AMP is the leading organization in the field of molecular diagnostics, and our annual meeting is widely considered the “premier gathering” of molecular professionals. As always, we will explore how cutting-edge technology and developments in molecular testing continue to have a major and direct impact on patient care. The AMP 2023 Program Committee is planning an impressive program to spark dialogue and engagement amongst attendees and exhibitors from around the world, and we look forward to welcoming you to discuss the latest in molecular diagnostics and network with friends and colleagues.
Whether you’re using PCR or NGS, targeted panels or whole-genome sequencing, mono- or multiplex testing, we have a solution to empower your workflow. Stop by booth #607 to explore and demo some of our products, including QCI Interpret.
Sip, mingle, and connect while gearing up for an exciting weekend of events, which include three QIAGEN-sponsored Corporate Workshops and two QIAGEN Innovation Stage Spotlights.
In a not-to-be-missed talk, Dr. Fergus Couch of the Mayo Clinic will discuss the current challenges and opportunities of liquid biopsy in oncology research.
Meet us at the Innovation Stage on November 1st.
Learn about QIAGEN Clinical Insight (QCI), a flexible clinical decision support suite that is compatible with any NGS platform, running any assay, targeting any indication, including somatic, hereditary, hematological or childhood cancers. During this talk, Dan Richards, Vice President of Biomedical Informatics at QIAGEN and co-founder of Ingenuity Systems, will present a lung cancer case study to show how QCI allows you to optimize and scale your pipeline for the clinical interpretation of genetic variants—from sequence data to report sign-off—without sacrificing accuracy or utility.
We are days away from one of the largest gatherings of molecular pathologists and diagnostic professionals and we couldn’t be more excited to support your path to precision medicine.
Visit us at booth #607 to demo our solutions or chat with our experts.
Learn more at our AMP 2018 event page.
See you in San Antonio!
The contest was called to address a current industry challenge: standardizing variant interpretation and reporting. The increasing demand for next-generation sequencing (NGS)-based tests has led to a high degree of variability in how members of the global molecular genetics and pathology community classify variants and prepare final reports. To better understand the limitations of standardization and move forward in the same direction, Agilent Technologies, Thermo Fisher Scientific, and QIAGEN engaged in a friendly competition to determine which company had the most accurate and consistent NGS analysis and interpretation platform: the Alissa Interpret platform, Ion Torrent platform, and QIAGEN's Biomedical Genomics Workbench and QIAGEN Clinical Insight (QCI™) Interpret, respectively.
Erasmus University Medical Center (Erasmus MC) Rotterdam generated sequence data from five clinical samples using Thermo Fisher’s Ion Torrent platform. The three contestants were given this sequence data and instructed to identify clonal and subclonal mutations in the tumors down to an allele frequency level of at least five percent. Then, the contestants were asked to identify and annotate the variants, calculate allele frequency, and interpret the variants according to a five-tier classification system ranging from “benign” to “clinically significant.”
This was no easy task.
Initially, seven companies expressed interest in meeting the challenge. In the end, only three crossed the finish line. According to Professor Winand Dinjens, the organizer of this year’s competition, and head of molecular diagnostics in the Department of Pathology at Erasmus MC Rotterdam, most contenders dropped out after struggling to analyze the sequencing data, which was produced with the Ion S5 XL System, a version of the Ion Torrent platform. As the race unfolded, unfamiliarity with the provided sequencing data caused more than half of the competitors to exit the track.
So, was there a home advantage?
The sequencing data in question was produced by the Ion Torrent platform, which means the Thermo Fisher team analyzed the data using tools custom-built to work with this type of sequence data. For example, during the variant calling process, the Thermo Fisher team was able to apply “flow space” information for each base as it related to Ion Torrent chemistry.
Even so, QIAGEN didn’t back down.
While Thermo Fisher may have had greater familiarity with this particular “track,” QIAGEN’s bioinformatics solutions are open platforms and have experienced over 750,000 “races” on all types of “tracks” across the world. The QIAGEN Knowledge Base is the industry’s largest, most up-to-date clinical database with the direct experience of analyzing over 750,000 human samples. This cumulative experience, in addition to more than 16 million knowledge base findings across 23,000 genes, gives QCI Interpret greater scope and depth.
For each of the five cancer samples, Erasmus supplied FASTQ files plus aligned BAM files, from which the task was to perform variant calling and interpretation and to generate a list of clinically reportable findings. Tim Bonnert, QIAGEN’s Associate Director of Bioinformatics Field Application Scientists, EMEA first used QIAGEN’s Biomedical Genomics Workbench to process the FASTQ files and perform the variant calling. Then he assessed the variants with QCI Interpret, which has curated content that triggered built-in ACMG/AMP and AMP/ASCO/CAP guidelines.
When the results from all contenders were in, none were identical.
QIAGEN’s software solutions performed significantly better than the competition. The organizers stated that there were a total of 12 variants across the five samples. QIAGEN reported 11 of the 12 variants; the variant had been identified in a homopolymer region, and the QIAGEN team identified this variant as a potential false positive. However, this classification does not change the overall clinical actionability recommendation for the patient. By contrast, Agilent and Thermo Fisher missed multiple calls. In some cases, neither platform detected variants in a sample that did in fact have clinically actionable findings; for example, the Torrent Variant Caller pipeline generated no calls for three clinically meaningful variants.
Even though QIAGEN outperformed competitors and achieved almost 100% concordance, these kinds of “battles” illustrate the importance of having pre-defined and clear standards for bioinformatics workflows. Classification and reporting of variants to healthcare providers is critical for patient care. This process requires: accurate reporting of the tumor response to targeted therapy; establishment of professional guidelines for patient care; and collaborative institutional clinical trials, thereby supporting the need for standardization among laboratories performing these tests.
According to Bonnert, “While Erasmus MC no doubt had these standards nailed down in their routine testing pipelines, for this competition there was, for example, uncertainty about required depth of coverage, acceptable distance into the intron, and other confidence metrics and standards that we believe are essential to any routine clinical bioinformatics approach. The need for standards in routine testing also extends to employing clearly defined rules and assessment criteria supported by curated clinical evidence.”
Standards are important for ensuring consistency of secondary and tertiary analysis workflows and for generating actionable data. The faithful detection of variants from Ion Torrent data by the Biomedical Genomics Workbench and the standardized clinical decision support provided by QCI Interpret proved the winning combination.
We are honored to have participated in the Battle of the Bioinformatics Pipelines. Here at QIAGEN, we are committed to building the most reliable, robust and technologically-advanced bioinformatics tools that are sequencer-agnostic because we want to empower more labs, more clinicians, and more patients to do and know more. Just as our pipeline proved victorious with Ion Torrent data in this battle, our research and clinical solutions work successfully with QIAGEN’s own GeneReader platform, as well as with data from Illumina.
Get in touch with one of our experts today! CONTACT US
The recent AMP Europe 2018 conference was a wonderful chance to catch up with old friends and establish new relationships—our team provided demos at the booth and we had a wonderful symposium. We also participated in a fun challenge, known as “Innovation Lab: Battle of the Bioinformatics Pipeline.” According to this story by Julia Karow in GenomeWeb, the aim of the exercise was “to provide commercial vendors of NGS analysis and interpretation pipelines with sequencing data from real patient samples, generated by a routine molecular diagnostics laboratory, and to see how similar or different their results would be.”
QIAGEN was one of three vendors who participated, using Biomedical Genomics Workbench data analysis platform and Qiagen Clinical Insight (QCI) Interpret software to identify mutations in tumor sequence data, down to a level of 5 percent. Participants were instructed to name and annotate the variants, state their allele frequencies and interpret them according to a five-tier classification system ranging from “benign” to “clinically significant.”
The session was organized and led by Winand Dinjens, head of molecular diagnostics in the Department of Pathology at Erasmus University Medical Center (Erasmus MC) Rotterdam, whose lab also analyzed the data, to establish a benchmark against which the other outcomes were compared. During the session, all three vendors presented their results and compared them to those of Erasmus MC. Though there was plenty of overlap amongst the three vendors’ results, none were identical. The session concluded with all participants agreeing that context (of a patient’s disease) is important in variant interpretation, and that laboratories must define their own thoughtful criteria to effectively frame a clinical report.
We are honored to have been included in the #AMPEurope2018 challenge, and that Biomedical Genomics Workbench and QCI were part of the process. We are also very proud of our team’s positive results—this is our third such challenge, 1) ECP 2017 and 2) AG MolPath, and we welcome the chance to compete again!
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
Austin, here we come!
We’re getting AMPed up for the upcoming Association for Molecular Pathology 2015 annual meeting! Held at the Austin Convention Center from November 5-7, AMP offers molecular pathologists the chance to catch up on the latest industry and research developments.
This year, AMP’s theme is “Realizing the Dream of Precision Medicine,” and we couldn’t imagine a more timely topic. Precision medicine is becoming a reality, and we’re proud to be forging the tools for this revolution, particularly where cancer is concerned.
Our theme for AMP is “Insights in Oncology,” and we’ll be focusing on both somatic and hereditary cancers during the show. In addition to several key news announcements, we’ve scheduled a number of activities for AMP attendees. We hope you’ll stop by to hear our speakers and check out our demos. Here are some events where you can find us during AMP:
Workshop:
November 4, 4:00-4:50 p.m.
Austin Convention Center, Grand Ballroom E
“Practical Considerations When Using a Clinical Decision Support System for NGS Variant Analysis, Interpretation, and Reporting”
Speakers: Andrea Ferreira-Gonzalez, PhD, Director Molecular Diagnostics Lab, Chair Molecular Diagnostics Division, Virginia Commonwealth University; Jason D. Peterson, M.S., Genomic Informaticist, Clinical Genomics and Advanced Technology (CGAT), Dartmouth-Hitchcock Medical
Dr. Ferreira-Gonzalez and others will discuss practical aspects involved during the evaluation and use of NGS data analysis tools in the clinical laboratory. Learn about their firsthand experiences with QIAGEN® Clinical Insight – a new, scalable clinical decision support platform intended to assist molecular pathologists in interpreting and reporting NGS variants from any targeted gene panel run on any next-gen sequencing instrument.
Evening reception:
November 4, 6:30 -8:30 p.m.
Hilton Austin, Salon A & B, 500 E 4th St, Austin, TX 78701
Networking event with QIAGEN executives
RSVP required: NATradeshows@qiagen.com
In-booth presentations:
November 5, 3:45-4:00 p.m. and November 6, 9:45-10:00 a.m.
Booth #922 and #923 — QIAGEN Bioinformatics
“Enabling Precision Medicine – Through Scalable NGS Assay Interpretation & Reporting in Oncology”
Speaker: Dan Richards, PhD, VP of Biomedical Informatics, QIAGEN
Next-generation sequencing (NGS) based clinical tests are increasingly being adopted in clinical labs, but there are significant challenges in unraveling the complexity of genetic information to offer actionable insights for healthcare professionals. The time spent on assessment of NGS variants continues to be a rate-limiting step to reporting. To address this issue, in May 2015 the American College of Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP) developed and published standards for the classification of sequence variants. The computational assessment of NGS variants according to ACMG and AMP guidelines promises to significantly reduce the amount of time from sequence result analysis to reporting. In this presentation, Dr. Dan Richards will discuss our manual curation and data-driven approach to pathogenicity classification using QIAGEN® Clinical Insight, a clinical decision support software tool developed to streamline the variant interpretation and reporting process for clinical laboratories. QIAGEN Clinical Insight leverages the comprehensive QIAGEN Knowledge Base with over 10 million biomedical findings of curated data to compute classifications based on the ACMG-reported criteria and classification system.
Learn more about QIAGEN Clinical Insight
