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 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.

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 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.

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.

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.

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.

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.

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.

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.

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 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.

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

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.