Complex structural variants(CSVs)are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural variants.How-ever,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match strategy.As a result,there has been limited progress for CSV discovery com-pared with simple structural variants.Here,we systematically analyzed the multi-breakpoint con-nection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read sequencing.Specifically,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined models.Comprehensive evaluations on both simulated and real datasets revealed that Mako outperformed other algorithms.Notably,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70％,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,respectively.Moreover,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed duplication.Further analysis of these CSVs also revealed the impact of sequence homology on the formation of CSVs.Mako is publicly available at https://github.com/xjtu-omics/Mako.

Background/Aims: A calcineurin inhibitor may alter pancreatic function and inflammatory reaction. This study aimed to determine the possible pharmacologic effect of the calcineurin inhibitor, tacrolimus, on pancreatic function, and to determine its preventive effect on post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis in liver transplantation (LT) patients. Methods: The serum amylase and lipase values before and after LT were compared. The frequency of post-ERCP pancreatitis was compared between non-LT and LT patients, using propensity score matching method. Results: Median serum amylase values (normal range, 19 to 86 U/L) were 49.0 U/L (38.0 to 68.0) before LT and 27.0 U/L (19.3 to 36.8) after LT, and median serum lipase values (normal range, 7 to 59 U/L) were 40.0 U/L (26.5 to 54.0) before LT and 10.5 U/L (6.0 to 21.0) after LT. Both serum amylase and lipase values significantly decreased after LT (p < 0.001), and to a level comparable to chronic pancreatitis. There was a marginal significant difference between the non-LT and LT groups before the propensity score matching with respect to frequency of post-ERCP pancreatitis (16 [3.2%] in non-LT group vs. 2 [0.9%] in LT group, p = 0.069). After propensity score matching, a marginal significant difference still existed with respect to frequency of post-ERCP pancreatitis (7 [4.8%] in non-LT group vs. 1 [0.7%] in LT group, p = 0.067). Conclusions The immunosuppression with calcineurin inhibitor may reduce not only the pancreatic enzyme dynamics but also inciting inflammatory event including post-ERCP pancreatitis.

BACKGROUND: Chronic kidney disease (CKD) is associated with fluid retention, which increases total body water (TBW) and leads to changes in intracellular water (ICW) and extracellular water (ECW). This complicates accurate assessments of body composition. Analysis of bioelectrical impedance may improve the accuracy of evaluation in CKD patients and multiple machines and technologies are available. We compared body composition by bioimpedance spectroscopy (BIS) against multi-frequency bioimpedance analysis (BIA) in a multi-ethnic Asian population of stable, non-dialysis CKD patients. METHODS: We recruited 98 stable CKD patients comprising 54.1% men and 70.4% Chinese, 9.2% Malay, 13.3% Indian, and 8.2% other ethnicities. Stability was defined as no variation in serum creatinine > 20% over three months. Patients underwent BIS analyses using a Fresenius body composition monitor, while BIA analyses employed a Bodystat Quadscan 4000. RESULTS: Mean TBW values by BIS and BIA were 33.6 ± 7.2 L and 38.3 ± 7.4 L; mean ECW values were 15.8 ± 3.2 L and 16.9 ± 2.7 L; and mean ICW values were 17.9 ± 4.3 L and 21.0 ± 4.9 L, respectively. Mean differences for TBW were 4.6 ± 1.9 L (P < 0.001), for ECW they were 1.2 ± 0.5 L (P < 0.001), and for ICW they were 3.2 ±1.8 L (P < 0.001). BIA and BIS measurements were highly correlated: TBW r = 0.970, ECW r = 0.994, and ICW r = 0.926. Compared with BIA, BIS assessments of fluid overload appeared to be more associated with biochemical and clinical indicators. CONCLUSION: Although both BIA and BIS can be used for body water assessment, clinicians should be aware of biases that exist between bioimpedance techniques. The values of body water assessments in our study were higher in BIA than in BIS. Ethnicity, sex, body mass index, and estimated glomerular filtration rate were associated with these biases.
Adult ; Asian Continental Ancestry Group ; Bias (Epidemiology) ; Body Composition ; Body Mass Index ; Body Water ; Creatinine ; Electric Impedance ; Glomerular Filtration Rate ; Humans ; Kidney Diseases ; Male ; Methods ; Nutrition Assessment ; Renal Insufficiency, Chronic ; Spectrum Analysis ; Water

The number of patients undergoing percutaneous coronary intervention (PCI) who mandate additional oral anticoagulant therapy has been increasing. Dual antiplatelet therapy (DAPT) is associated with reduced ischemic events including stent thrombosis, myocardial infarction and stroke following PCI. However, the tradeoff is an increased risk for bleeding while on DAPT. The addition of a novel oral anticoagulant (NOAC) further increases the likelihood of bleeding while on antiplatelet therapy. Thus, the overall risks and benefits for each patient undergoing PCI on NOAC must be assessed and therapy individualized to ensure optimal therapy for each unique situation. Patients on NOAC undergoing PCI should undergo routine assessment with intravascular imaging as the role of high-risk lesion-related features have increased importance prior to determining optimal duration of treatment with DAPT. We review the best practices for the pharmacologic management of patients requiring anticoagulation with NOAC who are treated with PCI and require antiplatelet therapy.
Anticoagulants ; Hemorrhage ; Humans ; Myocardial Infarction ; Percutaneous Coronary Intervention ; Practice Guidelines as Topic ; Risk Assessment ; Stents ; Stroke ; Thrombosis

The Asia-Pacific Working Group on inflammatory bowel disease (IBD) was established in Cebu, Philippines, under the auspices of the Asian Pacific Association of Gastroenterology with the goal of improving IBD care in Asia. This consensus is carried out in collaboration with Asian Organization for Crohn's and Colitis. With biologic agents and biosimilars becoming more established, it is necessary to conduct a review on existing literature and establish a consensus on when and how to introduce biologic agents and biosimilars in the conjunction with conventional treatments for ulcerative colitis (UC) and Crohn's disease (CD) in Asia. These statements also address how pharmacogenetics influence the treatments of UC and CD and provide guidance on response monitoring and strategies to restore loss of response. Finally, the review includes statements on how to manage treatment alongside possible hepatitis B and tuberculosis infections, both common in Asia. These statements have been prepared and voted upon by members of IBD workgroup employing the modified Delphi process. These statements do not intend to be all-encompassing and future revisions are likely as new data continue to emerge.
Adalimumab ; Asia ; Asian Continental Ancestry Group ; Biological Factors ; Biosimilar Pharmaceuticals ; Colitis ; Colitis, Ulcerative ; Consensus ; Cooperative Behavior ; Crohn Disease ; Gastroenterology ; Hepatitis B ; Humans ; Immunologic Factors ; Inflammatory Bowel Diseases ; Infliximab ; Pharmacogenetics ; Philippines ; Practice Guidelines as Topic ; Tuberculosis ; Ulcer

BACKGROUND/AIMS: The epidemiology and pathogenesis of eosinophilic esophagitis (EoE) remain unclear in Asian countries. We investigated clinicopathological characteristics and diagnostic trends of EoE, and evaluated 3 tissue biomarkers for correlation with disease activity and treatment response in Korean patients with EoE. METHODS: We retrospectively reviewed 25 271 esophageal biopsies performed during upper endoscopies between 2006 and 2017. We diagnosed EoE based on ≥ 15 eosinophils/high-power field (HPF) and, symptoms of esophageal dysfunction. We performed immunohistochemical analysis for tryptase, eosinophilic derived neurotoxin (EDN), and eotaxin-3. RESULTS: We diagnosed EoE in 72 patients (53 men and 19 women; mean age, 46.2 years) with presenting symptoms of, dysphagia (15.3%), epigastric pain (31.9%), and heartburn (30.6%). The diagnostic rate of EoE considerably increased between 2006 and 2017, from 0.29 diagnoses to 7.99 diagnoses per 1000 esophageal biopsies (P < 0.001). The mean peak eosinophil count (PEC) was 56.0 (± 77.8)/HPF. Whereas the EDN (rho = 0.667, P < 0.001) and eotaxin-3 levels (rho = 0.465, P < 0.001) correlated with PEC, tryptase and PEC were weakly correlated (rho = 0.291, P = 0.013). EDN (rho = 0.279, P = 0.017), and tryptase (rho = 0.279, P = 0.033) correlated with the inflammatory score of Eosinophilic Esophagitis Endoscopic Reference Score. Immunohistochemical analysis and changes in tryptase, EDN, and eotaxin-3 levels were associated with histologic and endoscopic improvements. CONCLUSIONS: EoE incidence considerably increased during the 12-year period, regardless of endoscopic esophageal biopsy rate. Tryptase, EDN, and eotaxin-3 levels in esophageal biopsy specimens could be promising biomarkers for disease activity, symptom, and endoscopic response in Korea.
Asian Continental Ancestry Group ; Biomarkers ; Biopsy ; Deglutition Disorders ; Diagnosis ; Endoscopy ; Eosinophilic Esophagitis ; Eosinophils ; Epidemiology ; Esophagus ; Female ; Heartburn ; Humans ; Incidence ; Korea ; Male ; Retrospective Studies ; Tryptases

The number of patients undergoing percutaneous coronary intervention (PCI) who mandate additional oral anticoagulant therapy has been increasing. Dual antiplatelet therapy (DAPT) is associated with reduced ischemic events including stent thrombosis, myocardial infarction and stroke following PCI. However, the tradeoff is an increased risk for bleeding while on DAPT. The addition of a novel oral anticoagulant (NOAC) further increases the likelihood of bleeding while on antiplatelet therapy. Thus, the overall risks and benefits for each patient undergoing PCI on NOAC must be assessed and therapy individualized to ensure optimal therapy for each unique situation. Patients on NOAC undergoing PCI should undergo routine assessment with intravascular imaging as the role of high-risk lesion-related features have increased importance prior to determining optimal duration of treatment with DAPT. We review the best practices for the pharmacologic management of patients requiring anticoagulation with NOAC who are treated with PCI and require antiplatelet therapy.

BACKGROUND/AIMS: This study aimed to determine the risk of post-endoscopic retrograde cholangiopancreatography (post-ERCP) bleeding among patients taking antiplatelet agents (APAs), particularly in the era of multiple APAs. METHODS: The primary outcomes were the frequency, type, and severity of ERCP-related bleeding according to the use of APAs. RESULTS: The frequencies of post-ERCP bleeding among the four different groups were 16 of 2,083 (0.8%) in the no drug group, 12 of 256 (4.7%) in the aspirin group, 3 of 48 (6.3%) in the single APA group, and 4 of 48 (8.3%) in the multiple APA group (p<0.001). In the univariate analysis, post-ERCP bleeding was associated with age, pull-type sphincterotomy, and APA and was inversely associated with balloon dilation of the biliary orifice. In the multivariate analysis, pull-type sphincterotomy (odds ratio [OR], 7.829; 95% confidence interval [CI], 1.411 to 43.453; p=0.019) and country (Korea: OR, 0.124; 95% CI, 0.042 to 0.361; p<0.001) were associated with post-ERCP bleeding. CONCLUSIONS: The frequency of post-ERCP bleeding was statistically higher in patients on any APA within 6 days prior to ERCP. However, in the multivariate analysis, APA use was not associated with post-ERCP bleeding. Until a large, adequately powered study to detect differences is performed, caution is recommended when considering invasive procedures during ERCP in patients on APAs.
Aspirin ; Cholangiopancreatography, Endoscopic Retrograde ; Hemorrhage* ; Humans ; Multivariate Analysis ; Platelet Aggregation Inhibitors*

BACKGROUND/AIMS: This study aimed to evaluate the diagnostic role of low serum amylase and lipase values in the detection of chronic pancreatitis. METHODS: Patients underwent endoscopic retrograde cholangiopancreatography and were diagnosed with non-calcific chronic pancreatitis (NCCP; n=99) and calcific chronic pancreatitis (CCP; n=112). Patient serum amylase and lipase values were compared with those of healthy controls (H; n=170). RESULTS: The median serum amylase (normal range, 19 to 86 U/L) and lipase values (7 to 59 U/L) (P₂₅–P₇₅) were 47.0 (39.8 to 55.3) and 25.0 (18.0 to 35.0) for H, 34.0 (24.5 to 49.0) and 19.0 (9.0 to 30.0) for NCCP, and 30.0 (20.0 to 40.8) and 10.0 (3.0 to 19.0) for CCP, respectively. The cutoff values with the highest diagnostic accuracy for discriminating NCCP from H were 40 U/L for amylase and 20 U/L for lipase, respectively, and for CCP from H were 38 U/L for amylase and 15 U/L for lipase, respectively. For the diagnosis of NCCP with a criterion of serum amylase < 40 and lipase < 20 U/L, the sensitivity, specificity, positive predictive value, and negative predictive values were 37.4%, 88.8%, 66.1%, and 70.9%, respectively. CONCLUSIONS: Serum amylase and/or lipase levels below the normal serum range are highly specific for chronic pancreatitis patients. Clinicians should not ignore low serum pancreatic enzyme values.
Amylases* ; Cholangiopancreatography, Endoscopic Retrograde ; Diagnosis ; Humans ; Lipase* ; Pancreatitis ; Pancreatitis, Chronic* ; Sensitivity and Specificity

INTRODUCTIONA complex relationship exists between chronic kidney disease-mineral and bone disorder (CKD-MBD) and adverse outcomes among dialysis patients. This study aimed to report the prevalence of CKD-MBD and examine the impact of achieving target CKD-MBD parameters on morbidity and mortality one year after peritoneal dialysis (PD) initiation.

METHODSIn this retrospective cohort study, patients electively initiated on PD were followed up for one year. Laboratory parameters were collected and the prevalence of CKD-MBD 4-6 months after PD initiation was determined based on the Kidney Disease Outcomes Quality Initiative (KDOQI) and Kidney Disease: Improving Global Outcomes (KDIGO) guidelines. Linear regression and Cox proportional hazards model were used to evaluate the effects of achieving CKD-MBD targets 4-6 months after PD initiation on hospitalisation, the incidence of peritonitis or exit-site infections (ESIs), and mortality at one year.

RESULTSThe prevalence of CKD-MBD among the 86 patients in this study was 86.0% (KDOQI) and 54.7% (KDIGO). There was no significant difference in hospitalisation duration between patients who achieved targets and those who did not. Patients who failed to meet all the KDIGO CKD-MBD or calcium serum targets had a higher incidence of peritonitis or ESI. A trend toward shorter time to death was observed among patients who failed to meet the KDIGO phosphorus serum targets.

CONCLUSIONThere was moderate (KDIGO) to high prevalence (KDOQI) of CKD-MBD among the patients. Achievement of all the KDIGO CKD-MBD or calcium serum targets was associated with reduced peritonitis or ESI, while achievement of the KDIGO phosphorus serum targets was associated with improved survival.

Adult ; Aged ; Aged, 80 and over ; Chronic Kidney Disease-Mineral and Bone Disorder ; complications ; epidemiology ; Female ; Humans ; Kidney Failure, Chronic ; complications ; therapy ; Linear Models ; Male ; Middle Aged ; Peritoneal Dialysis ; Prevalence ; Proportional Hazards Models ; Quality Control ; Retrospective Studies ; Treatment Outcome