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Multiplex generation and single-cell analysis of structural variants in mammalian genomes.
Science
January 2025
Department of Genome Sciences, University of Washington, Seattle, WA, USA.
Studying the functional consequences of structural variants (SVs) in mammalian genomes is challenging because (i) SVs arise much less commonly than single-nucleotide variants or small indels and (ii) methods to generate, map, and characterize SVs in model systems are underdeveloped. To address these challenges, we developed Genome-Shuffle-seq, a method that enables the multiplex generation and mapping of thousands of SVs (deletions, inversions, translocations, and extrachromosomal circles) throughout mammalian genomes. We also demonstrate the co-capture of SV identity with single-cell transcriptomes, facilitating the measurement of SV impact on gene expression.
View Article and Find Full Text PDFGenetic diversity, population structure in a historical panel of Brazilian soybean cultivars.
PLoS One
January 2025
The Sainsbury Laboratory-TSL, University of East Anglia, Norwich, United Kingdom.
Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years.
View Article and Find Full Text PDFNovel genetic insight for psoriasis: integrative genome-wide analyses in 863 080 individuals and proteome-wide Mendelian randomization.
Brief Bioinform
November 2024
Department of Dermatology, Daping Hospital, Army Medical University, No. 10, Changjiang Branch Road, Yuzhong District, Chongqing 400042, China.
Psoriasis affects a significant proportion of the worldwide population and causes an extremely heavy psychological and physical burden. The existing therapeutic schemes have many deficiencies such as limited efficacies and various side effects. Therefore, novel ways of treating psoriasis are urgently needed.
View Article and Find Full Text PDFCausal relationships between plasma lipidome and diabetic neuropathy: a Mendelian randomization study.
Front Endocrinol (Lausanne)
January 2025
Department of Endocrinology, Affiliated Wujin Hospital of Jiangsu University, Changzhou, Jiangsu, China.
Background: Dyslipidemia is closely related to diabetic neuropathy. This study examined the potential causal relationship involving 179 lipid species and the disease.
Methods: The pooled data on 179 lipid species and diabetic neuropathy were obtained from previous genome-wide association studies (GWAS).
Exploring the Causal Relationship Between Frailty and Chronic Obstructive Pulmonary Disease: Insights From Bidirectional Mendelian Randomization and Mediation Analysis.
Int J Chron Obstruct Pulmon Dis
January 2025
Department of Thoracic Surgery, Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, Jiangsu, 215000, People's Republic of China.
Background: Observational studies have underscored a robust association between frailty and chronic obstructive pulmonary disease (COPD), yet the causality remains equivocal.
Methods: This study employed bidirectional two-sample Mendelian randomization (MR) analysis. Univariable MR investigated the causal relationship between frailty and COPD.
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