17/06/13: SureFISH for FFPE Samples
June 17, 2013 by Peter · Leave a Comment
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)
17/06/13: HaloPlex Disease Research Panels Overview & Demonstration Webinar
June 17, 2013 by Peter · Leave a Comment
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.
If you are interested, please Register Here!
17/06/13: Introducing HaloPlex Disease Research Panels
June 17, 2013 by Peter · Leave a Comment
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
24/05/13: Notification of Genomics eSeminar Series: the Latest in Clinical Research and miRNA Analysis
May 24, 2013 by Peter · Leave a Comment
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
17/05/13: New App Note – Whole transcriptome analysis – RNA library prep kit and Ribo Zero
May 17, 2013 by Peter · Leave a Comment
Here is an application note using Agilent’s SureSelect Strand-Specific RNA Library Prep Kit (PDF opens in new tab / window)
11/03/13: Nice Article About the New Agilent Encore
March 11, 2013 by Peter · Leave a Comment
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.
05/03/13: Exciting New Developments in Agilent’s Sequence Capture Range for NGS
March 5, 2013 by Peter · Leave a Comment
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).
Download a Data Sheet on HaloPlex Exome here.
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
Learn some more at Agilent’s website.
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
Download a Data Sheet on The Strand Specific RNA Library Prep Kit here.
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.
05/03/13: Agilent Launch SureScan Dx Microarray Scanner
March 5, 2013 by Peter · Leave a Comment
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.
27/02/13: Agilent Release SureCall Software for NGS Data Analysis
February 27, 2013 by Peter · Leave a Comment
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:
SureCall Webpage at Agilent’s website
SureCall Flyer – An Overview
SureCall Application Note – Technical
13/02/13: Protocols for High Throughput Reproducible Next Gen Sequencing Sample Preparation
February 13, 2013 by Peter · Leave a Comment
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.
You can learn more and register at this page
A summary description of the seminar is as follows:
16/01/13: Notification of Agilent Automation Roadshow – Discover the New Encore Liquid Handling System
January 16, 2013 by Peter · Leave a Comment
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:
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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.
11/01/13: Agilent Online Seminars on Single Cell Analysis by aCGH, Plus a Couple on Methylation
January 11, 2013 by Peter · Leave a Comment
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
When
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”
13/11/12: Agilent Release SureSelect Human All Exon V5 & V5+UTRs
November 13, 2012 by Peter · Leave a Comment
Not much of a surprise this one, since the previous kit was based on 2011 RefSeq database information (though to my mind it doesn’t seem to have been out that long that V4 was released, which only goes to show that time really does fly). Agilent’s latest addition to the Human All Exon SureSelect range is sure to be a very strong product in the market for All Exon capture kits. Those customers that have used the V4 have had very positive results, based on the feedback I’ve received. The amount of work that Agilent has put into the design really reduces the amount of sequencing required, with associated cost reduction.
If you wish to learn more about this kit, please click on the banner below and you will be sent to a page where you will be asked to fill in a form (which means, if you are in Denmark, that I will be contacting you…)
08/11/12: Agilent Technologies and Roche Establish Agreement to Provide Continued Service and Support to Roche NimbleGen Microarray Customers
November 8, 2012 by Peter · Leave a Comment
For the second time in two days, I am left saying “wow” at developments in my immediate business world. This definitely took me by surprise:
Agilent Technologies and Roche Establish Agreement to Provide Continued Service and Support to Roche NimbleGen Microarray Customers
It makes a lot of sense for Agilent of course and it is great that Roche are prepared to put their customers needs over the obvious commercial rivalries.
07/11/12: The New Agilent Encore Liquid Handler: Looks Kind of “Wow!”
November 7, 2012 by Peter · 1 Comment
I did not see this coming, though there were rumours that Agilent were working on something that could handle larger volumes routinely. However, I imagined that it would be an adaptation of the existing excellent Bravo platform. How wrong I was.
Take a look at the video below of the new Encore system. It looks great:
A data sheet on the Encore can be downloaded here (PDF opens in new window/tab)
31/10/12: Excellent data reproducibility & concordance between Agilent miRNA microarrays
October 31, 2012 by Peter · Leave a Comment
For researchers interested in miRNA research, the Agilent microarrays are an excellent product for looking at expression of miRNAs across samples. Below is a link to an article describing how the high quality and consistency of Agilent’s microarray production pays off, when comparing data from arrays that represent different updates of the miRBase microRNA database.
Excellent data reproducibility and concordance between Agilent SurePrint G3 Human miRNA microarrays
31/10/12: First SureSelectXT Human Methyl-Seq Publication & Video!
October 31, 2012 by Peter · Leave a Comment
Over the past year I have been unsure about the SureSelectXT Human Methyl-Seq product from Agilent, to be honest. It did not seem to be hitting the spot with customers. There are a few groups in Denmark for whom it might be of interest, but none of them were motivated enough to try it out. Perhaps taking a “wait and see” approach? Funnily enough, just yesterday I was asked by a Danish customer in Copenhagen if there were any publications showing the use of this kit. I had to tell him no, but…
Just 24 hours later I learned the following: the first publication has been released using the SureSelectXT Human Methyl-Seq kit from the Max Planck Institute! In this paper, SureSelect was used to investigate methylation in the miRNA-26a region. Not only that, but there is actually a video available of a talk given by Michal Schweiger at this year’s ESHG meeting.
09/10/12: Agilent Release SureDesign Online Design Software for SureSelect and HaloPlex
October 9, 2012 by Peter · Leave a Comment
I’m just a little late with this news (funny how a few relatives visiting and having twins can send your schedule haywire…) In short, Agilent has decided to separate their array design software (e-Array) from their targeted sequencing capture design software (for HaloPlex and SureSelect). In the future, all designs for HaloPlex and SureSelect will be done through SureDesign. This tool looks quite straightforward to use and allows collaborations, so sharing of designs should be easier.
27/09/12: Gene Expression Profiling of Prokaryotic Samples
September 27, 2012 by Peter · Leave a Comment
Agilent have released a new application note, illustrating how the LIQA WT* kit can be used to perform expression analysis on prokaryotes. It is great to see this officially, since I have had a couple of customers in Denmark using the kit to do just that for quite some time.
This would also be the kit I would recommend trying out for longer non-coding RNAs too (not microRNAs), but there is nothing official from Agilent on that application yet.
The application note can be downloaded from Agilent’s website here (opens PDF file in new window)
*Please note that Agilent have two versions of the LIQA (Low Input Quick Amp) Kits available. If you are planning on working with prokaryotes, make sure you order the WT version I’ve linked above, otherwise you will end up spending a lot of money and waste a lot of time and samples.
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26/09/12: HaloPlex Training/Workshop in Uppsala, October 24th 2012
September 26, 2012 by Peter · Leave a Comment
Agilent are organising a HaloPlex training/workshop, from 1230-1700 on the above date.
All parts of the HaloPlex workflow, from panel design to data analysis, will be discussed. The training will be of interest for everyone doing or planning to do target enrichment using the HaloPlex technology.
You will meet representatives from Agilent/HaloPlex R&D as well as from Agilent technical support. This is important – the HaloPlex product was developed in Uppsala, so you will get the opportunity to speak to people who developed the product from start to finish and are working on developing it further.
If you want to attend, please send a short email to Peter via the web form on the contact page (yes, it works and I read them all 
)
You might want to combine your visit to Uppsala with attending the NGS symposium arranged by the Swedish Society for Medical Genetics in Uppsala on October 25th;“Next generation sequencing: Biomedical and clinical implications”, http://www.igp.uu.se/Seminars/ngs-symposium.
The course is free, as is the NGS Symposium. Could be an inexpensive and productive two days!
Don’t forget to sign up for You Do Bio’s Newsletter to get a regular – monthly, if I keep my act together – summary of all that is new and splendid in the product lines represented by You Do Bio.
