Sponsored by Tecan
Whole-Genome Sequence and Electronic Health Record Machine Learning for Hospital Outbreak Detection: A Novel Paradigm
Approaches for hospital outbreak detection have remained unchanged for years. When an outbreak is suspected, a method to establish genetic relatedness such as whole-genome sequencing (WGS) may be performed. This approach can miss outbreaks and falsely identify suspected outbreaks that are refuted by WGS.
In late 2016, University of Pittsburgh Professor of Medicine and Epidemiology, Dr. Lee Harrison and colleagues began developing the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines WGS surveillance with data mining and machine learning of the electronic health record (EHR) to detect outbreaks and correctly identify their routes of transmission, respectively. The team found EHR machine learning useful for transmission routes that cannot be identified by traditional means. The purpose of this talk is to describe the results of using this novel approach for detecting hospital outbreaks.
Participants can expect to learn:
- The difference between reactive WGS and WGS surveillance
- The advantages of reactive WGS and WGS surveillance
- How data mining of the electronic health record with machine learning can be used to identify transmission routes that are not readily apparent
- How EDS-HAT identifies outbreaks that are missed by traditional hospital infection prevention methods
Sponsored by PGDx
Decentralizing Precision Oncology Trials: Opportunities and Challenges for Implementing a Patient-Centric Model
The COVID-19 pandemic restricted clinical trial operations around the world but reignited efforts among researchers and industry players to explore new tools and decentralized strategies that can bring trials closer to where patients live and receive treatment. Such approaches may be useful for the development of precision oncology drugs, especially when these therapies are for rare, biomarker-defined tumor types and require a broad biomarker testing strategy to identify the treatment-eligible population.
Please join us on December 6th to hear four experts discuss the present challenges and opportunities in decentralizing precision cancer therapy trials: Dr. Sameek Roychowdhury, medical oncologist and member of the Translational Therapeutics Program, Ohio State University Comprehensive Cancer Center – James; Dr. Kristen Deak, associate director of clinical cytogenetics and molecular diagnostics, Duke University; Dr. Jonathan Cotliar, chief medical officer, Science 37; and Dr. Lee Schwartzberg, chief medical officer, OneOncology.
The panelists will discuss the value of distributed and centralized comprehensive genomic profiling, liquid biopsy testing, and telemedicine in improving clinical trial participation; highlight decentralized precision oncology trials currently underway and how they differ from traditional site-based trials; reflect on effective strategies for engaging and building trust among communities typically left out of research; and discuss how to involve community oncologists in decentralized trial approaches who usually don't have the time or resources to conduct research.
Sponsored by Allelica
Current clinical risk models rely heavily on traditional risk factors and only rarely incorporate genetic information. However, evidence that genome-wide variation contributes substantially to disease risk is mounting, with polygenic risk scores (PRS) emerging as a robust and accurate method to assess the genetic liability of disease. This webinar will explore how integrating PRS into clinical risk assessments leads to greater precision by enabling greater numbers of people at high genetic risk of disease to be identiﬁed and treated with disease-reduction interventions.
Dr. Noura Abul-Husn, clinical director of the Institute for Genomic Health at the Icahn School of Medicine at Mount Sinai, will provide insights on how PRS can be used to increase precision in risk assessment compared to current clinical genetic screening approaches, describe diverse patients’ perspectives on the use of clinical PRS, and discuss ongoing efforts to implement clinical PRS for common diseases in diverse populations. Professor Pradeep Natarajan, director of preventive cardiology at Massachusetts General Hospital, will discuss the limitations of contemporary guidelines in identifying patients at high risk of coronary artery disease and how PRS can help address this problem. Dr. George Busby, CSO & co-founder at Allelica, will discuss software available to enable PRS analysis implementation in-house at genetics laboratories and health systems and the best practices for clinical application.
Attendees will learn about:
- The role of PRS in estimating risk for cardiovascular and other common diseases.
- How PRS has been used to identify and rectify limitations in current risk assessments.
- How PRS is currently being integrated into patient care at leading healthcare institutions.
Sponsored by Qiagen
Tuberculosis (TB) is a leading cause of morbidity and mortality due to an infectious agent, with nearly 10 million new cases and 1.4 million deaths worldwide in 2019. Type 2 diabetes is a risk factor for the development of active TB. The global increase in type 2 diabetes, with 642 million cases predicted worldwide by 2040, poses a challenge for TB control. The elderly are an understudied and vulnerable population with a high prevalence of diabetes and are highly susceptible to TB, with 20 to 30 percent dying from the disease.
In this webinar, Blanca I. Restrepo will describe the epidemiological landscape of TB and diabetes, with contrasting observations between adults and the elderly. Most notably, the elderly have a high prevalence of type 2 diabetes, yet this is not associated with higher odds of TB in this population. Also, Restrepo and colleagues find that elderly vaccinated with the BCG vaccine at birth appear to be more protected from developing TB. These provocative findings require further testing in other cohorts. Finally, Restrepo will discuss the challenges for latent TB infection testing in the elderly and the performance of the QuantiFERON-Gold Plus TB test.
Sponsored by Illumina
Collaboratively Designed Genomic Tools to Maximize Both Genetic Gain and Economic Efficiency in Aquacultural Breeding Programs
Genomics can deliver great benefits to aquacultural breeding programs, including efficient management of diversity and inbreeding, accurate parentage assignment, optimal mating designs, improved breeding value prediction, selection decisions, and breeding strategies. Using the appropriate platform for the population of interest is critical. It is often expected that optimal results require a customized tool with a higher level of initial investment and larger ongoing costs. However, it is possible to keep costs reasonable with optimal outcomes through the creation or use of a collaboratively designed universal genotyping platform.
Collaborative genotyping solutions for specific species are created using diverse populations to ensure a design that contains a core set of markers with broad utility among all populations along with markers that capture specific population characteristics. The design also provides the ability to capture published markers associated with key traits. Many industry parties can benefit through using such platforms, creating a sample volume to keep costs reasonable and enabling results and outcomes that are easily compared and evaluated. As the platform is updated and improved, the benefit flows to all users. A successful example of this approach is in the livestock domain, where the widely used, collaboratively designed Illumina BovineSNP50 BeadChip array allows for high-throughput, cost-effective genetic screening for many genomic applications — including genomic selection — across both the dairy and beef industries. More recent extensions of this concept have been deployed as GeneSeek Genomic Profiler (GGPs) arrays. The updated content over time can leverage the continuously developing knowledge base about the genomic structure of a species as new tools and resources become available.
In this talk, Dr. Klara Verbyla, director of genomics and breeding and associate vice president of genetics at The Center for Aquaculture Technologies, will discuss the benefits of using such an approach for aquaculture species, as exemplified by the recent creation of a collaborative genotyping platform for L. vannamei shrimp designed using samples from 11 populations. Verbyla will discuss the design of the array, validating the array’s results, achieving maximal benefit from such an array, and the economic impacts of creating and using such genotyping platforms.
Sponsored by Tecan
DNA methylation profiling is an important tool in understanding various diseases, including neurodegenerative diseases such as multiple systems atrophy (MSA). Research has shown that the 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) methylation states play different roles in gene expression, but traditional bisulfite conversion methods result in a single readout of total methylation level without differentiating 5mC and 5hmC.
In this webinar, Jörg Tost, director of the Laboratory for Epigenetics and Environment at the Centre National de Recherche en Genomique Humaine, will discuss a cost-effective and streamlined method of integrating Tecan’s TrueMethyl oxBS module upstream of methylation arrays such as Infinium MethylationEPIC. He will present results from studies utilizing this method on prefrontal cortex brain tissue to examine 5mC and 5hmC changes in MSA disease progression. He will also demonstrate the successful combination of the TrueMethyl oxBS module with amplicon sequencing to analyze regions identified through methylation arrays and whole genome oxidative bisulfite sequencing.
- Learn about the important roles of 5mC and 5hmC in the regulation of gene expression.
- Understand the significance of differentiating between 5mC and 5hmC in epigenome-wide association analyses.
- Become familiar with the methods of integrating Tecan’s TrueMethyl oxBS module with various downstream applications to analyze 5mC and 5hmC levels at single-nucleotide resolution.
Tecan genomics reagents are for Research Use Only. Not for diagnostic procedures.
Sponsored by BioLegend
CD4 and CD8 T cells play critical roles in the mammalian immune system. While their development within the thymus from the CD4+CD8+ stage has been widely studied as a model of lineage commitment, the underlying mechanism remains unclear.
In this webinar, Aaron Streets of UC Berkeley will discuss how this process can be deconstructed by applying CITE-seq to measure the transcriptome and over 100 surface proteins in thymocytes from wild-type and lineage-restricted mice. Streets will explain how totalVI can be used to jointly analyze the paired measurements to build a comprehensive timeline of RNA and protein expression in each lineage. This data supports a sequential model of lineage determination in which both lineages go through an initial phase of CD4 lineage audition, which is followed by divergence and specification of CD8 lineage cells.Participants can expect to learn:
- How the totalVI computational pipeline can be used to interpret CITE-seq data.
- How single-cell multiomic measurements can be integrated with traditional flow cytometry to generate a hypothesis.
- A comprehensive model for T-cell development in the thymus.
Sponsored by Invitae
Error Corrected Sequencing and Variant Calling Approaches to Characterize Evolution of Clonal Hematopoiesis
In this webinar, Kelly Bolton, assistant professor of oncology at Washington University, will discuss the development and validation of a custom next-generation sequencing panel that targets genes commonly mutated in clonal hematopoiesis. She will address the challenges, approaches, and pitfalls of variant calling in clonal hematopoiesis. Finally, Bolton will discuss the application of this panel to a study of how clonal hematopoiesis evolves under the selective pressure of different oncologic therapies, including PARPi therapy, in 500 solid tumor patients.
Sponsored by Tecan
Understanding the Role of the Microbiome in Deficient and Proficient Mismatch Repair Colorectal Cancers
Links between colorectal cancer (CRC) and the gut microbiome have been established, but the specific microbial species and their roles in carcinogenesis remain active areas of inquiry. Part of the mystery behind these links relates to the different methods of study that bias toward different signatures. In this webinar, Nicholas Chia will present work that elucidates the role of specific subtypes of CRC and discuss the implications of these findings for future research.
Chia and colleagues collected paired colon tumor and normal-adjacent tissue and mucosa samples from 83 individuals who underwent partial or total colectomies for CRC. Mismatch repair (MMR) status was determined in each tumor sample and classified as either deficient MMR (dMMR) or proficient MMR (pMMR) tumor subtypes. Samples underwent 16S rRNA gene sequencing and a subset of samples from 50 individuals were submitted for targeted metabolomic analysis to quantify amino acids and short-chain fatty acids. A PERMANOVA was used to identify the biological variables that explained variance within the microbial communities. dMMR and pMMR microbial communities were then analyzed separately using a generalized linear mixed-effects model that accounted for MMR status, sample location, intra-subject variability, and read depth.
Sponsored by Thermo Fisher Scientific
Acute myeloid leukemia (AML) is an aggressive, heterogeneous disorder involving clonal expansion of progenitor myeloblasts in the bone marrow and peripheral blood. Research over the last decade has uncovered several recurrent somatic mutations associated with the disease biology. Hence, it may be increasingly important for labs to be able to efficiently profile AML samples for a growing number of diverse mutations, spanning single nucleotide variants, indels, tandem duplications, and gene fusions.
During this presentation, Diana Morlote, assistant professor of pathology at the University of Alabama at Birmingham, will discuss the recent implementation of a rapid, automated next-generation sequencing (NGS) assay in her research laboratory for genomic profiling of AML and other related hematological disorders. The data collected from several cases using the Oncomine Myeloid Assay GX v2 by Thermo Fisher Scientific will be presented. Analytical performance will be discussed for various key mutations detected using DNA inputs. Morlote will describe how this solution addresses key challenges with molecular analysis of AML and other related malignancies. This research furthers our understanding of malignant hematological disorders and may lead to better care in the future.
Sponsored by LGC, Biosearch Technologies
Marker-assisted breeding – a technique by which trait selection is aided by linking the trait with an associated genetic marker – requires access to high-throughput, low-cost genotyping of a genome-wide sample of DNA polymorphisms. Next-generation sequencing (NGS) approaches are often more cost-effective for large-scale applications compared to SNP arrays.
During this webinar, Mitchell J. Feldmann, postdoctoral researcher at the University of California, Davis, will discuss how targeted, medium-high density, multiplexed genotyping platforms can avoid several shortcomings of both SNP arrays and NGS-based genotyping by sequencing for heterozygous, outbred cultivated strawberry.
Learn how a high-throughput, medium-high density genotyping platform populated with 5,000 sub-genome specific SNPs connected to the 50K FanaSNP Axiom array for cultivated strawberries was designed and tested. Markers were selected to best reproduce genomic relationship matrices calculated with the 50K FanaSNP array and to cover the linkage landscape in a large diversity panel of exotic, heirloom, and modern cultivars.
Attendees will learn about:
- Marker-assisted breeding.
- Platform development and testing.
- The analyses enabled by a high level of connectivity across platforms.
Sponsored by Beckman Coulter
Like any sufficiently understood system, human innate and adaptive immunity can be tweaked. As researchers move from understanding the components and interactions within these programs to manipulating them, engineering principles like iterative design and scalability are raising new possibilities to influence the biological determinants of health. Join us for a discussion among experts on how synthetic biology, driven by a new generation of lab tools, is helping scientists push towards new therapies and diagnostics.