Results 51 to 60 of about 184,715 (310)

Optical Genome Mapping for Cytogenetic Diagnostics in AML

Cancers, 2023
The classification and risk stratification of acute myeloid leukemia (AML) is based on reliable genetic diagnostics. A broad and expanding variety of relevant aberrations are structural variants beyond single-nucleotide variants. Optical Genome Mapping is an unbiased, genome-wide, amplification-free method for the detection of structural variants.
Verena Nilius-Eliliwi, Wanda M. Gerding, Roland Schroers, Huu Phuc Nguyen, Deepak B. Vangala   +4 more
openaire   +2 more sources

Optical mapping as a routine tool for bacterial genome sequence finishing

BMC Genomics, 2007
Background In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts.
Gaudriault Sophie, Forst Steve, Du Zijin, Darby Creg, Bode Helge B, Barbazuk Brad, Miller Nancy, Henkhaus John, Goldman Barry S, Norton Stacie, Latreille Phil, Goodner Brad, Goodrich-Blair Heidi, Slater Steven   +13 more
doaj   +1 more source

Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions

Plants, 2023
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors.
Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne   +10 more
doaj   +1 more source

OMSim : a simulator for optical map data [PDF]

, 2017
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire ...
Audenaert, Pieter, Fostier, Jan, Miclotte, Giles, Plaisance, Stéphane, Rombauts, Stephane, Van de Peer, Yves   +5 more
core   +2 more sources

Feasibility of Optical Genome Mapping in Cytogenetic Diagnostics of Hematological Neoplasms: A New Way to Look at DNA

Diagnostics, 2023
Optical genome mapping (OGM) is a new genome-wide technology that can reveal both structural genomic variations (SVs) and copy number variations (CNVs) in a single assay.
Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Francesco Tarantini, Cosimo Cumbo, Giuseppina Tota, Crescenzio Francesco Minervini, Angela Minervini, Maria Rosa Conserva, Immacolata Redavid, Elisa Parciante, Maria Giovanna Macchia, Giorgina Specchia, Pellegrino Musto, Francesco Albano   +14 more
doaj   +1 more source

DeepOM: Single-molecule optical genome mapping via deep learning

Bioinformatics, 2022
AbstractEfficient tapping into genomic information from a single microscopic image of an intact DNA molecule fragment is an outstanding challenge and its solution will open new frontiers in molecular diagnostics. Here, a new computational method for optical genome mapping utilizing Deep Learning is presented, termed DeepOM.
Yevgeni Nogin, Tahir Detinis Zur, Sapir Margalit, Ilana Barzilai, Onit Alalouf, Yuval Ebenstein, Yoav Shechtman   +6 more
openaire   +2 more sources

AGORA: Assembly Guided by Optical Restriction Alignment

BMC Bioinformatics, 2012
Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs).
Lin Henry C, Goldstein Steve, Mendelowitz Lee, Zhou Shiguo, Wetzel Joshua, Schwartz David C, Pop Mihai   +6 more
doaj   +1 more source

Towards many colors in FISH on 3D-preserved interphase nuclei [PDF]

, 2006
The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process.
Albiez, H., Benecletti, P. A., Bolzer, A., Cremer, M., Cremer, T., Joffe, B., Müller, Stefan, Solovei, Irina, Speicher, Michael R., Walter, J.   +9 more
core   +1 more source

Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum [PDF]

Applied and Environmental Microbiology, 2005
ABSTRACT Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production.
Reslewic, Susan, Zhou, Shiguo, Place, Mike, Zhang, Yaoping, Briska, Adam, Goldstein, Steve, Churas, Chris, Runnheim, Rod, Forrest, Dan, Lim, Alex, Lapidus, Alla, Han, Cliff S., Roberts, Gary P., Schwartz, David C.   +13 more
openaire   +4 more sources

The hidden perils of read mapping as a quality assessment tool in genome sequencing [PDF]

, 2017
This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are ...
A Bankevich, AV Karlyshev, D Antipov, EW Myers, HC Lin, IJ Tsai, J Parkhill, K Rutherford, M Hunt, M Land, MT Swain, S Lin, S Meader, TD Otto, TJ Carver   +14 more
core   +1 more source