GenomeWeb/ABRF 2016 Webinar Series
About the Series
GenomeWeb partnered with the Association of Biomolecular Resource Facilities to produce a series of online seminars highlighting methods, techniques, and instrumentation that support life science research.
This series was sponsored by New England BioLabs. All the webinars were recorded, so we encourage you to view them below.
Recorded May 17, 2016 | 1:00 PM ET
This online seminar will provide a practical approach to implementing lean management tools in the life science laboratory.
Unlike some management trends and tools, the scientific method is deeply engrained in lean management, making it an effective strategy for lab workflows.
In this webinar, Robert Carnahan, associate professor of cancer biology at the Vanderbilt University School of Medicine, outlines three simple lean techniques that his team has implemented for project management, inventory and ordering, and equipment maintenance.
Attendees of this webinar will learn about specific tools to begin implementation in their own working environment.
Recorded June 7, 2016 | 1:00 PM ET
This online seminar, part of the GenomeWeb/ABRF 2016 Webinar Series, will provide an overview of experimental and computational standards for metagenomics that have been developed as part of the Genomes in a Bottle standards consortium.
Over the last decade, major advances in sequencing technology have led to a surge in large-scale metagenomics and microbiome studies. As these studies continue to grow both in number and in scope, researchers face methodological and computational challenges for experimental design and interpretation. Recently, several groups have come together to address these challenges and develop standardized samples and methods for DNA sequencing, including the Association of Biomolecular Resource Facilities Research Groups on next-generation sequencing and metagenomics, the Food and Drug Administration, and the National Institute of Standards and Technology, all of whom work together in the Genome in a Bottle standards consortium.
These efforts encompass multiple stages of genomics and metagenomics work including study design, sample collection, DNA extraction, library preparation, sequencing, and computational analysis.
In this webinar, Christopher Mason of Weill Cornell Medical College and Scott Tighe of the University of Vermont will provide an overview of metagenomics standards that leverage a titrated mixture of known bacteria and eukaryotes. These have been sequenced across multiple next-generation sequencing platforms and characterized with ten different algorithms for taxonomic classification. The consortium members have also aggregated a set of 30 control samples for additional classification.
Dr. Mason and Dr. Tighe will report on a number of findings from the project, including the fact that sites of cross-algorithm agreement can lead to the most accurate estimate of the number of species from a new sample. They will also present an online resource for these tools, methods, and data sets; all of which are freely available. These methods and standards can help the many large-scale metagenomics projects around the world (and even some in space).
Recorded July 19, 2016 | 1:00 PM ET
This online seminar will cover the history of gene editing methods like TALENs and CRISPR/Cas and provide an overview of various gene editing technologies.
The emergence of these new technologies in the last decade "has triggered a veritable revolution as laboratories worldwide have begun to introduce or correct mutations in cells and organisms with the level of ease and efficiency not previously possible,” the Journal of the American Medical Association noted in 2015.
In this webinar, Eric Kmiec, Ph.D., of Christiana Care Health System’s Helen F. Graham Cancer Center & Research Institute and Channabasavaiah Gurumurthy of the University of Nebraska Medical Center will discuss some of the origins of gene editing and how the field emerged from a series of basic science observations to the dynamic fast-paced field dominating research journals today.
Kmiec and Gurumurthy will also discuss some of the factors that can influence the frequency and efficacy with which gene editing takes place, including cell cycle progression, and the introduction of specific double-strand breaks at specified sites relative to the target.
The second part of the webinar will focus on the latest developments in genome editing technologies: specifically, different genome editing technologies will be compared with a special emphasis on the CRISPR/Cas system.
Recorded August 4, 2016 | 11:00 AM ET
This online seminar will provide an overview of A3 problem solving, a lean management tool that can be used to improve efficiencies in life science core labs.
Developing a culture of continuous improvement in the core lab involves winning the hearts and minds of researchers and administrators and aligning their efforts around delivering value to the customer as quickly, cost-effectively, and flawlessly as possible. Along the way, performance gaps present themselves.
The A3 lean approach — so-called because it limits all documentation to a single piece of 11 x 17 inch, or A3, paper — offers a consistent and effective means by which to address these gaps.
Using a hypothesis-driven approach, the A3 tool guides inquiry into the root cause of performance gaps, and the identification of proposed countermeasures and targets to improve. It also serves as a means by which to monitor progress toward goals and share results with others so that all may benefit from what has been learned.
Our panelists for this webinar will be Sean Jackson, Chief Information Officer at the University of Virginia Medicine & Physicians Group, and Jay W. Fox, Professor of Medicine, Immunology & Cancer Biology at the University of Virginia School of Medicine. They will describe how the A3 tool works, and how your organization can benefit from its adoption and use.
Recorded September 13, 2016 | 1:00 PM ET
Clinical metagenomics is still in its infancy, and maturation of the field requires an appropriate accreditation program to ensure quality testing and patient safety. This on-demand webinar provides an overview of how one metagenomics lab — the Alkek Center for Metagenomics & Microbiome Research (CMMR) at Baylor College of Medicine — is pursuing CLIA/CAP accreditation.
An integral component of the accreditation process is proficiency testing (PT), which utilizes pre-established criteria, or measurement standards, for inter-laboratory comparisons. To date, commercially available metagenomic PT offerings are not available, which puts the burden on individual laboratories to develop an alternative assessment. In order to address the need for PT in metagenomics, the CMMR utilized a combination of previously sequenced samples (e.g. “blinded generous donor samples”), synthetic DNA standards, and mock communities to evaluate microbial DNA extraction, library preparation, and sequencing.
In addition to developing PT specific to metagenomic analyses, the CMMR developed a quality system with standard operation procedures (SOPs), competency testing, a laboratory information management system (LIMS), and asset management software in compliance with CLIA/CAP standards.
The complexity of metagenomic analyses are compounded by a limited understanding of the sources of variance and their impact on downstream analyses. Therefore, it is critical that the community adopt a universal set of standards for PT. Common sets of standards will enable identification of variation introduced by lab processes, thus allowing for the safe adaptation to clinical use.
This webinar is the second on metagenomics under the GenomeWeb/ABRF 2016 Webinar Series.
Recorded November 1, 2016 | 1:00 PM ET
This webinar will outline new strategies for genome editing in mammalian cells using CRISPR/Cas9, with talks focused on point mutation repair in human cell lines and the design of knock-in animal models.
During this webcast, Dr. Eric Kmiec will discuss a new approach to the correction of point mutations using single-stranded oligonucleotides and a partially synthetic form of CRISPR/ Cas9, a ribonucleotideprotein (RNP) complex. The experimental design, including the process of RNP assembly and the workflow, will be presented.
Dr. Kmiec will share details of a case study in which a point mutation in an integrated copy of the mutated eGFP gene in a human cell line is corrected using this approach, and a reaction pathway that is likely distinct from that of homology-directed repair. The use of short single-stranded oligonucleotides may be a strategy of choice when the desired endpoint is correction of point mutations in chromosomal genes.
Our second speaker, Dr. CB Gurumurthy, will discuss the latest trends and CRISPR tools available for animal genome editing, with a particular emphasis on strategies for increasing the homology-directed repair mechanism to enable insertion of longer sequences at the Cas9 cut sites. A few examples of designing knock-in animal models and the workflow of generating the models will be presented.
This webinar is the second on gene editing under the GenomeWeb/ABRF 2016 Webinar Series.
Recorded November 15, 2016 | 1:00 PM ET
This webinar will provide an update on Phase 2 of the ongoing ABRF Next Generation Sequencing Study, an effort to evaluate the performance of NGS platforms and to identify optimal methods and best practices. Phase 1 of the study focused on RNA sequencing, while Phase 2 is focusing on genomic DNA samples.
In particular, Phase 2 of the ABRF NGS study aims to address three questions applicable to most technologies being used for deep sequencing of genomic DNA:
1) for a typical combination of sample preparation method and sequencing instrument (a “platform”), what levels of intra- and inter-laboratory variation should be expected;
2) how is a platform affected by DNA exposed to formalin fixation ; and
3) how is a platform affected by DNA that contains a skewed nucleotide composition?
Sequencing for the study is being performed by independent academic service laboratories not affiliated with reagent or instrument vendors. The use of well-characterized, publicly available reference samples and uniform protocols within each platform will generate baseline data sets against which alternative methods, hardware upgrades, and any sequencing lab’s performance can be compared.