Journal of Clinical Pathology

Background: Classification of central nervous system (CNS) tumors has become increasingly complex, raising concerns about the sustainability of comprehensive molecular diagnostics. We have evaluated nanopore whole genome sequencing (nWGS) as a single workflow to replace multiple diagnostic assays. Methods: We performed nWGS on DNA extracted from 90 adult CNS tumor samples (58 retrospective, 32 prospective) and compared the results to findings from standard of care (SoC) diagnostic work-up. Analysis was done through an automated workflow that consolidated diagnostically and therapeutically relevant genomic alterations, including copy-number variation, structural, and single-nucleotide variants, chromosomal aberrations, gene fusions, and methylation-based classification. Results: nWGS supported final diagnostic classification in all samples with >15% tumor cell content, requiring ~3 hours of hands-on library preparation, parallel sample processing, and sequencing times within 72 hours. Methylation-based classification was available within 1 hour and was concordant with the integrated final diagnosis in 89% of cases (80/90). All diagnostically relevant copy-number variations, single-nucleotide variants, and gene fusions were concordant with SoC testing. MGMT promoter methylation status matched in 94% of cases. In addition, nWGS identified prognostic and potentially actionable variants that were not reported or covered by SoC. Conclusions: nWGS delivers comprehensive genetic and epigenetic results with a fast turn-around compared to standard methods. This enables efficient, accurate, and scalable molecular diagnostics of CNS tumors using a single platform. This data supports its implementation in routine clinical practice and may be extended to other cancer types requiring complex genomic profiling.

Objective The decline of the perinatal demise rate is slowing and demises are often unexplained. Significant research has been done regarding diagnostic yield and genetic causes of demise, but little is known about how Geneticist involvement impacts outcomes. The goal of the study was to evaluate post-mortem genetic testing practices and effects of the geneticists involvement. Methods Retrospective data from 111 perinatal demise cases was examined, including rates of prenatal genetic counseling, post-delivery genetics consult, genetic testing, and autopsy investigation. Results In this cohort 54% received genetic testing and 25% received a genetics consult. When compared to those without, cases with genetic specialist involvement were associated with significant increases in testing uptake (p=0.007), diagnostic yield (p<0.001), and patient education (p<0.001). Second trimester stillbirths and those with fewer ultrasound (US) abnormalities were less likely to receive genetic testing (both p values <0.001) and consults (p<0.001, p=0.020). Conclusion Though it was not possible to avoid ascertainment bias, this data demonstrates that geneticist involvement correlates with a higher rate of testing, greater diagnostic yield, and more thorough counseling. These findings underscore the importance of integrating genetics providers into perinatal postmortem healthcare teams.

Digital Pathology (DP) is a fast-emerging branch of pathology focused on digitizing pathology data. A key challenge of DP usage for pathology laboratories, especially mid- to small-sized clinical labs, are the upfront costs associated with instrumentation and the logistical challenges of implementation. In the current project, we built an end-to-end DP solution using low-cost, open-source components that is user-friendly at a small scale. We repurposed readily available microscopy components in a pathology lab to assemble a fully functional DP pipeline for translational research applications. We tested multiple low-cost complementary metal-oxide semiconductor (CMOS) cameras in this project and chose a user-friendly Canon camera for image acquisition. An open-source DP server solution, OMERO v.5.6.4, was used as the image management system (IMS) to host and serve the WSIs on an Ubuntu 22.04 operating system. The server-hosted WSI images were evaluated remotely and asynchronously by multiple pathologists physically situated in Albuquerque, NM; Salt Lake City, UT; and Palo Alto, CA. Each pathologist assessed the quality of the WSI pipeline, image quality, and WSI interaction experience using a 23-question survey. Overall, the custom, low-cost WSI pipeline was noted to be a robust and user-friendly experience by the pathologists. The current DP setup is unlikely to be useful as a commercial, scalable DP pipeline for large-scale clinical applications. However, it demonstrates the feasibility of creating customized, small-scale DP solutions (at a low price point) for asynchronous translational pathology research applications. Additionally, building customized DP pipelines provides excellent educational opportunities for pathology residents to gain in-depth knowledge of the various technical elements of a DP workflow. In summary, we have established a low-cost, end-to-end WSI DP pipeline useful for spatiotemporally asynchronous translational pathology research, in an academic setting.

We completed a video-based, four-night, in-home, level 3 sleep apnea study of healthy, low-risk pregnant participants and their bed partners in order to characterize sleep physiology in the third trimester of pregnancy. Demographic, anthropometric, and baseline sleep health characteristics were recorded, and the NightOwl home sleep apnea test device was used to measure sleep breathing, posture, and architecture parameters. Symptoms of restless legs syndrome were elicited in the exit interview. Forty-one pregnant participants and 36 bed partners completed the study. Bed partners had a significantly higher prevalence of sleep apnea than their pregnant co-sleepers (31% vs. 5.9%). Bed partners also had more severe sleep apnea than their pregnant co-sleepers, and this persisted on an adjusted analysis for baseline differences in factors known to increase risk of sleep apnea. In pregnant participants, increasing gestational age was found to be protective against mild respiratory events but not more severe events. While the correlation between STOP-Bang score and measures of sleep apnea severity was weak, an affirmative response to the witnessed apneas item on the STOP-Bang questionnaire was a strong predictor of more severe sleep apnea for all participants. Smoking history also increased sleep apnea risk. Pregnant participants had lower sleep efficiency and longer self-reported sleep onset latency. Restless legs syndrome was experienced by 39.5% of the pregnant participants but no bed partners. From a sleep breathing perspective, people with healthy, low-risk pregnancies have better sleep than their bed partners despite lower sleep efficiency and higher rates of restless legs syndrome.

STRUCTURED ABSTRACTO_ST_ABSImportanceC_ST_ABSSexual dysfunction can occur after midurethral sling (MUS) and transvaginal prolapse surgery. It remains unclear whether these procedures impact the clitoris, despite its role in sexual function and proximity to the MUS and vagina. ObjectivesTo compare postoperative sexual function and clitoral features by MUS and vaginal surgery approach after transvaginal prolapse repair with/without concomitant MUS. DesignCross-sectional ancillary study of magnetic resonance imaging (MRI) and sexual function data from the Defining Mechanisms of Anterior Vaginal Wall Descent study. SettingEight clinical sites in the US Pelvic Floor Disorders Network. Participants: 88 women with uterovaginal prolapse who underwent vaginal mesh hysteropexy or vaginal hysterectomy with uterosacral ligament suspension with/without MUS between 2013-2015. Data were analyzed between September 2021-June 2023. ExposuresBetween June 2014-May 2018, participants underwent pelvic MRI 30-42 months after surgery, or earlier if reoperation was desired. Sexual activity and function at baseline and 24-48-month follow-up were evaluated using the Pelvic Organ Prolapse/Incontinence Sexual Questionnaire, IUGA-Revised (PISQ-IR). Clitoral features were obtained from postoperative MRI-based 3-dimensional models. Main Outcomes and MeasuresPISQ-IR scores and clitoral features (size, position). ResultsEighty-two women (median [range] age, 65 [47-79] years) were analyzed: 45 MUS (22 hysteropexy, 23 hysterectomy) and 37 No-MUS (19 hysteropexy, 18 hysterectomy). Postoperatively, 25 MUS, 12 No-MUS, 20 hysteropexy, and 17 hysterectomy patients were sexually active (SA). Overall, within the MUS and vaginal surgery groups, sexual function remained unchanged or improved (most PISQ-IR change from baseline scores were [&ge;]0) among SA and NSA women. Among SA women after surgery, the MUS group (vs No-MUS) had a poorer PISQ-IR arousal/orgasm (SA-AO) score (median, 3.5 vs 4.3; P=.02). The hysteropexy group (vs hysterectomy) had less improvement in PISQ-IR SA-AO score (median, 0.0 vs 0.3; P=.01). Women with MUS (vs without) had a smaller clitoral glans thickness (median, 9.0 mm vs 10.0 mm; P=.008) and clitoral body volume (median, 2783.5 mm3 vs 3587.4 mm3; P=.01). Conclusions and RelevanceSA women with MUS (vs without) or hysteropexy (vs hysterectomy) experienced poorer postoperative sexual function. MUS was linked to a smaller clitoris. Future studies should explore surgery-induced changes in clitoral anatomy and sexual function. KEY POINTSO_ST_ABSQuestionC_ST_ABSHow do sexual function and clitoral anatomy differ by midurethral sling placement and vaginal surgery approach? FindingsThis cross-sectional study compared patient-reported sexual function outcomes and 30-42-month postoperative magnetic resonance imaging-based 3-dimensional clitoral models of 82 women after vaginal prolapse surgery with or without concomitant midurethral sling. Midurethral sling (vs no sling) and vaginal mesh hysteropexy (vs vaginal hysterectomy) were associated with poorer postoperative sexual function outcomes. Additionally, midurethral sling was associated with a smaller clitoral glans and body. MeaningMidurethral sling and vaginal mesh hysteropexy were associated with, and may adversely alter, postoperative sexual function and/or clitoral anatomy. VISUAL ABSTRACT/PROMOTIONAL IMAGE O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/26351291v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@904497org.highwire.dtl.DTLVardef@187514aorg.highwire.dtl.DTLVardef@e9e799org.highwire.dtl.DTLVardef@640f1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

Abstract: Background: Vascular access is essential in treating patients undergoing prolonged endovenous therapy such as chemotherapy, antibiotics, and parenteral nutrition. Since the 1990s, when PICCs (peripherally inserted central catheters) appeared, vascular access options have expanded significantly, revolutionizing the treatment landscape for all types of patients. Objective: To analyze and describe the profile of the use of PICCs in a Brazilian quaternary hospital over 10 years with data collected by the infusion therapy team. Evaluating the number of PICCs implanted over the years, patients epidemiology and clinical characteristics, insertion details, associated complications, and the reason for removal. Methods: A retrospective cohort study that employs a quantitative, non-experimental approach to classify and statistically analyze past events associated with 21,652 PICCs implanted from January 2012 to December 2021 in a quaternary hospital at Sao Paulo - Brazil. All the catheters were implanted, and the data was collected by a team of nurses specializing in infusion therapy. We analyzed the number of catheters implanted over the years, insertion characteristics, patients epidemiology and clinical data, possible associated complications, and the reason for removal. Statistical analyses were conducted using R software (version 4.4.1) and SPSS (version 29) for Windows (IBM Corp, Armonk, NY). Results: During the specified period, 21,652 catheters were analyzed. The patients gender distribution was nearly balanced (48.2% versus 51.8%), and the average age was 66 years. Cardiovascular and metabolic issues were the most common comorbidities, and between 2020 and 2021, 29.3% of the sample tested positive for COVID-19. The most common location of hospitalization and implantation was the medical-surgical clinic (31.6% - 41.4%), and the most used type of catheter was the Power Picc (83.9%). The estimated complication incidence density is 2.94 complications per 1,000 catheter-days. Almost all the PICCs (98,2%) were adequately located at the cavo-atrial junction after the first attempt, 82.2% of catheters were removed after therapy, and the median duration of catheter use was 12 days. Conclusion: PICCs are widely employed for drug infusion, with their use growing progressively due to specialized teams greater availability and training. The high efficiency of these devices with a relatively low risk of complications already observed in previous studies was reinforced by the findings of this study of more than 20,000 catheters.

Genome-wide association studies of idiopathic pulmonary fibrosis (IPF) have identified 35 common genetic risk loci associated with IPF susceptibility. In this study, we evaluated the effects of the reported variants in clinically curated non-European individuals. Despite limited sample sizes, we observed partial replication, limited transferability of some variants and evidence of ancestry-specific effects. The MUC5B promoter variant rs35705950 emerged as the dominant and most consistent signal across ancestries. Our findings highlight the need for larger, well-characterised studies in understudied populations to support robust discovery and translation.

Background Regulatory inconsistency across African countries contributes to duplicative scientific assessments, prolonged approval timelines, and delayed access to essential medical products. To inform the operationalisation of the African Medicines Agency (AMA), the African Medicines Regulatory Harmonisation (AMRH) programme implemented Africa's first continental pilot study for the scientific evaluation and listing of human medicinal products. This study evaluates the pilot's procedural performance and examines how continental scientific opinions were translated into national regulatory decisions through reliance mechanisms. Methods and Findings A mixed-methods programme evaluation was conducted using regulatory datasets generated during the pilot study. Quantitative data included assessment timelines, GMP inspection outcomes and national post-listing regulatory actions. Retrospective qualitative thematic analysis was applied to governance documents and National Regulatory Authority (NRA) feedback to identify legal, institutional and procedural determinants influencing uptake. Of 64 expressions of interest, 24 products progressed to full evaluation and 12 received positive continental scientific opinions. Ten met the predefined performance target of [&le;]210 working days. Twenty-four GMP inspections identified no critical deficiencies and aligned with global regulatory benchmarks. National uptake demonstrated active reliance: full reliance (continental opinion as primary basis for national approval) for 7 products (58%); sequential reliance (continental assessment supplemented with targeted national queries) for 3 products (25%); and supplemented national review (separate national assessment undertaken) for 2 products (17%). Products with broader market strategies achieved registration in up to 23 African countries within a median of 77 working days post-listing. Variability in uptake reflected national legal authority, administrative requirements, and applicant submission strategies Conclusions The pilot study demonstrates the feasibility of a continent-wide regulatory assessment mechanism capable of producing trusted scientific outputs and enabling reliance-based national decision-making in Africa. While reliance was widely applied, heterogeneity in national procedures and administrative sequencing affected time to national registration. Findings provide empirical evidence to inform the AMA scale-up, highlighting the need for harmonised reliance pathways, streamlined administrative processes, and coordinated digital regulatory infrastructure.

The immunohistochemistry (IHC) methods widely used in diagnostic medicine and biomedical research are kinetically complex reaction-diffusion processes that, ideally, produce stain intensities correlated with the local antigen concentration. Yet after 75 years of use, practical theoretical tools to rigorously plan and interpret IHC experiments are still lacking. Because modeling the reactions requires time-consuming computer simulation, impractical for regular use, most protocols are optimized empirically, without detailed knowledge of the reaction rates and antigen-antibody equilibria. The resulting stain intensities can be calibrated against standards with known antigen abundance, but they are typically not interpretable in terms of chemical antigen concentrations. To address these limitations, we developed a fast interpolation method to model reaction-diffusion behavior, and experimental methods to characterize IHC kinetic parameters in formalin-fixed paraffin-embedded (FFPE) samples. Used together, these allow experimental measurement of both the chemical concentration of antigen in the sample and the reaction-diffusion parameters consistent with the assay results. Results show 1) direct immunofluorescent detection has low nanomolar sensitivity with >1000-fold dynamic range, and 2) antibody diffusion rates in FFPE samples can be >1000-fold slower than in aqueous solutions, producing diffusion-limited conditions in which the IHC reaction time course may depend on the sample antigen concentration. Awareness of these details is necessary to avoid potential underestimation of both the absolute and relative antigen concentrations in different samples that may occur if staining is stopped before reaching equilibrium. Software tools are provided to allow users to rapidly model IHC reaction time courses and to fit experimental time course data with candidate reaction parameters. The principles described here apply equally to other tissue-based "spatial omics" analyses and should be considered when designing and interpreting experiments requiring any macromolecule to diffuse into and react in a tissue section. SIGNIFICANCEThe theoretical and experimental framework described here advances IHC staining from a qualitative or semi-quantitative method towards a more rigorously quantitative assay. The practical ability to predict IHC reaction kinetics and fit reaction parameters to experimental data has the potential to advance IHC applications in diagnostic medicine and biomedical research in three ways: 1) interpretation of experimental and diagnostic samples stained under different conditions can be more objective, facilitating comparison of results from different protocols and different laboratories; 2) IHC staining can be interpreted as molar chemical antigen-antibody concentrations calculated from the reaction parameters measured in the studied sample; 3) the correlation between antigen concentration and biological behavior can be examined more reliably. Practical software tools are provided.

Background: The etiology and nosological status of seasonal affective disorder (SAD) as a specifier of depressive episodes versus a transdiagnostic disorder are the subject of debate. In this study, we investigated the underlying etiology of SAD and dimensional seasonality by examining their association with latitude and genetic risk for a range of traits, and investigated gene-environment interactions. Methods: This study included 12,460 adults aged 18-90 with a history of depression from the Australian Genetics of Depression Study. Regression models included predictors for latitude (distance from equator) and polygenic scores for eight traits; major depressive disorder, bipolar disorder, anxiety disorders, chronotype, sleep duration, body mass index, vitamin D levels, and educational attainment. Outcomes were SAD status and general seasonality score. Results: SAD was positively associated with latitude (OR[95%CI] = 1.05[1.03-1.06], padjusted<0.001), and there was nominal evidence of additive and multiplicative interactions between chronotype genetic risk and latitude (OR = 0.99[0.99-0.99], padjusted=0.381; OR=0.98[0.97-0.99], padjusted=0.489). General seasonality score was associated with latitude (IRR=1.01[1.01-1.01], padjusted 0.001) and genetic risk for major depressive disorder (IRR =1.02[1.01-1.03], padjusted<0.001), bipolar disorder (IRR=1.02[1.01-1.03], padjusted=0.001), anxiety disorders (IRR=1.03[1.01-1.04], padjusted<0.001), vitamin D levels (OR=0.89[0.80-0.95], padjusted=0.048), and educational attainment (IRR=0.97[0.96-0.99], padjusted<0.001). Conclusions: These findings enhance understanding of SAD etiology, highlighting contributions of psychiatric genetic risk and geographic measures on seasonal behavior, and support examining seasonality as a continuous dimension.

BackgroundExcessive accumulation of fibrillar collagen causes pathological scarring and fibrosis. A promising anti-fibrotic strategy targets the extracellular assembly of collagen fibrils rather than intracellular synthesis pathways. We previously developed a chimeric monoclonal antibody targeting the C-terminal telopeptide of the 2(I) chain of human collagen I that effectively disrupts fibrillogenesis. This study details the engineering of a humanized antibody variant optimized for therapeutic application, augmented with a collagen-binding peptide (CBP) to enhance targeted retention in fibrotic tissues. MethodsA humanized ACA was engineered by in silico homology modeling, complementarity-determining region grafting, and sequence optimization to eliminate chemical liabilities. Variants were expressed in mammalian cells and evaluated for binding kinetics and specificity. To improve spatial localization, the CBP was fused to the antibody. The lead variant was assessed for in vitro cytotoxicity, matrix retention, and in vivo efficacy using a rabbit model of post-traumatic knee arthrofibrosis. ResultsThe humanized ACA variants maintained high specificity and affinity for the 2Ct target domain. Fusing the CBP to the C-terminus of the light chain (C-cbpACA) successfully enhanced matrix retention without compromising target engagement or causing cellular toxicity. In the rabbit arthrofibrosis model, intra-articular C-cbpACA delivery significantly reduced flexion contracture and decreased total collagen deposition in the joint capsule compared to untreated controls. ConclusionWe successfully engineered a clinically viable, humanized, and matrix-targeted anti-fibrotic antibody that specifically inhibited extracellular collagen assembly and exhibited enhanced localization within fibrotic tissues. This construct represents a promising therapeutic strategy for mitigating pathological scarring and improving post-traumatic functional outcomes.

A Wearable Monitoring System (WMS), comprising a chest patch, wrist-worn pulse oximeter, and arm-worn blood pressure device, was developed in preparation for a pilot Randomised Controlled Trial (RCT) on a UK surgical ward. The system was designed to support continuous physiological monitoring and early detection of deterioration. An initial prototype user interface was developed by the research team based on prior clinical experience and engineering knowledge. To ensure suitability for clinical practice, iterative user-centred refinement was undertaken through a series of clinician focus groups and wearability assessments. Six focus groups were conducted between November 2019 and May 2021 involving multidisciplinary healthcare professionals. Feedback from these sessions informed successive interface and system modifications. System development spanned the COVID-19 pandemic, during which the WMS was rapidly adapted and deployed to support clinical care on isolation wards. Feedback obtained during this period was incorporated into later versions of the system and provided a unique opportunity to examine changes in clinician priorities under pandemic conditions. Clinicians consistently prioritised alert visibility, alarm fatigue mitigation, parameter flexibility, and centralised monitoring. Notably, preferences regarding alert modality and access mechanisms evolved over time: early enthusiasm for mobile or smartphone-type devices shifted towards a preference for fixed, ward-based displays and audible alerts at the nurses station following pandemic deployment. Building on previous wearability testing in healthy volunteers, wearability testing using a validated questionnaire was completed by 169 patient participants during the RCT. The chest patch and pulse oximeter demonstrated high tolerability, whereas the blood pressure cuff showed poor wearability and was removed from the final system. These findings demonstrate the importance of iterative, clinician-led design for wearable WMS and highlight how extreme clinical contexts such as the COVID-19 pandemic can significantly reshape perceived requirements for safety-critical monitoring technologies.

BackgroundAn upsurge in Streptococcus pyogenes infections 2022-2023 highlighted potential benefits of point-of-care tests (POCT) to support clinical pathways, prevent outbreaks, and optimise antibiotic use. ObjectivesWe conducted a pilot research study in a west London paediatric emergency department (ED) to determine whether a molecular POCT had potential to alter management in children who were also having a conventional throat swab taken for culture. MethodsChildren <16 years presenting to ED who had a throat swab requested by a clinician were invited to have a second swab taken for research purposes only. Clinical management was unaffected by the research swab result, which was processed using a molecular POCT that was not approved for use in the host NHS Trust. ResultsPrevalence of streptococcal infection was low during the study (May 2023-June 2025); swab positivity in symptomatic children was 12.8% (6/47). Overall, 38/49 (77.6%) participants who had throat swabs received antibiotics. Of those children recommended to receive antibiotics, 29/38 (76.3%) had a negative POCT. Mean time to reporting of positive throat swab culture results was 3.67 days (range 3-5 days) leading to occasional delay in treatment, although POCT identified positive results within minutes. ConclusionAntibiotic use was frequent and could be avoided or stopped by use of a rule out POCT in over three-quarters of children in the ED, if suspicion of S. pyogenes is the main driver for prescribing. POCT were easy to process and produced immediate results compared with culture, in theory enabling timely decision-making and avoiding treatment delay.

Alternative-splicing events (ASE) increase transcriptomic variability and play key roles in biological functions. The contribution of ASE to bipolar disorder (BD) remains largely unexplored. We performed a Transcriptome-Wide Alternative-Splicing Analysis (TWASA) to identify ASEs and genes potentially involved in BD. The study comprised 635 individuals: a discovery sample (DS) of 31 individuals from eight multiplex BD families (16 BD cases; 15 unaffected relatives), and a replication sample (RS) of 604 subjects (372 BD cases; 232 controls). Sequencing was conducted on RNA from lymphoblastoid cell lines (DS) and whole blood (RS). TWASA was performed using VAST-TOOLS (VT), rMATS (RM), and MAJIQ/MOCCASIN (MCC). Gene-set association analyses of genes containing ASEs were performed across six psychiatric disorders. Novel ASE (nASE) were investigated in the DS using FRASER. Limited gene overlap was observed across TWASA tools. MCC identified 2,031 complex ASEs involving 1,508 genes, showing the strongest genetic association with BD across psychiatric phenotypes. Prioritization of MCC-identified ASE genes yielded 441 candidates, including DOCK2 as top candidate from the DS. Replication was obtained for 98 genes, five with an identical ASE, and four (RBM26, QKI, ANKRD36, and TATDN2) showing a concordant percentage-spliced-in direction with the DS. Finally, 578 nASE were identified in the DS, with no evidence of familial segregation or differences in ASE types. This first TWASA in BD reveals tool-specific variability, complex ASE for genes specifically associated with BD, and novel candidate genes for BD. Alternative transcript isoform abundance may represent a mechanism contributing to BD pathophysiology.

PurposeDiagnostic yield from exome and genome sequencing varies widely across studies. It remains unclear how much of this variation reflects patient-level factors (e.g., sex, clinical features, race/ethnicity, genetic ancestry) versus site-level practices such as sequencing modality or variant interpretation workflows. We aimed to quantify the contributions of these factors to diagnostic outcomes across five U.S. clinical sequencing sites. MethodsWe performed a cross-sectional analysis of 3,008 prenatal, neonatal, and pediatric cases from the NHGRI Clinical Sequencing Evidence-Generating Research (CSER) consortium (2017-2023). Clinical indications spanned neurodevelopmental, neurological, immunological, metabolic, craniofacial, skeletal, cardiac, prenatal, and oncologic presentations. Genetic ancestry was inferred from sequencing data, and variants were interpreted using ACMG/AMP guidelines to classify DNA-based diagnoses. Generalized linear mixed models were used to estimate associations between diagnostic yield and fixed effects (sex, prenatal status, isolated cancer, number of clinical indications, sequencing modality, race/ethnicity, and genetic ancestry), while modeling study site as a random effect to quantify between-site variation. ResultsThe overall diagnostic yield was 19.0%. Multiple clinical indications (OR=1.47, 95% CI 1.20-1.80, p<0.001) were associated with higher diagnostic yield, and male sex (OR=0.80, 95% CI 0.66-0.96, p=0.017) and prenatal status (OR=0.63, 95% CI 0.44-0.90, p=0.012) were associated with lower yield. Sequencing modality, race/ethnicity, genetic ancestry, and isolated cancer were not statistically significantly associated with diagnostic outcomes.. A model without fixed effects attributed [~]10% of variance in diagnostic yield to between-site differences. After adjusting for covariates, site-level variance decreased to 5.7%, indicating consistent variation across sites not explained by measured patient factors. ConclusionAcross five sites, patient-level clinical features influenced diagnostic yield, but substantial site-level variation remained even after adjustment. Differences in variant interpretation, or case-classification practices may contribute to this residual variability. Further efforts to increase consistency in exome- and genome-sequencing diagnostic workflows may help reduce inter-site differences.

A multiplex diagnostic test is evaluated for self-reported long COVID associated persistent symptoms and a poor recovery from a SARS-CoV-2 infection. A mass-standardised concentration of total antibodies (AC), high-quality (HQ) antibodies and percentage of HQ antibodies (HQ%) is assessed against a spectrum of spike proteins to the SARS-CoV-2 variants: Wuhan, , {delta}, and the Omicron variants BA.1, BA.2, BA.2.12.1, BA.2.75, BA.5, CH.1.1, BQ.1.1 and XBB.1.5 in three cohorts. A cohort of control patients (n = 46) recovered (CC) and a cohort of self-declared long COVID patients (n = 113) (LCC). A nested Receiver Operating Characteristic (ROC) analysis, performed for the variant with lowest HQ concentration in the spectrum, produced an area under the curve and AUC = 0.61 (0.53-0.70) for the CC vs LCC cohorts. For the LCC cohort, the cut-off thresholds for AC = 0.8 mg/L, HQ = 1.5 mg/L and HQ% of 34% were determined, leading to a 71% sensitivity and 66% specificity derived by the Youden metric. The cohorts may be fully classified based on ROC and outlier analysis to give an incidence of persistent virus 62% (95% CI 52% - 71%), hyperimmune 12% (95% CI 7% - 20%) and unclassified, 26% (95% CI 18% - 35%). The overall diagnostic accuracy for both the hyper and hypo immune is 69%. All clinical interventions can now be tailored for the heterogenous long COVID patient cohort.

PurposeTo characterize maternal transport patterns in Iowa, a state with levels of maternal care and without formal perinatal regions, and assess whether transport decisions reflect efficient, risk-appropriate coordination. MethodsWe analyzed 2010-2023 Iowa birth records, which included 2,251 maternal transports between obstetric facilities across 106 unique routes. We characterized transport patterns and applied a community detection algorithm to identify "communities" of obstetric facilities that disproportionately transport among themselves. FindingsSuburban and rural counties have elevated transport rates compared to urban counties. 2,189 transports (97%) were from lower-to higher-level facilities. Among these, 2,037 (93%) were to Level III tertiary care centers. 567 transports (25.2%) bypassed a closer facility offering an equivalent or higher level of care than its destination facility. Health system affiliation was associated with bypassing transport, indicating potential organizational rather than purely geographic drivers of transport decisions. Three "communities" of obstetric facilities largely shaped by geographic proximity were identified. ConclusionsAlthough Iowa does not have formal perinatal regions, patterns of maternal transport are mostly in line with three de facto regions. Some potential inefficiencies were identified, such as obstetric facilities transporting to a farther facility when a closer facility offered the same level of care or higher. These findings may help identify opportunities to enhance care coordination among obstetric facilities, optimize maternal transport networks, and improve regionalization of maternal care.

Background: Elevated lipoprotein(a) [Lp(a)] is a known risk factor for several cardiovascular-related diseases established from multiple genetic and observational studies. However, the underlying mechanisms mediating the effects of Lp(a) levels on cardiovascular disease risk and major adverse cardiovascular events (MACE) are unclear. The aim of this study was to identify proteins downstream of Lp(a) using mendelian randomization (MR) - a genetic causal inference approach. Methods: A two-sample MR was performed by initially identifying Lp(a) genetic instruments based on data from genome wide association studies (GWAS) of Lp(a) blood concentrations. These instruments were then tested for association with proteins from proteomic pQTL data (Olink from UK Biobank, 2940 proteins and SomaScan from deCODE, 4907 proteins). Results: A total of 521 proteins associated with Lp(a) were identified. Using pathway enrichment analysis, the following MACE-relevant pathways were identified comprising a total of 91 Lp(a) downstream proteins: oxidized phospholipid-related, chemotaxis of immune cells and endothelial cell activation, pro-inflammatory monocyte activation, neutrophil activity, coagulation, and lipid metabolism. Conclusion: The results suggest that the influence of Lp(a) treatments is primarily through modifying inflammation rather than lipid-lowering, thus providing insight into the mechanistic framework which mediates the effects of elevated Lp(a) on atherosclerotic cardiovascular disease.

This analysis evaluates the feasibility and psychometric properties of daily digital cognitive assessments (DCAs) delivered on smartphones using data from the large, international Identifying Digital Endpoints to Assess FAtigue, Sleep and acTivities of daily living in Neurodegenerative disorders and Immune-mediated inflammatory diseases (IDEA-FAST) study. The data we analyse were collected from patients with neurodegenerative diseases (NDDs) and immune-mediated inflammatory diseases (IMIDs), and healthy controls (a subset who participated in all phases of the study, total N=977) in their own homes. These data were obtained alongside data from other devices that monitored physiology, kinematics, and sleep quality. Following a baseline visit, participants were remotely monitored via three scheduled daily sessions for 6-7 days in each of 4 active assessment phases (APs). APs were separated by 6-week intervals. Daily schedules comprised a morning psychomotor vigilance task (PVT) with eDiary, afternoon session (eDiary only), and an evening digit symbol substitution task (DSST) with eDiary. We evaluated session coverage using logistic mixed effects, test-retest reliability using ICCs, disease impacts on performance using linear mixed effect ANCOVA, and familiarisation using linear mixed effects. Overall coverage was 67.5% for the PVT and 77.0% for the DSST, with no significant differences between the healthy volunteers and disease cohorts. Coverage varied significantly by time-of-day (Evening > Morning > Afternoon), and improved with age, with an interaction revealing session time-of-day affected older participants less, all p < .001. Coverage was highest in AP 1 and reduced in subsequent APs. AP-day effects on coverage interacted significantly with AP, with a modest decline over AP 1, and the pattern reversed in APs 2-4. Baseline reliability was good (> .70) for both PVT mean reaction time and DSST total correct across all cohorts, and the movement-based measure from the DSST ranged [.55, .75], with lower values in the Parkinson's Disease and Primary Sjogren's Syndrome cohorts. Both tasks showed significant cohort effects, with performance in IMID cohorts intermediate between healthy controls and NDD. Longitudinal analysis revealed significant familiarisation effects in DSST. This was greatest in healthy controls, with significant attenuation of these effects in disease cohorts. No effect of familiarisation was seen in the PVT. Collectively, these results support the usefulness of at-home cognitive assessment on smartphones. Brief measures of cognition can be captured remotely in disease as well as controls with good adherence and sensitivity to distinguish known patient groups from healthy controls.

Preconception weight loss by metabolic-bariatric surgery (MBS) improves maternal-fetal outcomes, but little is known about its impact on offspring growth and health. The preconception bariatric surgery and child health outcomes (POSIT) study aims to estimate the effects of maternal MBS-induced preconception weight loss on infant and childhood body size, growth, and related outcomes. This report presents the methods used to construct the POSIT cohort and its baseline characteristics. This retrospective cohort study sampled members from a United States healthcare system aged 18 and older with a singleton, live birth to create three study groups: 1) a treatment group including women who underwent preconception MBS and subsequently became pregnant (n=1,374); 2) a control group matched to the MBS pre-surgery body mass index (BMI) (pre-surgery controls, n=13,740); and 3) a second control group matched to the MBS post-surgical, pre-pregnancy BMI (pre-pregnancy controls, n=13,740). MBS and pre-surgery BMI controls showed slight imbalances in that pre-surgery BMI controls were on average ~6 months younger, had 0.6 lower BMI (44.5 kg/m2) at the time of their pregnancy and were more likely to have become pregnant in earlier years than the MBS group prior to surgery. MBS and pre-pregnancy controls had comparable age (mean {+/-} SD 33 {+/-} 5 years), pre-pregnancy BMI (33 {+/-} 6 kg/m2), and year of delivery. Following matching, the MBS group had similar socioeconomic and health disparities as the pre-surgery control group, and both were worse than pre-pregnancy control group. Pregestational maternal comorbidity index improved after MBS and matched the pre-pregnancy controls. Upon extraction of offspring growth patterns and mediation analyses of maternal weight loss and metabolic responses to MBS, study findings will investigate effects of preconception weight loss by MBS on short- and long-term child health outcomes. Results will guide future studies focusing on improving maternal preconception weight and maternal-fetal outcomes.