Results 61 to 70 of about 101,026 (352)

DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation

Genome Biology, 2021
Nanopore long-read sequencing technology greatly expands the capacity of long-range, single-molecule DNA-modification detection. A growing number of analytical tools have been developed to detect DNA methylation from nanopore sequencing reads.
Yang Liu, Wojciech Rosikiewicz, Ziwei Pan, Nathaniel L. Jillette, Ping Wang, A. Taghbalout, J. Foox, C. Mason, M. Carroll, A. Cheng, Sheng Li   +10 more
semanticscholar   +1 more source

Complementarity of Long‐Reads and Optical Mapping in Parkinson's Disease for Structural Variants

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Long‐read sequencing and optical genome mapping technologies have the ability to detect large and complex structural variants. This has led to the discovery of novel pathogenic variants in neurodegenerative movement disorders. Thus, we aimed to systematically compare the SV detection capabilities of OGM and ONT in Parkinson's disease.
André Fienemann, Theresa Lüth, Susen Schaake, Carolin Gabbert, Marius Möller, Hauke Busch, Katja Lohmann, Jonas A. Gustafson, Danny E. Miller, Kensuke Daida, Manabu Funayama, Nobutaka Hattori, Samia Ben Sassi, Faycel Hentati, Matthew J. Farrer, Kristian K. Ullrich, Christine Klein, Joanne Trinh   +17 more
wiley   +1 more source

MethPhaser: methylation-based long-read haplotype phasing of human genomes

Nature Communications
The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease.
Yilei Fu, Sergey Aganezov, Medhat Mahmoud, John Beaulaurier, Sissel Juul, Todd J. Treangen, Fritz J. Sedlazeck   +6 more
doaj   +1 more source

Epilepsy‐Associated Variants of a Single SCN1A Codon Exhibit Divergent Functional Properties

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT Objective Pathogenic variants in SCN1A, which encodes the voltage‐gated sodium channel NaV1.1, are associated with multiple epilepsy syndromes exhibiting a range of clinical severity. SCN1A variants are reported in different syndromes, including Dravet syndrome, which is associated with loss‐of‐function, whereas neonatal/infantile‐onset ...
Lanie N. Liebovitz, Christopher H. Thompson, Linda C. Laux, Alfred L. George Jr.   +3 more
wiley   +1 more source

Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires

Nature Communications
Borgs are huge extrachromosomal elements (ECE) of anaerobic methane-consuming “Candidatus Methanoperedens” archaea. Here, we used nanopore sequencing to validate published complete genomes curated from short reads and to reconstruct new genomes.
Marie C. Schoelmerich, Lynn Ly, Jacob West-Roberts, Ling-Dong Shi, Cong Shen, Nikhil S. Malvankar, Najwa Taib, Simonetta Gribaldo, Ben J. Woodcroft, Christopher W. Schadt, Basem Al-Shayeb, Xiaoguang Dai, Christopher Mozsary, Scott Hickey, Christine He, John Beaulaurier, Sissel Juul, Rohan Sachdeva, Jillian F. Banfield   +18 more
doaj   +1 more source

Nanopore sequencing in microgravity [PDF]

npj Microgravity, 2016
Abstract Rapid DNA sequencing and analysis has been a long-sought goal in remote research and point-of-care medicine. In microgravity, DNA sequencing can facilitate novel astrobiological research and close monitoring of crew health, but spaceflight places stringent restrictions on the mass and volume of ...
Alexa B R McIntyre, Lindsay Rizzardi, Angela M Yu, Noah Alexander, Gail L Rosen, Douglas J Botkin, Sarah E Stahl, Kristen K John, Sarah L Castro-Wallace, Ken McGrath, Aaron S Burton, Andrew P Feinberg, Christopher E Mason   +12 more
openaire   +4 more sources

Compound Heterozygote Friedreich Ataxia Patients With Covert Proximal FXN Gene Deletions

Annals of Clinical and Translational Neurology, EarlyView.
ABSTRACT We present Friedreich ataxia patients with frataxin gene deletions. Data and records were collected at the Children's Hospital of Philadelphia from patients enrolled in the FACOMS natural history study. Patients with proximal deletions initially diagnosed with only one GAA expanded allele had more severe disease than their homozygous expansion
Michael P. Lazaropoulos, Morgan C. Devore, Christina Lam, Courtney Park, Sanjay Bidichandani, David R. Lynch   +5 more
wiley   +1 more source

Microbial Characteristics and Genomic Analysis of an ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain Carrying blaKPC−2 Conjugative Drug-Resistant Plasmid

Frontiers in Public Health, 2022
BackgroundThe sequence type 11 (ST11) carbapenem-resistant Klebsiella pneumoniae (CRKP) carrying blaKPC−2 has been widespread all over the world, and it has been reported frequently in China.
Lingyi Zeng, Lingyi Zeng, Jisheng Zhang, Kewang Hu, Kewang Hu, Jie Li, Jianmin Wang, Chengru Yang, Chengru Yang, Wan Huang, Lining Yin, Lining Yin, Xiaoli Zhang   +12 more
doaj   +1 more source

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

Nature Biotechnology, 2020
Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool by reversing the voltage across individual nanopores to reject specific sequences, enabling enrichment and depletion to address biological questions.
Alexander Payne, N. Holmes, Thomas Clarke, R. Munro, Bisrat J. Debebe, M. Loose   +5 more
semanticscholar   +1 more source

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

Nature Methods, 2021
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo ...
Alan Tourancheau, E. Mead, Xue-Song Zhang, Gang Fang   +3 more
semanticscholar   +1 more source