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Inferring demographic and selective histories from population genomic data using a two-step approach in species with coding-sparse genomes: an application to human data.
G3 (Bethesda)
January 2025
School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ 85281, USA.
The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection.
View Article and Find Full Text PDFAdenine base editor corrected ADPKD point mutations in hiPSCs and kidney organoids.
Adv Biotechnol (Singap)
June 2024
MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.
Autosomal dominant polycystic kidney disease (ADPKD) is a dominant genetic disorder caused primarily by mutations in the PKD1 gene, resulting in the formation of numerous cysts and eventually kidney failure. However, there are currently no gene therapy studies aimed at correcting PKD1 gene mutations. In this study, we identified two mutation sites associated with ADPKD, c.
View Article and Find Full Text PDFVariation in cancer risk between organs can not be explained by the degree of somatic clonal expansion.
Adv Biotechnol (Singap)
May 2024
State Key Labratory of Biocontrol, School of Life Sciences, Sun Yat-San University, Guangzhou, 510275, China.
Somatic clonal expansion refers to the proliferation and expansion of a cell clone within a multicellular organism. Since cancer also results from the uncontrolled proliferation of few cell clones, it is generally believed that aging-associated somatic clonal expansion observed in normal tissues represents a precancerous condition. For instance, hematological malignancy is often preceded by clonal hematopoiesis.
View Article and Find Full Text PDFMulti-omics sequencing of gastroesophageal junction adenocarcinoma reveals prognosis-relevant key factors and a novel immunogenomic classification.
Gastric Cancer
January 2025
Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
Background: Gastroesophageal junction adenocarcinoma (GEJAC) exhibits distinct molecular characteristics due to its unique anatomical location. We sought to investigate effective and reliable molecular classification of GEJAC to guide personalized treatment.
Methods: We analyzed the whole genomic, transcriptomic, T-cell receptor repertoires, and immunohistochemical data in 92 GEJAC patients and delineated the landscape of genetic and immune alterations.
Iron oxide nanoparticles coated with bioactive materials: a viable theragnostic strategy to improve osteosarcoma treatment.
Discov Nano
January 2025
School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
Osteosarcoma (OS) is distinguished as a high-grade malignant tumor, characterized by rapid systemic metastasis, particularly to the lungs, resulting in very low survival rates. Understanding the complexities of tumor development and mutation is the need of the hour for the advancement of targeted therapies in cancer care. A significant innovation in this area is the use of nanotechnology, specifically nanoparticles, to tackle various challenges in cancer treatment.
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