Mapping the genome one molecule at a time — optical mapping

Samad, A; Cai, Wei; Hu, Xinghua; Irvin, Benjamin; Jing, Junping; Reed, Jason; Meng, Xiangying; Huang, Jehn-Yu; Huff, Edward J.; Porter, Burdett R.; Shenkar, Alex; Anantharaman, Thomas; Mishra, Bhubaneswar; Clarke, Virginia; Dimalanta, Eileen T.; Edington, Joanne; Hiort, Catharina; Rabbah, Roderic; Skiada, John; Schwartz, David C.

doi:10.1038/378516a0

Cited by 30 publications

(16 citation statements)

References 8 publications

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“…We also derived an independent estimate for the genome size from the whole-genome optical restriction mapping of the species [38] (Additional file 4). Alignment of contigs to the optical maps [39] suggested that the optical maps consistently overestimated sizes (2 to 10% on average).…”

Section: Resultsmentioning

confidence: 99%

Genomic characterization of the Yersinia genus

et al. 2010

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Section: Resultsmentioning

confidence: 99%

Genomic characterization of the Yersinia genus

et al. 2010

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“…In a pioneering experiment in 1993 (Schwartz et al, 1993;Samad et al, 1995;Aston et al, 1999), Schwartz and his team demonstrated the feasibility of optical mapping by constructing the maps for several yeast chromosomes. This experiment has been followed by many subsequent improvements in the physical and chemical processes, accurate mathematical modeling, efficient algorithmic development and high-throughput automation.…”

Section: Optical Mappingmentioning

confidence: 99%

Optical Mapping

Mishra¹

2005

Encyclopedia of Life Sciences

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Optical mapping generates an ordered restriction map of a DNA molecule, that is, an ordered enumeration of the restriction sites along with the estimated lengths of the restriction fragments between consecutive restriction sites and various statistics, which model the errors in estimating the restriction fragment lengths and due to unrepresented and misrepresented restriction sites in the map. They have applications in improving the accuracy and algorithmic efficiency of sequence assembly, validating assembled sequences, characterizing gaps in the assembly and identifying candidates for finishing steps in a sequencing project, etc.

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“…A faster diagnosis means that patients can receive the correct treatment earlier and that the further spread of antimicrobial resistance can be hindered (15,16). The reduction of manipulation through the automation of OM would eventually allow the miniaturization of the process, with expected increases in throughput as well as reductions in cost (1). …”

Section: General Considerationsmentioning

confidence: 99%

“…The use of OM in microbiology started in the 1990s as an auxiliary technique that, combined with Sanger nucleotide sequencing, supported reliable and cost-effective bacterial genome mapping (1). In 1999, Lin et al (2) reported the first de novo shotgun OM-generated map of a microorganism, Deinococcus radiodurans .…”

Section: Optical Mapping In Microbiology: the Beginningmentioning

confidence: 99%

Applications of Optical DNA Mapping in Microbiology

et al. 2017

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Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequence-based studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.

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Mapping the genome one molecule at a time — optical mapping

Cited by 30 publications

References 8 publications

Genomic characterization of the Yersinia genus

Genomic characterization of the Yersinia genus

Optical Mapping

Applications of Optical DNA Mapping in Microbiology

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