESSO (b = 0.011; FDR p-value = 0.028) and contamination mixture (b = 0.011; FDR p-value = 0.045) method. CONCLUSION: This MR study utilised multiple MR methods to obtain results suggesting bidirectional genetic genetically-predicted relationships for elevated lymphocyte counts and schizophrenia risk. In addition, moderate evidence also showed bidirectional genetically-predicted relationships between schizophrenia and monocyte counts, and unidirectional effect from genetic liability for eosinophil count to schizophrenia and from genetic liability for schizophrenia to neutrophil count. The influence of schizophrenia to eosinophil count is less certain. Our findings support the role of WBC in schizophrenia and concur with the hypothesis of neuroinflammation in schizophrenia.

CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies.

Genome-wide association studies (GWASs) have revolutionized the field of complex trait genetics over the past decade, yet for most of the significant genotype-phenotype associations the true causal variants remain unknown. Identifying and interpreting how causal genetic variants confer disease susceptibility is still a big challenge. Herein we introduce a new database, CAUSALdb, to integrate the most comprehensive GWAS summary statistics to date and identify credible sets of potential causal variants using uniformly processed fine-mapping. The database has six major features: it (i) curates 3052 high-quality, fine-mappable GWAS summary statistics across five human super-populations and 2629 unique traits; (ii) estimates causal probabilities of all genetic variants in GWAS significant loci using three state-of-the-art fine-mapping tools; (iii) maps the reported traits to a powerful ontology MeSH, making it simple for users to browse studies on the trait tree; (iv) incorporates highly interactive Manhattan and LocusZoom-like plots to allow visualization of credible sets in a single web page more efficiently; (v) enables online comparison of causal relations on variant-, gene- and trait-levels among studies with different sample sizes or populations and (vi) offers comprehensive variant annotations by integrating massive base-wise and allele-specific functional annotations. CAUSALdb is freely available at http://mulinlab.org/causaldb.

Bioleaching Performance of Titanium from Bauxite Residue Under a Continuous Mode Using Penicillium Tricolor.

The present study performed a continuous mode of bioleaching to investigate the leaching efficiency of Titanium (Ti) from bauxite residue using Penicillium Tricolor at between 4% and 12% pulp densities during a 120-day running. Obtained results of the current study showed that increased pulp density led to a decrease in biomass, dissolved oxygen, and amount of leaching Ti as well as an increase in pH value. Further, it was found that efficiency of bioleaching can be enhanced by increasing the rate of aeration, retention time, and concentration of carbon source. However, it was also evident that, at high pulp density, excessive agitation did not give an expected leaching efficiency but a collapse of biomass. In addition, results of the present study showed that the maximum leaching amount of Ti was 3202 mg/L with a corresponding leaching ratio of 50.35% during the whole bioleaching process. Moreover, it was noted that the biomass showed a significant negative correlation with the pH value and dissolved oxygen. However, the biomass showed a significant positive correlation with leaching amount of Ti and thus indicate that microbial metabolic activities are the uppermost factor affecting the continuous leaching performance.

Up-regulation of circRNA_0068481 promotes right ventricular hypertrophy in PAH patients via regulating miR-646/miR-570/miR-885.

CircRNA-0068481 and several miRNAs are important in the pathogenesis of right ventricular hypertrophy (VH), while the inhibition of eye absent transcriptional coactivator and phosphatase 3 (EYA3) was proved to reverse vascular remodelling in rats. In this study, we tried to study the diagnostic value and mechanistic role of circRNA_0068481 in the diagnosis of RVH in PAH patients. qPCR was done to measure circRNA-0068481, miR-646, miR-750, miR-885 and EYA3 mRNA expression. Luciferase assay was done to explore the regulatory relationship between circRNA-0068481/EYA3 and the miRNAs. Western blot was done to measure EYA3 expression in AC16 cells. The expression of circRNA-0068481, miR-646 and miR-570 showed a considerable capability to diagnose RVH in PAH patients. The luciferase activity of circRNA-0068481 was remarkably suppressed by miR-646, miR-570 or miR-885. The luciferase signal of EYA3 was also inhibited by miR-646, miR-570 and miR-885. Up-regulation of circRNA-0068481 expression in AC16 significantly decreased miR-646, miR-570 and miR-885 expression, and up-regulated EYA3 expression, whereas circRNA-0068481 down-regulation significantly increased miR-646, miR-570 and miR-885 expression, and repressed EYA3 expression. CircRNA_0068481 sponged several miRNAs including miR-646, miR-570 and miR-885. These miRNAs were all found to target the expression of EYA3 mRNA, which is involved in the onset of right ventricular hypertrophy. Therefore, it can be concluded that the up-regulation of circRNA_0068481 can predict the diagnosis of right ventricular hypertrophy in pulmonary arterial hypertension patients.

Vascular progenitor cell senescence in patients with Marfan syndrome.

Vascular progenitor cells (VPCs) present in the adventitia of the vessel wall play a critical role in the regulation of vascular repair following injury. This study aimed to assess the function of VPCs isolated from patients with Marfan syndrome (MFS). VPCs were isolated from control and MFS donors and characterized. Compared with control-VPCs, MFS-VPCs exhibited cellular senescence as demonstrated by increased cell size, higher SA-ß-gal activity and elevated levels of p53 and p21. RNA sequencing showed that several cellular process-related pathways including cell cycle and cellular senescence were significantly enriched in MFP-VPCs. Notably, the expression level of TGF-ß1 was much higher in MFS-VPCs than control-VPCs. Treatment of control-VPCs with TGF-ß1 significantly enhanced mitochondrial reactive oxidative species (ROS) and induced cellular senescence whereas inhibition of ROS reversed these effects. MFS-VPCs displayed increased mitochondrial fusion and decreased mitochondrial fission. Treatment of control-VPCs with TGF-ß1 increased mitochondrial fusion and reduced mitochondrial fission. Nonetheless, treatment of mitofusin2 (Mfn2)-siRNA inhibited TGF-ß1-induced mitochondrial fusion and cellular senescence. Furthermore, TGF-ß1-induced mitochondrial fusion was mediated by the AMPK signalling pathway. Our study shows that TGF-ß1 induces VPC senescence in patients with MFS by mediating mitochondrial dynamics via the AMPK signalling pathway.

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers.

Cancer therapies have experienced rapid progress in recent years, with a number of novel small-molecule kinase inhibitors and monoclonal antibodies now being widely used to treat various types of human cancers. During cancer treatments, mutations can have important effects on drug sensitivity. However, the relationship between tumor genomic profiles and the effectiveness of cancer drugs remains elusive. We introduce Mutation To Cancer Therapy Scan (mTCTScan) web server (http://jjwanglab.org/mTCTScan) that can systematically analyze mutations affecting cancer drug sensitivity based on individual genomic profiles. The platform was developed by leveraging the latest knowledge on mutation-cancer drug sensitivity associations and the results from large-scale chemical screening using human cancer cell lines. Using an evidence-based scoring scheme based on current integrative evidences, mTCTScan is able to prioritize mutations according to their associations with cancer drugs and preclinical compounds. It can also show related drugs/compounds with sensitivity classification by considering the context of the entire genomic profile. In addition, mTCTScan incorporates comprehensive filtering functions and cancer-related annotations to better interpret mutation effects and their association with cancer drugs. This platform will greatly benefit both researchers and clinicians for interrogating mechanisms of mutation-dependent drug response, which will have a significant impact on cancer precision medicine.

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies.

Genome-wide association studies (GWASs), now as a routine approach to study single-nucleotide polymorphism (SNP)-trait association, have uncovered over ten thousand significant trait/disease associated SNPs (TASs). Here, we updated GWASdb (GWASdb v2, http://jjwanglab.org/gwasdb) which provides comprehensive data curation and knowledge integration for GWAS TASs. These updates include: (i) Up to August 2015, we collected 2479 unique publications from PubMed and other resources; (ii) We further curated moderate SNP-trait associations (P-value < 1.0 × 10(-3)) from each original publication, and generated a total of 252,530 unique TASs in all GWASdb v2 collected studies; (iii) We manually mapped 1610 GWAS traits to 501 Human Phenotype Ontology (HPO) terms, 435 Disease Ontology (DO) terms and 228 Disease Ontology Lite (DOLite) terms. For each ontology term, we also predicted the putative causal genes; (iv) We curated the detailed sub-populations and related sample size for each study; (v) Importantly, we performed extensive function annotation for each TAS by incorporating gene-based information, ENCODE ChIP-seq assays, eQTL, population haplotype, functional prediction across multiple biological domains, evolutionary signals and disease-related annotation; (vi) Additionally, we compiled a SNP-drug response association dataset for 650 pharmacogenetic studies involving 257 drugs in this update; (vii) Last, we improved the user interface of website.

Predicting regulatory variants with composite statistic.

MOTIVATION: Prediction and prioritization of human non-coding regulatory variants is critical for understanding the regulatory mechanisms of disease pathogenesis and promoting personalized medicine. Existing tools utilize functional genomics data and evolutionary information to evaluate the pathogenicity or regulatory functions of non-coding variants. However, different algorithms lead to inconsistent and even conflicting predictions. Combining multiple methods may increase accuracy in regulatory variant prediction. RESULTS: Here, we compiled an integrative resource for predictions from eight different tools on functional annotation of non-coding variants. We further developed a composite strategy to integrate multiple predictions and computed the composite likelihood of a given variant being regulatory variant. Benchmarked by multiple independent causal variants datasets, we demonstrated that our composite model significantly improves the prediction performance. AVAILABILITY AND IMPLEMENTATION: We implemented our model and scoring procedure as a tool, named PRVCS, which is freely available to academic and non-profit usage at http://jjwanglab.org/PRVCS CONTACT: wang.junwen@mayo.edu, jliu@stat.harvard.edu, or limx54@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

iTRAQ proteomics analysis reveals that PI3K is highly associated with bupivacaine-induced neurotoxicity pathways.

Bupivacaine, a commonly used local anesthetic, has potential neurotoxicity through diverse signaling pathways. However, the key mechanism of bupivacaine-induced neurotoxicity remains unclear. Cultured human SH-SY5Y neuroblastoma cells were treated (bupivacaine) or untreated (control) with bupivacaine for 24 h. Compared to the control group, bupivacaine significantly increased cyto-inhibition, cellular reactive oxygen species, DNA damage, mitochondrial injury, apoptosis (increased TUNEL-positive cells, cleaved caspase 3, and Bcl-2/Bax), and activated autophagy (enhanced LC3II/LC3I ratio). To explore changes in protein expression and intercommunication among the pathways involved in bupivacaine-induced neurotoxicity, an 8-plex iTRAQ proteomic technique and bioinformatics analysis were performed. Compared to the control group, 241 differentially expressed proteins were identified, of which, 145 were up-regulated and 96 were down-regulated. Bioinformatics analysis of the cross-talk between the significant proteins with altered expression in bupivacaine-induced neurotoxicity indicated that phosphatidyl-3-kinase (PI3K) was the most frequently targeted protein in each of the interactions. We further confirmed these results by determining the downstream targets of the identified signaling pathways (PI3K, Akt, FoxO1, Erk, and JNK). In conclusion, our study demonstrated that PI3K may play a central role in contacting and regulating the signaling pathways that contribute to bupivacaine-induced neurotoxicity.

Pre-dry heat treatment alters the structure and ultimate in vitro digestibility of wheat starch-lipids complex in hot-extrusion 3D printing.

Herein, we proposed dry heat treatment (DHT) as a pre-treatment method for modifying printed materials, with a particular focus on its application in the control of starch-lipid interactions during hot-extrusion 3D printing (HE-3DP). The results showed that pre-DHT could promote the complexation of wheat starch (WS) and oleic acid (OA)/corn oil (CO) during HE-3DP and thus increase the resistant starch (RS) content. From the structural perspectives, pre-DHT could break starch molecular chains into lower relative molecular weight which enhanced the starch-lipids hydrophobic interactions to form the V-type crystalline structure during HE-3DP. Notably, pre-DHT could also induce the formation of complexed structure which was maintained during HE-3DP. Compared with CO, OA with linear hydrophobic chains was easier to enter the spiral cavity of starch to form more ordered structures, resulting in higher RS content of 27.48 %. Overall, the results could provide basic data for designing nutritional starchy food systems by HE-3DP.

Chlorogenic Acid/Linoleic Acid-Fortified Wheat-Resistant Starch Ameliorates High-Fat Diet-Induced Gut Barrier Damage by Modulating Gut Metabolism.

This study aimed to investigate alterations in gut microbiota and metabolites mediated by wheat-resistant starch and its repair of gut barrier dysfunction induced by a high-fat diet (HFD). Structural data revealed that chlorogenic acid (CA)/linoleic acid (LA) functioned through noncovalent interactions to form a more ordered structure and fortify antidigestibility in wheat starch (WS)-CA/LA complexes; the resistant starch (RS) contents of WS-CA, WS-LA, and WS-CA-LA complexes were 23.40 ± 1.56%, 21.25 ± 1.87%, and 35.47 ± 2.16%, respectively. Dietary intervention with WS-CA/LA complexes effectively suppressed detrimental alterations in colon tissue morphology induced by HFD and repaired the gut barrier in ZO-1 and MUC-2 levels. WS-CA/LA complexes could augment gut barrier-promoting microbes including Parabacteroides, Bacteroides, and Muribaculum, accompanied by an increase in short-chain fatty acids (SCFAs) and elevated expression of SCFA receptors. Moreover, WS-CA/LA complexes modulated secondary bile acid metabolism by decreasing taurochenodeoxycholic, cholic, and deoxycholic acids, leading to the activation of bile acid receptors. Collectively, this study offered guiding significance in the manufacture of functional diets for a weak gut barrier.

Transport and risk of airborne pathogenic microorganisms in the process of decentralized sewage discharge and treatment.

Sewage treatment processes are a critical anthropogenic source of bioaerosols and may present significant health risks to plant workers. Compared with the specialization and scale of urban sewage treatment, many decentralized treatment models are flexible and extensive. These treatment facilities are usually close to residential areas owing to the pipe network layout and other restrictions. Bioaerosols generated by these facilities may present a serious and widespread occupational and non-occupational exposure risk to nearby residents, particularly the elderly and children. An understanding of the characteristics and exposure risks of bioaerosols produced during decentralized sewage treatment is lacking. We compared bioaerosol emission characteristics and potential exposure risks under four decentralized sewage discharge methods and treatment models: small container collection (SCC), open-channel discharge (OCD), single household/combined treatment (SHCT), and centralized treatment (CT) in northwest China. The OCD mode had the highest bioaerosol production, whereas the CT mode had the lowest. The OCD model contained the most pathogenic bacterial species, up to 43 species, including Sphingomonas, Pseudomonas, Cladosporium, and Alternaria. Risk assessments indicated bioaerosol exposure was lower in the models with sewage treatment (SHCT and CT) than in those without (SCC and OCD). Different populations exhibited large variations in potential risks owing to differences in time spent indoors and outdoors. The highest risk was observed in males exposed to the SCC model. This study provides a theoretical basis and theories for the future joint prevention and control of the bioaerosol exposure risk from decentralized sewage treatment.

Susceptibility to myocardial ischemia reperfusion injury at early stage of type 1 diabetes in rats.

BACKGROUND: Large body of evidences accumulated in clinical and epidemiological studies indicate that hearts of diabetic subjects are more sensitive to ischemia reperfusion injury (IRI), which results in a higher rate of mortality at post-operation than that of non-diabetes. However, experimental results are equivocal and point to either increased or decreased susceptibility of the diabetic hearts to IRI, especially at the early stage of the disease. The present study was designed to test the hypothesis that the duration/severity of the indexed ischemia is a major determinant of the vulnerability to myocardial IRI at early stage of diabetes. METHODS: Four weeks streptozotocin (STZ)-induced diabetic (D) and non-diabetic (C) Sprague-Dawley rats were randomly assigned to receive 30 or 45 min of left anterior descending artery ligation followed by 2 or 3 hours of reperfusion, respectively. Cardiac function was recorded by using Pressure-Volume (PV) conduction system. Myocardial infarct size was determined with triphenyltetrazolium chloride staining. Plasma Creatine kinase-MB (CK-MB), Lactate dehydrogenase (LDH) release, myocardial nitric oxide(NO) content and nitrotyrosine formation, 15-F(2t)-Isoprostane and plasma superoxide dismutase (SOD) were measured with colorimetric assays. Cardiomyocyte apoptosis was assessed by TUNEL staining. Myocardial TNFα, Caspase-3, STAT3, Akt, and GSK-3ß were determined by Western blotting. RESULTS: Prolongation of ischemia but not reperfusion from 30 min to 45 min significantly increased infarct size in D compared to C rats (P < 0.05), accompanied with significantly increased plasma CK-MB (P < 0.05). Prolongation of the duration of either ischemia or reperfusion significantly increased plasma LDH release and myocardial 15-F(2t)-Isoprostane and reduced plasma SOD activity, with concomitant reduction of myocardial NO and increase of nitrotyrosine formation in D relative to C (P < 0.05). Prolongation of ischemia and reperfusion significantly reduced left ventricular ejection fraction and increased the peak rate of pressure, accompanied with increased end systolic pressure in D relative to C rats (P < 0.05) but reduced phosphorylations of myocardial STAT3 at site Ser727 and Akt at site Ser473 as well as GSK-3ß at Ser 9 (P < 0.05). CONCLUSIONS: Diabetic hearts, even at early stage of the disease are more sensitive to IRI, and this increased severity of post-ischemic myocardial injury depends more on the duration of ischemia than that of reperfusion.

Introduction of chlorogenic acid into thermal processed starch- oleic acid system controls the ordered structure and inhibits oleic acid oxidation through molecular interactions.

In this study, the effects of starch- oleic acid (OA)- chlorogenic acid (CA) molecular interaction on OA oxidation during thermal processing were investigated based on structural analysis, oxidation characteristics and quantum calculations. The results showed that in the ternary system, on the one hand, OA could enter the spiral cavity of starch through hydrophobic forces and form V-type crystalline structure, which delayed its oxidation. On the other hand, CA could further inhibit the oxidation of OA through free radical reaction and did not affect the molecular interactions between OA and starch due to the steric hindrance and hydrophily. Notably, starch-OA-CA interactions could effectively decrease total oxidation value (19.07), prolong the induction time of oxidation (114.6 min) and reduce the abundance of oxidation products through hydrogen atom transfer reactions with active phenolic hydroxyl to protect the α-methylene groups at C=C. Overall, these results provided insights into functional property regulation by the interaction of starch-based multi-component systems.

Reciprocal causation mixture model for robust Mendelian randomization analysis using genome-scale summary data.

Mendelian randomization using GWAS summary statistics has become a popular method to infer causal relationships across complex diseases. However, the widespread pleiotropy observed in GWAS has made the selection of valid instrumental variables problematic, leading to possible violations of Mendelian randomization assumptions and thus potentially invalid inferences concerning causation. Furthermore, current MR methods can examine causation in only one direction, so that two separate analyses are required for bi-directional analysis. In this study, we propose a ststistical framework, MRCI (Mixture model Reciprocal Causation Inference), to estimate reciprocal causation between two phenotypes simultaneously using the genome-scale summary statistics of the two phenotypes and reference linkage disequilibrium information. Simulation studies, including strong correlated pleiotropy, showed that MRCI obtained nearly unbiased estimates of causation in both directions, and correct Type I error rates under the null hypothesis. In applications to real GWAS data, MRCI detected significant bi-directional and uni-directional causal influences between common diseases and putative risk factors.

Control of starch-lipid interactions on starch digestibility during hot-extrusion 3D printing for starchy foods.

The nutritional design of personalized starchy foods has become a research hotspot in the field of food science. Driven by the immense functional and nutritional implications of starch-lipid binary interactions, this study is aimed at designing starch digestibility by controlling the interaction between starch and glycerol monostearate (GMS)/stearic acid (SA) using a hot-extrusion 3D printing (HE-3DP) environment. The results indicated that the thermal shear force in the HE-3DP environment promoted hydrophobic interactions between starch and lipids, forming a V-type starch-lipid complex with a compact and ordered structure, thus enhancing enzymatic resistance. Compared with GMS, SA with linear hydrophobic chains was inclined to compound with starch to form a more ordered structure. Interestingly, the slowly digestible starch (SDS) and resistant starch (RS) content reached 25.06% when the added SA content was 10%. Besides, correlations between the structural parameters and digestibility were established, which provided crucial information for designing nutritional starchy food systems using HE-3DP.

Visualizing Graph Neural Networks With CorGIE: Corresponding a Graph to Its Embedding.

Graph neural networks (GNNs) are a class of powerful machine learning tools that model node relations for making predictions of nodes or links. GNN developers rely on quantitative metrics of the predictions to evaluate a GNN, but similar to many other neural networks, it is difficult for them to understand if the GNN truly learns characteristics of a graph as expected. We propose an approach to corresponding an input graph to its node embedding (aka latent space), a common component of GNNs that is later used for prediction. We abstract the data and tasks, and develop an interactive multi-view interface called CorGIE to instantiate the abstraction. As the key function in CorGIE, we propose the K-hop graph layout to show topological neighbors in hops and their clustering structure. To evaluate the functionality and usability of CorGIE, we present how to use CorGIE in two usage scenarios, and conduct a case study with five GNN experts. Availability: Open-source code at https://github.com/zipengliu/corgie-ui/, supplemental materials & video at https://osf.io/tr3sb/.

Polygenic power calculator: Statistical power and polygenic prediction accuracy of genome-wide association studies of complex traits.

Power calculation is a necessary step when planning genome-wide association studies (GWAS) to ensure meaningful findings. Statistical power of GWAS depends on the genetic architecture of phenotype, sample size, and study design. While several computer programs have been developed to perform power calculation for single SNP association testing, it might be more appropriate for GWAS power calculation to address the probability of detecting any number of associated SNPs. In this paper, we derive the statistical power distribution across causal SNPs under the assumption of a point-normal effect size distribution. We demonstrate how key outcome indices of GWAS are related to the genetic architecture (heritability and polygenicity) of the phenotype through the power distribution. We also provide a fast, flexible and interactive power calculation tool which generates predictions for key GWAS outcomes including the number of independent significant SNPs, the phenotypic variance explained by these SNPs, and the predictive accuracy of resulting polygenic scores. These results could also be used to explore the future behaviour of GWAS as sample sizes increase further. Moreover, we present results from simulation studies to validate our derivation and evaluate the agreement between our predictions and reported GWAS results.

Effect of starch-catechin interaction on regulation of starch digestibility during hot-extrusion 3D printing: Structural analysis and simulation study.

Recent developments of hot-extrusion 3D printing (HE-3DP) have made it possible to manipulate starch digestibility. This work investigated the regulating mechanism of starch-catechin (EC) interactions on rice starch digestibility during HE-3DP by using modern analytical techniques and computational models. The results showed that the HE-3DP processing with starch-EC interactions could significantly decrease the starch digestibility (p < 0.05) due to the formation of ordered structures including short-range ordered structure, nano-aggregates and V-type crystalline structure. Meanwhile, molecular dynamics simulations were performed to reveal the mechanism of EC as an enzyme inhibitor to enhance the resistant starch contents of rice starch to 46.1%. Results showed that EC could loosely attach to starch chains, thereby facilitating binding to Trp59 of pancreatic α-amylase and preventing starch from binding to its active pocket. These findings provide useful structural information for EC to reduce starch digestibility in the HE-3DP environment.