Author Archives: mccalleygenohub

Bioinformatic Analysis: A New Option On the Genohub NGS Market

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The ability to list and purchase bioinformatic analysis services along with next-gen sequencing comes to Genohub. This additional feature set will further simplify the NGS project experience by offering capabilities for the bioinformatics project step, all in one roof. By launching this service, researchers on Genohub are now able to shop from full-service sequencing providers who offer the three main services required in every NGS project with options for Illumina, Ion, SOLiD, PacBio, and Roche454 platforms:

  1. Library prep
  2. Next generation sequencing
  3. Bioinformatic analysis

The addition of this service alleviates the burden many researchers face of shopping for three separate sequencing related services from multiple providers and efficiently managing the entire process.

The benefits of this feature for researchers includes:

  • Researchers save time and money purchasing sequencing and bioinformatic services simultaneously
  • By enabling next gen sequencing providers to list bioinformatic services, it becomes easier and faster for researchers to compare and select a provider for their project
  • Risk is mitigated, as researchers are able to purchase bioinformatic services along with NGS services by providers that have gone through the Genohub vetting process

Providers also benefit:

  • Providers are now able to better highlight their unique services by listing specific bioinformatic services. These include basic primary analysis that may be included with every sequencing order, as well as more complex secondary and custom bioinformatics services that can be ordered as add-ons to NGS projects.
  • The bioinformatics platform enables providers to more succinctly communicate bioinformatic services to researchers, cutting down on back and forth communication prior to the researcher opting to move forward with the services listed by the provider

Providers may now list bioinformatic analysis services on the familiar “Manage Services Offerings” page:

New manage services page includes bioinformatics analysis services

New Manage Services Page

Researchers will be able to view these services once they select to view details about a sequencing package found when shopping by project or technology.

At Genohub we constantly strive to improve the service we offer to the NGS community through the development of new features and functionality. When we launched Genohub in August, 2013 our goal was to launch a service that was useful to researchers and sequencing providers, and continue to enhance and improve our service based directly on feedback from our clients.

The bioinformatic analysis listing feature come as a direct result of our development methodology. Researchers asked for a one-stop-shop for all of their sequencing needs, and sequencing providers asked for more ways to highlight and differentiate their services on Genohub. You asked, we listened!

Please visit Genohub often as we are constantly adding new useful features to improve the next-gen sequencing shopping experience including upcoming features to further enable providers to differentiate themselves and mitigate risk in decision making for researchers. If you have any feedback on additional features you would like to see, please send us feedback by shooting us an email at info@genohub.com.

3 Top Factors Researchers Consider When Selecting an NGS Provider

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At Genohub, not only do we seek feedback from researchers, our development methodology is almost entirely based on this feedback. We receive this feedback via website forms as well as routine one-on-one conversations with some of the top researchers using next generation sequencing for their projects. Through this data and interaction, certain trends have begun to emerge which may be useful to an NGS provider seeking additional projects. This list is not based on a controlled experiment, however countless conversations indicate that these factors are extremely important:

  1. Turnaround time – this one is a toss up when compared with price, but we typically find turnaround time to be among the leading factors in a researcher’s decision to select an NGS provider. We have heard quite a few stories of researchers seeing turnaround times over several months for library prep and sequencing.
  2. Price – while this is one of the biggest factors for researchers, it must be qualified with established trust which is the next major factor.
  3. Trust – this one is a biggie for many researchers and often a non-starter if not established. The main reasons for this are that researchers are hesitant to ship their precious samples (ie human brain tissue) to an NGS provider for quite often costly sequencing if they are not confident in their abilities. Researchers have told us some of the things they look for which lend to building their confidence:
    • Referrals & Reviews – researchers seek out colleagues who have done similar projects and look for recommendations. Word of mouth is one of the biggest methods researchers rely on to select an NGS provider.
    • Publications – providers who are listed in publications involving similar projects.
    • What kind of QC will be run on the sample.
    • Overall experience indicators such as time in business and volume of samples regularly handled.
    • Data and sample security.
    • Location – this factor is considerably important if previous trust is not established. Some researchers have absolutely no problem shipping samples across the globe, while others might physically drive their samples to a local provider to ensure sample integrity.

We would love to hear your feedback on this topic whether you are an NGS provider, or a researcher actively using next sequencing. What other decision driving criteria have you found as a provider, or what are some other factors important to you as a researcher?

In a Nutshell: Life Tech Exome Certified Service Provider Program

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Life Technologies announced yesterday that they launched the Ion AmpliSeq Exome Certified Service Provider Program.

What the program is in a nutshell:

  • Goals: Offer a network of next gen sequencing providers able to help researchers get a high quality exome sequence at a reduced cost with fast turnaround times and low amounts of input material
  • Exome sequencing inputs: as little as 50ng of customer DNA
  • Library kit used: Ion AmpliSeq Exome kit
  • NGS Instrument used: Ion Proton
  • Exome sequencing outputs: high quality data, which of course can be used with Ion Reporter Software for mutation validation, annotation, and reporting

The Service Provider Program is intended to fill exome sequencing market demand which Life Tech argues has been under-serviced with exome sequencing currently going for $1,000+ , long turnaround times up to 8 weeks, and requiring up to 3mg of DNA. Dr. Candace Johnson, Deputy Director and the Wallace Chair of Translational Research at Roswell Park Cancer Institute states “Exome sequencing will be central to discoveries made in clinical research”. If the Exome CSP delivers as promised, it could have a major impact in accelerating discoveries made in clinical research.

For more information on the Life Tech Provider Program please see the entire press release.

8 Top Online Calculators for Next Gen Sequencing

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When it comes to next gen sequencing, here are the top 8 online calculators that we have found:

Coverage

  1. Genohub’s shop by project feature
  2. The Coverage Calculator by Clinical Genomics

Oligonucleotide

  1. The Oligo Calc: Oligonucleotide Properties Calculator by Northwestern University
  2. The OligoAnalyzer 3.1 by Integrated DNA Technologies

Primers

  1. NCBI/ Primer-BLAST: Finding primers specific to your PCR template (using Primer3 and BLAST) 
  2. Primer3: WWW primer tool by UmassMed

qPCR Efficiency

  1. The qPCR efficiency calculator by Thermo Scientific
  2. The QPCR Standard Curve Slope to Efficiency Calculator by Agilent Technologies

If you know of any other great online calculators for next gen sequencing please tell us about it!

Targeted Resequencing (TPS/WES) Tops Next Gen Sequencing Survey

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Oxford Gene Technology (NGS provider currently listed on Genohub) recently presented the results of their next gen sequencing survey which demonstrated targeted resequencing as the top use for next generation sequencing. The results are based on a survey of 596 researchers who responded regarding their current and expected use of NGS services. When compared to the results for whole genome sequencing the popularity of targeted resequencing is possibly attributed mostly to the lower cost of targeted resequencing. This infographic depicts the results:

OGT NGS Survey Results

OGT NGS Survey Results

Other interesting results point to a general data problem with 38% of respondents saying they lack trust in bioinformatics data. Bioinformatics also leads the field when researchers were asked about the biggest barrier to NGS usage (see below).

Barriers to NGS Usage

Barriers to NGS Usage

Undoubtedly this presents an immense opportunity for the bioinformatics sector to increase confidence in data accuracy and interpretation which could have a positive impact on the use of next gen sequencing as a whole.

You can find many more interesting survey results on the excellent infographic titled Oxford Gene Technology – NGS Survey 2013.

BaseClear Lists Next Gen Sequencing Services On Genohub

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Genohub would like to welcome BaseClear to the Genohub family. The sequencing services listed by BaseClear has added more available options for researchers on the Genohub next generation sequencing market.

BaseClear has listed the following next gen sequencing instruments and Illumina library prep options:

  • Instruments:
    • Illumina MiSeq paired end sequencing options
    • Illumina HiSeq paired end sequencing options
    • PacBio SMRT Cell
  • Library prep:
    • Illumina DNA
    • Illumina 16S V4
    • Illumina RNA (rRNA-depleted)

BaseClear is located in the BioSciencePark (BSP) of Leiden in the Netherlands. By using Illumina systems (HiSEQ2500 and MiSEQ) in combination with the PacBio RS system BaseClear can offer whole genome analysis and offer a wide variety of combinations of read lengths, number of tags and paired end size ranges. The lab has been ISO17025 accredited since 2006.

We are excited to include BaseClear’s high throughput sequencing services on the Genohub next gen sequencing market.

UTHSCSA Lists Next Generation Sequencing Services On Genohub

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Genohub would like to welcome the Genome Sequencing Facility (GSF) at Greehey Children’s Cancer Research Institute in the University of Texas Health Science Center at San Antonio to the Genohub family. The sequencing services listed by UTHSCSA has added more available options for researchers on the Genohub next generation sequencing market.

UTHSCSA listed the following next generation sequencing instruments and Illumina library preparation options:

  • Instruments:
    • Illumina MiSeq paired end sequencing options
    • Illumina HiSeq single read and paired end sequencing options
  • Library prep:
    • Illumina ChIP
    • Illumina Directional RNA (polyA-selected)
    • Illumina Directional RNA (rRNA-depleted)
    • Illumina DNA
    • Illumina Exome
    • Illumina RNA (polyA-selected)
    • Illumina RNA (rRNA-depleted)
    • Illumina Small RNA (microRNA)

The GSF has a stated mission to deploy NGS systems focusing on cancer genomics to benefit Greehey CCRI investigators and the wider research community. The NGS facility performs all protocols necessary for preparing a sample to be sequenced on the Illumina HiSeq 2000 system. The GSF is also a research group with experience in customizing experiments and developing new applications. They provide:

  • Complete project consultation for optimal experimental design and setup
  • Complete quality control analysis during library preparation and data generation
  • Secure website to download the sequencing data with quality information
  • Full project report
  • Bioinformatics analysis option available
  • NCBI GenBank submission option available

We are excited to include UTHSCSA high throughput sequencing services on the Genohub next generation sequencing market.

First XPRIZE Cancelled Due To Unexpected Innovation in Next Gen Sequencing

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For the first time ever, an XPRIZE has been cancelled. The reason — unexpected innovation in next generation sequencing. The Archon Genomics XPRIZE announced in 2006, had promised to award $10 mil to the first team that was able to accurately sequence 100 whole human genomes at a cost of $10,000 or less per genome in a short period of time. The competition was cancelled as XPRIZE CEO Peter Diamandis and team felt it was not serving its intended purpose to incentivize technological innovation in gene sequencing.

As stated by Peter Diamandis, “Every XPRIZE is carefully designed to address a market failure and hopefully create a new industry to achieve breakthroughs and solutions once thought to be impossible.” Although the Archon Genomics XPRIZE was conceived according to this criteria, the XPRIZE team felt that innovation in gene sequencing has been progressing independently of the XPRIZE incentive, therefore voiding the need for the competition.

The rapid innovation in next generation sequencing has caused sequencing times to decrease and prices to plummet to around $5,000 per genome. The XPRIZE team feels as if the targets laid out by the competition will be met in the very near future with or without their incentive, and have opted to cancel the XPRIZE and return the money to sponsors. The announcement by Peter Diamandis can be read in its entirety on the Huffington Post.

The logic behind the XPRIZE cancellation seems clear, however it remains to be seen what backlash, if any, arises from scientists who may have spent considerable time and effort devoted to meeting this challenge. Although next gen sequencing instruments are developed by large companies such as Illumina ($1.15B revenue), which may not be driven by a competition like the XPRIZE, innovation in this field must also be attributed to the wider research community, of which a team may have conceivably won the competition independent of any large commercial enterprise. In fact, in his cancellation announcement, Peter Diamandis thanks George Church and the Wyss Institute at Harvard for registering for the competition. Does the XPRIZE lose some of its ability to incentivize future competitions because of this cancellation? We welcome your comments on the matter.

How to Select the Best Next Generation Sequencing Platform For Your Project

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We often get questions from researchers on selecting the best next generation sequencing platforms for specific projects. We are glad to offer free consultation to researchers on inquiries such as these among others. We also offer a sequencing guide to get you started.

Another great resource is a YouTube talk by Dr Elaine Mardis, a professor of Genetics and Molecular Biology and the co-director of the Genome Institute at the Washington University School of Medicine. She begins by discussing next gen sequencing instrument similarities, such as library amplification, nucleotide detection, read lengths, and paired end sequencing. She then dives into the factors unique to individual next gen sequencing instruments by Roche 454, Life Technologies, Illumina, Ion Torrent, PacBio, and Oxford Nanopore. The discussion focuses on the benefits and dissimilarities among them associated with:

  • Paired end reads: linear vs circularized fragments
  • Sequencing technologies: DNA polymerase, DNA ligase, synthesis H+ detection, syntheses, and nanopore
  • Library amplification methods: emPCR, bridge amplification, and its absence in some 3rd gen platforms
  • Run times
  • Error rates
  • Read lengths

Below, you can view the video in its entirety which goes into quite some detail and discusses the best types of projects for each NGS platform.

Micro-Seq Lists Next Generation Sequencing Services On Genohub

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Genohub would like to welcome Micro-Seq Enterprises to the Genohub family. The sequencing services listed by Micro-Seq has added more available options for researchers on the Genohub next generation sequencing market.

Micro-Seq listed the following next generation sequencing instrument and Illumina library preparation options:

  • Instrument:
    • Illumina MiSeq paired end sequencing options
  • Library prep:
    • Illumina DNA
    • Illumina 16S V4
    • Illumina Small RNA (microRNA)
    • Illumina RNA (rRNA-depleted)
    • Illumina Bisulfite

Micro-Seq Enterprises was formed to help reduce the sometimes long delay researchers are forced to endure to get the results of their experiments that involve DNA or RNA sequencing (RNA-seq, RNAseq), including bacterial community analysis (16S sequencing). Micro-Seq is able to offer quick turnaround times for researchers with smaller sequencing projects. Unlike sequencers with enormous capacity, the economic scale of the Illumina MiSeq prevents researchers with smaller sequencing projects from enduring longer wait times and higher fees.

 

We are excited to include Micro-Seq’s high throughput sequencing services on the Genohub next generation sequencing market.