Monthly Archives: July 2013

Next Generation Sequencing Creates Opportunities for Software Entrepeneurs

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Earlier this year it was announced that a large biotechnology firm, Qiagen based in the Netherlands completed its purchase of Ingenuity Systems based in California which had built software exclusively. This event is one of many to signal the trend of a merging of the biotechnology and software industries which is presenting a large opportunity for software entrepreneurs.

This trend, as further discussed on the Washington Post, is being led by the next generation sequencing industry which continues to produce sequencing data at ever increasing rates and at lower costs. As sequencing data becomes more readily available, the demand continues to rise as some experts suggest DNA mapping will become standard medical practice. Previously it had been difficult for software companies to thrive in the biotech space as next generation sequencing hadn’t come along until massively parallel signature sequencing (MPSS) was developed in the 1990’s. Because previous methods were costly and not readily available, the demand for sequencing analysis was held equally low.

As vast amounts of next generation sequencing data are now produced at ever quicker rates, there arises a tremendous opportunity for software entrepreneurs who are able to produce usable results from this data. Although the industry is in its infancy, and has not yet produced a clear market winner, there are several new companies which are capitalizing on this demand. One of these is Enlis Genomics which was started two years ago in Berkeley, CA by Devon Jensen, a PhD in molecular and cell biology. Devon saw the demand for software which was easy enough to use by the average researcher. Another notable example would be Cypher Genomics out of San Diego, CA also formed two years ago which allows researchers to detect genetic variations which may signal health concerns.

Undoubtedly we will also continue to see biotech firms of all types continue to gobble up these new bioinformatics companies as they strive to offer a complete front to back solution for their clients. This is truly an exciting time in the bioinformatics industry with a host of opportunities yet to be discovered.

The Institute for Personalized and Predictive Medicine of Cancer (IMPPC) Lists High Throughput Sequencing Services On the Genohub Market

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We want to welcome The Institute for Personalized and Predictive Medicine of Cancer (IMPPC) to the Genohub family. The high throughput sequencing services listed by IMPPC will add more available options to the Genohub next generation sequencing market.

IMPCC listed the following next generation sequencing instruments and library prep options:

  • Instruments:
    • Illumina HiScanSQ
    • Ion PGM 314 Chip
    • Ion PGM 316 Chip
    • Ion PGM 318 Chip
  • Library prep:
    • Illumina Directional RNA (polyA-selected)
    • Illumina Small RNA (microRNA)
    • Ion DNA

The IMPCC is a publicly funded institute backed by a private foundation with a mission to advance in the understanding of genetic and epigenetic factors leading to higher predisposition or susceptibility to develop cancer. We look forward to matching IMPPC with the most compatible high throughput sequencing projects for their lab.

For Academic Genome Centers: How Genohub Fits into the NIH Circular A21 Picture

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Occasionally, we speak with directors at academic genome centers that express their interest in Genohub, yet are unsure whether listing their high throughput sequencing services would in some way be unauthorized under NIH Circular A21. This circular “Establishes principles for determining costs applicable to grants, contracts, and other agreements with educational institutions”. Of course this directive does not affect all academic genome centers, but there are a substantial number which do receive grant funding from the NIH.

The general concern regarding how Genohub fits into the Circular A21 picture is understandable. The concern can likely be attributed to subsection J.46 which states:

Costs of selling and marketing any products or services of the institution are unallowable (unless allowed under subsection J.1 as allowable public relations costs or under subsection J.38 as allowable proposal costs).

Clearly, it would not be permissible for academic genome centers under Circular A21 to pay a third party to market their sequencing services. For this reason (among others), high throughput sequencing services are completely free to list on the Genohub Next Generation Sequencing Market. There are also currently no provisions whereby sequencing providers are able to pay Genohub for marketing services. Of course Genohub engages in marketing practices which happen to be aligned with the external facing goals of  many academic genome centers, namely attracting and offering the best value to researchers with projects involving next generation sequencing. Service providers do benefit from Genohub marketing, albeit at no cost.

Selling, on the other hand, can be viewed as permissible on Genohub under the subsection J.38 exception as an allowable proposal cost. Circular A21, J.38 states:

Proposal costs are the costs of preparing bids or proposals on potential federally and non federally funded sponsored agreements or projects, including the development of data necessary to support the institution’s bids or proposals. Proposal costs of the current accounting period of both successful and unsuccessful bids and proposals normally should be treated as F&A costs and allocated currently to all activities of the institution, and no proposal costs of past accounting periods will be allocable to the current period. However, the institution’s established practices may be to treat proposal costs by some other recognized method. Regardless of the method used, the results obtained may be accepted only if found to be reasonable and equitable.

Under the J.38 exception, Genohub offers the following service at a nominal fee per transaction through Genohub:

“Preparing bids or proposals”: One of the biggest reasons providers list services on Genohub is because they save valuable time and cost preparing bids or proposals. Services and pricing are listed one time only by the provider. Any time a researcher visits and shops for services via the Genohub shopping interface, Genohub instantly and automatically prepares and delivers bids from every NGS provider that meets the minimum search criteria. Of course Genohub only charges a small fee to the provider whose bid is chosen by the researcher.

The time and money saved on proposal costs by using Genohub has freed up resources for academic genome centers to allow them to refocus on their core objectives within their institution, yet fill those needed external sequencing orders to keep the engines running. Time and cost is further reduced as we offer researchers free consultation from our science team that might otherwise be required of the provider. We hope to continue to increase the value we provide to academic genome centers and researchers alike by creating a beautiful, simple, and cost effective next generation sequencing market.

If you have any additional questions on Circular A21 as it relates to Genohub, or have any feedback on how we can improve the services we offer to you, our valued customers, we encourage you to contact us at support@genohub.com.

 

Axeq Technologies Lists High Throughput Sequencing Services on the Genohub Market

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We want to welcome Axeq Technologies to the Genohub family. Axeq has listed high throughput sequencing services if offers on the Genohub next generation sequencing market. Axeq currently has 4 worldwide sites:

  • HQ – Axeq USA in Maryland
  • Axeq Europe in Amsterdam
  • Axeq Asia in Seoul
  • Axeq Japan in Tokyo

Macrogen is the parent company of Axeq which has been a phenomenal success in both the scientific services market and in the field of original genetic research. With devotion to molecular biology, cell biology, genetics research, and extensive investment in installations of cutting-edge research tools – including genotyping, Sanger sequencing and next-generation sequencing platforms, Macrogen successfully published numerous articles in leading journals. These include the publication of the first whole genome sequence of a Korean (Nature), and high resolution CNV analysis of the Asian population (Nature Genetics).

Axeq Technologies was formed in early 2011 as a premium brand to offer both scientific services and collaborations to researchers around the world. The company is dedicated to providing a whole new level of service experience based on its ability to provide publication-quality data and 24/7 client support. Currently, Axeq has listed high throughput sequencing services on an Illumina GAIIx instrument. We look forward to matching Axeq with sequencing projects on the Genohub next generation sequencing market.

Scientists Develop Method to Rapidly Analyze High Throughput Sequencing Data

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Scientists in Singapore have developed a method to rapidly analyze high throughput sequencing data. This method incorporates a mathematical technique which has long been used in industries outside biotechnology such as radar, electrical engineering, and cell phones.

While high throughput sequencing has revolutionized molecular biology, there has been a speed bump which slows the analysis of sequencing results. The high throughput sequencing process generates a massive amount of data which must be analyzed to filter signal from noise. Traditionally, researchers have treated each set of sequencing data as unique and requiring its own set of analytical methods to decipher. Because of this, it can take a lengthy period of time to produce meaningful sequencing data.

As published in Nature Biotechnology, the team of scientists was able to produce meaningful results from a variety of high throughput sequencing data sets using only one analytics technique, the pre-whitening match filter. The filter was demonstrated to produce data across several sequencing based functional profiles that is more accurate than assay-specific analysis methods.

This latest technique holds promise to reduce time and cost for patients who could benefit from an improved level of care due to sequencing.

The article can be found at: Kumar et al. (2013) Uniform, Optimal Signal Processing Of Mapped Deep-Sequencing Data.

 

University of Rochester Genomics Research Center Adds High Throughput Sequencing Services to Genohub

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We want to welcome the University of Rochester Genomics Research Center to the Genohub family. The high throughput sequencing services listed by the University of Rochester will add more available options to the Genohub next generation sequencing market.

The University of Rochester added the following instruments and library prep options:

  • Instruments: Illumina HiSeq
  • Library prep: a host of Illumina options
    • Directional RNA (rRNA-depleted)
    • Directional RNA (polyA-selected)
    • Small RNA (microRNA)
    • ChIP
    • Mate Pair (1-6 kb)
    • DNA
    • Bisulfite
    • RNA (polyA-selected)

We look forward to matching the University of Rochester with the most compatible high throughput sequencing orders for their lab.

Next Generation Sequencing Promises to Increase IVF Success Rates

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Next generation sequencing techniques hold promise for increasing the success rate of in-vitro fertilization (IVF). Dr Dagan Wells of the NIHR Biomedical Research Center at the University of Oxford announced on July 8, 2013 at the ESHRE annual meeting that an IVF birth had resulted, for the first time, due to embryo selection based on next generation sequencing results.

Historically, IVF success rates have stood at around 30%, thought to largely be due to DNA mutations in the embryo. Traditional sequencing techniques have been utilized in order to identify and utilize healthier embryos resulting in a higher success rate. The drawbacks, however, have been that these methods have been far too costly to be within reach of most patients.

Dr Wells and an international research team developed an embryo selection process using much faster and less costly next generation sequencing techniques. This process only takes about 16 hours avoiding the need for embryo freezing. Dr Wells technique also offers additional advantages when compared to previous techniques. Complete chromosome information can be produced and serious gene defects can be detected simultaneously.

As next generation sequencing has been revolutionizing many areas of genetic research, it looks poised to soon benefit IVF patients. “In the past few years, results from randomized clinical trials have suggested that most IVF patients would benefit from embryo chromosome screening, with some studies reporting a 50% boost in pregnancy rates. However, the costs of these genetic tests are relatively high, putting them beyond the reach of many patients. Next generation sequencing is a way which could make chromosome testing more widely available to a greater number of patients, improving access by cutting the costs. Our next step is a randomized clinical trial to reveal the true efficacy of this approach – and this will begin later this year.”  -Dr Wells

Genohub Next Generation Sequencing Market Open to Researchers

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RESEARCHERS! SAVE TIME & MONEY ON YOUR NEXT NEXT GENERATION SEQUENCING PROJECT!

The Genohub next generation sequencing market opens today to a number of researchers who could benefit from placing their next-gen sequencing order through Genohub. If you would like to take part in our initial launch please visit our shopping page, enter a few bits of information such as the number of samples to sequence and minimum number of reads, or coverage per sample, and we will instantly match you with the best providers for your project. You also have the ability to search by specific technology if you require a service provider with specific platforms and library types. It is 100% free to search and place an order, and we are currently offering free consultation from our science staff.

Here are some of the other ways we help researchers on Genohub:

  1. Save time shopping for the best price on costly sequencing projects

  2. Eliminate the need for researching the technologies in order to find suitable sequencing solutions

  3. Offer more predictability on turnaround time and quality

  4. Centralized per-project communication platform

Of course we realize that you have a number of options available when it comes to finding the best next generation sequencing provider for your project. In fact, we developed Genohub to help researchers in ways that have not been available up until now. Genohub is unique in that we offer:

  1. Structured service listings

  2. Intelligent technology-aware software that automatically matches project requirements with providers’ service listings

  3. Shopping, ordering and project management process tailored to sequencing projects

As a researcher, we encourage you to visit our shopping page and let us know what you think! And of course if you need any assistance along the way, we would be more than glad to help.

High Throughput Sequencing Locations

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If you get the inkling to know just where high throughput sequencing providers and sequencers themselves are located worldwide, there’s an excellent resource to help you do just that. If you haven’t come across this yet, Omicspaps.com is a crowd-sourced map which not only lists service providers globally, but also allows users to view the locations of selected individual sequencers. The site is aptly titled “Next Generation Genomics: World Map of High-Throughput Sequencers”. The home page is comprised of a map built on a Google Maps foundation that overlays the locations of sequencing providers and sequencers. Below is a screenshot of this view:

Omicsmaps - High Throughput Sequencing Locations

Omicsmaps – High Throughput Sequencing Locations

Users also have the option to filter by country. What is also quite interesting is the “Machine Statistics” link on the top right hand corner of the main screen which upon clicking, displays the total numbers of facilities per country, sequencers per provider, and many other interesting factoids. Here are a few highlights:

  • Largest genome center in the US: the Broad Institute of MIT and Harvard takes the cake on this one with a whopping 101 sequencing machines
  • The #1 high throughput sequencing platform in use today: this badge belongs to the Illumina HiSeq 2000 with 739 machines globally
  • There are more sequencing machines in the US than the next lower 6 countries on this list combined!

Each high throughput sequencing service provider also includes a link to their website which some might find useful. Another great way to get in touch with sequencing providers is through the Genohub shopping interface. Some of the best sequencing providers have already signed up with Genohub to also list their equipment along with the associated services, pricing, and additional value they offer. We encourage you to give it a try!

5 Next Generation Sequencing Market Drivers and Hindrances

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The next generation sequencing market is poised to reach $2.7 billion by 2017 as presented by marketsandmarkets.com. This represents an estimated growth of 16.3% from a market value of $1.3 billion in 2012. Marketsandmarkets presents a detailed analysis of their findings from which the following top next generation sequencing market drivers and hindrances are derived:

5 Top NGS Market Drivers:

  1. Continuous innovations and developments in the market aimed at higher throughput, increased accuracy, and affordable costs
  2. Improved turnaround time
  3. Government funding
  4. Increasing opportunities in NGS clinical applications
  5. Presence of dominant NGS platform players

Although the next generation sequencing market is growing rapidly, there are factors which have been weighing down the market as a whole.

5 Top NGS Market Hindrances:

  1. High reliability on grants and funding from the government
  2. Decrease in capital expenditure from academic institutions
  3. Accuracy and standardization concerns
  4. Data storage problems
  5. Issues in interpretation of complex data

The future of the NGS market promises to offer a simpler, less costly, and more integrated experience for researchers. The market is also poised to revolutionize applied markets like diagnostics, drug discovery, biomarker discovery, personalized medicine, and agriculture and animals research.