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)
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.
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:
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…)
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.
17/10/12: Barcode Crosstalk can Severely Affect Next Generation Sequencing Results
October 19, 2012 by Peter · Leave a Comment
I often tell my customers that Integrated DNA Technologies (IDT, www.idtdna.com) is the “best oligo house in the world.” However, because I operate in Denmark and Sweden, where many customers have not even heard of IDT, I usually get the response that (yeah, yeah) this is because I am trying to sell IDT oligos. Which must be partly true, since I can hardly claim to be unbiased. However, when you consider that no other company does 100% QC on its oligos (and can demonstrate that systematically to customers), has advanced oligonucleotide synthesis chemistry, whilst reducing prices and delivering fast turnaround times, I think I am on pretty solid ground. However, in addition to those things that “IDT is known for” (assuming you have heard of them), is their innovation in the use of chemically synthesized DNA.
Earlier this year, IDT released gBlocks, driving costs down and increasing turnaround time for synthetic biologists. However, the subject of this post is another recent innovation: IDT’s TruGrade™ Processing Service.
The TruGrade™ Processing Service is a proprietary production process that reduces the risk of oligonucleotide crosstalk during multiplex next generation sequencing applications. Oligo crosstalk is a potential cause of barcode misalignment, which can lead to inaccurate conclusions by associating sequencing data with the wrong sample.
Oligonucleotides manufactured using the TruGrade service are suitable for:
- Sample preparation using barcoded adapters for multiplex sequencing
- PCR using barcoded fusion primers for multiplex amplicon sequencing
The title of this post refers to an article that explains why standard oligonucleotide synthesis for NGS applications might lead to sample “crosstalk” when multiplexing, and how this can be reduced by using TruGrade™ Processing Service for your oligos. The article can be accessed here:
Barcode Crosstalk can Severely Affect Next Generation Sequencing Results
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.
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!
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21/09/12: Using the Bioanalyzer to Look at DNA from FFPE and Fresh-Frozen Samples
September 21, 2012 by Peter · Leave a Comment
Agilent has recently published a technical note on this very subject. The abstract reads as follows:
This Application Note describes the use of on-chip electrophoresis with the Agilent 2100 Bioanalyzer system for quality control of DNA samples from formalin-fixed paraffin-embedded and fresh-frozen tissues prior to and during SureSelect target enrichment in next generation sequencing workflows. Reliable DNA electrophoresis with the 2100 Bioanalyzer system provided smear profiles and details for library statistics, such as peak heights, average smear size, size distribution, and DNA concentration. FFPE DNA samples gave comparable results to DNA from fresh-frozen tissue and control DNA.
The full technote can be downloaded here as a PDF file.
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.
21/09/12: Seminar on Next Generation Sequencing, Aarhus, 21st November 2012
September 21, 2012 by Peter · Leave a Comment
The recently established organisation DSMOME (Dansk Selskab for Molekylær Medicin – Danish Society for Molecular Medicine) is organising a seminar on “Next Generation Sequencing,” 0930-1615 in Aarhus, just a few minutes walk from Aarhus central station.
Details of the meeting can be found here on DSMOME’s website, or you can go direct to the registration page. Note that registration is limited to 70 attendees.
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.
17/09/12: New SureSelect XT Protocol Available – Save More Time!
September 17, 2012 by Peter · 1 Comment
Agilent have released a new SureSelect XT protocol. There is one important and nice change – the protocol now has on-beads post-capture PCR. What this means is that SureSelect users will be able to amplify the captured DNA straight from the Dynal beads, eliminating elution, neutralization and the subsequent AMPure step. This can result in a time saving of about 75 minutes compared to the previous protocol.
The new protocol can be downloaded directly from here.
03/09/12: How Well Does SureSelect XT2 (pre-capture pooling) Work on FFPE Samples?
September 3, 2012 by Peter · Leave a Comment
Pretty well, according to this technical note from Agilent. (PDF file opens in a new window/tab)
30/08/12: Early Publication on the Use of HaloPlex
August 30, 2012 by Peter · Leave a Comment
This is an early (possibly the first) publication describing the use of Agilent’s HaloPlex technology to detect SNPs and inherited mutations in BRCA1 and BRCA2 genes: http://jmg.bmj.com/content/49/7/422.short.
There is a lot of interest coming from my customers in HaloPlex and there are a handful of early customers who have kits and are testing them .
09/08/12: Bravo Automated Liquid Handling System at DTU featured on Italian TV
August 9, 2012 by Peter · Leave a Comment
At the Technical University of Denmark’s (DTU) Multi Assay Core (DMAC) facility, they have had a Bravo automated liquid handling system installed for over 12 months for performing various functions, most notably sample preparation for next generation sequencing. One of DTU’s researchers, Thomas Sicheritz-Pontén was recently featured on Italian TV station RAI, in a science/medical slot.
The Bravo system features in the following video (starting about 00:03:45) if you are interested to see it in action: VIDEO
Thanks to Laurent Gautier for alerting me about this.
06/08/12: HaloPlex for Ion Torrent – Larger Designs Now Available
August 6, 2012 by Peter · Leave a Comment
Just a short note to mention that Agilent’s HaloPlex is now available for Ion Torrent capture sizes of up to 2.5Mb (previously, the limit was 250Kb)
20/06/12: New Agilent NGS Sample Prep eSeminar
June 20, 2012 by Peter · Leave a Comment
This from Agilent:
New NGS Sample Prep eSeminar
Wednesday, June 27, 2012, 5pm:
Automation Solutions for High Throughput Reproducible Next Gen Sequencing Sample Preparation
NGS sample preparation can be labour intensive and time consuming. Automated liquid handling can increase your laboratory throughput and decrease variability in sample preparation.
Join this live eSeminar and learn about:
| • | Available optimized protocols for automating NGS sample preparation | |
| • | Instrumentation to dramatically increase throughput and walk-away time |
> Register here. |
15/06/12: Going to the ESHG 2012? Two Symposiums of Interest
June 15, 2012 by Peter · Leave a Comment
The ESHG is one of the highlights of the conference season in Europe and is usually an incredibly popular meeting for researchers from Denmark and Sweden. So it should be again this year, with the conference being held in the German city of Nuremburg.
Two of the companies that are represented by You Do Bio will be holding their own satellite meetings at ESHG and both look good value:
1. Integrated DNA Technologies are holding the following satellite meeting: 
Saturday, June 23, 11.45 – 13.15 hrs, Room Budapest
Oligonucleotides for Clinical and Research Applications – Why Quality Matters
2. Agilent Technologies will be holding the following event:
Monday, June 25, 11.40 – 13.10 hrs, Room Istanbul
Revolutionizing Human Genetics Research with new target enrichment system and high-resolution Oligo FISH technologies
https://twitter.com/YouDoBio/status/213633335229034496
04/06/12: Agilent Technologies Expands HaloPlex Target Enrichment for Next-Generation Sequencers
June 5, 2012 by Peter · Leave a Comment
Of course, I am biased, but I think this looks really great news for researchers doing targeted resequencing. I’ve put the stuff I think is most interesting in bold:
Agilent Technologies Inc. (NYSE: A) today announced the expansion of the HaloPlex target enrichment system, which will now be available on Ion Torrent’s Personal Genome Machine, a benchtop sequencing solution.
The HaloPlex system features a unique paired-end design, which positions reads at both target ends using a single-end sequencing run. By taking advantage of the extra coverage that the paired-end design provides, researchers will be able to save sequencing costs and time.
“The HaloPlex technology makes it possible for us to capture specific sets of genes in a single reaction,” said Peter Ray, head of molecular genetics at The Hospital for Sick Children in Toronto, Canada. “So far we have gotten great coverage of the mutations we were looking for. By combining HaloPlex with Ion Torrent we are able to generate sequencing data for our targets in a single day.”
HaloPlex continues to break barriers common to other target enrichment technologies and can now enable larger capture sizes during desktop sequencing – up to 5Mb or approximately 2,000 genes on a MiSeq personal sequencer. HaloPlex offers greater efficiency and improved performance and, with the update released today, it allows researchers to process up to 250,000 amplicons in the same tube.
“HaloPlex is helping to transform target enrichment, especially for desktop sequencers,” said Olle Ericsson, director of marketing, DNA sequencing at Agilent. “We are overcoming previous barriers with the fastest, most flexible and most innovative target enrichment platform on the market.”
The Haloplex system’s fast-scaling target enrichment technology demonstrates Agilent’s ongoing commitment to enabling a better research workflow regardless of the sequencer platform being used.
HaloPlex is a flexible and customizable product that enables users to create designs in less than 10 minutes to enrich thousands of genomic targets, using the no-charge Web Design Wizard.
Agilent acquired Halo Genomics of Uppsala, Sweden, and the HaloPlex platform in December, 2011. HaloPlex technology complements the existing Agilent SureSelect target-enrichment system.
For more information, visit www.agilent.com/genomics/ngs
