Results 111 to 120 of about 2,044,942 (306)

K-mer analysis of long-read alignment pileups for structural variant genotyping

Nature Communications
Accurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes.
Adam C. English, Fabio Cunial, Ginger A. Metcalf, Richard A. Gibbs, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

Diffusion Approximations for Demographic Inference: DaDi [PDF]

, 2010
Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to
Carlos D. Bustamante, Ryan D. Hernandez, Ryan N. Gutenkunst, Scott H. Williamson   +3 more
core   +1 more source

Phenotypic and genotypic characterization of single circulating tumor cells in the follow‐up of high‐grade serous ovarian cancer

Molecular Oncology, EarlyView.
Single circulating tumor cells (sCTCs) from high‐grade serous ovarian cancer patients were enriched, imaged, and genomically profiled using WGA and NGS at different time points during treatment. sCTCs revealed enrichment of alterations in Chromosomes 2, 7, and 12 as well as persistent or emerging oncogenic CNAs, supporting sCTC identity.
Carolin Salmon, Rui P. L. Neves, Nikolas H. Stoecklein, Sven‐Thorsten Liffers, Jens Siveke, Jan D. Kuhlmann, Pauline Wimberger, Paul Buderath, Rainer Kimmig, Sabine Kasimir‐Bauer   +9 more
wiley   +1 more source

Investigating the interplay between prematurity and genetic variation in the context of rare developmental disorders

Genome Medicine
Background Rare damaging genetic variation accounts for a substantial proportion of the risk of rare developmental disorders (DDs), but common genetic variants as well as environmental factors, including prematurity, also contribute.
Olivia Wootton, Patrick Campbell, Sarah Richardson, Sarah J. Lindsay, Qin Qin Huang, Erwan Delage, Sana Amanat, Hilary S. Wong, Helen V. Firth, Matthew E. Hurles, Michael A. Simpson, Elizabeth J. Radford, Hilary C. Martin   +12 more
doaj   +1 more source

Correlation of the differential expression of PIK3R1 and its spliced variant, p55α, in pan‐cancer

Molecular Oncology, EarlyView.
PIK3R1 undergoes alternative splicing to generate the isoforms, p85α and p55α. By combining large patient datasets with laboratory experiments, we show that PIK3R1 spliced variants shape cancer behavior. While tumors lose the protective p85α isoform, p55α is overexpressed, changes linked to poorer survival and more pronounced in African American ...
Ishita Gupta, Yang Song, Madeleine Ndahayo, Anirudh Saxena, Theresa Guo, Dylan Z. Kelley, Jessica Gore, Andrew Hennigan, Alexa Anderson, John C. Papadimitriou, Daria A. Gaykalova   +10 more
wiley   +1 more source

Measuring (Mis)trust in the age of COVID-19: viewpoints of vaccine clinical trial participation among individuals living with sickle cell disease

BMC Public Health
Background COVID-19 vaccine efficacy was determined by the participation of individuals from diverse backgrounds in clinical trials. While these trials recruited participants with chronic conditions, little is known about how sentiments of mistrust ...
Khadijah Abdallah, Kiana Amini, Hasmin C. Ramirez, Madison Keller, Diba Seddighi, Marilyn S. Baffoe-Bonnie, Shameka Thomas, Vence L. Bonham, Ashley J. Buscetta   +8 more
doaj   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

Basroparib inhibits YAP‐driven cancers by stabilizing angiomotin

Molecular Oncology, EarlyView.
Basroparib, a selective tankyrase inhibitor, suppresses Wnt signaling and attenuates YAP‐driven oncogenic programs by stabilizing angiomotin. It promotes AMOT–YAP complex formation, enforces cytoplasmic YAP sequestration, inhibits YAP/TEAD transcription, and sensitizes YAP‐active cancers, including KRAS‐mutant colorectal cancer, to MEK inhibition.
Young‐Ju Kwon, Dong Young Kim, Yuna Kim, Uk‐Il Kim, Jae‐Sung Kim   +4 more
wiley   +1 more source

X chromosome inactivation across primary human tissues is mostly complete, with significant implications for genetic and clinical studies

BMC Genomics
Background X chromosome inactivation (XCI) refers to silencing of genes on one copy of the X chromosome in XX females, resulting in dosage compensation between XX females and XY males.
Daniel Shriner, Ayo P. Doumatey, Lin Lei, Mateus H. Gouveia, Karlijn A. C. Meeks, Elisabeth F. Heuston, Jie Zhou, Adebowale A. Adeyemo, Charles N. Rotimi   +8 more
doaj   +1 more source

Colorectal cancer‐derived FGF19 is a metabolically active serum biomarker that exerts enteroendocrine effects on mouse liver

Molecular Oncology, EarlyView.
Meta‐transcriptome analysis identified FGF19 as a peptide enteroendocrine hormone associated with colorectal cancer prognosis. In vivo xenograft models showed release of FGF19 into the blood at levels that correlated with tumor volumes. Tumoral‐FGF19 altered murine liver metabolism through FGFR4, thereby reducing bile acid synthesis and increasing ...
Jordan M. Beardsley, Michael W. Rohr, Joseph A. Goode, Sai Preethi Nakkina, Jignesh G. Parikh, Deborah A. Altomare   +5 more
wiley   +1 more source