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An augmented transformer model trained on protein family specific variant data leads to improved prediction of variants of uncertain significance.
Hum Genet
January 2025
TCS Research, Tata Consultancy Services, Hyderabad, India.
Variants of uncertain significance (VUS) represent variants that lack sufficient evidence to be confidently associated with a disease, thus posing a challenge in the interpretation of genetic testing results. Here we report an improved method for predicting the VUS of Arylsulfatase A (ARSA) gene as part of the Critical Assessment of Genome Interpretation challenge (CAGI6). Our method uses a transfer learning approach that leverages a pre-trained protein language model to predict the impact of mutations on the activity of the ARSA enzyme, whose deficiency is known to cause a rare genetic disorder, metachromatic leukodystrophy.
View Article and Find Full Text PDFTranscriptome of Anaplastic Thyroid Cancer Reveals Two Molecular Subtypes with Distinct Tumor Microenvironment and Prognosis.
Thyroid
January 2025
Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Gwanak-gu, Republic of Korea.
Although patients with anaplastic thyroid cancer (ATC) generally have a poor prognosis and there are currently no effective treatment options, survival and response to therapy vary between patients. Genomic and transcriptomic profiles of ATC have been reported; however, a comprehensive study of the tumor microenvironment (TME) of ATC is still lacking. This study aimed to elucidate the TME characteristics associated with ATC and their prognostic implications.
View Article and Find Full Text PDFMultifractal Spectrum Analysis for Assessing Pulmonary Nodule Malignancy.
J Vis Exp
January 2025
Fever Outpatient Clinic, Dongzhimen Hospital, Affiliated to Beijing University of Chinese Medicine;
Non-invasive assessment of pulmonary nodule malignancy remains a critical challenge in lung cancer diagnosis. Traditional methods often lack precision in differentiating benign from malignant nodules, particularly in the early stages. This study introduces an approach using multifractal spectrum analysis to quantitatively evaluate pulmonary nodule characteristics.
View Article and Find Full Text PDFImpact of Age and Body Mass Index on the Outcomes of Laparoscopic Mesh Sacrocolpopexy.
Obstet Gynecol Int
January 2025
Department of Gynecology and Obstetrics, Hotel Dieu de France Hospital, Beirut, Lebanon.
Pelvic organ prolapse (POP) is a benign condition that can adversely affect women's quality of life. Mesh sacrocolpopexy is an effective surgical treatment for POP, but is considered a complex and risky surgery for obese and elderly women. The objective of this study was to assess the impact of age and obesity on the outcomes of minimally invasive sacrocolpopexy.
View Article and Find Full Text PDFTandem repeats are a highly polymorphic class of genomic variation that play causal roles in rare diseases but are notoriously difficult to sequence using short-read techniques . Most previous studies profiling tandem repeats genome-wide have reduced the description of each locus to the singular value of the length of the entire repetitive locus . Here we introduce a comprehensive database of 3.
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