Illumina Genomics Podcast

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.

Our biggest environmental challenges ultimately relate to microbes, so studying microbes in nature is important for understanding the health of our planet. Dr. James Tiedje is Distinguished Professor and Director of the Center for Microbial Ecology at Michigan State University. He joins me to discuss the use of genomics to better understand microbial functions in their environment.

2018 was an awesome year for genomics and genomics research. In this special compilation episode, I’ll share some of our 2018 podcast highlights and future predictions for genomics – where we were in 2018, and where we’re going in 2019 and beyond.

Dr. Tõnu Esko is Deputy Director of Research at the Estonian Biobank of the University of Tartu. He joins me to talk about the Estonian Biobank and to explain how Estonia aims to create a national system to enable precision healthcare through genomic profiling.

Dr. Joshua Weiner is Professor of Biology at the University of Iowa and Associate Director of the Iowa Neuroscience Institute. His lab uses a wide range of molecular and cell biology techniques to study the brain. Josh is a cell biologist by training, but he joins me to share his experiences on recently incorporating next-generation sequencing, or NGS, to complement his cell biology work.

The CRISPR-Cas9 genome editing system is enabling scientists to make specific DNA changes in the genomes of plants and animals and has the potential to greatly impact our world. Dr. Sam Sternberg, Assistant Professor of Biochemistry and Molecular Biophysics at Columbia University, joins me to discuss the biology and impact of CRISPR and genome editing.

In noninvasive prenatal testing (NIPT), a maternal blood sample provides maternal DNA as well as DNA from the pregnancy to screen prenatal chromosomal abnormalities using next-generation sequencing, or NGS. Dr. Ronald J. Wapner, Vice Chair of Research in Obstetrics and Gynecology for Columbia University, joins me to share his perspective on prenatal screening and NIPT.

Long-term memories can last from minutes to a lifetime, and they are associated with changes in synaptic activity and formation of neuronal circuits in the brain. Dr. Ted Abel is Professor at the University of Iowa and Director of the Iowa Neuroscience Institute. Ted joins me to discuss the transcriptional and epigenetic changes that are also associated with long-term memory.

Sequencing a human genome requires 300 billion bases of DNA sequence, all of which need to be assembled – like a giant genomic jigsaw puzzle. Dr. Aleksey Zimin is Associate Research Scientist at Johns Hopkins University, and he joins me to discuss whole genome sequencing and assembly. He also discusses a novel method for creating phased genome assemblies.

Hereditary deafness is a relatively common disorder that affects about 1 in 1000 newborns. Dr. Richard J. Smith is Professor of Otolaryngology at the University of Iowa, and he joins me to discuss the genetic basis of deafness. He also discusses the development of genomic tools to aid in genetic testing of heritable forms of hearing loss.

Autism is a complex psychiatric disorder that affects 1 in 59 children in the United States. Dr. Jacob Michaelson is Associate Professor of Psychiatry at the University of Iowa and uses genomic and computational techniques to study autism and other psychiatric disorders. He joins me to discuss the genetics of autism and (sparkforautism.org).