CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

BACKGROUND

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

RESULTS

Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.

CONCLUSIONS

Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

Multi-trait analysis characterizes the genetics of thyroid function and identifies causal associations with clinical implications

To date only a fraction of the genetic footprint of thyroid function has been clarified. We report a genome-wide association study meta-analysis of thyroid function in up to 271,040 individuals of European ancestry, including reference range thyrotropin (TSH), free thyroxine (FT4), free and total triiodothyronine (T3), proxies for metabolism (T3/FT4 ratio) as well as dichotomized high and low TSH levels. We revealed 259 independent significant associations for TSH (61% novel), 85 for FT4 (67% novel), and 62 novel signals for the T3 related traits. The loci explained 14.1%, 6.0%, 9.5% and 1.1% of the total variation in TSH, FT4, total T3 and free T3 concentrations, respectively. Genetic correlations indicate that TSH associated loci reflect the thyroid function determined by free T3, whereas the FT4 associations represent the thyroid hormone metabolism. Polygenic risk score and Mendelian randomization analyses showed the effects of genetically determined variation in thyroid function on various clinical outcomes, including cardiovascular risk factors and diseases, autoimmune diseases, and cancer. In conclusion, our results improve the understanding of thyroid hormone physiology and highlight the pleiotropic effects of thyroid function on various diseases.

Genotype imputation methods for whole and complex genomic regions utilizing deep learning technology

The imputation of unmeasured genotypes is essential in human genetic research, particularly in enhancing the power of genome-wide association studies and conducting subsequent fine-mapping. Recently, several deep learning-based genotype imputation methods for genome-wide variants with the capability of learning complex linkage disequilibrium patterns have been developed. Additionally, deep learning-based imputation has been applied to a distinct genomic region known as the major histocompatibility complex, referred to as HLA imputation. Despite their various advantages, the current deep learning-based genotype imputation methods do have certain limitations and have not yet become standard. These limitations include the modest accuracy improvement over statistical and conventional machine learning-based methods. However, their benefits include other aspects, such as their "reference-free" nature, which ensures complete privacy protection, and their higher computational efficiency. Furthermore, the continuing evolution of deep learning technologies is expected to contribute to further improvements in prediction accuracy and usability in the future.

Multifaceted analysis of cross-tissue transcriptomes reveals phenotype-endotype associations in atopic dermatitis

Atopic dermatitis (AD) is a skin disease that is heterogeneous both in terms of clinical manifestations and molecular profiles. It is increasingly recognized that AD is a systemic rather than a local disease and should be assessed in the context of whole-body pathophysiology. Here we show, via integrated RNA-sequencing of skin tissue and peripheral blood mononuclear cell (PBMC) samples along with clinical data from 115 AD patients and 14 matched healthy controls, that specific clinical presentations associate with matching differential molecular signatures. We establish a regression model based on transcriptome modules identified in weighted gene co-expression network analysis to extract molecular features associated with detailed clinical phenotypes of AD. The two main, qualitatively differential skin manifestations of AD, erythema and papulation are distinguished by differential immunological signatures. We further apply the regression model to a longitudinal dataset of 30 AD patients for personalized monitoring, highlighting patient heterogeneity in disease trajectories. The longitudinal features of blood tests and PBMC transcriptome modules identify three patient clusters which are aligned with clinical severity and reflect treatment history. Our approach thus serves as a framework for effective clinical investigation to gain a holistic view on the pathophysiology of complex human diseases.

Multiancestry analysis of the HLA locus in Alzheimer's and Parkinson's diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson's disease (PD) and Alzheimer's disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.

Genome-wide association study identifies risk loci within the major histocompatibility complex region for Hunner-type interstitial cystitis

Hunner-type interstitial cystitis (HIC) is a rare, chronic inflammatory disease of the urinary bladder with unknown etiology and genetic background. Here, we conduct a genome-wide association study of 144 patients with HIC and 41,516 controls of Japanese ancestry. The genetic variant, rs1794275, in the major histocompatibility complex (MHC) region (chromosome 6p21.3) is associated with HIC risk (odds ratio [OR] = 2.32; p = 3.4 × 10^-9). The association is confirmed in a replication set of 26 cases and 1,026 controls (p = 0.014). Fine mapping demonstrates the contribution to the disease risk of a completely linked haplotype of three human leukocyte antigen HLA-DQβ1 amino acid positions, 71, 74, and 75 (OR = 1.94; p = 5 × 10^-8) and of HLA-DPβ1 amino acid position 178, which tags HLA-DPB1∗04:02 (OR = 2.35; p = 7.5 × 10^-8). The three HLA-DQβ1 amino acid positions are located together at the peptide binding groove, suggesting their functional importance in antigen presentation. Our study reveals genetic contributions to HIC risk that may be associated with class II MHC molecule antigen presentation.

A genome-wide association study for allergen component sensitizations identifies allergen component-specific and allergen protein group-specific associations

Background

Allergic diseases are some of the most common diseases worldwide. Genome-wide association studies (GWASs) have been conducted to elucidate the genetic factors of allergic diseases. However, no GWASs for allergen component sensitization have been performed.

Objective

We sought to detect genetic variants associated with differences in immune responsiveness against allergen components.

Methods

The participants of the present study were recruited from the Tokyo Children's Health, Illness, and Development study, and allergen component-specific IgE level at age 9 years was measured by means of allergen microarray immunoassays. We performed GWASs for allergen component sensitization against each allergen (single allergen component sensitization, number of allergen components analyzed, n = 31), as well as against allergen protein families (allergen protein group sensitization, number of protein groups analyzed, n = 16).

Results

We performed GWAS on 564 participants of the Tokyo Children's Health, Illness, and Development study and found associations between Amb a 1 sensitization and the immunoglobulin heavy-chain variable gene on chromosome 14 and between Phl p 1 sensitization and the HLA class II region on chromosome 6 (P < 5.0 × 10-8). A GWAS-significant association was also observed between the HLA class II region and profilin sensitization (P < 5.0 × 10-8).

Conclusions

Our data provide the first demonstration of genetic risk for allergen component sensitization and show that this genetic risk is related to immune response genes including immunoglobulin heavy-chain variable gene and HLA.

Genetic Risk of Primary Aldosteronism and Its Contribution to Hypertension: A Cross-Ancestry Meta-Analysis of Genome-Wide Association Study

BACKGROUND

Hypertension imposes substantial health and economic burden worldwide. Primary aldosteronism (PA) is one of the most common causes of secondary hypertension, causing cardiovascular events at higher risk compared with essential hypertension. However, the germline genetic contribution to the susceptibility of PA has not been well elucidated.

METHOD

We conducted a genome-wide association analysis of PA in the Japanese population and a cross-ancestry meta-analysis combined with UK Biobank and FinnGen cohorts (816 PA cases and 425 239 controls) to identify genetic variants that contribute to PA susceptibility. We also performed a comparative analysis for the risk of 42 previously established blood pressure-associated variants between PA and hypertension with the adjustment of blood pressure.

RESULTS

In the Japanese genome-wide association study, we identified 10 loci that presented suggestive evidence for the association with the PA risk (P<1.0×10^-6). In the meta-analysis, we identified 5 genome-wide significant loci (1p13, 7p15, 11p15, 12q24, and 13q12; P<5.0×10^-8), including 3 of the suggested loci in the Japanese genome-wide association study. The strongest association was observed at rs3790604 (1p13), an intronic variant of WNT2B (odds ratio, 1.50 [95% CI, 1.33-1.69]; P=5.2×10^-11). We further identified 1 nearly genome-wide significant locus (8q24, CYP11B2), which presented a significant association in the gene-based test (P=7.2×10^-7). Of interest, all of these loci were known to be associated with blood pressure in previous studies, presumably because of the prevalence of PA among individuals with hypertension. This assumption was supported by the observation that they had a significantly higher risk effect on PA than on hypertension. We also revealed that 66.7% of the previously established blood pressure-associated variants had a higher risk effect for PA than for hypertension.

CONCLUSIONS

This study demonstrates the genome-wide evidence for a genetic predisposition to PA susceptibility in the cross-ancestry cohorts and its significant contribution to the genetic background of hypertension. The strongest association with the WNT2B variants reinforces the implication of the Wnt/β-catenin pathway in the PA pathogenesis.

Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection.

Genetic mechanisms influencing COVID-19 susceptibility are not well understood. Here, the authors analyzed whole blood RNA-seq data of 465 Japanese individuals with COVID-19, highlighting thousands of fine-mapped variants affecting expression and splicing of genes, as well as the presence of COVID-19 severity-interaction eQTLs.

Comparative whole transcriptome analysis of Parkinson's disease focusing on the efficacy of zonisamide

OBJECTIVE

Interindividual variations in responsiveness to zonisamide in patients with Parkinson's disease (PD) have been observed in clinical settings. To decipher the molecular mechanisms determining the efficacy of zonisamide, we conducted whole transcriptome sequencing analysis of patients with PD.

METHODS

We selected 23 super-responders (SRs) and 25 non-responders (NRs) to zonisamide from patients with PD who had participated in a previous clinical trial for the approval of zonisamide for the treatment of 'wearing-off'. Whole transcriptome analysis of peripheral blood was conducted on samples taken before and 12 weeks after zonisamide treatment. We performed differential gene expression analysis to compare between the SRs and NRs at each time point.

RESULTS

Differentially expressed genes in the pre-treatment samples were significantly enriched for glutamatergic synapses and insulin-like growth factor binding (P_adj=7.8 × 10^-3 and 0.029, respectively). The gene sets associated with these functions changed more dynamically by treatment in SRs than NRs (p=7.2 × 10^-3 and 8.2 × 10^-3, respectively).

CONCLUSIONS

Our results suggest that the efficacy of zonisamide in PD patients is associated with glutamate-related synaptic modulation and p53-mediated dopaminergic neural loss. Their transcriptomic differences could be captured before treatment, which would lead to the realisation of future personalised treatment.

Decoding the diversity of killer immunoglobulin-like receptors by deep sequencing and a high-resolution imputation method

The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We construct a KIR imputation reference panel (n_reference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (n_total = 169,907), and perform phenome-wide association studies of 85 traits. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10^-4). Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets.

HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases

Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.

Trans-Ethnic Fine-Mapping of the Major Histocompatibility Complex Region Linked to Parkinson's Disease

BACKGROUND

Despite evidence for the role of human leukocyte antigen (HLA) in the genetic predisposition to Parkinson's disease (PD), the complex haplotype structure and highly polymorphic feature of the major histocompatibility complex (MHC) region has hampered a unified insight on the genetic risk of PD. In addition, a majority of the reports focused on Europeans, lacking evidence on other populations.

OBJECTIVES

The aim of this study is to elucidate the genetic features of the MHC region associated with PD risk in trans-ethnic cohorts.

METHODS

We conducted trans-ethnic fine-mapping of the MHC region for European populations (14,650 cases and 1,288,625 controls) and East Asian populations (7712 cases and 27,372 controls). We adopted a hybrid fine-mapping approach including both HLA genotype imputation of genome-wide association study (GWAS) data and direct imputation of HLA variant risk from the GWAS summary statistics.

RESULTS

Through trans-ethnic MHC fine-mapping, we identified the strongest associations at amino acid position 13 of HLA-DRβ1 (P = 6.0 × 10-15 ), which explains the majority of the risk in HLA-DRB1. In silico prediction revealed that HLA-DRB1 alleles with histidine at amino acid position 13 (His13) had significantly weaker binding affinity to an α-synuclein epitope than other alleles (P = 9.6 × 10-4 ). Stepwise conditional analysis suggested additional independent associations at Ala69 in HLA-B (P = 1.0 × 10-7 ). A subanalysis in Europeans suggested additional independent associations at non-HLA genes in the class III MHC region (EHMT2; P = 2.5 × 10-7 ).

CONCLUSIONS

Our study highlights the shared and distinct genetic features of the MHC region in patients with PD across ethnicities. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes

Conventional human leukocyte antigen (HLA) imputation methods drop their performance for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic major histocompatibility complex (MHC) fine-mapping due to inter-ethnic heterogeneity in allele frequency spectra. We develop DEEP*HLA, a deep learning method for imputing HLA genotypes. Through validation using the Japanese and European HLA reference panels (n = 1,118 and 5,122), DEEP*HLA achieves the highest accuracies with significant superiority for low-frequency and rare alleles. DEEP*HLA is less dependent on distance-dependent linkage disequilibrium decay of the target alleles and might capture the complicated region-wide information. We apply DEEP*HLA to type 1 diabetes GWAS data from BioBank Japan (n = 62,387) and UK Biobank (n = 354,459), and successfully disentangle independently associated class I and II HLA variants with shared risk among diverse populations (the top signal at amino acid position 71 of HLA-DRβ1; P = 7.5 × 10^-120). Our study illustrates the value of deep learning in genotype imputation and trans-ethnic MHC fine-mapping.

Further Reduction in Help-Seeking Behaviors Amidst Additional Barriers to Mental Health Treatment in Asian Populations: A Contemporary Review

Under diagnosis and treatment of mental health illnesses lead to chronic presentations and consequences. Multiple factors contribute to gaps in treatment, including the role culture plays in the development or suppression of help-seeking behaviors (HSBs). In the Asian community, conversation and recognition of mental health and its disorders are considered shameful. This review presents an analysis of literature to identify barriers to mental health treatment pronounced in Asian populations and discusses how culture influences these barriers and treatment-seeking behaviors, particularly in the context of the Asian-origin Coronavirus disease 2019 (COVID-19) global pandemic. It is the purpose of this review to discuss Asian American underutilization of mental health services and understand the factors the contribute to psychiatric care resistance in Asian communities.

Modulation of methotrexate-induced intestinal mucosal injury by dietary factors

Methotrexate (MTX)-induced intestinal mucosal injury in animals has been studied to understand how MTX can cause gastrointestinal disorders, but the pathogenesis of gastrointestinal disorders is still uncertain. We have attempted to reveal how dietary factors influence intestinal toxicity due to MTX. Mice were fed normal chow (NC) or a high-fat high-sucrose diet (HFHSD) before oral administration of MTX. While MTX significantly decreased the survival rates of mice fed HFHSD, the intestinal epithelial injury was detected. MTX excretion in the feces of mice fed HFHSD was reduced. Change of diets between NC and HFHSD influences the survival. The survival rates of the mice fed a high-sucrose diet or control diet were higher than those fed HFHSD. Higher survival rates were observed in mice fed a high-fat high-sucrose diet modified (HFHSD-M) in which casein was replaced by soybean-derived proteins. The survival rates of mice treated with vancomycin were lower than those administered neomycin. Microbiome and metabolome analyses on feces suggest a similarity of the intestinal environments of mice fed NC and HFHSD-M. HFHSD may modify MTX-induced toxicity in intestinal epithelia on account of an altered MTX distribution as a result of change in the intestinal environment.

P4678The hemodynamic improvement with balloon pulmonary angioplasty in chronic thromboembolic pulmonary hypertension depends on the lesion location

Background

Pulmonary endarterectomy (PEA) is a treatment of choice for patients with chronic thromboembolic pulmonary hypertension (CTEPH). Patients with proximal pulmonary artery disease are considered to be good candidates for PEA because of their generally excellent outcomes. However, not all patients can be operated because of patients' advanced age, comorbidities and poor general condition. Balloon pulmonary angioplasty (BPA) has become an alternative treatment for CTEPH patients especially whose lesions locate in the distal site. The effectiveness of BPA in patients who have lesions in the proximal pulmonary arteries but cannot be a candidate for PEA remains unclear.

Purpose

The aim of this study was to investigate the outcome of BPA in CTEPH patients whose lesions appears operable but ineligible for PEA.

Methods

A total of 370 patients who underwent BPA in our institute from November 2004 to January 2018 were enrolled. All the patients were divided into operable group and inoperable group according to the difference of lesion location based on the findings of perfusion scintigraphy, computed tomography and pulmonary angiography. Hemodynamic effects of BPA in both groups were investigated. We also conducted survival analyses using the Kaplan-Meier method with the log-rank test.

Results

Among 370 patients, 90 patients deemed operable. The main reasons why not operated in the PEA operable group were patient's refusal (44%), advanced age (14%), and comorbidities (27%). There were no baseline characteristic differences between two groups except for the history of acute pulmonary embolism. Mean pulmonary artery pressure (mPAP) and pulmonary vascular resistance (PVR) equally improved after BPA in both groups (operable: 38.2±10.8 mmHg to 21.5±4.7mmHg, inoperable: 42.4±11.3 mmHg to 21.8±4.8 mmHg, p<0.001, operable: 8.0±4.2 wood unit to 3.5±1.5 wood unit, inoperable: 9.1±4.6 wood unit to 3.4±1.3 wood unit, p<0.001). Furthermore, five-year cumulative survival rates were not different between two groups (inoperable vs. operable: 93% vs. 88%, p=0.23, median follow-up period was 23.0 months (range: 5–136 months)). Meanwhile, the absolute change of mPAP and PVR in inoperable group were greater than those in operable group (inoperable: 20.7±11.2 mmHg, operable: 16.6±11.0 mmHg, p=0.010, inoperable: 5.6±4.4 wood unit, operable: 4.5±3.9 wood unit, p=0.015).

Conclusions

Although the outcome of BPA for CTEPH patients with operable lesions appears acceptable, absolute change in hemodynamics was lower than that of the patients with inoperable lesions. CTEPH with proximal lesions should be treated with PEA rather than BPA.

P4675The utility of additional balloon pulmonary angioplasty for residual hypoxemia in normohemodynamic chronic thromboembolic pulmonary hypertension patients after invasive treatments

Background

Balloon pulmonary angioplasty (BPA) improves hemodynamics, symptoms and exercise capacity in patients with chronic thromboembolic pulmonary hypertension (CTEPH) who are ineligible for pulmonary endarterectomy (PEA). However, certain patients still have hypoxemia after BPA or PEA despite normalization of hemodynamics. In CTEPH, hypoxemia is related increased dead space ventilation caused by vascular obstruction.

Purpose

This study was aimed to clarify whether additional BPA can improve hypoxemia of CTEPH patients after normalization of hemodynamics.

Methods

A total of 335 patients who underwent initial series of BPA in our institute were followed up. Sixty-four patients with mean pulmonary artery pressure (mPAP) <30mmHg and percutaneous oxygen saturation (SpO2) <95% without oxygen inhalation at more than 6 months after the initial series of BPA and of patients who could reevaluate hemodynamics and oxygenation after additional BPA were enrolled. These patients were divided into two groups with or without additional BPA procedures. Change of hemodynamics and SpO2 were retrospectively investigated.

Results

Thirty-three of 64 patients underwent additional BPA procedures. Patients' age was older in BPA group than those in non-BPA group (71.3±10.4 vs. 66.5±9.4 years old, p=0.02). mPAP and pulmonary vascular resistance (PVR) was significantly higher in BPA group (mPAP: 23.9±3.2 vs. 20.7±3.8 mmHg, p=0.001, PVR: 4.2±1.2 vs. 3.5±1.4 wood unit, p=0.03, respectively). Among the 1.8±1.4 BPA procedures per person, total 6.6±3.8 segmental pulmonary arteries per person were treated. While no obvious improvements were observed in non-BPA group, PVR and SpO2 in BPA group were significantly improved (4.2±1.2 to 3.7±1.3 wood unit, p=0.002, 90.7±3.1% to 94.1±3.6%, p<0.001, respectively). In the multivariate logistic regression analysis, additional BPA procedures were associated with further improvement of SpO2 (hazard ratio, 3.7; 95% confidence interval, 1.2–11.5; P=0.02).

Conclusions

Additional BPA procedure was associated with improvement of hypoxemia in CTEPH patients after normalization of hemodynamics. Treating as many lesions as possible in BPA might relieve the patients' residual dyspnea.

Predicting the impact of single nucleotide variants on splicing via sequence-based deep neural networks and genomic features

Single nucleotide mutations in exonic regions can significantly affect gene function through a disruption of splicing, and various computational methods have been developed to predict the splicing-related effects of a single nucleotide mutation. We implemented a new method using ensemble learning that combines two types of predictive models: (a) base sequence-based deep neural networks (DNNs) and (b) machine learning models based on genomic attributes. This method was applied to the Massively Parallel Splicing Assay challenge of the Fifth Critical Assessment of Genome Interpretation, in which challenge participants predicted various experimentally-defined exonic splicing mutations, and achieved a promising result. We successfully revealed that combining different predictive models based upon the stacked generalization method led to significant improvement in prediction performance. In addition, whereas most of the genomic features adopted in constructing machine learning models were previously reported, feature values generated with DSSP, a DNN-based splice site prediction tool, were novel and helpful for the prediction. Learning the sequence patterns associated with normal splicing and the change in splicing site probabilities caused by a mutation was presumed to be helpful in predicting splicing disruption.

Assessing predictions of the impact of variants on splicing in CAGI5

Precision medicine and sequence-based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. In the past, few CAGI challenges have addressed the impact of sequence variants on splicing. In CAGI5, two challenges (Vex-seq and MaPSY) involved prediction of the effect of variants, primarily single-nucleotide changes, on splicing. Although there are significant differences between these two challenges, both involved prediction of results from high-throughput exon inclusion assays. Here, we discuss the methods used to predict the impact of these variants on splicing, their performance, strengths, and weaknesses, and prospects for predicting the impact of sequence variation on splicing and disease phenotypes.

Postpartum psychosis in a non-native language-speaking patient: A perspective on language barriers and cultural competency

Postpartum psychosis is a condition characterised by rapid onset of psychotic symptoms several weeks after childbirth. Outside of its timing and descriptions of psychotic features, minimal research exists due to its relative rarity (1 to 2 per 1000 births in the USA), with greater emphasis on postpartum sadness and depression. With the existing literature, cultural differences and language barriers previously have not been taken into consideration as there are no documented cases of postpartum psychosis in a non–English-speaking patient. Correctly differentiating postpartum psychosis from other postpartum psychiatric disorders requires adeptly evaluating for the presence of psychotic symptoms with in-depth history taking. Here, we present a case of postpartum psychosis in a Japanese-speaking only patient, with an associated clinical course and culturally appropriate approach to treatment. A review of postpartum psychosis and language/cultural considerations are also discussed, with attention on the Japanese concept of ‘Satogaeri bunben’.

Factors associated with a positive willingness to practise oral health care in the future amongst oral healthcare and nursing students

OBJECTIVES

The purpose of this study was to identify the weak points in the knowledge and attitudes of first-year oral health care and nursing students towards oral health care and to identify the factors associated with their positive willingness to practise oral health care after becoming a health professional in order to develop oral healthcare curricula.

MATERIALS AND METHODS

The subjects were 88 first-year dental students (DSs), 64 dental hygiene students (DHSs) and 119 nursing students (NSs) enrolled in schools in Japan, as of April 2017. A questionnaire was distributed to subjects in each school to assess their knowledge and attitudes towards oral health care.

RESULTS

Less than half knew that oral health care was also provided in cancer hospitals, hospices, acute care hospitals, maternity wards and psychiatric wards. Only 46.2% knew that oral health care was effective in the prevention of aspiration pneumonia. The level of knowledge and attitudes in NSs regarding oral health care were likely to be lowest amongst the student groups. Only NSs' high interest towards oral health care was associated with their positive willingness to practise oral health care in the future although oral health students' high perceptions and interest regarding oral health care were associated with the willingness.

CONCLUSION

This study showed oral healthcare and nursing students' weak points regarding their attitudes and knowledge of oral health care at early stages. Oral health academic staff and professionals should develop effective oral healthcare curricula for oral healthcare students and help nursing staff develop a collaborative nursing oral healthcare curriculum to motivate nursing students.

Human Splice-Site Prediction with Deep Neural Networks

Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site. The length of input is 140 nucleotides, with the consensus sequence (i.e., "GT" and "AG" for the donor and acceptor sites, respectively) in the middle. Each input sequence model is applied to the pretrained DNN model that determines the probability that an input is a splice site. The model consists of convolutional layers and bidirectional long short-term memory network layers. The pretraining and validation were conducted using the data set tested in previously reported methods. The performance evaluation results showed that the proposed method can outperform the previous methods. In addition, the pattern learned by the DNNs was visualized as position frequency matrices (PFMs). Some of PFMs were very similar to the consensus sequence. The trained DNN model and the brief source code for the prediction system are uploaded. Further improvement will be achieved following the further development of DNNs.

Endogenous protein and enzyme fragments induce immunoglobulin E-independent activation of mast cells via a G protein-coupled receptor, MRGPRX2

Mast cells play a central role in inflammatory and allergic reactions by releasing inflammatory mediators through 2 main pathways, immunoglobulin E-dependent and E-independent activation. In the latter pathway, mast cells are activated by a diverse range of basic molecules (collectively known as basic secretagogues) through Mas-related G protein-coupled receptors (MRGPRs). In addition to the known basic secretagogues, here, we discovered several endogenous protein and enzyme fragments (such as chaperonin-10 fragment) that act as bioactive peptides and induce immunoglobulin E-independent mast cell activation via MRGPRX2 (previously known as MrgX2), leading to the degranulation of mast cells. We discuss the possibility that MRGPRX2 responds various as-yet-unidentified endogenous ligands that have specific characteristics, and propose that MRGPRX2 plays an important role in regulating inflammatory responses to endogenous harmful stimuli, such as protein breakdown products released from damaged or dying cells.

A Case of Antiphospholipid Antibody Syndrome Diagnosed after Thrombosis of an Arteriovenous Shunt

A 32-year-old male dialysis patient with lupus nephritis was admitted because of shunt obstruction. The arteriovenous fistula was reconstructed, but obstruction recurred twice within several hours after surgery. A high blood level of anticardiolipin β2-glycoprotein I antibody suggested that shunt obstruction was caused by a thrombotic tendency related to the antiphospholipid antibody syndrome. Accordingly, for the third shunt procedure, antiplatelet therapy (which had been commenced for systemic lupus erythematosus) was combined with dalteparin sodium from before surgery and warfarin was added postoperatively. This regimen prevented shunt obstruction. In conclusion, hemodialysis patients who suffer repeated shunt obstruction should be examined for antiphospholipid antibody syndrome.

Isolation of new ligands for orphan receptor MRGPRX1-hemorphins LVV-H7 and VV-H7

The human MAS-related G protein-coupled receptor X1 (MRGPRX1) is a member of the GPCR family. The receptor is primate specific and expressed in the sensory neurons of dorsal root ganglion and trigeminal ganglion, where it is considered to be involved in the pain perception. The MRGPRX1 has unusual binding mechanism, as it is activated by several different ligands as well as several different fragments of precursor proteins. Thus, we hypothesize that it is activated by several unknown compounds as well since the receptor is still classified as orphan. Here, we describe the isolation of two novel endogenous ligands for the MRGPRX1 from human platelet preparation. The isolated ligands are hemoglobin β-chain fragments, known members of the hemorphin family.