Taylor & Francis

Welcome to part 2 of this two-part episode on whole-genome sequencing (WGS) in rare disease research and treatment. In part one we discussed the impacts the technology has had on both improving the clinical diagnosis and management of rare diseases and on drug development and basic research studies. 

This episode goes beyond the technology's capabilities and into the debates surrounding how, when and why they should be used. What needs to change for the technique to be applied equitably? And how does reality stack up against science fiction in terms of people's perceptions of ubiquitous WGS.

To do this I speak with David Dimmock, Senior Medical Director of the Rady Children's Institute for Genomic Medicine (CA, USA); Christine Stanley, Chief Director of Clinical Genomics, Variantyx (MA, USA); and Take Ogawa, Vice President of Sales & Marketing at Psomagen (MD, USA). Each of these speakers provides their opinions on the impacts of race, religion and way of life on the application of WGSand how much data is too much data.

Contents:

Introductions: 00:00-02:20

Gauging public perceptions of routine WGS 02:20-05:40

The role of industry in improving WGS accessibility and capabilities: 05:40-07:35

The appropriate use of pre-symptomatic and predictive risk findings: 08:00-11:15

Debating the discovery of untreatable diseases: 11:15-12:45

The impact of data biases in gene sequencing and the lack of gene references for different populations: 12:45-14:45

The impact of religion and lifestyle on ethical considerations in the use of WGS data: 14:45-16:00

Dealing with unintended findings or results that impact relatives: 16:00-16:45

The value of WGS in pharmacogenomic variant findings and challenging the ACMG59 list: 16:45-19:20

Striking the balance between fully utilizing WGS for all potential findings and ensuring maximum participation for all groups: 19:20-22:45

Filtering data to avoid exclusion: 22:45-24:10

Who owns WGS data? 24:10-25:15

Consent conversations: 25:15-26:30

Final comments: 26:30-27:15

Love it or hate it, western blotting forms the bedrock of countless studies across numerous disciplines. Explore its history, development and applications in this episode all about the marmite of life science techniques.

Guiding me through the hand wringing, hair follicle destroying history and process of western blotting, and hopefully explaining the beauty and potential of the technique - is Kenneth Oh, Senior Project Manager at Bio-Rad Laboratories.

Kenneth reveals some of the latest developments in western blotting. Revealing how researchers are now able to validate the success of each stage of a western blot and work with smaller samples, Kenneth provides key tips for ensuring each of your western blots is a triumph.

Contents:

Intro: 00:00-01:15

History of western blotting: 01:15-3:50

What makes western blotting so tricky? 03:50-05:30

Stepwise optimization: 05:30-06:50

Stain-free western blotting: 06:50-08:50

The different variants of western blotting: 08:50-10:20

The right blot for the right application: 10:20-11:30

The most exciting developments in western bloting:11:30-13:35

New horizons for western blotting: 13:35-15:25

The impact of multiplex-western blotting: 15:25-16:30

Tips for best practice: 16:30-18:10

The future of western blotting: 18:10-20:30

Yearning for automation: 20:30-21:30

In this episode, we take a look at one of the key steps of infectious disease research, sample collection; exploring the challenges associated with the step and the solutions available to improve infectious disease research around the globe.

Exploring the trials and tribulations of infectious disease sample collection with me is Stanislav Forman, Product Developer at Zymo Research (CA, USA). Stan explains the extreme environments in which sample collection often occurs; revealing the difficult transit and storage requirements – often involving cold chain logistics – that can derail infectious disease studies early on.

Find out how key solutions to these problems have been successfully workshopped with the US military and have even been used in work with NASA to conduct safe sample collection in space. And discover just how successful these solutions can be when faced with the blazing wreckage of a transit vehicle…

Contents

Introductions: 00:00-01:20Key challenges of sample collection for infectious disease research: 01:20-02:30Additional challenges presented by COVID-19: 02:30-05:00The emergence of at-home testing: 05:00-07:00Established practices for sample collection and introducing DNA/RNA shield: 07:00-09:00Protecting DNA/RNA samples: 09:00-11:00Working with NASA on sample collection and protection in space: 11:00-14:20Protecting samples in a blazing transit van: 14:20-15:25The impact of inactivating and preserving sample collection products on infectious disease research: 15:30-16:30Areas for improvement in sample collection: 16:30-17:30Closing statements: 17:30-19:20

Explore the realm of epigenetics and gene expression, discovering the different omic ‘lenses’ used to examine these processes and the power of single-cell studies to reveal provide a comprehensive multiomic view of cells and their biology.  

This episode features the ever-buoyant Will Greenleaf, Associate Professor of Genetics at Stanford University School of Medicine (CA, USA) and head of the Greenleaf Lab. Will takes us through his lab’s work, detailing his attempts to understand the compacting of DNA into cell nuclei and how this impacts gene expression and epigenetic regulation.

Discover the emerging new research focus that Will has coined the “Regulome” – the collection of physical molecular components that control gene expression through factors such as chromatin accessibility.

To explore these new frontiers Will often encounters questions with no technologies available to ask them. So what does he do? Invent the technologies he needs! Find out how his lab came to develop the, now widely used, ATAC-Seq and learn of the new tools that he is looking to develop to solve even more perceptive questions.

This episode has it all, and also reveals the potential of Will’s single-cell multiomic approaches in cancer research, virology and HIV.

Contents:

·      Introductions: 00:00-02:00

·      The exploring the physical genome: 02:00-03:15

·      Chromatin accessibility: 03:15-05:15

·      Introducing the ‘Regulome’: 05:15-07:15

·      The importance of multiomics for the study of gene expression: 07:15-07:55

·      DNA methylation and histone organization: 07:55-10:30

·      Real-world impact of this research:  10:30-12:30

·      Will’s varied career path: 12:30-16:15

·      Combining multiomic datasets with computational biology and physics experience: 16:15-18:40

·      Single-cell techniques: 18:40-21:50

·      Developing ATACC-Seq: 21:50-23:50

·      New tools in development: 23:50-27:30

·      Insights into the epigenetics of cancer: 27:30-29:35

·      Insights into virology and HIV latency: 29:35-32:10

·      One wish to help explore the regulome. 32:10-33:00

Cryopreservation of advanced therapy medicinal products: an interview with Brian Hawkins by Taylor & Francis Group

This episode, supported by Bethyl, delves into the realm of the tumor microenvironment (TME), exploring the cells that reside there and how they interact to promote tumor growth and metastasis. Discover how immune cells are attracted and manipulated by tumor cells enabling the cancer to invade neurons where they can then travel throughout the body.

Providing an expert's insight into this topic is Moran Amit, Assistant Professor at the MD Anderson Cancer Center (TX, USA). Moran exposes the nebulous interactions in the TME and describes the techniques that he uses to interrogate it, in the hope that by further understanding these interactions we will be able to design more successful, targeted therapies for neurotropic cancers.

Contents:

·      Introductions: 00:00-01:20

·      The key cells of the TME:  01:20-02:50

·      How cells of the TME  support the tumor: 02:50-05:45

·      How cancer cells influence and impact immune cells: 05:45-07:25

·      The invasion of cancers into the neurons: 07:27-9:45

·      Recruitment of neurons to the TME: 09:45-10:55

·      The evolution of neuron recruitment to the TME: 10:55-15:00

·      Techniques involved in the study of the TME: 15:00-17:00

·      Tips for best practice: 17:00-18:00

·      Tumors with neural networks: 18:00-20:05

·      Clinical impact of research: 20:05-21:50

·      The cancers impacted the most by this research: 21:50-23:25

·      The impact of neural invasion on patients and neurons: 23:25-25:30

·      One thing to improve our understanding of the TME: 25:30-28:00

Rare diseases present a series of challenges on numerous fronts. From simply deciphering what a patient is affected by to considering how best to manage a rare condition with limited pre-existing medications available for a rare disease, each new development or breakthrough brings clinicians to a new question. While these conditions are, in isolation, rare; in total rare diseases impact 25-30million people in the USA alone.

Supported by Psomagen and featuring four fascinating guests from across the spectrum of topics and focuses in the rare disease space, this episode explores the updates to whole-genome sequencing technology that have improved the "Diagnostic Oddysey" experienced by some patients, enabled more accurate drug development and provides insight into the diagnosis and characterization of undefined rare diseases, before exploring the clinical impact whole-genome sequencing can have on clinical outcomes.

This episode features insight from four field-leading experts in rare disease research, whole-genome sequencing technologies and clinical practice for patients with rare diseases, including:

Alan Beggs: Director of The Manton Center for Orphan Disease Research, Sir Edwin and Lady Manton Professor of Pediatrics at Harvard medical school Christine Stanley: Chief Director of Clinical Genomics at VariantyxDavid Dimmock: Senior Medical Director of Rady Children's Institute for Genomic MedicineTake Ogawa: Vice President, Sales & Marketing at Psomagen 

Contents

Introduction: 00:00-02:30Defining the Diagnostic Oddysey: 02:30-06:20Rare disease discovery: 06:20-09:20Techniques involved in Rare disease discovery: 09:20-12:05Whole-genome sequencing updates impacting clinical diagnosis: 12:05-18:30Currently required improvements in techniques for rare disease research and management: 18:30-24:10Explaining long-read and short-read sequencing: 24:10-26:00Developing therapeutics for rare diseases: 26:00-30:00Whole-genome sequencing in animal model validation: 30:00-31:20Improving access to whole-genome available to researchers and clinicians: 31:20-33:40Whole-genome sequencing improving management and outcomes for rare diseases: 33:40-38:27

In the Zone: phosphorylated biomarkers by Taylor & Francis Group

In this episode, we explore the often overlooked technique of environmental sequencing for infectious diseases and how it is being applied to the response to COVID-19. Taking the state of California and a case study of this application, I speak to Micheal Lisek, Project Manager Environmental Microbiomics at Zymo Research Corp.

Micheal outlines the basis of environmental sequencing, predominantly the screening of wastewater for signs of viral RNA, the key techniques involved in the process and challenges associated with it. Micheal also explains the key pieces of information that can be obtained by environmental sequencing and the benefits of the approach vs exclusively using clinical testing.

Micheal highlights the value of environmental sequencing for monitoring variants, understanding transmission patterns and identifying outbreaks, providing examples of the information provided to the public health officials in California that were used to successfully manage rising infections and limit the impact of a surge in cases.

Contents

Introduction: 00:00-01:58Introducing environmental surveillance for infectious diseases: 01:58-03:30COVID-19 response vs previous environmental sequencing work and how it has prepared people for COVID-19: 03:30-06:18The benefits of wastewater screening over clinical testing: 06:18-07:10Challenges of wastewater testing: 07:10-09:10Monitoring for SARS-CoV-2 variants: 09:10-10:55Understanding transmission patterns: 10:55-12:00Identifying signs of viral vaccine escape and tracing transmission: 12:00-14:50PCR vs NGS techniques for environmental sequencing: 14:50-16:05Tips for best practice when conducting environmental sequencing: 16:05-17:50Practical results of environmental sequencing data on outbreak suppression: 17:50-20:40Investigating mutation rates in the environmental samples: 20:40-23:20Emerging techniques in wastewater surveillance: 23:20-25:10Developing standard protocols and structure for wastewater surveillance: 25:10-28:20

In this podcast, Tristan Free – Digital Editor at RegMedNet – speaks to Abbie Underhill (Scientific Bioprocessing) about the role that sensors have in regenerative medicine, including the biggest challenges behind implementing sensors in cell culture systems.