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Sensitivity to Environmental Stress and Adversity and Lung Cancer.
JAMA Netw Open
January 2025
Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland.
Importance: Sensitivity to environmental stress and adversity may influence lung cancer risk, highlighting a critical link between psychosocial factors and cancer etiology.
Objective: To evaluate whether genetically estimated sensitivity to environmental stress and adversity is associated with lung cancer risk.
Design, Setting, And Participants: Data were obtained from a genome-wide association study identifying 37 independent genetic variants strongly associated with sensitivity to environmental stress and adversity and a cross-ancestry genome-wide meta-analysis from the International Lung Cancer Consortium.
Fibroblast transcriptomics uncovers pathogenic genomic variants in individuals with exome-negative childhood onset epilepsy.
Epilepsia
January 2025
Applied Translational Neurogenomics Group, Vlaams Instituut voor Biotechnology (VIB) Center for Molecular Neurology, VIB, Antwerp, Belgium.
Objective: This study aims to improve genetic diagnosis in childhood onset epilepsy with neurodevelopmental problems by utilizing RNA sequencing of fibroblasts to identify pathogenic variants that may be missed by exome sequencing and copy number variation analysis.
Methods: We enrolled 41 individuals with childhood onset epilepsy and neurodevelopmental problems who previously had inconclusive genetic testing. Fibroblast samples were cultured and analyzed using RNA sequencing to detect aberrant expression, aberrant splicing, and monoallelic expression using the Detection of RNA Outlier Pipeline (DROP) pipeline.
Noncoding variants and sulcal patterns in congenital heart disease: Machine learning to predict functional impact.
iScience
February 2025
Division of Newborn Medicine, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
Neurodevelopmental impairments associated with congenital heart disease (CHD) may arise from perturbations in brain developmental pathways, including the formation of sulcal patterns. While genetic factors contribute to sulcal features, the association of noncoding variants (ncDNVs) with sulcal patterns in people with CHD remains poorly understood. Leveraging deep learning models, we examined the predicted impact of ncDNVs on gene regulatory signals.
View Article and Find Full Text PDFNext-Generation Sequencing Analysis on Image-Guided Biopsy Samples in Early-Stage Lung Cancer: Feasibility Study and Comparison With Surgical Samples.
JTO Clin Res Rep
February 2025
Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, New York.
Introduction: Limited information exists on next-generation sequencing (NGS) success for lung tumors of 30 mm or less. We aimed to compare NGS success rates across biopsy techniques for these tumors, assess DNA sequencing quality, and verify reliability against surgical resection results.
Methods: We used data from the Initiative for Early Lung Cancer Research on Treatment study, including patients with lung tumors measuring 30 mm or less who had surgery and NGS on biopsies since 2016.
Context-specific eQTLs provide deeper insight into causal genes underlying shared genetic architecture of critically ill COVID-19 and idiopathic pulmonary fibrosis.
HGG Adv
January 2025
Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA. Electronic address:
Most genetic variants identified through genome-wide association studies (GWAS) are suspected to be regulatory in nature, but only a small fraction colocalize with expression quantitative trait loci (eQTLs, variants associated with expression of a gene). Therefore, it is hypothesized but largely untested that integration of disease GWAS with context-specific eQTLs will reveal the underlying genes driving disease associations. We used colocalization and transcriptomic analyses to identify shared genetic variants and likely causal genes associated with critically ill COVID-19 and idiopathic pulmonary fibrosis.
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