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Argus™ Optical Mapping System MapIt™ Services - Sample Preparation - Sample Transport - Request a MapIt Quote - Payment + Terms | ||
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OpGen: Frequently Asked Questions
General Questions
MapIt Optical Mapping Services Questions
- If I order an Optical Map, what happens next, and what do I receive from MapIt Optical Mapping Services?
- Can I place an order via the website?
- What is the average turn around time when I place an order?
Sample Types and Preparation Questions
- What sample preparation is required for submission?
- What sample types are acceptable to ship to OpGen for Optical Mapping?
- Is it true that you can accept mixed microbial or metagenomic samples?
- What sort of resolution is possible using a single restriction enzyme?
- How is a restriction enzyme chosen?
- Is it possible to use multiple enzymes in one map? Is each restriction enzyme used in an individual digest?
- Does using a second enzyme increase the cost and if so, by how much?
- How do you generate an Optical Map from “unculturable” or “fastidious” samples?
- Can specimens be retrieved from the slide after analysis (or can ANY subsequent experiments be performed on the restriction fragments such as hybridization reactions)?
Sample Transport Questions
- Do international shipments pose any problems with sample transportation?
- Why does OpGen provide MapIt Sample Transport Kits?
Applications and Technical Questions
- After I sequence, I have numerous contigs to assemble — how does Optical Mapping help with contig placement and closure?
- Is it also possible to use FISH in combination with Optical Mapping?
- Can Optical Mapping provide Maps of plasmids or viruses?
- Can you detect SNPs?
- What is the upper limit of genome size amenable to Optical Mapping?
- Does OpGen generate in silco maps that form part of the MapViewer database or is this something I need to generate for my specific Optical Map project?
General Questions
Optical Maps are high resolution, ordered whole genome restriction maps that are well suited for finding novel insertions, deletions and rearrangements. Because Optical Mapping is a de novo process, no previous sequence information is required. top
OpGen is not a software production company; however, OpGen’s proprietary Map Analysis Software is used to analyze and view all Optical Maps. This software is highly functional and ideal for comparing whole genomes to one another as well as for placing sequence contigs along the Optical Map scaffold to determine order, alignment and orientation. top
MapIt Optical Mapping Services
If I order an Optical Map, what happens next, and what do I receive from MapIt Optical Mapping Services?
Upon receipt of an Optical Mapping order, Customer Support will provide instructions for sample preparation specific to the Customer’s needs and that will ensure sample integrity for shipping. A MapIt Sample Transport Kit that meets all regulatory requirements for the transport of biological and/or infectious substances is then forwarded to the Customer for forwarding samples to the OpGen Laboratory. An Order Form, instructions, and all required labeling accompanies each Kit. Once the samples have been “Mapped”, MapIt provides each Customer with two CDs — the first, an Install Disc containing the company’s proprietary software, and the second, the MapIt Data Disc containing whole genome physical maps for each isolate tested and a comparative analysis, if appropriate to the service ordered. top
Can I place an order via the website?
No, it is best to contact OpGen to discuss your project and needs — each project is customized to your project needs. Specific preparation of your samples for processing may vary depending on your sample type or your specific microbe — tell us about your project and we will be able to provide you with the sample prep method specific to your needs to ensure high molecular DNA is obtained.
Also, it is very important that we know when you plan to ship samples to our laboratory for processing — we want ensure sample integrity in the transit process. Additionally, samples must be cleared by our safety officer in advance due to safety concerns associated with some sample types. top
What is the average turn around time when I place an order?
Turn around time is totally dependent on the scope of your project, the microbes and size of the genome(s) Mapped. Bacterial Maps typically are smaller than the genomes of yeast or fungi and require less processing. Quotations and time tables will be provided to you. top
Sample Types and Preparation
What sample preparation is required for submission?
Specific preparation of your samples for processing may vary depending on your sample type or your specific microbe — tell us about your project and we will be able to provide you with the sample prep method specific to your needs to ensure high molecular DNA is obtained. If you have special requirements or want to know if we can accept specific types of samples or end-products, please don’t hesitate to ask us. top
What sample types are acceptable to ship to OpGen for Optical Mapping?
Microbial Safety Level Classification BSL-1 or BSL-2 are acceptable for live organisms. For microbes otherwise classified, you must provide signed documentation as proof that only non-viable microbes are provided to OpGen. When you contact Customer Support, we will provide the protocol for rendering the cells non-viable. top
Is it true that you can accept mixed microbial or metagenomic samples?
Yes, that is true. Optical Mapping technology is able to distinguish strains in a mixed sample. T Wagner’s poster presented at the 2008 ICAAC “Use of Optical Mapping to Identify Bacteria from Complex Mixture and Clinical Samples”. (link to publications page) top
What sort of resolution is possible using a single restriction enzyme?
The “resolution” of Optical Mapping using a single restriction enzyme is approximately 2Kb. Optical Mapping begins with immobilizing DNA to an optical glass surface. Because all wet chemistry occurs on this surface, very small fragments of the immobilized DNA can occasionally become detached and wash away. While small fragments may be retained that <2Kb in size, 100% will be retained that 2Kb and larger. top
How is a restriction enzyme chosen?
Enzymes are chosen that will generate an overall average fragment size of 7-10Kb which tends to be optimal for Optical Mapping. Additionally, enzyme selection is based sequenced strain data and/or Customer-provided sequence data if available. top
Is it possible to use multiple enzymes in one map? Is each restriction enzyme used in an individual digest?
Maps are generated using one restriction enzyme per Optical Map. However some Customers find that it is advantageous to have Optical Maps generated using different restriction enzymes, particularly for sequence closure projects. If all sequence contigs are not placed with a particular enzyme, it is possible another enzyme may complete the contig placement. top
Does using a second enzyme increase the cost and if so, by how much?
Maps are generated using one restriction enzyme per Optical Map, so producing more than one map with an additional enzyme(s) adds some additional cost. However, the second enzyme map would cost considerably less and we can generate a customized quote for you when we discuss your overall project and needs. top
How do you generate an Optical Map from “unculturable” or “fastidious” samples?
Genomic analysis using Optical Mapping may be performed on uncultured bacteria or other organisms. High molecular weight (HMW) DNA may be obtained using specific microbial or organism sample preparation methods without the need for culture and isolation techniques. top
Can specimens be retrieved from the slide after analysis (or can ANY subsequent experiments be performed on the restriction fragments such as hybridization reactions)?
“Specimens” are prepared to generate High molecular weight DNA. HMW DNA is then loaded into the channels of a microfluidics Optical Chip and captured in parallel arrays in long, as single DNA molecules. Immobilized DNA molecules are retained electrostatically, interrogated with a restriction endonuclease, digested, and then stained. If the entire original specimen is used for sample preparation, there will be no specimen remaining for other testing. Because the HMW DNA is attached to the Optical Chip, and has been further processed, DNA retrieval and/or other testing would not be possible. top
Sample Transport
Do international shipments pose any problems with sample transportation?
Transportation of live cells internationally requires a permit from the CDC. We currently hold a worldwide permit without country limitations but there are limitations relative to the specific organisms listed on our permit.
If you wish to ship a sample that is not listed on our permit, we can provide a sample preparation method that will render the cells non-viable for transport. top
Why does OpGen provide MapIt Sample Transport Kits?
There are several important reasons why we provide free sample transport kits to you: There are several types of transport kits and not all types meet all regulatory requirements for the transport of biological and/or infectious substances as regulated by law — ours do. Next, we want to ensure that specimens are packed and transported per DOT and IATA rules and regulations to minimize risk and ensure safety of all persons involved in the transportation chain. And, your sample integrity is very important — OpGen wants to make sure your samples are not jeopardized in transit and arrive safely to our laboratory. top
Applications and Technical Questions
After I sequence, I have numerous contigs to assemble — how does Optical Mapping help with contig placement and closure?
Your sequence and contig data can be converted into an in silico sequence contig Optical Map. Utilizing the proprietary Map Analysis Software, the Map will be analyzed and the contigs will be aligned and oriented quickly on the Map scaffold in their appropriate, ordered location. Gap size and location will be determined. Mis-assemblies, repetitive sequences, insertions, deletions and mobile elements will be visually identified. Contigs less than 50Kb may not be placed. Your map may also be compared to other available sequenced organisms very easily. top
Is it also possible to use FISH in combination with Optical Mapping?
Not currently, our Research and Development team is continually exploring potential opportunities for expanding our applications. top
Can Optical Mapping provide Maps of plasmids or viruses?
Optical Mapping requires very high molecular weight DNA (200Kb at minimum). Our imaging software automatically excludes molecules of sizes less than 200Kb. In our past experience, we have mapped plasmids and extra chromosomal elements approximately 150Kb in size, but ordinarily, we would be looking for molecules 200Kb or higher. top
Optical Mapping technology enables whole genome analysis that is both complimentary and additive to existing microarray and SNP genotyping systems. Where these technologies detect small changes in DNA sequence, Optical Mapping finds novel insertions, deletions and genomic rearrangements within the genome that other techniques are unable to find. top
What is the upper limit of genome size amenable to Optical Mapping?
Prokaryotes and small eukaryotes can be Mapped, with the larger genome projects of 50-100Mb requiring more sample preparation, processing and Mapping time. Bacterial genomes contain a single chromosome and typically range up to about 6Mb in size, contrasted to Yeast and fungal genomes which contain multi-chromosomes and the genomes are much larger. top
Does OpGen generate in silico maps that form part of the Optical Mapping database or is this something I need to generate for my specific Optical Map project?
Let us know which sequenced strains you are interested in and we will include those with your final data package. The Optical Mapping Software allows you to upload sequence data from Genbank files directly into the Database, so if there are additional strains of interest, this is a nice benefit of the Software. top
If you don’t see your question here, just ask us at CustomerSupport@OpGen.com or call us at 1.888.856.2748 or 301.813.1270.