RESUMEN
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network and Genomics Research to Elucidate the Genetics of Rare Disease Consortium. Across six routinely collected biospecimens, 61% of quantified genes were not influenced by genome build. However, we identified 1,492 genes with build-dependent quantification, 3,377 genes with build-exclusive expression, and 9,077 genes with annotation-specific expression across six routinely collected biospecimens, including 566 clinically relevant and 512 known OMIM genes. Further, we demonstrate that between builds for a given gene, a larger difference in quantification is well correlated with a larger change in expression outlier calling. Combined, we provide a database of genes impacted by build choice and recommend that transcriptomics-guided analyses and diagnoses are cross referenced with these data for robustness.
RESUMEN
Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.
RESUMEN
BACKGROUND: Hip fractures are one of the most common injuries experienced by the general population. Despite advances in surgical techniques, postoperative mortality rates remain high. identifying relevant clinical factors associated with mortality is essential to preoperative risk stratification and tailored post-surgical interventions to improve patient outcomes. The purpose of this study aimed to identify preoperative risk factors and develop predictive models for increased hip fracture-related mortality within 30 days post-surgery, using one of the largest patient cohorts to date. METHODS: Data from the American College of Surgeons National Surgical Quality Improvement Program database, comprising 107,660 hip fracture patients treated with surgical fixation was used. A penalized regression approach, least absolute shrinkage and selection operator was employed to develop two predictive models: one using preoperative factors and the second incorporating both preoperative and postoperative factors. RESULTS: The analysis identified 68 preoperative factor outcomes associated with 30-day mortality. The combined model revealed 84 relevant factors, showing strong predictive power for determining postoperative mortality, with an AUC of 0.83. CONCLUSIONS: The study's comprehensive methodology provides risk assessment tools for clinicians to identify high-risk patients and optimize patient-specific care.
