Genomics via Optical Mapping II: Ordered Restriction Maps

1997 ◽  
Vol 4 (2) ◽  
pp. 91-118 ◽  
Author(s):  
THOMAS S. ANANTHARAMAN ◽  
BUD MISHRA ◽  
DAVID C. SCHWARTZ
Keyword(s):  
Optical Mapping ◽  
Restriction Maps

scholarly journals Finding Overlapping Rmaps via Gaussian Mixture Model Clustering

2021 ◽  
Author(s):  
Kingshuk Mukherjee ◽  
Massimiliano Rossi ◽  
Daniel Dole-Muinos ◽  
Ayomide Ajayi ◽  
Mattia Prosperi ◽  
...  
Keyword(s):  
Single Molecule ◽  
Optical Mapping ◽  
Gaussian Mixture ◽  
Restriction Maps ◽  
Entire Genome ◽  
Cpu Time ◽  
Genome Wide ◽  
Genomic Location ◽  
Optical Maps ◽  
Mixture Model Clustering

Optical mapping is a method for creating high resolution restriction maps of an entire genome. Optical mapping has been largely automated, and first produces single molecule restriction maps, called Rmaps, which are assembled to generate genome wide optical maps. Since the location and orientation of each Rmap is unknown, the first problem in the analysis of this data is finding related Rmaps, i.e., pairs of Rmaps that share the same orientation and have significant overlap in their genomic location. Although heuristics for identifying related Rmaps exist, they all require quantization of the data which leads to a loss in the precision. In this paper, we propose a Gaussian mixture modelling clustering based method, which we refer to as OMclust, that finds overlapping Rmaps without quantization. Using both simulated and real datasets, we show that OMclust substantially improves the precision (from 48.3% to 73.3%) over the state-of-the art methods while also reducing CPU time and memory consumption. Further, we integrated OMclust into the error correction methods (Elmeri and cOMet) to demonstrate the increase in the performance of these methods. When OMclust was combined with cOMet to error correct Rmap data generated from human DNA, it was able to error correct close to 3x more Rmaps, and reduced the CPU time by more than 35x. Our software is written in C++ and is publicly available under GNU General Public License at https://github.com/kingufl/OMclust

scholarly journals A Whole-Genome Shotgun Optical Map of Yersinia pestis Strain KIM

2002 ◽  
Vol 68 (12) ◽  
pp. 6321-6331 ◽  
Author(s):  
Shiguo Zhou ◽  
Wen Deng ◽  
Thomas S. Anantharaman ◽  
Alex Lim ◽  
Eileen T. Dimalanta ◽  
...  
Keyword(s):  
Yersinia Pestis ◽  
Optical Mapping ◽  
Early Stage ◽  
Sequence Assembly ◽  
Whole Genome ◽  
Restriction Maps ◽  
Sequencing Project ◽  
Genome Sequence Assembly ◽  
Optical Map ◽  
Guide Sequence

ABSTRACT Yersinia pestis is the causative agent of the bubonic, septicemic, and pneumonic plagues (also known as black death) and has been responsible for recurrent devastating pandemics throughout history. To further understand this virulent bacterium and to accelerate an ongoing sequencing project, two whole-genome restriction maps (XhoI and PvuII) of Y. pestis strain KIM were constructed using shotgun optical mapping. This approach constructs ordered restriction maps from randomly sheared individual DNA molecules directly extracted from cells. The two maps served different purposes; the XhoI map facilitated sequence assembly by providing a scaffold for high-resolution alignment, while the PvuII map verified genome sequence assembly. Our results show that such maps facilitated the closure of sequence gaps and, most importantly, provided a purely independent means for sequence validation. Given the recent advancements to the optical mapping system, increased resolution and throughput are enabling such maps to guide sequence assembly at a very early stage of a microbial sequencing project.

scholarly journals Optical Mapping of Plasmodium falciparum Chromosome 2

1999 ◽  
Vol 9 (2) ◽  
pp. 175-181 ◽  
Author(s):  
Junping Jing ◽  
Zhongwu Lai ◽  
Christopher Aston ◽  
Jieyi Lin ◽  
Daniel J. Carucci ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
High Resolution ◽  
Genome Sequencing ◽  
Large Scale ◽  
Dna Analysis ◽  
Optical Mapping ◽  
Chromosome 2 ◽  
Dna Molecules ◽  
Restriction Maps ◽  
Plasmid Library

Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping withNheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.

Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping

Science ◽  
1993 ◽  
Vol 262 (5130) ◽  
pp. 110-114 ◽  
Author(s):  
D. Schwartz ◽  
X Li ◽  
L. Hernandez ◽  
S. Ramnarain ◽  
E. Huff ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Optical Mapping ◽  
Restriction Maps

scholarly journals Super-resolved Optical Mapping of Reactive Sulfur-Vacancies in Two-Dimensional Transition Metal Dichalcogenides

ACS Nano ◽  
2021 ◽  
Author(s):  
Miao Zhang ◽  
Martina Lihter ◽  
Tzu-Heng Chen ◽  
Michal Macha ◽  
Archith Rayabharam ◽  
...  
Keyword(s):  
Transition Metal ◽  
Optical Mapping ◽  
Transition Metal Dichalcogenides ◽  
Two Dimensional ◽  
Metal Dichalcogenides

Acute detection of optical tissue changes in real-time during pulsed field ablation (PFA)

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
K.L Hong ◽  
O Amirana ◽  
T Ransbury ◽  
B Glover
Keyword(s):  
Real Time ◽  
Right Atrium ◽  
Optical Mapping ◽  
Energy Levels ◽  
Optical Signal ◽  
Lesion Formation ◽  
Pulsed Field ◽  
Tissue Changes ◽  
Rf Energy ◽  
The Right

Abstract Background It has been established in previous animal and human studies that it is possible to assess lesion formation in real-time using optical means during the application of radiofrequency (RF) energy in cardiac ablation procedures. The optical interrogation was accomplished using a novel catheter and instrument system whereby the catheter has embedded optical fibers that transmit and receive light from the instrument. Purpose The aim of this study was to see if there are similar indications of lesion formation, detected by the same optical means, during the application of pulsed field ablation (PFA) energy to cause lesions through electroporation. Methods A series of 3 anesthetized pigs underwent PFA in the right atrium. An 8-electrode circular catheter was placed high in the right atrium, near the superior vena cava, to simulate pulmonary vein isolation as part of an AF ablation procedure. The optical catheter was placed adjacent to the circular catheter between stimulation electrode pairs. A bolus of adenosine was administered to create a window of asystole to avoid stimulation on the T-wave. Bipolar PFA was delivered immediately post drug infusion and the optical signature from the catheter was recorded and displayed in real-time. Electrograms were recorded and the mapping of the lesion was performed with the optical catheter at the following time intervals post PFA delivery: 0 min, 15 min, 1 hour, and 3 hours. Necropsy and histology followed the procedure. Results The optical signal is distinctly higher in intensity during the PFA pulse train. The optical signal showed an immediate significant decrease and a slow but steady decay over the mapping interval. Electrogram reduction accompanied PFA application and also showed a marked reduction over the mapping interval. The optical signal amplitudes were markedly lower when on the lesion compared to healthy non-ablated myocardium as predicted. Conclusions Preliminary results indicate that optical mapping detects immediate tissue changes during PFA at these energy levels and hence could be is a viable method of evaluating lesion formation during and after PFA energy application. The optical signal indicates that cell damage occurs immediately at these energy levels and continues to progress slowly in lesions made by PFA energy compared to those made by RF energy. The findings also suggest that optical mapping can identify acute lesions made with PFA energy in real-time implying that optical mapping could evolve as a PFA gap detector. Funding Acknowledgement Type of funding source: None

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