Agilent have now updated their SureFISH manual to include recommendations for formalin fixed paraffin embedded (FFPE) samples.
Check out the updated protocol here. (opens a PDF file)
Join Agilent’s webinar on Tuesday, June 18, 2013 5:00 pm. Crikey, that is already tomorrow! Well, if you are interested, here is a preview:
Agilent’s integrated solution for clinical genomics research also includes SureCall, an easy-to-use desktop application that combines best in class open source algorithms for end-to-end NGS data analysis from alignment to categorization of mutations. With this complete workflow, customers can rapidly deploy studies for clinical research.
Great news! I’m excited that Agilent have launched HaloPlex Disease Research panels recently (official launch at ESHG 2013)! The panels are a series of 7 comprehensive panels developed in collaboration with clinical research experts, focusing on targeted gene sets for specific disease research applications. All panels should provide premium coverage and performance for accurate and reliable variant calling.
Agilent offers two catalog HaloPlex panels, the Cancer Research Panel and the Cardiomyopathy panel.
In addition, pre-designed panels for other disease gene sets are available in SureDesign and can be ordered as custom designs.
Below is a summary of what is available with this launch
I think that this is a great new release by Integrated DNA Technologies (IDT, www.idtdna.com).
It’s been a long-awaited release. IDT has announced the launch of PrimeTime® qPCR Assay Plates, for high throughput qPCR analysis. Primers and probes for 5’-nuclease and intercalating dye assays (e.g., SYBR®) can now be directly ordered online in a 96 well plate format, eliminating the time-consuming transfer of primers and probes from reagent stocks, and streamlining the reaction set-up. PrimeTime qPCR Assay Plates offer an ideal solution for many applications that generate large quantities of data, such as validation of NGS and microarray data, as well as high throughput gene expression screening.
Addressing the needs of each particular qPCR assay requirement, a range of primer and/or probe concentrations are available, delivered lyophilized within a 96 deep-well plate. For additional flexibility, different dye-quencher combinations can also be ordered on the same plate, extending the range of assays that can be performed during a single run. The researcher does not even need to purchase a complete 96 well plate, just 24 assays is the minimum per plate order. Further cost savings are possible once a plate layout has been designed, since replicate plates can be generated at a lower total cost per reaction, making this format particularly suited to high throughput applications in academia and industry.
Designing and ordering your custom assays in this new plate format is rapid and intuitive with the online PrimeTime® qPCR assay tool, which allows users to easily create a master plate via simple copy and paste actions from source data. Alternatively, researchers can select from a specialized library of predesigned human, mouse, or rat assays generated by IDT’s sophisticated design engine. In addition to incorporating accurate Tm and secondary structure prediction data, this assay design engine takes into account the latest data from the NCBI RefSeq database, to avoid off- target amplification and SNPs, thus ensuring maximum assay performance.
As standard, IDT ensures the highest quality oligonucleotide synthesis, with full QC assessment by mass spectrometry, and results available free of charge on our website.
Integrated DNA Technologies (IDT) is proud to be an iGEM Corporate Sponsor for 2013. IDT are also partnering with iGEM 2013 teams to help them achieve their goals. This year IDT are offering 50% off gBlocks® Gene Fragments. Learn more at this link
Any iGEM teams in Denmark and Sweden who are interested in help, please contact me via the contact page.
24/05/13: Notification of Genomics eSeminar Series: the Latest in Clinical Research and miRNA Analysis
Here is notification of some upcoming eSeminars on genomics-related subjects, arranged by Agilent. They all look pretty interesting:
Focusing Cytogenomic Analyses for Clinical Research Relevance
June 4, 2013 – 5:00 pm CET
Differences in MicroRNA Detection Levels are Technology and Sequence Dependent
June 13, 2013 – 3:00 pm CET
Clinical Research Panels Overview and Demo: How to customize the HaloPlex Cancer Research Panel
June 18, 2013 – 5:00 am CET
Each of these subjects will be presented by an external (i.e., non-Agilent) speaker.
To learn some more (read abstracts) and take the opportunity to register, follow this link: Upcoming e-Seminars in Genomics
BioCision keep on adding new products to their existing line. As always, the quality is excellent and if you really care about your biological samples, as well as reproducibility in your experiments. You can get a copy of the latest version of their catalog online by clicking on the picture above, or the link below. For once, I actually prefer the online version, because it allows you to see the figures rather better than print version, where they are a bit small.
Why not ask for a demonstration? I have most of the BioCision product lines available for testing. These are really excellent products that work as described, but you are welcome to try them out first.
Here is an application note using Agilent’s SureSelect Strand-Specific RNA Library Prep Kit (PDF opens in new tab / window)
From May 13th, 2013, the following changes regarding Genes and MiniGene Synthetic Genes will take effect:
|Product||Previous Length||New Length||Previous Guaranteed Yield||New Guaranteed Yield|
|MiniGene™ Synthetic Genes||25–400 bp||25–500 bp||
|Genes||401+ bp||501+ bp||
Please check IDT’s website for updated pricing (as far as I can see it has not changed).
As always, all Genes and MiniGene constructs are sequence verified on both strands prior to shipping. Sequence information, including chromatograms, a plasmid map, and a FASTA file, is available.
If you have any questions about these changes or IDT’s gene synthesis service in general, please contact IDT at email@example.com.
Below is the text from a recent joint press release from IDT and SGI-DNA.
The awesome bit is that soon, synthetic DNA constructs up to 2 Mbp will be available from IDT. I might be wrong, but that is a huge leap in the potential size of synthetic genes.
CORALVILLE, IA AND LA JOLLA, CA (February 27, 2013). Integrated DNA Technologies, Inc. (IDT) and SGI-DNA announce an expanded partnership to develop, manufacture, and market a variety of synthetic DNA products.
IDT is the world’s leader in custom oligonucleotide synthesis and SGI-DNA is a newly formed subsidiary of Synthetic Genomics, Inc. (SGI), which focuses on genomic-driven solutions to a variety of global needs.
In February of 2012, IDT and SGI began to co-manufacture, commercialize, and market small synthetic gene products of up to 5 kb. IDT also launched its gBlocks™ Gene Fragments product line, for use in combination with SGI’s proprietary DNA technologies, including Gibson Assembly™, to assemble small gene constructs efficiently. gBlocks™ Gene Fragments have already revolutionized synthetic biology applications by substantially lowering DNA synthesis costs and making DNA assembly more efficient and reliable.
IDT and SGI-DNA are now extending this collaboration to manufacture and co-brand cloned synthetic DNA constructs up to 2 Mbp, and to make them available through IDT. This product offering has not been available until today and will make possible new applications including metabolic and whole genome engineering through de novo DNA synthesis. SGI-DNA will manufacture and become IDT’s exclusive supplier of the larger constructs. The two companies will also work together on the launch of an expanded IDT gBlocks Gene Fragments offering, expected later in 2013.
Dr. Joseph Walder, IDT’s Founder and Chief Executive Officer, noted, “By joining forces, IDT and SGI-DNA will enable the research community by providing a complete solution, from short genes to very large synthetic constructs, at prices and with delivery times simply unavailable in the market today.” “Enabling new and better research has always been the essence of IDT’s mission, so it’s the perfect fit.”
“Over the last year, we have grown our in-house gene synthesis business, and effectively worked together with IDT to co-manufacture and co-market smaller synthetic gene products. This is the natural next step in that collaboration,” agreed J. Craig Venter, Ph.D., SGI’s Founder and Chief Executive Officer. He continued, “We are excited about what we’ll accomplish through the combination of SGI-DNA’s unique expertise with large, complex gene products and IDT’s experience in manufacturing and delivering small DNA products to researchers around the globe.”
SGI is also announcing the official launch of SGI-DNA, which will be responsible for all aspects of the development, manufacture, and commercialization of SGI’s synthetic DNA business.
IDT and SGI-DNA did not disclose the financial details of their arrangement.
For more information about how to order IDT/SGI-DNA products, please visit https://www.idtdna.com/pages/products/genes/custom-gene-synthesis.
Follow us on twitter @idtdna for real-time updates and insights.
About IDT Integrated DNA Technologies, Inc. (IDT) is the largest supplier of custom synthetic nucleic acids in the world, serving the areas of academic research, biotechnology, clinical diagnostics, and pharmaceutical development. IDT’s primary business is the manufacture of custom primers, probes, and genes for research and diagnostic applications. Today, IDT synthesizes and ships an average of 36,000 custom oligos per day to more than 86,000 customers worldwide. IDT’s manufacturing locations include facilities in Coralville, Iowa; San Diego, Calif.; Leuven, Belgium; and Singapore. For more information, visit www.idtdna.com.
SGI-DNA, a wholly owned subsidiary of Synthetic Genomics, Inc. (SGI) founded in 2013 and headquartered in La Jolla, CA, provides differentiated synthetic DNA solutions to leading organizations with demands for large and/or complex DNA constructs. Building on the scientific breakthroughs from leading scientists J. Craig Venter, Hamilton Smith, Clyde Hutchison, Dan Gibson and their teams, SGI-DNA utilizes unique and proprietary DNA synthesis technologies from SGI to produce synthetic genes, genetic pathways, and whole genomes quickly and costeffectively. SGI-DNA is responsible for all commercial aspects of SGI’s synthetic DNA business and focuses on strategic business relationships with both academic and commercial researchers.
For more information, visit www.sgidna.com.
About Synthetic Genomics Inc.
SGI, a privately held company founded in 2005, is dedicated to developing and commercializing genomic-driven solutions to address a wide range of global challenges. The company is focused on several key research and business programs including: developing new synthetic DNA products and technologies through SGI-DNA, algae biofuels, new and improved food and nutritional products, and clean water technology. SGI is also involved in synthetically derived vaccine development through Synthetic Genomic Vaccines Inc. (SGVI), a business unit cofounded with the J. Craig Venter Institute; and in developing sustainable crops such as castor and sweet sorghum and agricultural products through AgraCast, a company co-founded with Plenus S.A. de C.V. For more information go to: www.syntheticgenomics.com
Media Contact for SGI and SGI-DNA
Media Contact for IDT
A couple of weeks ago, there was a stop of the Agilent Encore roadshow in Copenhagen. There was a live demo, a product presentation and a very nice presentation by Laurent Gautier of DTU on his experience with automation.
Recently, Agilent sent out a newsletter and it has a link to a nice short article explaining the main features and benefits of the Encore system. Read it here.
Agilent was saving up some interesting announcements for the genomics world (as so many other companies were) at this years AGBT meeting. I have tried summarize those of most interest in this post:
1. HaloPlex Cancer Research Panel
Hooray! This has been the subject of some discussion. The content of HaloPlex is so flexible that the need for a pre-designed panel did not seem to be there. On the other hand, I heard from some researchers that they choose an Agilent competitor product simply because the other company made the choice easy. I guess if something is missing from a company-designed “cancer” panel, it is easier to blame the company than oneself.
Anyway, I’m reliably informed that this product will be released March 29th 2013 and hope to have some more information then. You can always email me if you want some more inside information.
2. HaloPlex has now been expanded to target the Human Exome
OK, I did hear a rumour about this one and it has been launched quickly (relative to the rumour, I mean).
Take home information is: HaloPlex has now been expanded to target the Human Exome. The HaloPlex Exome is ideal for clinical research with streamlined workflow and low input requirements.
• Outstanding coverage with less sequencing – only 4Gb to achieve 80% at 20X coverage
• Samples ready for sequencing the next day
• Minimal hands on time and only 200ng of input DNA
3. Introducing SureSelect Strand-Specific RNA Library Prep Kit
The new SureSelect Strand Specific RNA Library Prep kit has been announced at AGBT 2013! These library prep kits can be used for whole transcriptome or targeted RNA-Seq and are a new addition to Agilent’s Gene Regulation portfolio. The kits were apparently very well received at AGBT and provide the advantages of:
• High strand specificity for greater understanding of gene regulation
• Greater library complexity using small amounts of starting material
• Improved uniformity of coverage and less 5’/3’ bias
Once again, I’m informed that this product will be released in March (whoops, that’s now) and hope to have some more information “soon.” You can always email me if you cannot wait.
Agilent have launched a new microarray scanner!
What’s so special about that, you might ask? Well, this is the first scanner from Agilent that is CE marked for in vitro diagnostic use in Europe. Or more specifically “The SureScan Dx Microarray Scanner is CE- marked and is currently marketed in Belgium, Denmark, Finland, France, Germany, Italy, Netherlands, Spain, Sweden, and the United Kingdom.”
I guess I shouldn’t say anymore, because the whole diagnostics (Dx) area seems to be a minefield of what you can and cannot claim. So, if you are interested, go to the SureScan Dx Microarray Scanner page on Agilent’s genomics website.
You can also download a Technical Note on the SureScan Dx Microarray Scanner.
This is the first release of a new software package from Agilent that is designed to streamline the analysis of sequencing data from genomic DNA. This first release only covers samples that have been enriched with HaloPlex. It remains to be seen if later versions will cover Agilent’s other target enrichment product, SureSelect, but that will not be available in this first release.
I have no data to test this software on, but I think it sounds pretty good. For a start, it is FREE! Not bad. Furthermore, it can take raw reads from Illumina HiSeq/MiSeq instruments or the Ion Torrent and convert it to something meaningful. To learn a bit more about SureCall, please check out the following pieces of information:
This is notification of a new webinar from IDT:
It is often necessary to select primers using specific parameters; e.g., a particular GC content or Tm, forcing the start or stop position of a primer end. However, not all primer design tools provide this flexibility. In this interactive webinar, we will demonstrate several primer customization scenarios using the free, highly popular PrimerQuest™ Design Tool, including:
• When to use default design parameters, and when to customize assay design
• How to design primers for one, two, or up to 50 sequences at a time
• How to approach specific customized design scenarios suggested by and voted on by participants of this webinar
Tuesday, February 26th – 7:00pm CST
Wednesday, February 27th – 8:00am CST (This is the best one for European-based researchers)
Wednesday, February 27th – 1:00pm CST
This webinar could be interesting to researchers who have been using IDT’s PrimerQuest, as this has been updated.
Ahram Biosystems, the inventors of the Palm PCR have done an incredible job in reducing the price of the instrument, so that I am able to make a special price offer to anyone who wants to purchase an instrument. And yes, you can try it out first!
For those who don’t know, the Palm PCR is probably one of the coolest instruments currently available to life scientists. However, like many new technologies, it seems to be a product in search of an application. So far, less than a handful of researchers have tried the instrument out, or have discussed applications with me, which is somewhat disappointing. I always thought scientists were meant to be curious and pushing the boundaries. Here is a device that allows the user to run a PCR at the same spot that a test sample is located. There are possibilities for detecting the product of the PCR reaction on-site too. Isn’t that interesting to someone?
Check out this video to see the Palm PCR in action.
The above title is from an upcoming Agilent online seminar that will cover available automation protocols for various NGS sample preparation reagents and gives an overview of how manual NGS methods were optimized for automation.
A summary description of the seminar is as follows:
16/01/13: Notification of Agilent Automation Roadshow – Discover the New Encore Liquid Handling System
Agilent are doing a European-wide tour of their new Encore Liquid Handling System. That means it will be possible for customers in Denmark to view the new instrument on Thursday February 21st, in Copenhagen. Attendance at the meeting is free. The overview of the roadshow is as follows:
Personally, I think this looks like a great instrument and I think anyone interested in laboratory automation would be crazy to pass up the chance to see it in action.
You can register for the meeting here, or by clicking on the banner above.
This is notification of an upcoming “e-Seminar” from Agilent: High-Resolution Oligonucleotide-Based aCGH Analysis of Single Cells in Under 24 Hours
Take the opportunity to learn about Agilent’s cytogenetic solution for single cell analysis by attending this free e-seminar. Sounds good! There seems to be a good deal of interest in this subject.
During this e-seminar you will learn:
- How experimental conditions were empirically optimized for performing oligonucleotide-based array comparative genomic hybridization (aCGH) on single cells with 8x60K microarrays
- How to analyze single-cell data in Agilent CytoGenomics 2.5 software
January 15, 2013
5pm (Central Europe)
Registration for the two seminars on Methylation is also at the same link. The subjects here are
- “Genome-Wide Increase in Differential DNA Methylations in TMPRSS:ERG Negative Prostate Cancers” and
- “Complete Sample to Analysis Solutions for Targeted DNA Methylation Discovery using Next Generation Sequencing”
BioCision have launched a new promotion for the New Year! It is very simple – spend just EUR 150 on a BioCision product and receive a free mini (1L) ice pan, or a free multi-pack of TruCoolTM cryoboxes.