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-The MiraiBio Team

• MicroPlex Beads
• Lumavidin Beads
• SeroMAP Beads
• xTAG Beads
• Calibration Beads
• Control Beads
• Luminex 200 Calibration Kit (25 doses)
• Luminex 200 Performance Verification Kit (25 doses)
• Automated Maintenance Plate
• Luminex Sheath Fluid, 1X, 20L

We regret to inform you that Hitachi Solutions America, Ltd. (HISAL) must stop accepting orders for the above mentioned products at 12:00pm PST on December 27^th, 2011**. HISAL has the most competitive prices for most of the products affected and due to the long shelf life of some of the products (up to 3 years) you may want to consider purchasing extra inventory at our competitive prices before our distribution rights end.

Please be aware that the product descriptions, part numbers and prices for the affected products will change when you source them from another supplier. You can contact HISAL at info@miraibio.com to receive a matrix that correlates HISAL product descriptions, part numbers and prices to the manufacturer’s respective descriptions, numbers and prices.

We greatly value your business and will do our very best to facilitate the transition to a new supplier of the products affected by this announcement.

Thank you again for your business and loyalty. We look forward to serving you with HISAL products and services in the future.

Regards,

The MiraiBio Group of Hitachi Solutions America, Ltd.

**After December 27^th, 2011 we recommend that you purchase these products directly from the manufacturer, Luminex Corporation. In order to facilitate the transition, Luminex Corporation has assigned 2 contacts, Debra Asgari and David Mendoza, to handle any inquiries, process initial orders and communicate the ordering process for ongoing orders:

Debra Asgari – dasgari@luminexcorp.com or 512-381-4386

David Mendoza – dmendoza@luminexcorp.com or 512-381-4302

Although sequencing technology and price performance per base-pair-sequenced continue to advance at an impressive rate, Finished whole genome sequencing projects are still costly and lengthy endeavors. Next Gen sequencing technology (and even next-next gen technology) isn’t addressing some of the common issues faced with creating a “Finished” quality genome, namely Contig Placement, Gap Closure and Validation.  Addressing these issues takes several months and a substantial amount of the budget in a sequencing project.

Consider the current workflow for generating a Finished whole genome in the figure below.

As you can see, generating the initial sequence data is no longer the bottle neck. Small genomes can be sequenced using shot gun methods in a couple of days. After the initial assembly the hard part starts: Closing gaps between your contigs, navigating regions with a high number of repeats, resequencing for validation etc. These tasks can represent over 50% of the length of a sequencing project and over 50% the cost!

I wanted to see if other researchers had found novel and/or more cost effective ways of dealing with these challenges. Especially labs that are resource constrained. I came across an interesting paper titled Finishing genomes with limited resources:  lessons from an ensemble of microbial genomes that was published last year in BMC Genomics^1. It discusses how using Whole Genome Mapping technology, also called Optical Mapping, can significantly reduce the length of sequencing projects. Before we get into what the paper presents let’s learn more about Whole Genome (Optical) Mapping.

Whole Genome (Optical) Mapping is a de novo process that generates whole genome, ordered, restriction maps with no requirement for previous sequence information & provides a comprehensive view of genomic architecture. An Optical Map or Whole Genome Map (WGM) is displayed in the unique MapCode™ pattern below where the vertical lines indicate the locations of restriction sites, and the distance between the lines represent the fragment size.

The WGM acts as a scaffold for your sequencing project. How? The contigs generated from your sequence assembly are converted to Optical Maps in silico and then are aligned and assembled to the de novo WGM. The WGM acts as an independent validation tool for contig placement and length of repeat regions while also helping to easily identify gaps in your assembly. By taking unordered sequence contigs and aligning them to an ordered WGM you quickly orient the contigs.  When aligned, you can then identify any possible misassemblies that may have occurred in the initial assembly portion of your project.

You might be wondering how the scaffold concept as it applies to Whole Genome Mapping is different from scaffolds obtained with mate-pairs. To quote Nagarajan et al in the paper referenced above “It should be noted that unlike scaffolds obtained with mate-pairs, the scaffolds here are genome-wide and one per genome and therefore well suited for finishing efforts.”(p3) Additionally “While paired-end reads can be invaluable to scaffold contigs, they provide local order information [only] and using them to recreate a genome wide ordering of contigs is computationally challenging.”(p7) Finally “In addition, for time-critical applications in a biodefense or clinical setting, the time to construct paired-end libraries can be a limiting factor. In such settings, Optical Restriction Mapping [22], a form of ordered restriction maps (see Figure 5), can be a promising alternative as it can quickly provide genome wide restriction site information that can be used to order and orient contigs [8].”(p7)

We are starting to get a picture of how using just one single WGM can save time and reduce the need for computationally intensive bioinformatic steps thereby saving money. Let’s look in more detail about how these time savings are gained.

Contig Placement and Validation

With shotgun sequencing, genomic rearrangements, like inversions, can be missed due to incorrect reconstruction of repeats. A WGM can help you validate your whole genome and identify any possible inversions, insertions, translocations and deletions that sequencing may not have identified.  In the example below the contiguous map in the middle was generated de novo using Whole Genome (Optical) Mapping technology. The contigs were generated in silico. Notice the missassemblies for example in Contig980. You can see an example of an inversion in Contig1253. You can also see examples of insertions, deletions and run of the mill gaps that will have to be spanned in resequencing efforts.

Gap Closure

Another example Nagarajan et al describe is using WGMs to reduce the number of PCR experiments needed.  “Working with the original assembly (59 large contigs) could have necessitated on the order of 592 ≈ 3000 PCR experiments.” (p4) That’s a lot of PCR kits and a lot of time.  Using WGMs as scaffolds, they were able to finish the genome using only 43 PCR experiments and 26 sequencing reactions to close 33 of the gaps.  “From a finishing perspective, these (Optical Mapping) scaffolds are particularly useful, as for a set of n contigs, they help reduce the number of PCR experiments needed from roughly n² to n.” (p7)

Let’s go back to our original figure describing the steps and average time to complete a sequencing project, this time comparing current methods to a workflow that uses a WGM.