Here is an application note using Agilent’s SureSelect Strand-Specific RNA Library Prep Kit (PDF opens in new tab / window)
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.
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:
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.
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.
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.
Pretty well, according to this technical note from Agilent. (PDF file opens in a new window/tab)
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 .
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.
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
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
A short bulletin from Agilent:
- XT2 available for order!
- SureSelect XT2 in 16, 96, and 480 sample sizes for the Illumina HiSeq and MiSeq platform
- Available for Human All Exon V4/V4+UTRs and custom
- Custom Target Enrichment from 0.5Mb -> 24Mb (0.5-2.9Mb custom now available!)
The most crucial aspect of this is that it highlights the long-awaited pre-capture pooling protocol from Agilent. Now, as a representative of Agilent, I have been quite impatient about this, as have many others. Customers were already asking for this product at about the same time SureSelect was first released (Feb 2009, if my memory is correct). However, I will say this for Agilent: their protocols are usually rock-solid when they are released, so for labs that want a reliable method for pre-capture pooling, I am pretty confident that this is a good option.
Another interesting from Agilent, this time on RNA-seq. May 14, 2012, Central European Time.
You can register here: eSeminar on RNA-seq
The seminar abstract reads as follows:
Transcriptome sequencing, RNA-Seq, is a powerful tool to determine expression levels of various transcripts using shallow sequencing approaches. However to find novel splice variants, gene fusions and rare transcripts deeper sequencing is required. The SureSelect RNA Capture products allow you to achieve that depth by focusing your research on the regions that matter most to you. By focusing your research on smaller subsets you can find novel splice variants and gene fusions that are frequently associated with disease. Whether following whole transcriptome analysis or microarray studies the Agilent SureSelect RNA Capture products serve as an effective tool to provide more information and deeper coverage depth for your selected regions, while maintaining relative gene expression levels.
It is becoming very clear that the acquisition of Halo Genomics’ HaloPlex technology by Agilent was a great buy. The technology has already been updated with some outstanding new features that make it a very attractive solution for researchers doing targeted sequencing:
- Simple protocol – the entire protocol, targeting and library prep takes only 6 hours!
- Simple Design Wizard to create custom panels
- Simple to implement – just buy the kit, no additional instrument purchases required
- Automation protocol coming soon
- COMPATIBLE WITH CHALLENGING SAMPLES
- Only 200ng DNA required
- Demonstrated to work with FFPE Samples
- Complete Target Enrichment in Less than 6 hours!
- Go from Sample Prep to Sequencing in a single work shift
- Capture targets up to 500kb
- 96 indexes for sample multiplexing
- Compatible with desktop sequencing and High throughput platforms (today: Illumina platforms; coming soon: Ion Torrent)
- HIGH PERFORMING
- Capture all types of genetic variants (SNPs, INDELs, etc) with great allelic balance and great sensitivity
- Superior target coverage, with great specificity, and providing excellent sensitivity!
The SureSelect Human Methyl-Seq product looks like a great new tool for researchers in the methylation field. Learn about this technology direct from the people who have been working very hard to develop it:
The video below explains Agilent’s HaloPlex technology in a clear way:
Agilent has announced that e-Array v.7.8 has gone live from 23 February 2012. There are several new features and improvements, which are summarized below. They sound like very nice improvements:
A New eArray Workspace – Mutagenesis!
The eArray Mutagenesis workspace enables custom design for the Agilent QuikChange Oligo Library Mutagenesis System, a novel method for generating a rationally designed library of mutants. This new system enables researchers to precisely target and mutate every codon in up to 20 regions of 50 amino acids or less. It is an easy and rapid method for mid-throughput mutagenesis that allows customers to complete single amino acid scanning, codon saturation, or combinatorial mutagenesis in a single day. Please note that the QuikChange Oligo Library Mutagenesis System is currently available only through an early customer access program.
Three New Catalog SureSelect Kits – Human All Exon v4, Human All Exon v4 plus UTRs, and Human Methyl-Seq
These new SureSelect Target Enrichment kits are now available in eArray, along with a new SureSelect part number schema.
A New Zebrafish Genome version (Zv9) for Custom SureSelect Libraries!
eArray 7.8 now offers the Zebrafish (Danio rerio) Genome version Zv9 for custom SureSelect Target Enrichment, enabling customers to design their libraries using the most current Zebrafish content.
The eArray Development Team has implemented multiple performance and feature enhancements to improve customer experience.
Performance Optimizations for:
- Faster Bait and Probe Uploads
- Faster Creation of Bait Groups and Probe Groups
- Faster Probe Group Downloads
- Faster Design File Generation – Less waiting for new annotation files during “File Write in Progress.”
Longer Maintenance of Bait Tiling Parameters and Fate File Information for SureSelect Bait Tiling Jobs
- The storage time for design parameters and fate files for SureSelect bait tiling jobs is now six months. This was increased from two weeks and makes it more convenient for researchers to preserve the design parameters for important bait groups.
Increased Maximum Number of Baits that can be Downloaded from SureSelect Bait Search Results
- The limit for the number of baits that can be downloaded from bait search results has been increased to 50,000. Previous versions of eArray limited the maximum number to 10,000 baits.
Improved Packaging of Annotation File Download Archives
- Annotation file downloads are now packaged in a single .zip file archive. There are no longer multiple .zip archives nested within the main .zip archive.
Support for Tab-Text file for GenBank Accession Upload to RNA Enrichment Bait Tiling Wizard
- Users are no longer required to create a .zip archive of their gene list in order to upload it to the bait tiling wizard.
Updated Help and Info Links in the User Interface
- Embedded Help materials in the user interface have been thoroughly reviewed and updated.
Lots of new information and a very clear video explaining how HaloPlex technology works. I really needed that!
Sounds pretty good:
Agilent’s Pre-Conference Workshop at AGBT
Wednesday, February 15, 2012 | 9:00 am – 1:00 pm
Save the Date! Register for Agilent’s Pre-Meeting Workshop and be the first to hear about Halo Genomics’ revolutionary products for Next Gen Sequencing. Agilent will be hosting keynote researchers for an in-depth review of cutting-edge research.
Edwin Cuppen Ph.D., Hubrecht Institute
Alexander Hoischen Ph.D., Radboud University Medical Centre
Andrew Brown Ph.D., Ontario Institute for Cancer Research (OICR)
John Stamatoyannopoulos Ph.D., University of Washington
John Mcpherson Ph.D., The Ontario Institute for Cancer Research
Somasekar Seshagiri Ph.D., Genentech
And more keynotes TBA!
More details and Registration Here
I have just heard that Agilent is organising a Genomics User Meeting to be held at the Wellcome Trust Conference Centre at the Sanger Genome Campus on 1st and 2nd March 2012.
The two days will cover researchers’ entire genomics workflow for microarrays and next generation sequencing and Agilent will be announcing some new product launches during the meeting. Good reasons to go!
The meeting is FREE to attend and will include all meals and refreshments, including a 3 course dinner on the Thursday evening. However you should arrange your own travel and accommodation.
There are a number of hotels available nearby including the Holiday Inn Express in Whittlesford http://www.hiexpresscambridgeduxford.co.uk/ and the Red Lion in Hinxton http://www.redlionhinxton.co.uk/.
Rooms are also available on site at a rate of £88.50 per night including breakfast. To book please call the conference reception on 01223 495000.
Please book as soon as you can as there are only 50 rooms available. The venue provides complementary car parking for all delegates and free wifi in all rooms.
PLEASE NOTE: Places at the meeting are limited so Agilent will be accepting registrations on a first come first served basis. Thank you for your understanding.
Please reply to me through the contact page to register your interest in the meeting and state any special dietary requirements. Also please let me know if you would be interested in presenting your research using Agilent’s genomics solutions during the meeting, in the form of a talk or poster.