At the AGBT 2018 meeting in Orlando, the QIAGEN team soaked up the latest NGS advances.
AGBT is a marathon of cutting-edge scientific talks and posters, networking events, and legendary parties. One of our favorite talks came from John Martignetti, who spoke about efforts to develop a liquid biopsy for endometrial cancer to spare women the invasive, painful surgical procedure used today. (If you missed it, check out our profile of Martignetti’s work using IPA to detect a promising new biomarker for ovarian cancer patients.) At AGBT, he shared results of a prospective study of 107 patients. For all cases diagnosed through traditional means as having cancer, the liquid biopsy using uterine lavage fluid also detected driver mutations associated with cancer. It wasn’t all clear cut, though. One patient who had no signs of cancer according to traditional tests was found to have cancer-associated driver mutations from the liquid biopsy. Martignetti’s talk got attendees considering the medical challenges associated with cases like this, where there are no established standards of care yet.
There were many other excellent talks, but of course we’re partial to the ones that included new data analysis tools. Christina Curtis from Stanford presented an algorithm trained to differentiate between tumors evolving neutrally or under selective pressures, which could have implications for understanding metastasis and other traits of cancer progression. Michael Schatz from Johns Hopkins University presented the CrossStitch pipeline for rapid, reference-guided assembly of human genomes based on many different types of sequencing data. And Ami Bhatt from Stanford introduced Athena, a custom assembler for de novo metagenomics.
We’d like to thank the many attendees who spent time with us at the conference. It was a pleasure to hear about your research and let you know how QIAGEN’s bioinformatics tools might help. And we thoroughly enjoyed seeing so many people sporting their “Explore the RNA Universe” T shirts for the outer-space-themed closing party!
This week is the Advances in Genome Biology & Technology annual conference, taking place this year in Orlando. The QIAGEN Bioinformatics team always looks forward to this event for its commitment to cutting-edge science and meticulous genomic analysis, and we’re pleased to be a sponsor of this great meeting.
As usual, one of the concurrent sessions will focus on computational biology, the topic that resonates most for us. We’re eager to hear from scientists who think as deeply about the analysis and interpretation of DNA and RNA data as we do – and who don’t judge us for geeking out on equations, pathway diagrams and scripts! In other sessions, there will be lots of great results to consider from human genome analyses, cancer studies and microbiome interrogations, all areas that are near and dear to the QIAGEN team.
If you’ll be attending AGBT, we invite you to stop by our table at the morning coffee breaks on Tuesday and Wednesday at 10:20am. Grab a coffee and a free “Explore the RNA Universe” T-shirt, courtesy of QIAGEN! They’ll be the perfect look for rocking out at the space-themed farewell party on Thursday night.
We hope to see you in Orlando!
During our workshop at this year’s AGBT conference, scientist Chris Mason from Weill Cornell Medicine intrigued the audience with a look at several ongoing projects in his lab. Mason is best known in the genomics field for PathoMap, a study of the microbial inhabitants of New York City, and for the NASA twins study, which uses an integrative ’omics approach to analyze the effects of space travel by comparing twin astronauts — one in space and one here on Earth. He has also done considerable RNA methods work and was the first to coin the word “epitranscriptome.” His team has been using QIAGEN tools, and he shared his experiences with our solutions.
One of Mason’s major efforts is MetaSUB, or PathoMap on steroids. For MetaSUB, scientists are analyzing microbial communities in 45 cities around the world, using subways and other urban infrastructure to get a better understanding of how microbes live, move, and pass among humans. Among other things, these studies are shedding light on important traits such as drug resistance; non-resistant and antibiotic-resistant bacteria could be found living in the same subway station in New York. As part of this project, the lab has been using CLC Genomics Workbench and CLC Microbial Genomics Module to analyze 16S rRNA data. Thanks to our recent partnership with CosmosID, our solution will soon have whole metagenome taxonomic analysis capabilities as well. Mason’s team is also working on the Extreme Microbiome Project to conduct similar studies in unusual locations around the world.
A similar approach, including CLC Genomics Workbench, is being used to study previously collected patient samples that were never successfully cultured. Mason said 20 to 30 percent of patients with infectious disease fall into this category — waiting for weeks for culturing of their samples, only to get inconclusive results. This project will sequence 250 such samples and use metagenomics to determine the microbial content.
In separate work, the Mason lab is using RNA-seq to look at differentially expressed genes in clinical samples. One project used the QIAseq Targeted RNA Panels to look at samples from leukemia patients taken at the time of diagnosis and again at relapse. The goal was to find genes consistently dysregulated at relapse — something that previous exome studies had failed to detect. The protocol worked well even with samples as small as 10 nanograms, and the all-in cost of about 50 cents per target gave a good option for quickly and affordably measuring gene expression. This study led to the validation of 104 genes that appear to be a signature of relapse in these patients.
One of the essential features of the QIAseq panels is the ability to add unique molecular identifiers, or barcodes, to each molecule prior to library prep, according to Mason. This step helps scientists detect PCR artifacts and correct ratios later in the workflow, making the process more robust and reliable.
Thanks to Chris Mason for an excellent talk about some of the fascinating research going on in his lab!
Watch the presentation on Targeted RNA sequencing, Urban Metagenomics, and Astronaut Genomics:
https://clcbio.23video.com/v.ihtml/player.html?token=753d018adc990f968d90e9d98b3c65b5&source=embed&photo%5fid=13129410Learn more about our solution for metagenomics
Learn more about QIAseq Targeted RNA Panels
The 17th annual Advances in Genome Biology and Technology meeting was a whirlwind of stellar talks, great posters, and - of course - fabulous parties.
While all the talks were terrific, some really resonated with us. In the opening session, David Haussler made the case for sharing genomic data and rare variant information as much as possible, a message that we loved hearing as co-founders of the Allele Frequency Community. We believe that data sharing is essential for genomic medicine to have the kind of impact we all anticipate. In another talk, Stephan Schuster announced the launch of the GenomeAsia 100K, a new project to sequence 100,000 people in Asia for a better understanding of the genetic diversity in that population. We’re excited to see what this new trove of data contributes to the global genomics community.
Our team was busy during the conference and one of the highlights of our efforts was the lunch workshop featuring Chris Mason from Weill Cornell Medicine. He presented updates on some of his more unique projects, including efforts to sequence pathogens across New York City and more extreme environments and to unravel the biological effects of space travel through a study of twin astronauts. Mason has been beta testing the QIAseq Targeted RNA Panels, and during his presentation, he highlighted the benefits of the panels in delivering digital RNA sequencing for gene expression analysis, and he shared results from that metagenomics work as well. It was a great workshop thanks to Mason and all the attendees who took the time to join us!
We also participated in the software demo session, showcasing our QIAGEN Ingenuity® Variant Analysis™ application for sequencing data interpretation. With the connections to the Ingenuity Knowledge Base and HGMD, it relies on meticulously curated genomic and biological data to help scientists quickly home in on variants of interest to get at the root cause of disease or other phenotypes. We provided software demos at our hospitality suite as well, and we’d like to thank all the people who stopped by.
We had a great time in Orlando and we’re for sure looking forward to AGBT meeting next year – hope to see you there!
Learn more about QIAGEN Ingenuity Variant Analysis
Read more about the new QIAseq Targeted RNA Panels
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
Imagine Human Genome Interpretation minus the false positives. Allele Frequency Community is a freely accessible “opt-in” community resource designed to facilitate sharing of anonymized, pooled allele frequency statistics among laboratories for the benefit of patients and biomedical research.
Joining the community is free. Once you join, your NGS samples can be richly annotated with allele frequency information from the entire Community. Non-personally identifiable statistics from community members’ samples are used to expand the diversity of the database over time.
More informations about Allele Frequency Community is available here www.allelefreq.org
At AGBT 2015 in Florida, we'll be giving a presentation on Allele Frequency Community at the Software Demo Session. The presentation title is Genomic Crowdsourcing: Allele Frequency Community Provides Expansive, Ethnically Diverse, Freely Available Community Resource for Allele Frequency Annotation.
Time and place: February 26 Thursday 5:15 pm – 7:15 pm, Marco Island Hilton, Florida
Title: Genomic Crowdsourcing: Allele Frequency Community Provides Expansive, Ethnically Diverse, Freely Available Community Resource for Allele Frequency Annotation
Douglas Bassett1, G Eley2, R Felciano1, R Forsberg1, L Furmanski1, G Glusman3, D Goldstein4, M Hegde5, P Hieter6, A Joecker1, T Kaminski7, A Krämer1, S Letovsky7, T Love1, B Macy1, A Muthiah1, K Patel1, N Pearson8, V Rajaraman1, H Rehm9, D Richards1, F Schacherer1, E Schadt10, S Scott1, J Shendure11, D Shiffman1, A Subramanian1, P van der Spek12, JG Vockley2, R Yip1
Abstract Text
A key challenge in genome interpretation is the lack of an extensive, high quality, ethnically-diverse collection of human genomes as a reference set. A prospective disease-causing variant that appears to be “rare” based on publicly available sequence may in fact be a polymorphism in an ethnic population under-represented in public databases. Resources such as the Exome Variant Server and the 1000 Genomes Project have been immensely valuable to the community, and Kaviar combines such datasets into integrated allele frequencies, but public databases have not been funded to provide broad and deep ethnic representation. QIAGEN’s Variant Analysis™ genome interpretation solution (www.ingenuity.com/variants) has been used to interpret 300,000 ethnically diverse human samples. However, these NGS datasets are private and most are never publicly released. Labs often collect their own private allele frequency libraries, but infrastructure and incentives have historically not existed for integrating these resources into a freely-available community asset. The Allele Frequency Community has been formed to address this interpretation need. Founding members have pooled extensive human exome- and genome-wide variant call datasets in a secure, anonymized, pooled fashion to create the largest integrated, freely-accessible, hosted community database of allele frequencies ever available. To enable this community resource to grow over time, users have the opportunity to opt-in to join the Allele Frequency Community and benefit from the extensive database, agreeing in return to allow their sequences to contribute to the database. Only anonymous, pooled allele frequencies are provided, protecting patient privacy. QIAGEN Bioinformatics agreed to host the content and make it available free of charge via its HIPAA and Safe Harbor compliant genome interpretation ecosystem, which includes QIAGEN’s Variant Analysis, Cancer Research Workbench (www.clcbio.com/products/) and Clinical Decision Support (www.ingenuity.com/ngs-clinical-beta) offerings. Analyses made possible by this large diverse dataset will be presented, and ethnic diversity of the resource will be reviewed.
For more info, please write to marketingbiox@qiagen.com
