This is my last product update for now, but perhaps it is the most important, since it concerns a significant development that Agilent have introduced to their library preparation step for the SureSelect product range. Called SureSelect QXT, it enables a 90 minute hybridization step producing same day sample-to-sequencing-ready-libraries from only 50 ng of input gDNA. So, the big news is that input DNA has dropped a lot and the whole protocol is complete in a single day. What’s not to like?
Agilent have made a QXT Resource Page. There, you will find, amongst other stuff, a recording that explains the salient details of the product and why you might find it interesting.
This teaches me that I need to update my website more regularly…
There was a webinar held on September 11th, 2014, based around the subject of Agilents new SureSelect XT Inherited Disease Panel. The good, no great, news is that if you missed it, you can view the recording of how this panel was developed and used – direct from the research group in Berlin where it was developed.
At only 24 minutes long, this can easily be combined with your coffee break. Perhaps you will even find out why “The Answer” is “at Your Fingertip.”
The abstract from the webinar reads as follows:
Less than half of individuals presenting with suspected genetic disease receive an etiological diagnosis. Though next-generation sequencing (NGS), and in particular whole exome sequencing (WES), has enabled an unprecedented acceleration in the pace of Mendelian disease gene discovery, extensive challenges remain to integrate NGS, bioinformatics, and clinical data into effective workflows.
Today, only variants in the ~3000 established Mendelian disease genes can be interpreted in a clinical context. In our research, we have established an approach that targets variants in these causative genes and developed a target enrichment panel that enabled us to achieve coverage of 20-fold or better for 98% of bases. Furthermore, we established a computational method termed Phenotypic Interpretation of eXomes (PhenIX, http://compbio.charite.de/PhenIX) that evaluates and ranks variants based on variant pathogenicity and semantic similarity of phenotypic presentation as described by Human Phenotype Ontology (HPO) terms to those of 3991 Mendelian diseases associated with the ~3000 disease genes. We retrospectively tested PhenIX on 52 individuals with previously identified causal mutations, achieving a mean rank of 2.1 for the correct gene. In a prospective study on a group of 80 individuals for whom no disease had been recognized despite intensive clinical workup and targeted genetic testing, PhenIX analysis was concordant with 23 cases (~29%).
26/09/14: Webinar: The Utility of Exome Sequencing in Providing Deep Coverage of Disease-Relevant Targets
My dealings with customers would indicate that exome sequencing is one of the most popular uses for next gen sequencing equipment. There are several providers of exome sequencing kits, but I represent Agilent, as you may know, and have many customers who are more than satisfied with Agilent’s SureSelect XT Human All Exon kits. However, Agilent has now produced a version of their Human All Exon kit that now provides increased depth of coverage in disease-associated regions – SureSelect Clinical Research Exome (CRE).
So, why and when should you use the CRE? Find out, direct from the scientists who developed and optimized the content in a webinar to be held on Monday October 13, 2014, 1700 CET.
To anyone who cannot make it, but would like to hear the webinar, I suggest registering anyway and then getting access to the recording that you can view at a more convenient time.
Agilent are holding an Automation User Group Meeting to be held at and co-hosted by AstraZeneca in Mölndal, just outside Gothenburg, Sweden.
Date: Tuesday 21 October 2014, Time: 0830-1650
Highlights of the agenda
- Workshop with fellow automation users and Agilent staff including local engineer
- Guided tour of automation installations at AstraZeneca’s Mölndal site
- New applications in automation presented
- Bravo, Encore and BenchCel platforms presented
I have visited the Mölndal site three or four times in total, in different roles in different companies. The automation set-up there is very impressive. In my opinion, it is worth going to even if you don’t yet have budget, because it can show you what’s possible with lab automation.
I would also add that it is always fascinating to be inside a large and successful pharma company’s R&D site. Especially one that is heavily influenced by Scandinavian design. Plus, the canteen at AstraZeneca is quite something.
As I said recently, it has been a busy Summer at Agilent, with a number of new products released, almost all to do with Next Generation Sequencing (NGS). This post is about Agilent’s SureSelect Inherited Disease panel.
While exome sequencing is oftenthe most appropriate solution for comprehensive and unbiased detection of disease-associated variants, exome sequencing is generally not convenient for owners of benchtop sequencers, due to limited sequencing capacity.
The SureSelectInherited Disease, a 10.5Mb design developed in collaboration with researchers from Medical Genetics, Charite Berlin, one of the leading research hospitals in Germany, is Agilent’s answer to the requirement for comprehensive, yet targeted analysis, of about 2,700 genes known to cause Mendelian disorders. This design enables single sample deep sequencing to facilitate identification of variants of low frequency, and trio analysis, important in inherited disease research on a benchtop sequencer.
This highly targeted design can be used with Agilent’s efficient SureSelect workflows that enable greatly reduced hybridization times, as little as 90 minutes, providing faster time to results.
At a Glance:
- Expert-defined content
- Developed in collaboration with researchers from Medical Genetics, Charite Berlin
- Highly targeted content enabling analysis of regions implicated in rare disease pathogenesis
- Deep coverage
- Optimized design enables trio analysis or deep sequencing of one sample
- Compatible with high throughput or benchtop sequencers
- Fast track to answers
- 3.5x faster sample to sequencing with SureSelectQXT
- Accelerated sample to categorized variants with SureCall software
If you are interested to learn more, please download this datasheet on the Inherited Disease Panel
You can also learn more online here.
I’ll be honest. When I first heard that Agilent were releasing a SureSelect Clinical Exome product to supplement their already-excellent SureSelect Exome V.5 kit, I wasn’t quite sure what the reason could be (other than to make me confused). However, now I get it: this SureSelect kit covers the same targets as the popular SureSelect All Exome kit, but provides more coverage in disease-associated targets. Hence, the tagline:
“Definitive Answers WHERE IT MATTERS”
The SureSelectClinical Research Exome design, has been developed in collaboration with researchers from Emory University and The Children’s Hospital of Philadelphia, is your answer to the requirement for increased coverage of certain targets, 10% more in disease-associated targets with 4Gb of sequencing, enabling highly sensitive and accurate variant identification, resulting in definitive answers.
This exome design can be used with Agilent’s highly efficient SureSelect workflows that enable greatly reduced hybridization times providing faster time to results.
Key Benefits for Researchers and Clinicians:
- Expert-optimized content
- Contains additional targets identified in collaboration with researchers from Emory University and The Children’s Hospital of Philadelphia
- Most comprehensive design
- Gain deep coverage with only 4Gb: 80% at 20x, 10% more in disease-associated regions
- Fast track to answers
- Shorten your day with 2.5x faster workflows from sample to data, and break the analysis bottleneck with SureCall software
To learn more about the SureSelect Clinical Exome, try the following links:
Ever since Agilent first launched SureFISH (a couple of years ago now, I guess), customers have often asked the question about whether custom FISH* probes would be available. Up to now, the answer has been a straight NO, but I’m glad to say that this has changed and now Agilent has allowed for the possibility of custom FISH probes to be available.
To learn more, please click on the links below:
*Of course, you know I mean Fluorescent in situ Hybridisation, don’t you?
Notification about three interesting genomics seminars coming up from Agilent. In fact, one of them is tonight (bad timing on the notification then, but I only heard about it myself this morning). The good news is that the recordings for these eSeminars are available later if you register for them, which is probably a more realistic way to listen to them. My ability to attend seminars at 5 PM is usually quite limited, as it is for others with families etc.
Here are the details about the seminars:
|Breaking Barriers in Clinical Research Sequencing||Targeted Massively Parallel Sequencing to Identify Rare Genetic Variants in Autism Spectrum Disorder||Utility of a Custom Microarray to Study Neurodevelopmental Disorders|
|Thursday, June 26, 2014
05:00 pm CET
|Wednesday, July 16, 2014
05:00 pm CET
|Wednesday, July 23, 2014
05:00 pm CET
|Maria Celeste Ramirez, Ph.D.
Global NGS Product Manager, SureSelect
Michael Borns, Ph.D.
|Anthony Griswold, Ph.D.
Associate Scientist, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine
|Yiping Shen, Ph.D, FACMG
Director, Research & Development
|Detailed Abstract||Detailed Abstract||Detailed Abstract|
A collection of publications that used HaloPlex Target enrichment in Cancer Research and Inherited Disease Research.
Click Here or on the picture above to download a PDF with the HaloPlex Publication List.
Are you the owner of an Agilent 2100 Bioanalyzer instrument and based in Denmark? If yes, then you might be interested in a special offer on Agilent’s 2200 TapeStation. There is a great discount on the TapeStation if you already own a Bioanalyzer. Just contact me for details, using the form below and I’ll be happy to let you know what it is.
Note: this offer ends April 30th 2014 – so be quick!
A nice article on transitioning from manual NGS sample prep. to using automation, from Genetic Engineering and Biotechnology News
I’m posting this on behalf of Agilent. The WIN Symposium has a good reputation.
Agilent, being a proud founding member of the WIN consortium for personalized medicine, invites you to the WIN 2014 Symposium, in Paris, from June 23rd to 24th.
WIN Symposia are an initiative of the WIN Consortium, a non-profit global collaboration of academic, industry, health plan, and patient advocacy organizations dedicated to bringing the most promising advances in precision cancer medicine to patients worldwide.
Mr. Serota, President and CEO of Blue Cross and Blue Shield Association, joining other prestigious leaders, will present keynote lectures during the Symposium, including:
|Robert Weinberg, Cambridge, MA (USA)||Leroy Hood, Seattle (USA)|
|René Bernards, Amsterdam (NL)||Guido Kroemer, Villejuif (France)|
|Hans Clevers, Utrecht (Netherlands)||Bob Löwenberg, Rotterdam (Netherlands)|
See below some important links:
Discover the detailed WIN 2014 program with all lecture titles and speakers names here.
|Call to abstracts!
View abstract submission and abstract preparation guidelines here.
Join WIN Linkedin group to be informed about the Symposium, discover like-minded professionals and join discussions here.
Don’t miss this unique opportunity to interact directly with the world’s leaders in innovations in cancer patient management. Register now here.
24/03/14: Same Day, Cost-Effective Aneuploidy Detection with Agilent Oligonucleotide array CGH and MDA Single Cell Amplification Method
An interesting and potentially useful application coming from Agilent: the ability to analyze single cells for aneuploidy, using microarray-based comparative genomic hybridization (aCGH). There are several applications where this ability could be useful, for example pre-implantation (IVF), cancer and noninvasive prenatal testing.
Agilent have recently hosted a webinar, given by Ali Hellani, Founder, Viafet Genomic Center, Dubai. This webinar is now available to download and view for free (you need to fill in a few details at registration).
In light of the time sensitive nature of pre-implantation genetics research and the need for an economical method to screen many samples in a high throughput environment, Dr. Hellani developed a same-day, cost effective protocol using the Agilent SurePrint G3 Human CGH 8x60K or 4x180K Microarrays and a Multiple Displacement amplification (MDA) method. The total time from amplification to data analysis can be as short as 6.5 hours. Dr. Hellani’s method allows for the processing of more samples per slide and the generation of high molecular weight DNA suitable for CGH and other applications, such as next generation sequencing. Utilizing this short, cost-effective protocol, copy number changes in individual genomes amplified from single cells can be accurately identified.
I have put together a package of different research tools that are available to researchers in the cancer field. In the past, this would have involved talking to interested researchers and then sending an email with a whole bunch of attachments. Now, in “the interest of saving your mailbox,” I have assembled a number of useful documents in one place (nothing special, just a folder in my DropBox account). If you are interested to get access to this information, please fill in the contact form below.
Subjects covered include:
- ALK, ROS1 and RET flourescent in situ hybridization (FISH) probes
- Getting gene expression and DNA sequence data from formalin-fixed, paraffin embedded (FFPE) tissue samples
- Cancer research microarrays
- Next generation sequencing (NGS) on circulating tumor cells
- Automation of NGS
If any of this sounds interesting to you, please fill in this contact form and let me know:
Comments or questions are welcome.
My own experience has seen the difference that automation can make to throughput in next generation sequencing laboratories. For example, I’ve been told by one customer who set up an Agilent NGS Automation system in their laboratory, that it originally took two technicians three months to process 200 samples manually. After installation of an Agilent Bravo, they increased their throughput to 500 samples per week.
Agilent are currently running a campaign on automation, with resources, videos etc. that any researchers interested in this subject will find useful.
It seems that more and more labs are having to get some kind of certification. From what I can tell from talking to those of my customers who get GLP/GMP, it involves a lot of hard work and stress to put this in place. So, for those in Denmark who have already gone through the pain, or are thinking about it, Agilent’s upcoming Compliance Tour, stopping off in Copenhagen might be of interest.
Attendance is Free
28/02/14: Upcoming Webinar – Utility of an Automated SureSelect NGS Panel for Understanding Disorders Featuring Aortopathy
Agilent, together with GenomeWeb, are organising a webinar that encompasses targeted sequencing by NGS and automation of the next-gen sequencing workflow. The webinar will occur Tuesday March 25th 2014.
This webinar will detail how the aortopathy NGS research panel enables the identification of mutations in genes from individuals with disorders featuring aortopathy, including Marfan and Marfan-like syndromes.
A Q&A session will follow Dr. Wooderchak-Donahue’s presentation.Speaker:Whitney Wooderchak-Donahue
Adjunct Assistant Professor, Department of Pathology, University of Utah; research and development scientist, ARUP Laboratories
This is a good development in the story of Agilent’s free data analysis software, SureCall. Users of both HaloPlex and SureSelect will now be able to use the software, which is improving in quality all the time.
Highlights of New Features
- SureSelect support
- Exome analysis: HaloPlex and SureSelect
- Find copy number changes with an in-house developed algorithm
- Quickly identify somatic mutations in tumor versus normal sample analysis and de novo mutations with trio analysis
The Minimum You Need to Know About SureCall
- SureCall is a sequencer-to-results solution which will increase throughput without increasing costs or requiring extensive bioinformatics resources
- SureCall provides an end-to-end data analysis solution – from alignment to categorization of mutations
- SureCall is part of Agilent’s market leading NGS Target Enrichment solution for clinical research
- SureCall is available free-of-charge from Agilent’s website: www.agilent.com/genomics/surecall (available for PC 12Feb; Mac version available April)
Agricultural Biotechnology, which I guess means the application of biotechnology to agriculture, is of great interest because it is where research starts to be applied in ways that affect the food we eat, the energy we use and how we “do” agriculture. You Do Bio has quite a lot of customers who are working in this field – a couple of weeks ago I was at the Plant Biotech Denmark meeting as an exhibitor. With the general widening of the use of genomics research tools in research, it makes sense Agilent is planning their first European Animal and Plant Symposium which will be hosted in Amsterdam, February 25th and 26th 2014.
This Symposium will be over two days attracting leading scientists within the Agricultural Biology field, working in gene regulation, epigenetics, copy number/mutation detection and molecular biology using next-generation sequencing, microarrays and RT-qPCR/PCR. I think Agilent has done a great job in attracting some interesting outside speakers for this symposium. I know from experience how hard it is to get this number of speakers organized and available on those particular days of the meeting.
The meeting is open to all who work within the areas of:
|Microbiology||Animal Genomics Research|
Another focus is to investigate how such technologies and applications assist to address key concerns of the scientific community and to overcome current challenges in Agriculture Genomics Research.
|Discover the most up-to-date agenda here.|
To register for the meeting please submit your details here.
Participation is free of charge but seats are limited!
I lived in The Netherlands for 4½ years and really like Amsterdam. It is also a fairly inexpensive place to fly to and stay. I wish I was going myself!
11/11/13: Designing Custom Oligo FISH Probes for the Detection of Chromosomal Rearrangements in FFPE Tissues
Agilent presented some interesting new technology developments at the ASHG meeting held in Boston last month. Various R&D groups at Agilent also presented some of their technology-related work in the poster sessions. These posters are available (for now) on Agilent’s website.
The subject of FFPE always seems to be of interest, particularly for scientists who can get access to these samples and mine them for information.