Chinese normotensive and essential hypertensive reference intervals for plasma aldosterone and renin activity by liquid chromatography-tandem mass spectrometry.

OBJECTIVES: The renin-angiotensin-aldosterone system (RAAS) regulates blood pressure. Plasma renin activities (PRA) and plasma aldosterone concentrations (PAC) are biomarkers related to RAAS. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based measurements for PRA and PAC have become popular. Method-specific reference intervals (RIs) are required. METHODS: Routine PRA and PAC services in a Hong Kong teaching hospital were based on LC-MS/MS methods. PRA and PAC RIs were developed for normotensive subjects and essential hypertensive (EH) patients. Healthy volunteers were recruited to establish normotensive RIs. PRA and PAC results of hypertensive patients with urine aldosterone tests for primary aldosteronism (PA) screening were retrieved from the laboratory information system. Patients without PA were included. Patients with secondary hypertension and patients on medications affecting the RAAS were excluded. The central 95% RIs were established based on the recommendations of the Clinical and Laboratory Standards Institute guideline C28-A3. RESULTS: PRA and PAC of 170 normotensive volunteers and 362 EH patients were analysed. There was no sex-specific difference in PRA and PAC for normotensive and EH reference subjects. Differences for PRA and PAC were noted between normotensive subjects aged below 45 and their older counterparts. However, such a difference was only identified for PRA but not PAC in EH patients. Age-specific RIs were established accordingly. CONCLUSIONS: This study presented age-specific LC-MS/MS RIs of PRA and PAC for both normotensive and EH populations for local Chinese in Hong Kong.

Biological augmentation of meniscal repair: a systematic review.

PURPOSE: Orthopedic literature remains divided on the utility of biologic augmentation to optimize outcomes after isolated meniscal repair. The aim of this systematic review is to analyze the clinical outcomes and re-operation rates of biologically augmented meniscal repairs. METHODS: PubMed, CINAHL, Cochrane, and EMBASE databases were queried in October 2020 for published literature on isolated meniscal repair with biological augmentation. Studies were assessed for quality and risk of bias by two appraisal tools. Patient demographics, meniscal tear characteristics, surgical procedure, augmentation type, post-operative rehabilitation, patient reported outcome measures, and length of follow-up were recorded, reviewed, and analyzed by two independent reviewers. RESULTS: Of 3794 articles, 18 met inclusion criteria and yielded 537 patients who underwent biologic augmentation of meniscal repair. The biologically augmented repair rates were 5.8-27.0% with PRP augmentation, 0.0-28.5% with fibrin clot augmentation, 0.0-12.9% with marrow stimulation, and 0.0% with stem cell augmentation. One of seven studies showed lower revision rates with augmented meniscal repair compared to standard repair techniques, whereas five of seven found no benefit. Three of ten studies found significant functional improvement of biologically augmented repair versus standard repair techniques and six of ten studies found no difference. There was significant heterogeneity in methods for biologic preparation, delivery, and post-operative rehabilitation protocols. CONCLUSION: Patients reported significant improvements in functional outcomes scores after repair with biological augmentation, though the benefit over standard repair controls is questionable. Revision rates after biologically augmented meniscal repair also appear similar to standard repair techniques. Clinicians should bear this in mind when considering biologic augmentation in the setting of meniscal repair. LEVEL OF EVIDENCE: IV.

Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection.

BACKGROUND: Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-free DNA (cfDNA) molecules have jagged ends. METHODS: Jagged ends of cfDNA were detected by incorporating unmethylated cytosines during a DNA end-repair process, followed by bisulfite sequencing. Incorporation of unmethylated cytosines during the repair of the jagged ends lowered the apparent methylation levels measured by bisulfite sequencing and were used to calculate a jagged end index. This approach is called jagged end analysis by sequencing. RESULTS: The jagged end index of urinary cfDNA was higher than that of plasma DNA. The jagged end index profile of plasma DNA displayed several strongly oscillating major peaks at intervals of approximately 165 bp (i.e., nucleosome size) and weakly oscillating minor peaks with periodicities of approximately 10 bp. In contrast, the urinary DNA jagged end index profile showed weakly oscillating major peaks but strongly oscillating minor peaks. The jagged end index was generally higher in nucleosomal linker DNA regions. Patients with bladder cancer (n = 46) had lower jagged end indexed of urinary DNA than participants without bladder cancer (n = 39). The area under the curve for differentiating between patients with and without bladder cancer was 0.83. CONCLUSIONS: Jagged ends represent a property of urinary cfDNA. The generation of jagged ends might be related to nucleosomal structures, with enrichment in linker DNA regions. Jagged ends of urinary DNA could potentially serve as a new biomarker for bladder cancer detection.

Anticoagulation and antiplatelet therapy post coronary artery bypass surgery.

BACKGROUND: Coronary artery bypass grafting (CABG) is the gold standard treatment for patients with multivessel coronary heart disease. Although its use has proven long-term survival benefits, there is a relative degree of graft failure which increases morbidity and mortality rates. DISCUSSION: This review discusses clinical outcomes following antiplatelet and anticoagulant therapy after CABG. There is wide variation of evidence about the use of clopidogrel or ticagrelor to aspirin postoperatively in relation to improving graft patency rates or clinical outcomes over the use of aspirin alone. These dual therapies may have significant protective effects in patients undergoing off-pump CABG. Recent studies suggest that superior outcomes may be attained by combining prasugrel with aspirin. Further research is needed to evaluate this, as well as compare the effectiveness of different dual antiplatelet regimens. There is weak evidence for post-CABG anticoagulation, with warfarin and rivaroxaban providing no protection against graft failure but decreasing long-term major adverse cardiac events. Anticoagulation seems to be indicated only in post-CABG patients at high risk of future ischemic events. CONCLUSION: The use of dual anti-platelet therapy post coronary artery bypass surgery needs further research. Potentially, selective patient groups will benefit more from the addition of thienopyridine antiplatelets or anticoagulants to aspirin after CABG.

Rehabilitation variability after rotator cuff repair.

BACKGROUND: There has been increasing recognition of the importance for standardized postoperative rehabilitation protocols. Despite published guidelines in 2016 by the American Society of Shoulder and Elbow Therapists (ASSET), optimal postoperative rehabilitation after rotator cuff repair (RCR) remains an area of active academic debate. The goals of this study were (1) to assess the variability of RCR rehabilitation protocols published online, (2) to study the congruence between online RCR rehabilitation protocols and the ASSET consensus statement, and (3) to identify differences in online RCR rehabilitation protocols from before and after 2016. METHODS: A web-based search was conducted for publicly available RCR rehabilitation protocols from websites of all Accreditation Council for Graduate Medical Education (ACGME) academic orthopedic institutions. A supplemental 10-page Google search was also performed with the search terms "rotator cuff repair rehabilitation protocol." Collected protocols were grouped by tear size (small/medium or large/massive) and examined for information relating to the following categories: protocol demographics, adjunctive therapy use, immobilization/range of motion, and strengthening. Findings were compared to the ASSET statement's recommendations. Protocols published before and after ASSET's 2016 publication were compared for differences. RESULTS: A total of 66 online RCR rehabilitation protocols were collected. Only 16 of 187 (8.5%) ACGME institutions provided online RCR rehabilitation protocols. The collected protocols recommend more aggressive rehabilitation in comparison to ASSET, specifically regarding immobilization time, passive range of motion initiation, active assisted range of motion initiation, and strengthening initiation (P < .001). Protocols published after 2016 trended toward more conservative recommendations in comparison to protocols published before 2016. Regardless of this trend, the majority of these recommendations were still largely more aggressive than ASSET's recommendations. CONCLUSION: Despite an attempt by ASSET to provide standardization, this study highlights the marked variations that still exist regarding RCR rehabilitation. Additionally, online RCR rehabilitation protocols tend to make more aggressive recommendations than the ASSET consensus statement. Further research is needed to address these variations and to either validate, alter, or reject the ASSET recommendations.

Conventional versus miniaturized cardiopulmonary bypass: A systematic review and meta-analysis.

Objective: A meta-analysis of randomized controlled trials was performed to compare the effects of miniaturized extracorporeal circulation (MECC) and conventional extracorporeal circulation (CECC) on morbidity and mortality rates after cardiac surgery. Methods: A comprehensive literature search was conducted using Ovid, PubMed, Medline, EMBASE, and the Cochrane databases. Randomized controlled trials from the year 2000 with n > 40 patients were considered. Key search terms included variations of "mini," "cardiopulmonary," "bypass," "extracorporeal," "perfusion," and "circuit." Studies were assessed for bias using the Cochrane Risk of Bias tool. The primary outcomes were postoperative mortality and stroke. Secondary outcomes included arrhythmia, myocardial infarction, renal failure, blood loss, and a composite outcome comprised of mortality, stroke, myocardial infarction and renal failure. Duration of intensive care unit, and hospital stay was also recorded. Results: The 42 studies eligible for this study included a total of 2154 patients who underwent CECC and 2196 patients who underwent MECC. There were no significant differences in any preoperative or demographic characteristics. Compared with CECC, MECC did not reduce the incidence of mortality, stroke, myocardial infarction, and renal failure but did significantly decrease the composite of these outcomes (odds ratio, 0.64; 95% confidence interval [CI], 0.50-0.81; P = .0002). MECC was also associated with reductions in arrhythmia (odds ratio, 0.67; 95% CI, 0.54-0.83; P = .0003), blood loss (mean difference [MD], -96.37 mL; 95% CI, -152.70 to -40.05 mL; P = .0008), hospital stay (MD, -0.70 days; 95% CI, -1.21 to -0.20 days; P = .006), and intensive care unit stay (MD, -2.27 hours; 95% CI, -3.03 to -1.50 hours; P < .001). Conclusions: MECC demonstrates clinical benefits compared with CECC. Further studies are required to perform a cost-utility analysis and to assess the long-term outcomes of MECC. These should use standardized definitions of endpoints such as mortality and renal failure to reduce inconsistency in outcome reporting.

Glenoid Pathology, Skeletal Immaturity, and Multiple Preoperative Instability Events Are Risk Factors for Recurrent Anterior Shoulder Instability After Arthroscopic Stabilization in Adolescent Athletes.

PURPOSE: To identify risk factors for recurrent shoulder instability after arthroscopic stabilization in adolescent athletes. METHODS: A retrospective case-control study was undertaken of all patients younger than 18 years undergoing arthroscopic shoulder stabilization for anterior instability between 2009 and 2016. Two patient cohorts were identified: (1) patients with recurrent instability (frank dislocations or subluxations) after arthroscopic stabilization and (2) an age- and sex-matched cohort of patients with no recurrent instability at a minimum of 2 years' follow-up from index surgery. Patient demographic, injury, radiographic, and surgical variables were recorded. Variables with P < .10 on univariate analysis were entered into a binary logistic multivariate regression analysis. RESULTS: We identified 35 patients (20.5%) in whom arthroscopic stabilization failed at a mean of 1.2 ± 1.0 years after their index surgical procedure. A separate age- and sex-matched cohort of 35 patients with no evidence of recurrent instability was identified (mean follow-up, 5.4 ± 2.0 years; minimum follow-up, 2 years). Univariate analysis identified increased glenoid bone loss (P = .039), decreased glenoid retroversion (P = .024), and more than 1 instability event prior to surgery (P = .017) as significant risk factors for recurrent instability. Multivariate regression analysis revealed that glenoid retroversion less than 6°, skeletal immaturity, and more than 1 prior instability event significantly and independently predicted future recurrence. The risk of recurrence after arthroscopic stabilization was increased by 3 times in patients with 2 risk factors and by 4 times in patients with all 3 risk factors. CONCLUSIONS: Anterior glenoid bone loss, glenoid version, skeletal immaturity, and multiple preoperative instability events are risk factors for failed arthroscopic stabilization in adolescent athletes with anterior instability. LEVEL OF EVIDENCE: Level III, case-control study.

Mendelian randomization analyses suggest a role for cholesterol in the development of endometrial cancer.

Blood lipids have been associated with the development of a range of cancers, including breast, lung and colorectal cancer. For endometrial cancer, observational studies have reported inconsistent associations between blood lipids and cancer risk. To reduce biases from unmeasured confounding, we performed a bidirectional, two-sample Mendelian randomization analysis to investigate the relationship between levels of three blood lipids (low-density lipoprotein [LDL] and high-density lipoprotein [HDL] cholesterol, and triglycerides) and endometrial cancer risk. Genetic variants associated with each of these blood lipid levels (P < 5 × 10-8 ) were identified as instrumental variables, and assessed using genome-wide association study data from the Endometrial Cancer Association Consortium (12 906 cases and 108 979 controls) and the Global Lipids Genetic Consortium (n = 188 578). Mendelian randomization analyses found genetically raised LDL cholesterol levels to be associated with lower risks of endometrial cancer of all histologies combined, and of endometrioid and non-endometrioid subtypes. Conversely, higher genetically predicted HDL cholesterol levels were associated with increased risk of non-endometrioid endometrial cancer. After accounting for the potential confounding role of obesity (as measured by genetic variants associated with body mass index), the association between genetically predicted increased LDL cholesterol levels and lower endometrial cancer risk remained significant, especially for non-endometrioid endometrial cancer. There was no evidence to support a role for triglycerides in endometrial cancer development. Our study supports a role for LDL and HDL cholesterol in the development of non-endometrioid endometrial cancer. Further studies are required to understand the mechanisms underlying these findings.

Injury Incidence, Patterns, and Risk Factors in Functional Training Athletes in an Asian Population.

BACKGROUND: Functional training, also known as CrossFit, is a unique sport that combines weightlifting, gymnastics, and metabolic conditioning into a single program. There are an estimated 50 functional training centers in Malaysia. PURPOSE: To analyze the injury rates, patterns, and risk factors of functional training/CrossFit. STUDY DESIGN: Descriptive epidemiology study. METHODS: Electronic questionnaires were distributed to 244 participants from 15 centers in the country. Descriptive data regarding the athletes, injury occurrence within the past 6 months, injury details, and risk factors were collected. RESULTS: Of the 244 athletes, 112 (46%) developed at least 1 new injury over the previous 6 months. Injury rates were significantly higher in athletes from nonaffiliate training gyms compared with CrossFit-affiliated gyms, in athletes with previous injuries, and in those who perceived themselves as having more than average fitness. CONCLUSION: Coaches and athletes need to be more aware of risk factors for injury to enable safer and better training strategies.

Paget-Schroetter syndrome in athletes: a comprehensive and systematic review.

BACKGROUND: Paget-Schroetter syndrome (PSS) is a rare condition of axillosubclavian vein thrombosis often seen in athletes with a history of repetitive external rotation and abduction of the shoulder. The purpose of this review was to analyze the literature and characterize PSS in the athletic population, including risk of PSS by sport. We also provide a comprehensive review of PSS to inform clinicians on the pathophysiology, detection, and management of the condition. METHODS: Four databases were reviewed to identify cases of PSS occurring in athletes. Data on patient demographics, reported sport, diagnosis, treatment, management, return to sport, and complications were extracted and analyzed by 2 independent reviewers. RESULTS: Of the 123 cases of PSS identified, baseball and weight lifting had the highest incidence (26.8% and 19%, respectively), followed by swimming, football, and basketball. The average return to sport was 4.7 months, and 26.7% of subjects reported complications, most commonly pulmonary embolism. CONCLUSION: In athletes presenting with upper extremity pain and swelling with a history of playing baseball or weight lifting, PSS should be higher on a clinicians differential diagnosis list. Swimmers, football, and basketball players are less likely to present with PSS but are still more likely than other types of athletes to develop the condition. Clinician awareness of PSS in athletes is critical to avoid delays in treatment and misdiagnosis, and to allow for a timely return to sport with minimal complications.

Use of Virtual Reality Simulation to Identify Vision-Related Disability in Patients With Glaucoma.

Importance: Clinical assessment of vision-related disability is hampered by the lack of instruments to assess visual performance in real-world situations. Interactive virtual reality (VR) environments displayed in a binocular stereoscopic VR headset have been designed, presumably simulating day-to-day activities to evaluate vision-related disability. Objective: To investigate the application of VR to identify vision-related disability in patients with glaucoma. Design, Setting, and Participants: In a cross-sectional study, 98 patients with glaucoma and 50 healthy individuals were consecutively recruited from a university eye clinic; all participants were Chinese. The study was conducted between August 30, 2016, and July 31, 2017; data analysis was performed from December 1, 2017, to October 30, 2018. Exposures: Measurements of visual acuity, contrast sensitivity, visual field (VF), National Eye Institute 25-item Visual Function Questionnaire Rasch score, and VR disability scores determined from 5 VR simulations: supermarket shopping, stair and city navigations in daytime, and stair and city navigations in nighttime. Duration required to complete the simulation, number of items incorrectly identified, and number of collisions were measured to compute task-specific and overall VR disability scores. Vision-related disability was identified when the VR disability score was outside the normal age-adjusted 95% confidence region. Main Outcomes and Measures: Virtual reality disability score. Results: In the 98 patients with glaucoma, mean (SD) age was 49.8 (11.6) years and 60 were men (61.2%); in the 50 healthy individuals, mean (SD) age was 48.3 (14.8) years and 16 were men (32.0%). The patients with glaucoma had different degrees of VF loss (122 eyes [62.2%] had moderate or advanced VF defects). The time required to complete the activities by patients with glaucoma vs healthy individuals was longer by 15.2 seconds (95% CI, 5.5-24.9 seconds) or 34.1% (95% CI, 12.4%-55.7%) for the shopping simulation, 72.8 seconds (95% CI, 23.0-122.6 seconds) or 33.8% (95% CI, 10.7%-56.9%) for the nighttime stair navigation, and 38.1 seconds (95% CI, 10.9-65.2 seconds) or 30.8% (95% CI, 8.8%-52.8%) for the nighttime city navigation. The mean (SD) duration was not significantly different between the glaucoma and healthy groups in daytime stair (203.7 [93.7] vs 192.9 [89.1] seconds, P = .52) and city (118.7 [41.5] vs 117.0 [52.3] seconds, P = .85) navigation. For each decibel decrease in binocular VF sensitivity, the risk of collision increased by 15% in nighttime stair (hazard ratio [HR], 1.15; 95% CI, 1.08-1.22) and city (HR, 1.15; 95% CI, 1.08-1.23) navigations. Fifty-eight patients (59.1%) with glaucoma had vision-related disability in at least 1 simulated daily task; a higher proportion of patients had vision-related disability in nighttime city (27 of 88 [30.7%]) and stair (27 of 90 [30.0%]) navigation than in daytime city (7 of 88 [8.0%]) and stair (19 of 96 [19.8%]) navigation. The overall VR disability score was associated with the National Eye Institute 25-item Visual Function Questionnaire Rasch score (R2 = 0.207). Conclusions and Relevance: These findings suggest that vision-related disability is associated with lighting condition and task in patients with glaucoma. Virtual reality may allow eye care professionals to understand the patients' perspectives on how visual impairment imparts disability in daily living and provide a new paradigm to augment the assessment of vision-related disability.

Factors Influencing Attitude Toward Organ and Tissue Donation Among Patients in Primary Clinic, Sabah, Malaysia.

INTRODUCTION: Worldwide, the gap between organ supply and demand has widened over the years. Malaysia has one of the lowest deceased organ donation rates. Success rate of organ or tissue procurement depends on not only the approach rate by health care providers but also the awareness among the public, whereby it can be a platform for family initiation of organ donation. The purpose of this study is to assess the knowledge of and determine the factors influencing attitude toward organ and tissue donation among patients in a primary clinic. METHODS: A cross-sectional analytical study was carried out. Self-administered questionnaires were given to 400 patients who registered at an outpatient clinic in April 2018. Convenience sampling was applied. RESULTS: Monthly income, education level, occupation, and knowledge level are significantly associated with attitude of the respondents toward organ and tissue donation. Occupation influenced attitude toward organ donation. Knowledge of organ donation and brain death both significantly affected attitude toward organ donation. CONCLUSION: The greater the knowledge of organ donation and brain death, the more positive impression or attitude toward organ donation. Education level and income are the main predictors that influence attitude toward organ donation. Hence, it is important for public health units to promote and deliver public education on organ donation, change public misconceptions, and work parallel with hospitals to increase organ donation rates in Sabah.

Comprehensive characterization and resolution of discrepant spectrophotometric bilirubin results in patients on eltrombopag therapy.

Background Eltrombopag is a thrombopoietin receptor agonist used for the treatment of thrombocytopenic conditions. It can cause pH-dependent discoloration of plasma/serum. Eltrombopag is potentially hepatotoxic. It can affect the assessment of hyperbilirubinemia because of its (i) absorbance at ~450 nm (bilirubin), (ii) absorbance at ~550 nm (diazo-bilirubin) and (iii) it can cause yellowish discoloration of the eyes at normal circulating bilirubin levels. Methods We collected 66 samples from patients on a range of eltrombopag dosages up to 150 mg daily. Bilirubin was measured using multiple routine spectrophotometric analyzers, the Doumas reference method and high-performance liquid chromatography (HPLC). Plasma/serum eltrombopag concentrations were determined using liquid chromatography tandem mass spectrometry (LC-MS/MS). Spike-in and admixture experiments delineated the effects of eltrombopag and its metabolites. Results Forty-nine of 52 samples from patients on ≥50 mg daily eltrombopag therapy showed significantly discrepant inter-analyzer total bilirubin results, a difference up to 64 µmol/L (3.7 mg/dL). In one sample, total bilirubin varied from 8 to 65 µmol/L (0.4-3.8 mg/dL) by different routine analyzers, with direct bilirubin ≤4 µmol/L (0.2 mg/dL). There was a positive correlation between total bilirubin difference and plasma eltrombopag concentration (r = 0.679), and spike-in experiments demonstrated that Beckman AU and Doumas reference methods were susceptible to positive interference. HPLC can quantify bilirubin after separating eltrombopag, and results suggest different analyzers are affected to varying degrees by eltrombopag and its metabolites. Conclusions Eltrombopag and its metabolites can cause positive interference to the spectrophotometric measurements of total bilirubin. Accurate measurements of total bilirubin may improve our understanding of the prevalence of hyperbilirubinemia in patients on eltrombopag therapy.

Noninvasive Detection of Bladder Cancer by Shallow-Depth Genome-Wide Bisulfite Sequencing of Urinary Cell-Free DNA for Methylation and Copy Number Profiling.

BACKGROUND: The current diagnosis and monitoring of bladder cancer are heavily reliant on cystoscopy, an invasive and costly procedure. Previous efforts in urine-based detection of bladder cancer focused on targeted approaches that are predicated on the tumor expressing specific aberrations. We aimed to noninvasively detect bladder cancer by the genome-wide assessment of methylomic and copy number aberrations (CNAs). We also investigated the size of tumor cell-free (cf)DNA fragments. METHODS: Shallow-depth paired-end genome-wide bisulfite sequencing of urinary cfDNA was done for 46 bladder cancer patients and 39 cancer-free controls with hematuria. We assessed (a) proportional contribution from different tissues by methylation deconvolution, (b) global hypomethylation, (c) CNA, and (d) cfDNA size profile. RESULTS: Methylomic and copy number approaches were synergistically combined to detect bladder cancer with a sensitivity of 93.5% (84.2% for low-grade nonmuscle-invasive disease) and a specificity of 95.8%. The prevalence of methylomic and CNAs reflected disease stage and tumor size. Sampling over multiple time points could assess residual disease and changes in tumor load. Muscle-invasive bladder cancer was associated with a higher proportion of long cfDNA, as well as longer cfDNA fragments originating from genomic regions enriched for tumor DNA. CONCLUSIONS: Bladder cancer can be detected noninvasively in urinary cfDNA by methylomic and copy number analysis without previous knowledge or assumptions of specific aberrations. Such analysis could be used as a liquid biopsy to aid diagnosis and for potential longitudinal monitoring of tumor load. Further understanding of the differential size and fragmentation of cfDNA could improve the detection of bladder cancer.

Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin.

Cell-free DNA (cfDNA) in human plasma is a class of biomarkers with many current and potential future diagnostic applications. Recent studies have shown that cfDNA molecules are not randomly fragmented and possess information related to their tissues of origin. Pathologies causing death of cells from particular tissues result in perturbations in the relative distribution of DNA from the affected tissues. Such tissue-of-origin analysis is particularly useful in the development of liquid biopsies for cancer. It is therefore of value to accurately determine the relative contributions of the tissues to the plasma DNA pool in a simultaneous manner. In this work, we report that in open chromatin regions, cfDNA molecules show characteristic fragmentation patterns reflected by sequencing coverage imbalance and differentially phased fragment end signals. The latter refers to differences in the read densities of sequences corresponding to the orientation of the upstream and downstream ends of cfDNA molecules in relation to the reference genome. Such cfDNA fragmentation patterns preferentially occur in tissue-specific open chromatin regions where the corresponding tissues contributed DNA into the plasma. Quantitative analyses of such signals allow measurement of the relative contributions of various tissues toward the plasma DNA pool. These findings were validated by plasma DNA sequencing data obtained from pregnant women, organ transplantation recipients, and cancer patients. Orientation-aware plasma DNA fragmentation analysis therefore has potential diagnostic applications in noninvasive prenatal testing, organ transplantation monitoring, and cancer liquid biopsy.

A Targeted Gene Panel That Covers Coding, Non-coding and Short Tandem Repeat Regions Improves the Diagnosis of Patients With Neurodegenerative Diseases.

Genetic testing for neurodegenerative diseases (NDs) is highly challenging because of genetic heterogeneity and overlapping manifestations. Targeted-gene panels (TGPs), coupled with next-generation sequencing (NGS), can facilitate the profiling of a large repertoire of ND-related genes. Due to the technical limitations inherent in NGS and TGPs, short tandem repeat (STR) variations are often ignored. However, STR expansions are known to cause such NDs as Huntington's disease and spinocerebellar ataxias type 3 (SCA3). Here, we studied the clinical utility of a custom-made TGP that targets 199 NDs and 311 ND-associated genes on 118 undiagnosed patients. At least one known or likely pathogenic variation was found in 54 patients; 27 patients demonstrated clinical profiles that matched the variants; and 16 patients whose original diagnosis were refined. A high concordance of variant calling were observed when comparing the results from TGP and whole-exome sequencing of four patients. Our in-house STR detection algorithm has reached a specificity of 0.88 and a sensitivity of 0.82 in our SCA3 cohort. This study also uncovered a trove of novel and recurrent variants that may enrich the repertoire of ND-related genetic markers. We propose that a combined comprehensive TGPs-bioinformatics pipeline can improve the clinical diagnosis of NDs.

Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma.

Circulating tumor-derived cell-free DNA (ctDNA) analysis offers an attractive noninvasive means for detection and monitoring of cancers. Evidence for the presence of cancer is dependent on the ability to detect features in the peripheral circulation that are deemed as cancer-associated. We explored approaches to improve the chance of detecting the presence of cancer based on sequence information present on ctDNA molecules. We developed an approach to detect the total pool of somatic mutations. We then investigated if there existed a class of ctDNA signature in the form of preferred plasma DNA end coordinates. Cell-free DNA fragmentation is a nonrandom process. Using plasma samples obtained from liver transplant recipients, we showed that liver contributed cell-free DNA molecules ended more frequently at certain genomic coordinates than the nonliver-derived molecules. The abundance of plasma DNA molecules with these liver-associated ends correlated with the liver DNA fractions in the plasma samples. Studying the DNA end characteristics in plasma of patients with hepatocellular carcinoma and chronic hepatitis B, we showed that there were millions of tumor-associated plasma DNA end coordinates in the genome. Abundance of plasma DNA molecules with tumor-associated DNA ends correlated with the tumor DNA fractions even in plasma samples of hepatocellular carcinoma patients that were subjected to shallow-depth sequencing analysis. Plasma DNA end coordinates may therefore serve as hallmarks of ctDNA that could be sampled readily and, hence, may improve the cost-effectiveness of liquid biopsy assessment.

Identification of nine new susceptibility loci for endometrial cancer.

Endometrial cancer is the most commonly diagnosed cancer of the female reproductive tract in developed countries. Through genome-wide association studies (GWAS), we have previously identified eight risk loci for endometrial cancer. Here, we present an expanded meta-analysis of 12,906 endometrial cancer cases and 108,979 controls (including new genotype data for 5624 cases) and identify nine novel genome-wide significant loci, including a locus on 12q24.12 previously identified by meta-GWAS of endometrial and colorectal cancer. At five loci, expression quantitative trait locus (eQTL) analyses identify candidate causal genes; risk alleles at two of these loci associate with decreased expression of genes, which encode negative regulators of oncogenic signal transduction proteins (SH2B3 (12q24.12) and NF1 (17q11.2)). In summary, this study has doubled the number of known endometrial cancer risk loci and revealed candidate causal genes for future study.

Genetic overlap between endometriosis and endometrial cancer: evidence from cross-disease genetic correlation and GWAS meta-analyses.

Epidemiological, biological, and molecular data suggest links between endometriosis and endometrial cancer, with recent epidemiological studies providing evidence for an association between a previous diagnosis of endometriosis and risk of endometrial cancer. We used genetic data as an alternative approach to investigate shared biological etiology of these two diseases. Genetic correlation analysis of summary level statistics from genomewide association studies (GWAS) using LD Score regression revealed moderate but significant genetic correlation (rg  = 0.23, P = 9.3 × 10-3 ), and SNP effect concordance analysis provided evidence for significant SNP pleiotropy (P = 6.0 × 10-3 ) and concordance in effect direction (P = 2.0 × 10-3 ) between the two diseases. Cross-disease GWAS meta-analysis highlighted 13 distinct loci associated at P ≤ 10-5 with both endometriosis and endometrial cancer, with one locus (SNP rs2475335) located within PTPRD associated at a genomewide significant level (P = 4.9 × 10-8 , OR = 1.11, 95% CI = 1.07-1.15). PTPRD acts in the STAT3 pathway, which has been implicated in both endometriosis and endometrial cancer. This study demonstrates the value of cross-disease genetic analysis to support epidemiological observations and to identify biological pathways of relevance to multiple diseases.