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.
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.
