We'll be attending PAG XXV, the largest ag-genomics meeting in the world, January 14-18 in San Diego, CA, USA. PAG is one of our favorite events to meet researchers from all over the world within plant and animal genomics. As always, we've prepared scientific activities for you, which you can read more about below.
Monday, January 16. 12:50-3:00 pm
Royal Palm Salon 5-6
QIAGEN bioinformatics offers genome scientists continuity in their research. CLC Genomics Workbench and a series of specialized modules integrate all NGS data analysis capabilities required to power modern plant and animal research into a single platform – from DNA-seq and variant detection, advanced RNA-seq and epigenomics capabilities, to a comprehensive toolbox for metagenomics or plant pathogen analysis. The direct integration with Ingenuity Pathway Analysis (IPA) allows researchers to explore the biological consequences of the results of RNA-seq or epigenomics experiments.
For this workshop we have picked two NGS application areas that we will explore in greater depth: Dr. Jamie Hill (Product owner, CLC Genomics Workbench, QIAGEN) will focus on RNA-seq capabilities and best practices. And Dr. Mark Borodovski is presenting on gene finding and annotation of metagenomes or pathogen genomes.
Speaker: Jamie Hill, Senior Bioinformatics Scientist, QIAGEN Aarhus
For few areas of genomics, do best practices evolve as quickly and continuously as for RNA-seq applications. As a consequence of the rapid development within RNA-seq, researchers struggle to ensure that their analysis pipelines meet the latest standards. In the daily routine users often run a mix of different bioinformatics tools for the respective analysis step they perform best, from read mapping through isoform quantification to the detection of differential abundance. However, integrating and testing the best performers among a growing number of analysis solutions is complex and time consuming.
RNA-seq analysis is a declared focus area for QIAGEN bioinformatics. Users of CLC Genomics Workbench and Biomedical Genomics Workbench rely on us to constantly evaluate emerging bioinformatics approaches and integrate leading approaches into our solutions in a way that follows modern design control and quality assurance criteria. In our workshop we will share best practices as well as some of the recent improvements and underlying methods implemented into our RNA-seq solution.
Speaker: Mark Borodovsky, Georgia Institute of Technology, Atlanta, GA, USA, Gene Probe, Inc., Atlanta, GA, USA
Gene prediction and annotation plays central role in genomics. However, in spite of much attention, open problems still exist and stimulate development of new algorithmic solutions in all categories of gene finding. Particularly, gene prediction in short assemblies of NGS reads e.g. in short metagenomic sequences, is far from trivial.
The gene finder, MetaGeneMark, has been frequently used in individual labs for analysis of short sequences. It has also been used as a part of comprehensive pipelines, such as DOE JGI IMG/M pipeline for annotation of environmental metagenomes.
Implementation of MetaGeneMark in the CLC Genomic Workbench, its applications and the theory behind MetaGeneMark is the subject of this presentation.
Presenter: Marta Matvienko
Location: Grand Exhibit Hall
NGS assemblies of plant genomes often consist of thousands of contigs. Sequencing the segregating progenies is regularly used to anchor the de novo assembled contigs into chromosomescale assemblies. The analysis of sequencing data from segregating progenies usually involves custom scripting, and requires advanced bioinformatics skills. Here we present a userfriendly workflow that can be performed in CLC Genomics Workbench, enabling biologists to proceed with this type of data analysis.
We used the publicly available ddRADSeq data for sacred lotus, Nelumbo nucifera (Liu et al, 2016), and the corresponding genomic assembly consisting of 3,602 contigs. The alignments, as well as all variant calling and variant filtering were performed in CLC Genomics Workbench. The variants were called using the Fixed Ploidy Variant caller, filtered against control reads of the other parent, and selected for homozygosity and variant quality. This part of the workflow produced a known variants track, which was used to call variants in the progenies. We further filtered the variant tracks using the workbench's comparative tools, and ended up with 4K variants detected in at least 70% of F2 samples.
To assess the quality of variant calls, we exported the data from CLC Genomics Workbench and submitted them to the MadMapper program, which clustered contigs into chromosomes. Most of the genomic assembly (72.5%) was clustered into 9 lotus chromosomes; a similar number, 70.6% was anchored by Liu et al. This confirmed the quality of the marker data for chromosomescale assemblies outputted by the workbench using the user-friendly workflow.
The Association for Molecular Pathology (AMP) 2016 Annual Meeting is held in Charlotte, North Carolina, from November 10-12. The theme of this years meeting will be "Big World. Molecular Medicine. One Community."
We're looking forward to being there as the leading global provider of Sample to Insight solutions. Our experts will present our portfolio of consumables, instruments, and bioinformatics at booth #1119 - please stop by for a chat and a demonstration.
On Friday November 11, 9:00 a.m. to 4:00 p.m.* we're hosting workshops with invited speakers. You can find us in the Product Showcase Theater on the exhibit floor.
10:00 a.m. - 10:30 a.m.
Enabling precision medicine in oncology through accurate and scalable NGS variant interpretation and reporting with QIAGEN Clinical Insight (QCI™)
Speakers: Helen Fernandes, PhD, Weill Cornell Medicine and Andres Ferreira-Gonzalez, PhD, Virginia Commonwealth University
Next-generation sequencing (NGS) based tests are increasingly being adopted in clinical labs, but there are significant challenges in accurately classifying variants based on levels of evidence and offering actionable insights for healthcare professionals. In this showcase, Dr. Helen Fernandes (Weill Cornell Medicine) and Dr. Andrea Gonzales (Virginia Commonwealth University) will highlight some of the variant interpretation and reporting challenges that clinical testing labs encounter with implementing NGS tests and briefly review their concordance study results using the clinical decision support platform, QIAGEN Clinical Insight (QCI™). They will describe how QCI helps their labs to scale their testing services and improve the actionability of reporting through a comprehensive evidence-based approach and CLIA-CAP compliant reporting guidelines.
12:00 p.m. - 12:45 p.m.
New solutions for oncology and beyond - streamlined testing for CALR and targeted NGS using unique molecular indices
Speakers: Christoph Menzel, PhD, QIAGEN and Fergus Couch, PhD, Mayo Clinic
Advances in molecular analysis have increased understanding of the complex molecular signatures of cancers. In this showcase, Dr. Christoph Menzel (QIAGEN) and Dr. Fergus Couch (Mayo Clinic) will talk about new technologies and applications relevant for oncology research. Dr. Menzel will discuss features of the new CALR qPCR assay from QIAGEN, which offers reliable detection of CALR mutations in exon 9 and identification of Types 1 & 2 in one qPCR run in <4 h. Dr. Couch will introduce a unique PCR chemistry for targeted NGS that improves variant detection and uniformity, and ensures robust enrichment of GC-rich regions.
2:45 p.m. - 3:15 p.m.
Colorectal cancer testing using liquid biopsies - how Clinical Genomics is improving patient outcomes through better recurrence monitoring
Speaker: Lawrence LaPointe, PhD, Clinical Genomics
Analysis of circulating tumor DNA (ctDNA) has the potential to improve detection and monitoring of cancers, with significant impact on patient outcomes. This is especially important for cancers with a high rate of recurrence, such as colorectal cancer where between 30% and 40% of cases recur. However, the only currently available monitoring blood test misses 74% of resectable recurrences. In this showcase, Dr. Lawrence LaPointe (CEO Clinical Genomics) will discuss how his team are working with QIAGEN to harness the power of ctDNA to allow Clinical Genomics to develop a test with twice the recurrence detection rate.
We're looking forward to seeing you at AMP and discuss how our solutions can benefit your research.
Learn more about QCI
Visit the official event website: AMP 2016
The European Human Genetics Conference 2016 is taking place in Barcelona, Spain, on May 21-24. We'll be there and we have prepared a number of scientific activities to take place. ESHG has become one of the premier events in the field of human genetics and will set the scene for discussions about the latest developments within human and medical genetics.
You can find us at booth #550 and #552 and we encourage you to stop by for a chat, a demo, or to share your HGMD experiences on our poster-board. We'll also be presenting posters and hosting a Satellite Meeting as well.
Title: Using next-generation sequencing bioinformatics solutions to compare exomes in rare and inherited diseases and identify the cause of the disease
Speakers: Dr. Anika Joecker, PhD, Global Solution Manager, QIAGEN Bioinformatics - Céline S. Reinbold, MSc, PhD Student, Department of Biomedicine, University Hospital Basel, Switzerland - Dr. Andreas Rump, PhD, Head of Molecular genetics group, Institute of Clinical Genetics, Technical University of Dresden, Germany
Date and time: Saturday, May 21 at 12:15 p.m. - 1:45 p.m. (lunch will be available)
Join us, together with Mrs. Reinbold and Dr. Rump, for noteworthy presentations on the use of next-generation sequencing in clinical applications. We'll start the workshop with a brief introduction to our clinical genomics portfolio of solutions, presented by Dr. Joecker. Then Mrs. Reinbold will present her compelling data on a comprehensive comparison of three different exome sequencing pipelines. Dr. Rump will conclude the workshop with an exciting presentation on Exome and Mendeliome sequencing in rare genetic diseases where he will present the work from his recent publication in the Journal of Medical Genetics.
Identification of potential immune targets in controlling Endometrioid Endometrial Carcinoma metastatic progression
Presenter: Elodie Dubus
Presentation time: Sunday, May 22 at 10:15 a.m. - 11.15 a.m.
Location: Poster section 16 - Omics/Bioinformatics, poster board #P16.25A
Leveraging network analytics to infer patient syndrome and identify causal mutations using patient DNA sequence and phenotype data
Presenter: Sohela Shah
Presentation time: Sunday, May 22 at 4:45 p.m. - 5:45 p.m.
Location: Poster section P14 - New diagnostic approach, technical aspects & quality control, poster board #P14.086B
A efficient and accurate end-to-end next-generation sequencing solution for identifying and interpreting disease causing variants in rare diseases
Presenter: Anika Joecker
Presentation time: Sunday, May 22 at 4:45 p.m. - 5:45 p.m.
Location: Poster section P15 - Personalized/Predictive Medicine and Pharmacogenomics, poster board #P15.06B
QIAGEN and PreAnalytiX will host a joint Corporate Satellite where you can join us and hear how our customers are using our new technologies to advance molecular genetics research!
Title: Sample to Insight - The journey where biological samples are transformed into valuable insights
Speakers: Dr. Elena García-Arumí, Department of Clinical and Molecular Genetics and Rare Disease Unit, Hospital Vall d ́Hebron, Barcelona, Spain - Dr. Daniel Groelz, QIAGEN, Hilden, Germany
Date and time: Sunday May 22, 2016 at 11.15 a.m. – 12.45 p.m. in room 131
Dr. Elena García-Arumí, Hospital Vall d ́Hebron, will talk about molecular genetics approaches to mitochondrial OXPHOS system diseases using QIAGEN NGS strategies and Dr. Daniel Groelz, QIAGEN will present a new technology and workflow for integrated collection, stabilization, and purification of circulating cell-free DNA - the PAXgene® Blood ccfDNA System.
We're looking forward to seeing you in Barcelona!
Follow us on Twitter at @QIAGENbiox and @QIAGENscience for updates during the event
Get more details about ESHG
The Advances in Genome Biology and Technology (AGBT) meeting will be held at the JW Marriott Grande Lakes from February 10-13. We look forward to being there, and we hope you’ll drop by to attend our workshop, software demo and poster session for a peek at our solutions.
Our workshop will include a presentation from Dr. Chris Mason, an associate professor at Weill Cornell Medicine whose work has been recognized with awards from the NIH and the CDC and has been featured in Nature, Science, The New York Times, the Wall Street Journal, and more. His 100-plus peer-reviewed papers have been cited more than 5,500 times; he has also co-founded three biotechnology startup companies and serves as an advisor to several others. You don’t want to miss his talk!
Below is a quick glance at QIAGEN highlights on the AGBT agenda. We really hope to see you there!
Workshop (complimentary lunch provided)
Thursday, February 11, 12:05 p.m. - 1:05 p.m.
Coquina North
Presenter: Dr. Chris Mason, Associate Professor at Weill Cornell Medicine
“Targeted RNA Sequencing, Urban Metagenomics, and Astronaut Genomics”
In this presentation, Mason will cover the QIAseq Targeted RNA Panel beta testing, QIAGEN’s sample-to-insight solution for metagenomics sequencing, as demonstrated in the MetaSUB project. He will also discuss his latest endeavor, a comprehensive genomic study of the impact of spaceflight on the human body. Astronaut Scott Kelly will be studied during the course of his year-long stay at the International Space Study, as will his twin brother, Mark Kelly, a former NASA astronaut who will remain on earth. Check out more about this study on NPR.
Poster Presentation: Metagenomics Sample to Insight: MetaSUB 2.0
Thursday, February 11, 5-7 p.m.
Friday, February 12, 4:45-6:45 p.m.
Coquina North
Presenters: Nan Fang & Rumeysa Akinci-Tolun
Metagenomics Sample to Insight: “Ribosomal RNA Depletion from Single-cell RNA-Sequencing Library”
Software Demo Session
Thursday, February 11, 5-7 p.m.
Coquina North
Presenter: Sohela Shah
Ingenuity Variant Analysis, leveraging the Knowledge Base and HGMD, achieves over 30x enrichment in biologically relevant variants from whole genome and exome sequence data from patients with rare disease.
Demo Sessions & Complimentary refreshments
Thursday, February 11 - Saturday, February 13
Del Lago 4
Thursday, February 11 from 10 a.m.-7 p.m.
Friday, February 12 from 10 a.m.-7 p.m.
Saturday, February 13 from 9 a.m.-2 p.m.
For additional updates on QIAGEN at AGBT, please visit the Biomarker Insights blog.
QIAGEN is pleased to sponsor AGBT 2016 and we're looking forward to seeing you in Orlando.
More information
It was a pleasure attending PAG 2016. We had a poster presentation and were hosting a workshop on advanced NGS data analysis where invited guest speakers presented their research and agrigenomics software solutions from QIAGEN Bioinformatics.
Poster presentation
CLC Microbiome Genomics Module: Interactive Metagenome Analysis Tools
Now researchers are able to examine sample from a variety of resources such as soil, river water and gut microbiome. There are several analysis tools however those tools are not easy to use for everyone. Therefore interactive and intuitive tool can overcome the difficulties. We created CLC Microbial Genomics Module (MGM) that is metagenomics analysis module for CLC Genomics Workbench.
Presenter: Mari Miyamoto, QIAGEN
Workshop
Advanced NGS data analysis - integrated and user friendly bioinformatics toolbox for the analysis and visualization of multi-omics data
Analysis of next generation sequencing data typically requires the use of a range of different open source algorithms and bioinformatics software applications. Particularly making maximum sense of several different datatypes, such as genomic and variant data, transcriptomic and epigenomic data, can be challenging.
In our workshop we had two presentations:
Learn more about CLC Genome Finishing Module
Learn more about CLC Microbial Genomics Module
ASHG 2015 was everything we hoped it would be: interesting and inspiring scientific presentations and a place to reconnect with friends and customers. When we weren’t manning a busy booth, our team had a wonderful time soaking in the latest and greatest in human genetics.
Here is a recap of our scientific line up at the show:
Tuesday October 6, Dan Richards, PhD., VP of Biomedical Informatics, QIAGEN Bioinformatics, gave a presentation about “Genome-scale ACMG pathogenicity classification using comprehensive curated clinical evidence and data.”
Wednesday October 7, we hosted a workshop with two guest speakers: Yuval Itan from Rockefeller University and Ben Solomon from Inova.
Yuval Itan talked about “NGS Diagnostic Odyssey - From Bench to Beside: Join fellow investigators in an educational overview of how bioinformatic solutions transform NGS results into actionable hereditary disease insights”.
Ben Solomon gave a presentation on “Solving Diagnostic Odysseys in the Neonatal Intensive Care Unit Achieving Valuable Insight from a Single Cell Genome.”
And Thursday October 8 was the time for our three poster presentations:
How can our solutions help you?
The solutions featured in our speakers presentations may also further your NGS studies. Take a look here and get inspired:
Of course you're also more than welcome to contact us for any questions you might have. Hope to see you next year in Vancouver - we’re already looking forward to it!
Oct 6th - Oct 10th, 2015
ASHG 2015 will be held in Baltimore, Maryland from Tuesday, October 6 through Saturday, October 10, 2015.
It's the 65th ASHG and the meeting provides a forum for the presentation and discussion of cutting-edge science in all areas of human genetics: at invited platform and poster sessions, on the trade show floor, and at interactive workshops and events.
QIAGEN Bioinformatics team will be in Booth #1622 ready to show you how our Sample to Insights solutions can help you in your research. We will be demonstrating Ingenuity® Variant Analysis™, Biomedical Genomics Workbench, HGMD, and Inova Genomes — and we’d be happy to answer your questions.
We also invite you to stop by the QIAGEN booth #1621 across the aisle to learn about sample to insight solutions for exosomes, FFPE, circulating nucleic acids and single cells.
We have a number of QIAGEN Bioinformatics executives participating in educational sessions.
10-min presentation:
Workshop:
This event will be held in room Loch Raven, 2nd floor, Sheraton Inner Harbor Hotel.
Poster sessions:
For more than six decades, the American Society of Human Genetics Annual Meeting has offered the latest news and views about all areas of human genetics. This year, in its 65th iteration, ASHG promises to uphold that tradition: it will take place from October 6-10 at the Baltimore Convention Center, where more than 6,500 attendees from around the globe will learn about and discuss cutting-edge research in the field. For QIAGEN Bioinformatics, the conference offers a chance to focus on hereditary diseases, including cancer, and our various platforms, tools, and partnerships that allow researchers to further their work, including hereditary and rare disease analysis and interpretation in one solution with Biomedical Genomics Workbench and Variant Analysis with HGMD®, Inova Genomes, QIAGEN® Clinical Insight (hereditary cancer application) and collaborative enterprises like the Allele Frequency Community.
Listed as one of the best conferences to attend by a GenomeWeb survey, ASHG is well known for its broad scope and insightful content. The 2015 agenda offers a number of intriguing sessions — from symposia and workshops to keynotes and poster sessions — with topics including the genetics of disease, science communication, and policy updates, among many others. In addition to its abundant opportunities for scientists to network and learn through interactive sessions, ASHG features a large exhibition space, where more than 3,000 posters will be on display and more than 200 companies will provide updates on their products and services.
Several sessions stand out on the ASHG agenda this year. Kicking off the meeting, ASHG President Neil Risch will address how, through research and clinical practice, genetics is poised to make a significant impact on society and technology. Immediately following that session, Risch will host a symposium about the progress of genomics and electronic health records with four thought leaders in this space. In addition, several sessions will drill down into the genetics of disease, which is helping to move the needle on more effective medical treatment.
We’re particularly pleased to see such a focus on NGS analysis and interpretation — several of the scientific sessions will report on new methods as well as case studies of how high-quality analysis and interpretation made a difference. Many of the sessions also touch on the importance of analyzing more diverse populations. As co-founders of the Allele Frequency Community, we heartily support efforts to expand our public genetic databases to reflect variation seen in even very small ethnic populations.
For more information on ASHG, click here.
