Results 1 to 10 of about 1,250,987 (119)

Expression of concern for global biomedical research by the human genome organization (HUGO) [PDF]

Human Genomics
Cuts to US science funding will stall advances in genomics affecting public health, rare disease and cancer diagnostics and therapeutics in the US and around the world.
Ada Hamosh, Fabiana Arzuaga, Karen B. Avraham, Zilfalil Bin Alwi, Anne Bowcock, Sir John Burn, Piero Carninci, Collet Dandara, Iscia Lopes-Cendes, Leon Mutesa, Partha P. Majumder, Juergen K.V. Reichardt, Joris A. Veltman   +12 more
doaj   +2 more sources

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Nature Communications, 2021
Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph.
Tsung-Yu Lu, The Human Genome Structural Variation Consortium, Mark J. P. Chaisson   +2 more
doaj   +1 more source

Truvari: refined structural variant comparison preserves allelic diversity

Genome Biology, 2022
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same.
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

The effects of common structural variants on 3D chromatin structure

BMC Genomics, 2020
Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs).
Omar Shanta, Amina Noor, Human Genome Structural Variation Consortium (HGSVC), Jonathan Sebat   +3 more
doaj   +1 more source

Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach

BMC Bioinformatics, 2021
Background The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remains challenging.
Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, NISC Comparative Sequencing Program, Jennifer J. Johnston, Leslie G. Biesecker   +9 more
doaj   +1 more source

The Warburg effect is necessary to promote glycosylation in the blastema during zebrafish tail regeneration

npj Regenerative Medicine, 2021
Throughout their lifetime, fish maintain a high capacity for regenerating complex tissues after injury. We utilized a larval tail regeneration assay in the zebrafish Danio rerio, which serves as an ideal model of appendage regeneration due to its easy ...
Jason W. Sinclair, David R. Hoying, Erica Bresciani, Damian Dalle Nogare, Carli D. Needle, Alexandra Berger, Weiwei Wu, Kevin Bishop, Abdel G. Elkahloun, Ajay Chitnis, Paul Liu, Shawn M. Burgess   +11 more
doaj   +1 more source

Phenotypic variance explained by local ancestry in admixed African Americans

Frontiers in Genetics, 2015
We surveyed 26 quantitative traits and disease outcomes to understand the proportion of phenotypic variance explained by local ancestry in admixed African Americans. After inferring local ancestry as the number of African-ancestry chromosomes at hundreds
Daniel eShriner, Amy R. Bentley, Ayo Priscille Doumatey, Guanjie eChen, Jie eZhou, Adebowale eAdeyemo, Charles N. Rotimi   +6 more
doaj   +1 more source

SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads

BMC Genomics, 2017
Background Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing.
Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski, Richard A. Gibbs   +10 more
doaj   +1 more source

Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease

Nature Communications, 2021
PU.1 is a master regulator of myeloid development but its role in disease-relevant neutrophils is not well known. Here, the authors look at primary neutrophils from a human population and find that genetic variants affecting binding of PU.1 are ...
Stephen Watt, Louella Vasquez, Klaudia Walter, Alice L. Mann, Kousik Kundu, Lu Chen, Ying Sims, Simone Ecker, Frances Burden, Samantha Farrow, Ben Farr, Valentina Iotchkova, Heather Elding, Daniel Mead, Manuel Tardaguila, Hannes Ponstingl, David Richardson, Avik Datta, Paul Flicek, Laura Clarke, Kate Downes, Tomi Pastinen, Peter Fraser, Mattia Frontini, Biola-Maria Javierre, Mikhail Spivakov, Nicole Soranzo   +26 more
doaj   +1 more source

Genetic variants associated with Hermansky-Pudlak syndrome

Platelets, 2020
Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder characterized by defective biogenesis of lysosome-related organelles. Clinical manifestations include a bleeding diathesis due to a platelet delta storage pool deficiency ...
Melissa A. Merideth, Wendy J. Introne, Jennifer A. Wang, Kevin J. O’Brien, Marjan Huizing, Bernadette R. Gochuico   +5 more
doaj   +1 more source