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FAQ

General Questions

What is a Whole Genome Map?

Whole Genome Maps (previously Optical Maps) are high-resolution, ordered, whole genome restriction maps that are well suited for finding novel insertions, deletions, and rearrangements. Because Whole Genome Mapping is a de novo process, no previous sequence information is required.

Are you a software company?

OpGen is not a software production company; however, OpGen’s proprietary MapIt® Analysis Software is used to view and analyze all Whole Genome Maps. This software is highly functional and ideal for comparing whole genomes to one another, as well as for placing sequence contigs along the Whole Genome Map scaffold to determine order, alignment, and orientation.

MapIt® Services

If I order a Whole Genome Map, what happens next, and what do I receive from MapIt® Services?

Upon receipt of a Whole Genome Map 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. An order form, instructions, and all required labeling accompanies each kit. The customer should fill out all forms and follow all instructions to safely ship samples for mapping to the OpGen Laboratory. 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.

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 weight DNA is obtained.

Also, it is very important that we know when you plan to ship samples to our laboratory for processing; we want to 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.

What is the average turnaround time when I place an order?

Turnaround time is totally dependent on the scope of your project, the target species, 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.

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—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 weight 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.

What sample types are acceptable to ship to OpGen for Whole Genome 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.

Is it true that you can accept mixed microbial or metagenomic samples?

Yes, that is true. Whole Genome Mapping technology is able to distinguish strains in a mixed sample. See T. Wagner’s poster presented at the 2008 ICAAC, “Use of Whole Genome Mapping to Identify Bacteria from Complex Mixture and Clinical Samples.”

What sort of resolution is possible using a single restriction enzyme?

The “resolution” of Whole Genome Mapping using a single restriction enzyme is approximately 2Kb. Whole Genome 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 that are less than 2Kb in size may be retained, 100% of fragments 2Kb and larger will be retained.

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 Whole Genome Mapping. Additionally, enzyme selection is based on sequenced strain data and/or customer-provided sequence data if available.

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 Whole Genome Map. However, some customers find that it is advantageous to have Whole Genome 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 that another enzyme may complete the contig placement.

Does using a second enzyme increase the cost and, if so, by how much?

Maps are generated using one restriction enzyme per Whole Genome 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. We can generate a customized quote for you when we discuss your overall project and needs.

How do you generate a Whole Genome Map from “unculturable” or “fastidious” samples?

Genomic analysis using Whole Genome 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.

Can specimens be retrieved from the slide after analysis (or can any subsequent experiments, such as hybridization reactions, be performed on the restriction fragments)?

“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 as extended, 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.

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.

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. Finally, your sample integrity is very important; OpGen wants to make sure your samples are not jeopardized in transit and arrive safely to our laboratory.

Application and Technical Questions

After I sequence, I have numerous contigs to assemble. How does Whole Genome Mapping help with contig placement and closure?

Your sequence and contig data can be converted into an in silico sequence contig Whole Genome Map. Through 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. Misassemblies, repetitive sequences, insertions, deletions, and mobile elements will be visually identified. Contigs less than 50Kb may not be placed. Your map can also be compared to other available sequenced organisms very easily.

Is it also possible to use FISH in combination with Whole Genome Mapping?

Not currently. Our Research and Development team is continually exploring potential opportunities for expanding our applications.

Can Whole Genome Mapping provide Maps of plasmids or viruses?

Whole Genome 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 extrachromosomal elements approximately 150Kb in size, but ordinarily, we would be looking for molecules 200Kb or larger.

Can you detect SNPs?

Whole Genome Mapping technology enables whole genome analysis that is both complementary and additive to existing microarray and SNP genotyping systems. Where these technologies detect small changes in DNA sequence, Whole Genome Mapping finds novel insertions, deletions, and genomic rearrangements within the genome that other techniques are unable to find.

What is the upper limit of genome size amenable to Whole Genome Mapping?

Prokaryotes, small eukaryotes and, as of fall 2011, human and plant samples can be mapped, with the larger genome projects requiring more sample preparation, processing and mapping time.

Does OpGen generate in silico maps that form part of the Whole Genome Mapping database or is this something I need to generate for my specific Whole Genome Map project?

Let us know which sequenced strains you are interested in and we will include those with your final data package. The Whole Genome Mapping Software allows you to upload sequence data from GenBank files directly into the database; if there are additional strains of interest, this is a nice benefit of the software.

 

If you don’t see your question here, just ask us at CustomerSupport@OpGen.com or call 1.888.856.2748 or 301.813.1270.

“Physical map and genetic map still should be emphasized as an important parts of a reference genome. Recent progress in technologies, such as the whole genome mapping high-throughput platform offered by OpGen, now provide the tools for efficient physical map construction. This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing. We applied this technology as an assistant tool of the NGS to assemble bacterial, plant and large mammalian genome with reliable accuracy and generate the sub-chromosome graded assembly. The experience in these genome assembly projects shows that the physical map should be the standard for any reference genome to be assembled in further.”

Xun Xu, Ph.D.

Deputy Director at BGI
 

This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing.

Xun Xu, Ph.D.
Deputy Director at BGI

“Our research focuses on a wide variety of projects from viruses and microbes to crop plants and mammals. Many of our projects are de novo assembly projects, where, without a closely related genome sequence, it can be difficult to critically assess the results. We often combine different sequencing technologies, and we are finding that regardless of the sequencing platform, error correction, or assembler used, OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.”

Matthew Clark, Ph.D.

Team Leader, Sequencing Technology Development

The Genome Analysis Centre (TGAC), Norwich, UK

OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.

Matthew Clark, Ph.D.
Team Leader, Sequencing Technology Development

“We adopted OpGen’s Argus System as the most advanced way of adding Whole Genome Mapping to improve whole genome sequences. We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences as part of our program in the Human Microbiome Project. We are now moving the technology into larger genome projects.”


George Weinstock, Ph.D.

Associate Director
 The Genome Institute at Washington University

We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences. This is part of our program from the Human Microbiome Project.

George Weinstock Ph.D.

Associate Director

The Genome Institute at Washington University

“Certain things you just have a tough time answering with de novo sequencing. And assembly doesn’t always work out as sweetly as you would like. So definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map optically as well as de novo assembly. And the amount of money you would save is in the thousands of dollars in finishing.”

Stefan Green

Director of DNA Services

University of Illinois Chicago Research Resources Center (UIC RRC)

Definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map.

Stefan Green
Director of DNA Services

“Physical map and genetic map still should be emphasized as an important parts of a reference genome. Recent progress in technologies, such as the whole genome mapping high-throughput platform offered by OpGen, now provide the tools for efficient physical map construction. This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing. We applied this technology as an assistant tool of the NGS to assemble bacterial, plant and large mammalian genome with reliable accuracy and generate the sub-chromosome graded assembly. The experience in these genome assembly projects shows that the physical map should be the standard for any reference genome to be assembled in further.”

Xun Xu, Ph.D.

Deputy Director at BGI
 

This independent technology provides not only the validation of the genome sequencing, but also provides the large-scale chromosome structure information that cannot be detected by sequencing.

Xun Xu, Ph.D.
Deputy Director at BGI

“Our research focuses on a wide variety of projects from viruses and microbes to crop plants and mammals. Many of our projects are de novo assembly projects, where, without a closely related genome sequence, it can be difficult to critically assess the results. We often combine different sequencing technologies, and we are finding that regardless of the sequencing platform, error correction, or assembler used, OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.”

Matthew Clark, Ph.D.

Team Leader, Sequencing Technology Development

The Genome Analysis Centre (TGAC), Norwich, UK

OpGen’s Whole Genome Mapping identifies misassemblies and provides the highest quality de novo assembly for further research.

Matthew Clark, Ph.D.
Team Leader, Sequencing Technology Development

“We adopted OpGen’s Argus System as the most advanced way of adding Whole Genome Mapping to improve whole genome sequences. We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences as part of our program in the Human Microbiome Project. We are now moving the technology into larger genome projects.”


George Weinstock, Ph.D.

Associate Director
 The Genome Institute at Washington University

We combined Whole Genome Maps with sequence assemblies to correct errors and misassemblies in bacterial genome sequences. This is part of our program from the Human Microbiome Project.

George Weinstock Ph.D.

Associate Director

The Genome Institute at Washington University

“Certain things you just have a tough time answering with de novo sequencing. And assembly doesn’t always work out as sweetly as you would like. So definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map optically as well as de novo assembly. And the amount of money you would save is in the thousands of dollars in finishing.”

Stefan Green

Director of DNA Services

University of Illinois Chicago Research Resources Center (UIC RRC)

Definitely for any whole genome de novo project that people are insistent on closing we would do a Whole Genome Map.

Stefan Green
Director of DNA Services

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