Biology subjects

Sweeney, N.

Publications and source records attributed to Sweeney, N..

3 recordsLinked to original sources

bioRxiv2026

An end-to-end framework for single-cell-resolution, whole-transcriptomic spatial profiling in post-mortem human brain

Single-cell resolution spatial transcriptomics enables transcriptome-wide molecular profiling within intact tissue architecture, providing unprecedented opportunities to investigate cellular organization and disease-associated molecular states in the human brain. However, applying these technologies to post-mortem human brain tissue remains challenging due to RNA degradation, heterogeneity in tissue preservation, and a lack of standardized analytical workflows. These challenges are particularly pronounced for whole-transcriptome platforms, where successful implementation requires optimization of both experimental and computational procedures. Here, we present an end-to-end framework for single-cell-resolution, whole-transcriptome spatial transcriptomics of fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) post-mortem human brain tissue. The framework combines an optimized experimental workflow with a preservation-agnostic bioinformatics pipeline for data processing, integration, and annotation. Experimentally, we show that a condensed two-day Visium HD workflow provides improved library quality, lowered qPCR cycle thresholds, and more consistent fragment size distributions. Sequencing saturation analyses further identified cost-effective sequencing depths that maximize transcript recovery while minimizing redundant sequencing. Computationally, we established a scalable workflow incorporating DAPI-based nuclear segmentation, transcript assignment, quality control, reference-guided integration, clustering, and cell-type annotation. We implemented a reference-based highly variable gene selection strategy to enable robust cross-sample harmonization independent of tissue preservation method. Application of this framework to seven Alzheimers disease frontal cortex specimens (five FF and two FFPE) generated a unified single-cell spatial transcriptomic atlas comprising more than 530,000 spatially resolved cells. The integrated dataset resolved major neuronal, glial, and vascular cell populations, recapitulated expected cortical architecture, and enabled direct comparison of FF- and FFPE-derived spatial transcriptomic profiles. Together, this work provides a practical experimental and computational framework for single-cell resolution, whole-transcriptome spatial transcriptomics in post-mortem human brain tissue and delivers a publicly available resource that expands the utility of archived and frozen specimens for studies of neurodegeneration and other neurological disorders. ImportanceSpatial transcriptomics of human post-mortem brain tissue is limited by RNA degradation, preservation variability, and lack of standardized workflows. Here, we present an end-to-end framework combining an optimized two-day Visium HD protocol with a preservation-agnostic bioinformatics pipeline. This approach improves library quality, defines efficient sequencing strategies, and enables robust spatial profiling across both FF and FFPE samples. Applied to Alzheimers disease brain tissue, it generates high-resolution single-cell spatial data and expands the utility of archived and frozen specimens for studying neurodegenerative diseases.

neuroscience↗

bioRxiv2018

Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants

BACKGROUNDGenetic disorders are a leading cause of morbidity and mortality in infants. Rapid Whole Genome Sequencing (rWGS) can diagnose genetic disorders in time to change acute medical or surgical management (clinical utility) and improve outcomes in acutely ill infants.\n\nMETHODSRetrospective cohort study of acutely ill inpatient infants in a regional childrens hospital from July 2016-March 2017. Forty-two families received rWGS for etiologic diagnosis of genetic disorders. Probands received standard genetic testing as clinically indicated. Primary end-points were rate of diagnosis, clinical utility, and healthcare utilization. The latter was modelled in six infants by comparing actual utilization with matched historical controls and/or counterfactual utilization had rWGS been performed at different time points.\n\nFINDINGSThe diagnostic sensitivity was 43% (eighteen of 42 infants) for rWGS and 10% (four of 42 infants) for standard of care (P=.0005). The rate of clinical utility for rWGS (31%, thirteen of 42 infants) was significantly greater than for standard of care (2%, one of 42; P=.0015). Eleven (26%) infants with diagnostic rWGS avoided morbidity, one had 43% reduction in likelihood of mortality, and one started palliative care. In six of the eleven infants, the changes in management reduced inpatient cost by $800, 000 to $2,000,000.\n\nDISCUSSIONThese findings replicate a prior study of the clinical utility of rWGS in acutely ill inpatient infants, and demonstrate improved outcomes and net healthcare savings. rWGS merits consideration as a first tier test in this setting.

clinical trials↗

bioRxiv2017

The NSIGHT1 Randomized Controlled Trial: Rapid Whole Genome Sequencing for Accelerated Etiologic Diagnosis in Critically Ill Infants

ImportanceGenetic disorders, including congenital anomalies, are a leading cause of morbidity and mortality in infants, especially in neonatal and pediatric intensive care units (NICU and PICU). While genomic sequencing is useful for diagnosis of genetic diseases, results are usually reported too late to guide inpatient management.\n\nObjectiveTo test the hypothesis that rapid whole genome sequencing (rWGS) increases the proportion of infants in NICUs and PICUs receiving a genetic diagnosis within 28 days.\n\nDesignAn investigator-initiated, partially blinded, pragmatic, randomized controlled study with enrollment from October 2014 - June 2016, and follow up until December 2016.\n\nSettingA regional neonatal and pediatric intensive care unit in a tertiary referral childrens hospital.\n\nParticipantsSixty five of 129 screened families with infants aged less than four months, in neonatal and pediatric intensive care units, and with illnesses of unknown etiology, completed the study.\n\nInterventionParent and infant trio rWGS.\n\nMain Outcome and MeasureThe hypothesis and end-points were formulated a priori. The primary end-point was rate of genetic diagnosis within 28 days of enrollment or first standard test order.\n\nResultsTwenty six female proband infants, 37 male infants, and two infants of undetermined sex were randomized to receive rWGS plus standard tests (n=32, cases) or standard tests alone (n=33, controls). The study was terminated early due to loss of equipoise: 63% (21) controls received genomic sequencing as standard tests. Nevertheless, intention to treat analysis showed the rate of genetic diagnosis within 28 days to be higher in cases (31%, ten of 32) than controls (3%, one of 33; difference, 28% [95% CI, 10% to 46%]; p=0.003). Among infants enrolled in the first 25 days of life, the rate of neonatal diagnosis was higher in cases (32%, seven of 22) than controls (0%, zero of 23; difference, 32% [95% CI, 11% to 53%]; p=0.004). Age at diagnosis (median in cases 25 days, range 14-90 days vs median in controls 130 days, range 37-451) and time to diagnosis (median in cases thirteen days, range 1-84 days vs median in controls 107 days, range 21-429 days) were significantly less in cases than controls (p=0.04).\n\nCONCLUSIONSrWGS increased the proportion of infants in a regional NICU and PICU who received a timely diagnosis of a genetic disease. Additional, adequately powered studies are needed to determine whether accelerated diagnosis is associated with improved outcomes in this setting. ClinicalTrials.gov Identifier: NCT02225522.

clinical trials↗