Illumina Genomics Podcast

In this episode, Theral Timpson dives into the burgeoning field of multiomics and its massive data challenges with a veteran of digital pathology, Joachim Schmid. Schmid was recently appointed as vice president of multiomics data solutions at Illumina. Schmid discusses how sequencing costs are plummeting, leading to an explosion in multiomics applications. Yet, with all the data being generated, biologists often lack the computational background to make sense of it. Schmid highlights Illumina's acquisition of Partek, a company that has been developing multiomics data analysis tools, and he emphasizes that empowering researchers with accessible analysis tools is crucial to advancing the field. AI is poised to play a key role in moving multiomics forward. Schmid discusses both the opportunities and limitations of AI, noting that while AI can streamline data processing, there are still areas for improvement, particularly in developing more intuitive and user-friendly tools for biologists. He shares some exciting applications of multiomics in personalized medicine and cancer research.

In this episode of the Illumina Genomics Podcast Illumina’s Amadou Gueye, Marketing Lead for the Middle East & Africa speaks to Professor Martin Nyaga, Head of the Next Generation Sequencing (NGS) Unit at the School of Biomedical Sciences at the University of the Free State. This interview takes a close look at how NGS is revolutionizing public health in Africa and how genomics has been a game-changer in identifying, tackling and tracking associated disease outbreaks. Hear as Professor Nyaga explains the impact of infectious diseases in Africa and how his establishment of the NGS Unit at the University of the Free State is supporting advanced research in genomics and address pressing public health challenges in South Africa. Learn more about how he and his team implemented their NGS lab from scratch, with key considerations for others looking to expand in-lab NGS capacity.

In this podcast, Mendelspod’s Theral Timpson is joined by Sam Strom, a principal scientist at Illumina with a background in clinical testing. In this interview, Sam addresses two of the big challenges in clinical sequencing, which are variant calling and variant interpretation. Sam says Illumina has created its own multi-sample genomic reference and is also making use of artificial intelligence to improve variant calling. He also shares how Illumina supports scaling variant interpretation for genomes and other assays with an AI and automation comprehensive solution, enabling high-quality genetic testing workflows to reach next level accessibility.

In this podcast, Mendelspod’s Theral Timpson speaks to Kyle Farh, VP and distinguished scientist leading Illumina’s Artificial Intelligence Lab. Farh says the company began the AI lab seven years ago when deep learning was just taking off. Two of the team’s AI algorithms, PrimateAI-3D and SpliceAI, published in Cell and Nature Genetics, were among the first examples of deep learning algorithms in genomics. This interview takes a close look at Illumina’s activities in AI and delves into the long-term impact of AI on genomics.

In this podcast, Mendelspod’s Theral Timpson speaks to Cara Statz from JAX and Erica Schnettler from Illumina about how their combined technologies are helping researchers and oncologists deal with the increasing complexity of cancer genomic data. They discuss oncologists' experience dealing with an overwhelming amount of new scientific data, and both guests give their advice for new labs setting up cancer testing and oncology clinical research.

Rachel E. Sanborn, MD, presents the journey of a patient diagnosed with atypical carcinoid with brain metastases who benefited from the detection of a KIF5B-RET fusion by comprehensive genomic profiling. Rachel E. Sanborn, MD is the medical director of the Thoracic Oncology and Phase I Clinical Trials Programs at the Earle A. Chiles Research Institute at Providence Cancer Institute.

Jeanne Tie, MD, discusses the DYNAMIC trial and areas of unmet needs for minimal residual disease (MRD) to become the standard of care for patients with colorectal cancer. The DYNAMIC trial showed that a ctDNA-guided approach reduces the use of adjuvant treatment in patients with stage II colon cancer without compromising their clinical outcome. Jeanne Tie is a medical oncologist and professor at Peter MacCallum Cancer Centre.

Atocha Romero, PharmD, PhD, explains the value of liquid biopsy-based comprehensive genomic profiling. Dr. Romero provides an overview of the results of the NADIM II clinical trials and discusses ctDNA testing to monitor disease and guide treatment. Atocha Romero, PharmD, PhD, is the director of the Liquid Biopsy Laboratory of the Medical Oncology Department at the Hospital Universitario Puerta de Hierro in Madrid, Spain.

Pashtoon Kasi, MD, MS, explains how liquid biopsy next-generation sequencing (NGS)-based testing can benefit cancer patients. Dr. Kasi presents four colorectal cancer patient cases for whom comprehensive genomic profiling (CGP) was done via liquid biopsy and results for clinically-relevant biomarkers were obtained in 7-8 days.

Listen to Genetic Counsellors Katie Ellis and Patricia Winters, Illumina discuss how more resource-efficient counselling methods are needed to support patient informed consent for genetic testing during pregnancy. They discuss the resources available for healthcare providers and expectant parents that allows them to make informed decisions.

Vivek Subbiah, MD, explains how patients with rare and common tumors can benefit from next generation sequencing (NGS)-based testing for NTRK gene fusions. He presents the case of a patient who benefited from precision medicine based on the detection of a NTRK1 fusion by comprehensive genomic profiling.

Isabelle Ray-Coquard, MD, PhD, explains how comprehensive genomic profiling (CGP) simultaneously provides HRD and BRCA status in ovarian cancer patients. She presents the case of a patient who benefited from CGP testing for these biomarkers and shares the recent findings of the PAOLA-1 trial.

Dr. Ronald Leopold discusses implementation of pharmacogenomic screening in the healthcare industry. The conversation explores barriers to pharmacogenomic (PGx) program adoption, the future of precision medicine, and a paradigm shift away from reimbursement to value-based healthcare.

Why does a medication effectively “cure” one patient while having little to no effect, or worse, an adverse effect, on another? The answer may be found in our genome. Pharmacogenomics research aims to understand how genetic variations affect responses to medications, and can provide vital information for physicians as they choose a therapy regimen and prescribe dosage. Dr. Howard McLeod shares his thoughts on pharmacogenomics and the future of precision medicine.

Robert Schlaberg and Lauge Farnaes from IdByDNA join us to talk about the evolution of metagenomics technology. The is the second half of their interview, where the focus shifts towards the application of metagenomics in facing the threat of emerging pathogens

Robert Schlaberg and Lauge Farnaes from IdByDNA join us in a two-part interview to talk about the evolution of metagenomics technology. In the first part of this interview, the discussion focuses on the application of metagenomics on infectious diseases in the clinical realm.

Christopher Mason from Weill Cornell Medicine discusses his multifaceted approach to the urgent need for testing when the COVID-19 pandemic broke out in early 2020. Chris also discusses finding from a paper that was published in Nature Communications this year, entitled “Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions.” (https://www.nature.com/articles/s41467-021-21361-7).

Although Africa is the continent with the highest amount of genetic diversity, it is underrepresented in global genomic databases. H3Africa is one of several initiatives, founded in 2010, that responded to the challenge of narrowing this gap. To discuss their efforts at H3Africa, we are joined by Zané Lombard Professor at the University of the Witwatersrand in Johannesburg, South Africa, and Neil Hanchard at the Baylor College of Medicine in Houston, TX.

Although most developmental genes are silenced in adult somatic cells, some can be reactivated in cancer cells and promote tumor growth. Listen to Dr. Guo-Liang Chew of the Cancer Science Institute of Singapore discuss the discovery of a novel role for developmental genes in regulating the immune response to cancer.

Whole genome sequencing can help diagnose genetic diseases in days and holds the promise of helping parents avoid months or years of inconclusive tests. Listen to Dr. Vandana Shashi of Duke University and Kimberly LeBlanc of the Undiagnosed Diseases Network and learn how whole genome sequencing can short-circuit the diagnostic odyssey for patients with rare diseases.

Whole genome sequencing has the potential to supplant the traditional stepwise approach to genetic testing, but standard laboratory guidelines and clinical best practices are critical for implementing the technology. Listen to Dr. Christian Marshall of The Hospital for Sick Children explain how laboratory and clinical best practices can help enable whole genome sequencing for diagnosing genetic diseases.

Genetic diseases are the leading cause of death among infants that are hospitalized in intensive care, and an estimated four percent of newborns in North America may be affected. Listen to Dr. Shimul Chowdhury, of Rady Children's Institute for Genomic Medicine, explain how rapid whole genome sequencing can help pinpoint the causes of rare diseases in children.

Behavioral medicine holds the promise of helping scientists better understand how genomics outputs impact on individuals and their lives. Listen to Professor Catharine Wang of Boston University explain her research on how individuals adopt new health technologies, including genomics and molecular diagnostics.

Invertebrates make up 95% of all animal species. They’ve been around for hundreds of millions of years and help to maintain the health of our planet. Listen to Professor Gonzalo Giribet of Harvard College and the Harvard Museum of Comparative Zoology explain how genomic and morphological data from living and extinct animals is helping scientists to better understand invertebrate evolution and diversity.

Structural variants are relatively large changes in DNA sequence across the genome, and they play a significant role in human disease. Listen to Dr. Michael Talkowski of Massachusetts General Hospital and Harvard Medical School explain how genomics is helping us to understand the biology of DNA structural variation and its impact on human developmental and psychiatric disorders.

According to the California Healthcare Institute, up to 10% of the population may be affected by a rare disease. But because each individual disease is rare, it can be challenging for health care professionals to correctly diagnose and treat them. Listen to Dr. Christine Stanley of Variantyx explain how whole genome sequencing can impact on the understanding and diagnosis of rare genetic disorders.

According to the CDC, up to 40% of adults in the United States are obese. Diet and exercise play critical roles in obesity and in our general health, but what is the best diet; and, is that diet best for everyone? Listen to Dr. José M. Ordovás of Tufts University discuss nutrigenomics, the study of how our genomes impact on our nutrition and health.

Targeted drug discovery has traditionally focused on inhibiting or modulating the function of abnormal proteins. But many more diseases could potentially be treated by controlling the expression of abnormal and normal genes. Listen to Dr. Eric R. Olson of Syros Pharmaceuticals explain how epigenomics is enabling a paradigm shift in drug discovery.

In 2019, NGS continued to enable scientists to make great strides in understanding human biology and disease. In this special compilation episode, I’ll share some of our 2019 podcast highlights. We’ll also share our expert guests’ predictions for science, medicine, and genomics – where we were in 2019, and where we’re going in 2020 and beyond.

NGS-based genomics assays can help characterize the genetic profile of a tumor, and these technologies are poised to supplant single-gene testing in oncology. But, what impact will this revolutionary technology have on patients, clinicians, and the entire healthcare system? Listen to Dr. Brian Piening of the Providence Cancer Institute explain how NGS is changing the standard of care in oncology.

Understanding the mutational profile of a tumor can help to guide therapeutic options. Genomics has enabled the simultaneous analysis of multiple mutations across multiple genes, providing a comprehensive genomic profile of a given tumor. Listen to Dr. Rachel Sanborn of the Providence Cancer Institute explain how genomics technologies are empowering precision oncology.

Agriculture has sustained and enhanced human life for thousands of years, but a changing environment and expanding population is increasing demand for more productive and more sustainable farming. Listen to Dr. Andrzej Kilian of Diversity Arrays Technology describe how NGS-based genotyping is helping to develop more sustainable agriculture practices.

Cancer is one of the leading causes of death around the world, and 38% people will be diagnosed with cancer at some point in their lives. Listen to Dr. Ramanuj DasGupta and Dr. Shumei Chia of the Genome Institute of Singapore describe how patient-derived tumor models and NGS can combine to offer new insights in precision oncology.

Sepsis is a serious medical condition typically caused by a bloodstream infection. The World Health Organization estimates that sepsis affects 30 million people worldwide every year, leading to 6 million deaths. Listen to Jean-François Brepson of PathoQuest discuss the challenges in infectious disease diagnostics and how NGS technology can improve pathogen detection and antibiotic stewardship.

To ensure global scientific benefit from genomics, we need a better understanding of human genetic diversity, yet some communities remain underrepresented in genetics studies. Listen to Professor Simon Easteal of the Australian National University explain how studying DNA in collaboration with Indigenous Australian communities can improve the health and well-being of Australia's First Peoples.

The average risk of miscarriage in a healthy woman is 10-25%, and risk increases with increasing maternal age. In vitro fertilization (IVF) is a set of technologies that can be used to overcome female or male infertility. Listen to Dr. Mark Bowman of Genea explain the science and technology behind IVF, and how next-generation sequencing can improve IVF through preimplantation genetic testing.

Genetic carrier screening is used to identify recessive mutations linked to genetic disorders. It can be performed for women and men who want to know if their future children might be at risk for genetic diseases. Listen to Zoe Milgrom of Eugene Labs discuss the technology and genetic counseling behind carrier screening.

The epigenome is the chemicals and proteins that bind DNA and regulate gene expression. Gene regulation, also called epigenetics, is critical for diseases like cancer. Dr. Susan Clark is Research Director of Genomics at the Garvan Institute of Medical Research. She’s an expert in the genomics of DNA methylation, and she joins me to discuss the role of epigenetics in human biology and cancer.

Tigers are apex predators in the wild and vital to maintaining biodiversity, but fewer than 3,000 tigers remain in areas of southeast Asia. Dr. Dibesh Karamcharya is Executive Director of the Center for Molecular Dynamics Nepal, and he joins me to explain how the Nepal Tiger Genome Project is helping scientists to better understand these amazing animals and to aid in their conservation.

Parents of children who suffer from a rare disease can sometimes find it difficult to find a diagnosis, sometimes spending years living in a diagnostic limbo land. Heather Renton is the executive officer of Syndromes Without A Name (SWAN) Australia, and she joined me to discuss her daughter’s rare disease and the impact of NGS-based testing on her and her family.

The immune system is skilled at determining friend from foe. But, our immune systems can sometimes turn against us, leading to autoimmune disease. Dr. Carola Vinuesa is Professor of Immunology at the Australian National University, and she joins me to discuss how NGS can unravel the complex interaction of cells and molecules that regulate antibody response and autoimmunity.

NGS-based single cell genomics techniques can characterize the genetic material of millions of individual cells isolated from bulk tissues. These techniques have revolutionized our understanding of the type and nature of cells that exist in our bodies. Dr. Shalin Naik of the Walter and Eliza Hall Institute of Medical Research joined me to discuss his use of single cell omics to understand the immune system.

Neglected tropical diseases primarily impact the world’s poor, and more than 1 billion people currently suffer from one of these neglected diseases. Professor Warwick Grant of La Trobe University joined me to discuss how genomics is being used to maximize the impact of treatment for river blindness, a neglected disease that affects as many as 35 million people in Africa.

Rare diseases affect millions of people around the world. Dr. Matt Might is Professor and Director of the Hugh Kaul Precision Medicine Institute at the University of Alabama Birmingham. His son, Bertrand, was the first person to be diagnosed with NGLY1 deficiency, an ultra-rare disorder. Matt joined me to discuss Bertrand’s diagnostic odyssey and the impact of genomics on rare disease research.

At the recent European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) conference, I talked with microbiology experts employing next-generation sequencing (NGS) in clinical microbiology. Dr. Agathe Jouet of Genoscreen and Dr. Christophe Rodriguez of University Hospital Henri-Mondor joined me to discuss amplicon and shotgun sequencing to help diagnose infectious diseases.

An average risk woman in the US has about a 1 in 8 chance of developing breast cancer. Breast tumors are genetically heterogeneous and can be classified into subtypes based on patterns of gene expression, DNA methylation, nucleotide substitutions and genomic rearrangements. Dr. Åke Borg is Professor of Oncology and Pathology at Lund University, and he joined me to discuss the genetics of breast cancer.

Science, technology, engineering, and math (STEM) industries need creative and innovative employees now and into the future. Randy Schregardus is Student Programs Manager at the Van Andel Education Institute (vaei.vai.org), and he joined me to discuss advances in K-12 science education, the next generation science standards, and innovative science education programs at VAEI.

Who am I, and where do I come from? We’re all interested in these fundamental human questions. Recently, genomic analysis of ancient human DNA has refined our understanding of human history and biology. Dr. Eske Willerslev of the Universities of Cambridge and Copenhagen joins me for a fascinating discussion about ancient DNA, human biology, and human history.

We all start life as a single egg cell, but after fertilization we grow into a large organism containing about 40 trillion diverse and specialized cells. Embryogenesis is the developmental process by which an embryo forms and develops, and it’s enabled by stem cells. Dr. Amy Ralston of Michigan State University joins me to talk about genomics, stem cells, and embryogenesis.

Metabolic changes in immune cells can alter immune system biology. So, understanding how immune cells get energy is important for understanding immune. Drs. Connie Krawczyk and Rusty Jones of the Van Andel Research Institute (vari.vai.org) talk about omics technologies for studying immunometabolism. To learn more about the Metabolic and Nutritional Programming team visit russelljoneslab.vai.org.