A fine-scale genetic map of the Japanese population.

Genetic maps are fundamental resources for linkage and association studies. A fine-scale genetic map can be constructed by inferring historical recombination events from the genome-wide structure of linkage disequilibrium-a non-random association of alleles among loci-by using population-scale sequencing data. We constructed a fine-scale genetic map and identified recombination hotspots from 10 092 551 bi-allelic high-quality autosomal markers segregating among 150 unrelated Japanese individuals whose genotypes were determined by high-coverage (30×) whole-genome sequencing, and the genotype quality was carefully controlled by using their parents' and offspring's genotypes. The pedigree information was also utilized for haplotype phasing. The resulting genome-wide recombination rate profiles were concordant with those of the worldwide population on a broad scale, and the resolution was much improved. We identified 9487 recombination hotspots and confirmed the enrichment of previously known motifs in the hotspots. Moreover, we demonstrated that the Japanese genetic map improved the haplotype phasing and genotype imputation accuracy for the Japanese population. The construction of a population-specific genetic map will help make genetics research more accurate.

Simultaneous determination of heparan sulfate, chondroitin/dermatan sulfates, and hyaluronan glycosaminoglycan disaccharides by high-performance liquid chromatography using a reverse-phase column with adamantyl groups.

Glycosaminoglycans (GAGs), which are one of the major components of proteoglycans, play a pivotal role in physiological processes such as signal transduction, cell adhesion, growth, and differentiation. Characterization of GAGs is challenging due to the tremendous structural diversity of heteropolysaccharides with numerous sulfate or carboxyl groups. In this present study, we examined the analysis of 2-aminobenzamide (2-AB) labeled GAG disaccharides by high-performance liquid chromatography (HPLC) using a reverse-phase (RP)-column with adamantyl groups. Under the analytical conditions, 17 types of 2-AB labeled GAG disaccharides derived from heparan sulfate, chondroitin/dermatan sulfates, and hyaluronan were sequentially separated in a single analysis. The analysis time was fast with high retention time reproducibility. Moreover, the RP-HPLC column with adamantyl groups allowed the quantification of GAGs in various biological samples, such as serum, cultured cells, and culture medium.

Impact of GERAADA score in patients with acute type A aortic dissection.

BACKGROUND: Despite continuous developments and advances in the perioperative management of patients suffering from acute aortic dissection type A (AADA), the associated postoperative morbidity and mortality remain high and strongly depend on the preoperative clinical status. The associated postoperative mortality is still hard to predict prior to the surgical procedure. The so-called German Registry of Acute Aortic Dissection Type A (GERAADA) score uses very basic and easily retrievable parameters and was specifically designed for predicting the 30-day mortality rate in patients undergoing surgery for AADA. This study evaluated impact of the GERAADA score in the authors' institutional results. METHODS: Among 101 acute type A aortic dissection patients treated at our hospital during August 2015-March 2021, the GERAADA was calculated individually and retrospectively. Predicted and actual mortalities were assessed, and independent predicted factors were searched. The primary endpoint was defined as comparison of GERAADA scores and early mortality, and the secondary endpoints were defined as comparison of GERAADA scores and other postoperative results, and comparison of preoperative factors and postoperative results regardless to GERAADA scores. RESULTS: While the overall 30-day mortality for the entire study cohort calculated by the GERAADA score was 14.3 (8.1-77.6)%, the actual mortality rate was 6%. However, the GERAADA score was significantly high in some postoperative complications and showed significant correlation with some peri- and post-operative factors. In addition, factors not belonging to GERAADA score such as time from onset to arrival at the hospital, time from onset to arrival at the operation room, spouse presence, and hemodialysis were significantly associated with 30-day mortality. CONCLUSIONS: Although the actual mortality was lower than predicted, GERAADA score may impact on the postoperative course. In addition, it would be desirable to add parameters such as the time from onset to arrival, family background, and hemodialysis for further accuracy.

Free-wall perforation of the left ventricle after acute myocardial infarction complicated with pericardial tamponade that mimicked ascending aortic dissection: A case report.

Life-threatening cardiac events may be misdiagnosed as acute aortic dissection because of notable symptom mimicry. We report the case of a 72-year-old male patient with presentations presumed to be of aortic origin. However, surgery revealed posterior free-wall perforation in the left ventricle caused by the occlusion of an obtuse marginal branch.

Heterozygous calcyclin-binding protein/Siah1-interacting protein (CACYBP/SIP) gene pathogenic variant linked to a dominant family with paucity of interlobular bile duct.

Paucity of interlobular bile ducts (PILBD) is a heterogeneous disorder classified into two categories, syndromic and non-syndromic bile duct paucity. Syndromic PILBD is characterized by the presence of clinical manifestations of Alagille syndrome. Non-syndromic PILBD is caused by multiple diseases, such as metabolic and genetic disorders, infectious diseases, and inflammatory and immune disorders. We evaluated a family with a dominantly inherited PILBD, who presented with cholestasis at 1-2 months of age but spontaneously improved by 1 year of age. Next-generation sequencing analysis revealed a heterozygous CACYBP/SIP p.E177Q pathogenic variant. Calcyclin-binding protein and Siah1 interacting protein (CACYBP/SIP) form a ubiquitin ligase complex and induce proteasomal degradation of non-phosphorylated ß-catenin. Immunohistochemical analysis revealed a slight decrease in CACYBP and ß-catenin levels in the liver of patients in early infancy, which almost normalized by 13 months of age. The CACYBP/SIP p.E177Q pathogenic variant may form a more active or stable ubiquitin ligase complex that enhances the degradation of ß-catenin and delays the maturation of intrahepatic bile ducts. Our findings indicate that accurate regulation of the ß-catenin concentration is essential for the development of intrahepatic bile ducts and CACYBP/SIP pathogenic variant is a novel cause of PILDB.

Effect of intensive care provided by nurse practitioners for postoperative patients: A retrospective observational before-and-after study.

Nurse practitioners are increasingly now members of intensive care teams in Japan, but no data exist about their effect on the outcomes for critically ill patients. This study aimed to compare the outcomes of postoperative patients on mechanical ventilators before and after the participation of nurse practitioners in intensive care teams. We retrospectively identified 387 patients who underwent postoperative mechanical ventilation at a University Hospital in Japan, using data from medical records from 1 April 2015 to 31 March 2017. We extracted data and compared patients' length of stay in the intensive care unit and the hospital, mechanical ventilation days, postoperative rehabilitation start date, rehabilitation prescription, intensive care unit and hospital mortality, and intensive care unit readmission. Multiple regression analysis was used to analyze the factors affecting length of stay in the intensive care unit. Patients who received care from nurse practitioners and physicians had significantly shorter stays in intensive care (4.8 ± 4.8 days versus 6.7 ± 10.3 days, p < 0.021). Mechanical ventilation days, total length of hospital stay, rehabilitation prescription, mortality in intensive care and hospital, and readmission to intensive care were all similar to those who received care only from physicians. The multiple regression analysis suggests that participation of nurse practitioners in intensive care reduced the length of stay in the unit by 2.6 days (p = 0.003). These findings could help to increase use of non-physician healthcare providers in intensive care. Our results demonstrated that it is both effective and safe for nurse practitioners to participate in intensive care teams that provide care for postoperative patients receiving mechanical ventilation.

dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project.

To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called "dbTMM" that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts.

Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs.

Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5-5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.

Impact of direct carotid artery perfusion in acute type A aortic dissection involving the common carotid artery.

OBJECTIVES: Acute type A aortic dissection complicated with brain ischemia is associated with significantly higher mortality risks. Even if rescued with central aortic repair, some patients develop permanent postoperative neurological deficiency postoperatively. We recently introduced direct common carotid artery perfusion for acute type A aortic dissection involving the common carotid artery. This study introduced this technique to prevent postoperative neurological deficiency by comparing brain protection strategies. METHODS: Among 91 acute type A aortic dissection patients treated at our hospital during August 2015-October 2020, the common carotid artery was involved in 19 (21%), which had > 90% stenosis in either of the carotid arteries on preoperative contrast-enhanced computed tomography. Twelve patients underwent conventional selective cerebral perfusion during August 2015-December 2018 and seven patients underwent direct carotid artery perfusion during January 2019-October 2020. We assessed patient characteristics, surgical courses, clinical outcomes, and neurological outcomes. RESULTS: The mean age was 69 (range 39-84) years; 17 patients were male (89%). Eight patients (42%) had neurological symptoms. Concomitant procedures, postoperative neurological symptoms, and late mortality were significantly associated with conventional selective cerebral perfusion. Five selective cerebral perfusion patients experienced worsened neurological symptoms and two died of broad cerebral ischemia. No direct carotid artery perfusion patient died during hospitalization or experienced worsened neurological outcomes. CONCLUSIONS: Direct carotid artery perfusion may be useful in aortic dissection with brain ischemia because it does not aggravate neurological symptoms and is not associated with intraoperative cerebral infarction. However, it may be ineffective when cerebral infarction has already developed.

Surgical treatment for brachiocephalic artery aneurysm with Takayasu arteritis using isolated cerebral perfusion: a case study.

BACKGROUND: Takayasu arteritis (TA) is a chronic inflammatory disease that induces stenosis, occlusion, or aneurysmal degeneration of the aorta and its major branches. Though rarely reported, proximal aneurysmal lesions from the aortic root to the arch are more common in Asian populations than in Western populations. In the surgical treatment of TA, anastomotic aneurysm can be problematic. Furthermore, atherosclerotic complications should be considered in surgical treatment for elderly TA patients. CASE PRESENTATION: Here, we report a case of brachiocephalic artery (BCA) aneurysm with TA for which surgical treatment was successful. Though it was solely a lesion of the brachiocephalic artery, after considering the patient's clinical background and the features of TA, we chose a partial arch replacement. Further, for avoidance of anastomotic aneurysm, both distal and proximal anastomosis were reinforced with Teflon felt strips. Preoperative computed tomography detected severe atherosclerotic changes in the arch vessels. The patient underwent partial arch replacement using isolated cerebral perfusion (ICP) for brain protection and recovered without any neurological deficits. CONCLUSIONS: In avoidance with anastomotic aneurysm, reinforcement of the anastomosis was introduced. ICP was effective for brain protection in case with severe atherosclerotic changes.

ALOX12 mutation in a family with dominantly inherited bleeding diathesis.

The arachidonic acid (AA) cascade plays a significant role in platelet aggregation. AA released from membrane phospholipids is metabolized by cyclooxygenase (COX) pathway to thromboxane A2 (TXA2) or by 12S-lipoxygenase (ALOX12) to 12-hydroperoxyeicosatetraenoic acid (12-HPETE). In contrast to a well-known role of the COX pathway in platelet aggregation, the role of ALOX12 is not well understood. Platelets of ALOX12-deficient mice exhibit increased sensitivity for ADP-induced aggregation. However, recent evidence strongly suggests a significant role of ALOX12 in platelet aggregation and calcium signaling. 12-HPETE potentiates thrombin- and thromboxane-induced platelet aggregation, and calcium signaling. Inhibition experiments of ALOX12 demonstrated decreased platelet aggregation and calcium signaling in stimulated platelets. We studied a family with a dominantly inherited bleeding diathesis using next-generation sequencing analysis. Platelet aggregation studies revealed that the proband's platelets had defective aggregation responses to ADP, TXA2 mimetic U46619, collagen, and AA, normal affinity of TXA2 receptor for U46619, and normal induction of GTPase activity upon stimulation with U46619. However, the production of inositol 1,4,5-triphosphate (IP3) was only increased up to 30% of the control upon U46619 stimulation, suggesting a defect in phospholipase C-ß2 (PLCB2) activation downstream from TXA2 receptors. Affected family members had no mutation of PLCB2, but had a heterozygous c.1946A > G (p.Tyr649Cys) mutation of ALOX12. ALOX12 activity in platelets from the affected members was decreased to 25-35% of the control. Our data strongly suggested that a heterozygous c.1946A > G ALOX12 mutation was a disease-causing mutation; however, further experiments are required to confirm the pathogenesis of ALOX12 mutation in platelet aggregation.

Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.

The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using > 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.

Resternotomy and coronary artery bypass grafting after omental flap procedure: A case report.

Few studies have reported resternotomy after an omental flap procedure. We describe the case of a 78-year-old man who received resternotomy after omental flap procedure for deep sternal wound infection and successfully underwent coronary artery bypass grafting. Although preoperative computed tomography showed funnel chest and limited space between the sternum and omentum, resternotomy was performed safely using circular electric sternum saw under partial cardiopulmonary bypass. Because the omentum functioned as cushioning material between the sternum and mediastinal organs, no injuries of the mediastinal organs occurred. An ultrasonic scalpel effectively dissected between the omentum and mediastinal organs, especially above the ascending aorta. The targeted coronary arteries were easily detected. The patient experienced no major cardiac or infectious events for three months. An ultrasonic scalpel is recommended for dissecting between the omentum and mediastinal organs.

Clustering by phenotype and genome-wide association study in autism.

Autism spectrum disorder (ASD) has phenotypically and genetically heterogeneous characteristics. A simulation study demonstrated that attempts to categorize patients with a complex disease into more homogeneous subgroups could have more power to elucidate hidden heritability. We conducted cluster analyses using the k-means algorithm with a cluster number of 15 based on phenotypic variables from the Simons Simplex Collection (SSC). As a preliminary study, we conducted a conventional genome-wide association study (GWAS) with a data set of 597 ASD cases and 370 controls. In the second step, we divided cases based on the clustering results and conducted GWAS in each of the subgroups vs controls (cluster-based GWAS). We also conducted cluster-based GWAS on another SSC data set of 712 probands and 354 controls in the replication stage. In the preliminary study, which was conducted in conventional GWAS design, we observed no significant associations. In the second step of cluster-based GWASs, we identified 65 chromosomal loci, which included 30 intragenic loci located in 21 genes and 35 intergenic loci that satisfied the threshold of P < 5.0 × 10-8. Some of these loci were located within or near previously reported candidate genes for ASD: CDH5, CNTN5, CNTNAP5, DNAH17, DPP10, DSCAM, FOXK1, GABBR2, GRIN2A5, ITPR1, NTM, SDK1, SNCA, and SRRM4. Of these 65 significant chromosomal loci, rs11064685 located within the SRRM4 gene had a significantly different distribution in the cases vs controls in the replication cohort. These findings suggest that clustering may successfully identify subgroups with relatively homogeneous disease etiologies. Further cluster validation and replication studies are warranted in larger cohorts.

Genome-wide association study identifies new loci for albuminuria in the Japanese population.

BACKGROUND: Urinary albumin excretion (UAE) is a risk factor for cardiovascular diseases, metabolic syndrome, chronic kidney disease, etc. Only a few genome-wide association studies (GWAS) for UAE have been conducted in the European population, but not in the Asian population. Here we conducted GWAS and identified several candidate genes harboring single nucleotide polymorphisms (SNPs) responsible for UAE in the Japanese population. METHODS: We conducted GWAS for UAE in 7805 individuals of Asian ancestry from health-survey data collected by Tohoku Medical Megabank Organization (ToMMo) and Iwate Tohoku Medical Megabank Organization (IMM). The SNP genotype data were obtained with a SNP microarray. After imputation using a haplotype panel consisting of 2000 genome sequencing, 4,962,728 SNP markers were used for the GWAS. RESULTS: Eighteen SNPs at 14 loci (GRM7, EXOC1/NMU, LPA, STEAP1B/RAPGEF5, SEMA3D, PRKAG2, TRIQK, SERTM1, TPT1-AS1, OR5AU1, TSHR, FMN1/RYR3, COPRS, and BRD1) were associated with UAE in the Japanese individuals. A locus with particularly strong associations was observed on TSHR, chromosome 14 [rs116622332 (p = 3.99 × 10-10)]. CONCLUSION: In this study, we successfully identified UAE-associated variant loci in the Japanese population. Further study is required to confirm this association.

3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome.

The first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be useful to construct population-level allele frequency panels with easy-to-use interfaces. In the Tohoku Medical Megabank Project, we sequenced nearly 4000 individuals from a Japanese population and constructed an allele frequency panel of 3552 individuals after removing related samples. The panel is called the 3.5KJPNv2. It was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. Our database is the first large-scale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population. All the data are available on our original database at https://jmorp.megabank.tohoku.ac.jp.

Outlier detection for questionnaire data in biobanks.

BACKGROUND: Biobanks increasingly collect, process and store omics with more conventional epidemiologic information necessitating considerable effort in data cleaning. An efficient outlier detection method that reduces manual labour is highly desirable. METHOD: We develop an unsupervised machine-learning method for outlier detection, namely kurPCA, that uses principal component analysis combined with kurtosis to ascertain the existence of outliers. In addition, we propose a novel regression adjustment approach to improve detection, namely the regression adjustment for data by systematic missing patterns (RAMP). RESULT: Application to epidemiological record data in a large-scale biobank (Tohoku Medical Megabank Organization, Japan) shows that a combination of kurPCA and RAMP effectively detects known errors or inconsistent patterns. CONCLUSIONS: We confirm through the results of the simulation and the application that our methods showed good performance. The proposed methods are useful for many practical analysis scenarios.