Whereas the genome-era technologies have produced the sequence of complete human genome, the modern post-genome technologies aim at the understanding of mechanisms of processing of genetic information and elucidation of within-species variation. Single nucleotide polymorphisms (SNPs) comprise the majority of polymorphism in the human population. Non-synonymous coding SNPs together with SNPs in regulatory regions are believed to have the highest impact on complex disease etiology, quantitative traits and response to drug treatment. PolyPhen is a computational tool for prediction of putatively functional nsSNPs with application areas such as genetics of complex disease, birth defects, identification of functional mutations in model organisms and evolutionary genetics.
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JMIRx Med
January 2025
Department of Biochemistry and Medical Genetics, Cancer Center, University of Illinois Chicago, 900 s Ashland, Chicago, IL, 60617, United States, 1 8479124216.
Background: The causes of breast cancer are poorly understood. A potential risk factor is Epstein-Barr virus (EBV), a lifelong infection nearly everyone acquires. EBV-transformed human mammary cells accelerate breast cancer when transplanted into immunosuppressed mice, but the virus can disappear as malignant cells reproduce.
View Article and Find Full Text PDFThe Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the neonatal intensive care unit. After the MPSE was introduced, utilization of WGS increased, time to ordering WGS decreased, and WGS diagnostic yield increased.
View Article and Find Full Text PDFSci Rep
January 2025
School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kerala, India.
Pyomelanogenic P. aeruginosa, frequently isolated from patients with urinary tract infections and cystic fibrosis, possesses the ability to withstand oxidative stress, contributing to virulence and resulting in persistent infections. Whole genome sequence analysis of U804, a pyomelanogenic, multidrug-resistant, clinical isolate, demonstrates the mechanism underlying pyomelanin overproduction.
View Article and Find Full Text PDFNat Commun
January 2025
Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, USA.
Mechanisms related to tumor evasion from NK cell-mediated immune surveillance remain enigmatic. Dickkopf-1 (DKK1) is a Wnt/β-catenin inhibitor, whose levels correlate with breast cancer progression. We find DKK1 to be expressed by tumor cells and cancer-associated fibroblasts (CAFs) in patient samples and orthotopic breast tumors, and in bone.
View Article and Find Full Text PDFJ Immunother Cancer
January 2025
Heidelberg University Hospital Department of Hematology Oncology and Rheumatology, Heidelberg, Germany
Bispecific antibodies (BsAb) have emerged as a leading treatment modality in patients suffering from B-cell non-Hodgkin's lymphoma (B-NHL). However, treatment failure is common and may potentially be attributed to pre-existing or emerging T-cell exhaustion. CD39 catalyzes-together with CD73-the hydrolysis of immunogenic ATP into immunosuppressive adenosine and thus actively promotes an immunosuppressive micromilieu.
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