Dan Geraghty, a researcher at Fred Hutchinson Cancer Research Center and CEO of Scisco Genetics, has spent much of his career focused on the genetics of immune response. Recently he talked to Mendelspod host Theral Timpson as part of a series of podcasts on the rise of long-read sequencing.
Genomics luminary Mike Snyder, Profesor and Chair of the Genetics Department at Stanford University and Director of the Stanford Center for Genomics and Personalized Medicine, has been making strides in gene expression studies for years. His latest advance: analyzing whole human transcriptomes, which he calls personal transcriptomes, to better understand gene activity in an individual. Snyder says this approach could one day become a crucial element in clinical care. Dr. Snyder has published recent papers in Nature Biotechnology and PNAS using Single Molecule, Real- Time (SMRT) Sequencing for transcriptome analysis and demonstrated that long reads enable full coverage of RNA molecules. Recently he talked…
In an interview with Theral Timpson — part of Mendelspod’s series on long-read sequencing — Ulf Gyllensten, a professor in Medical Molecular Genetics at Uppsala University, spoke about using PacBio technology for HLA typing, human genome studies, transcriptomics, and more.
To understand the genetic factors underlying health and disease and to address hidden heritability, scientists require a more comprehensive view of all the variations in the human genome. Single Molecule, Real-Time (SMRT) Sequencing delivers the read lengths, uniform coverage, and accuracy needed for accessing the complete size spectrum of sequence variant types — from single nucleotides to complex structural variants. PacBio’s long single-molecule reads also provide direct variant phasing information across full-length genes and chromosome haplotype blocks. With SMRT Sequencing, scientists gain new insight into the genetic basis of health and disease.
The study of genomics has revolutionized our understanding of science, but the field of transcriptomics grew with the need to explore the functional impacts of genetic variation. While different tissues in an organism may share the same genomic DNA, they can differ greatly in what regions are transcribed into RNA and in their patterns of RNA processing. By reviewing the history of transcriptomics, we can see the advantages of RNA sequencing using a full-length transcript approach become clearer.
Listen to Mendelspod’s podcast with PacBio CEO, Mike Hunkapiller, as he recounts his memories from the first human draft genome project 15 years ago.
Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project. “I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of this Mendelspod interview. “The great excitement of next generation sequencing—which is deserved—has…
Marc Salit is the leader of the Genome Scale Measurement Group at the National Institute of Standards and Technology or NIST. In this Mendelspod podcast, he explains how NIST played a pivotal, foundational role in enabling the ‘Century of Physics.’ Now Marc and NIST are looking for the right set of standards to enable the already-upon-us “Century of Biology.” The human reference genome is an example of a standard that Marc and his team are developing. Currently they are piloting what they call “Genome in a Bottle,” a physical reference standard to which all other human genomes can be measured.…
By 2050, there will be 9 billion people on the planet. What will they eat? This is the question that led Rod Wing, Director of the Arizona Genomics Institute, into the field of plant genomics. What has been accomplished so far in the mission to come up with some super green crops? And how does Rod see anti-GMO sentiment and the recent trend toward gluten free diets factoring in? After answering these questions, he dives into a discussion on which sequencing instruments he has used for plant work. Unsurprisingly, Rod prefers the PacBio long reads even though the cost is…
Jim Lupski is a professor at Baylor College of Medicine where he’s on the frontline of incorporating genomic research into everyday clinical practice. The story begins with Jim’s own genome, which is perhaps the most sequenced genome ever. Jim’s life as a leading genomic researcher has been driven in part for a strong personal reason. He has a rare genetic disease named after three researchers who first defined it, Charcot Marie Tooth Neuropathy. What began as a personal journey to uncover the source of his own disease led Jim to seminal work that launched the field of structural variation. Working…
One of the popular questions on the Mendelspod program is how those doing sequencing decide between the quality of PacBio’s long reads and the cheaper short read technology, such as that of Illumina or Thermo Fisher. Steve Marsh, the Director of Bioinformatics at the Anthony Nolan Research Institute in London, provides the most clear and dramatic answer yet: use the PacBio system exclusively. Established in 1974 by the mother of a boy with a rare blood disease, the Anthony Nolan Institute is a world leader in blood crossmatching and donor/patient registries. Steve and his team at the Institute have dramatically…
Dan Geraghty explains that while there have been decades’ worth of studies associating the genetics of the major histocompatibility complex (MHC), and the highly polymorphic HLA class 1 and 2 genes, we still haven’t found the key mutations for a variety of different autoimmune diseases such as type 1 diabetes, rheumatoid arthritis, multiple sclerosis, and others. Enormous amounts of linkage disequilibrium in these regions are one factor, as is getting information in phase, so larger stretches of sequence are needed. Recently Geraghty has begun using SMRT Technology with hopes of drilling down to the causal genetics.
Ulf Gyllensten speaks about advances in screening for HPV, his predictions for the widespread use of genome sequencing in the clinic, and applications using Single Molecule, Real-Time (SMRT) Sequencing for human genome studies.
From Mendelspod: Jonas Korlach is a natural storyteller—a rare trait in a scientist who is more comfortable presenting data than talking of himself. Jonas is the co-inventor of PacBio’s SMRT (single molecule, real time) sequencing, and we wanted to hear from him directly how it all got started, and also when the team realized that they had something big with long reads and close to 100X coverage. How many of us can boast of hitting it out of the park on our first try?
The Mike Schatz lab at Cold Spring Harbor is well know for de novo genome assemblies and their work on structural variation in cancer genomes. In this Mendelspod podcast, lab leader, Mike Schatz, and doctorate student, Maria Nattestad tell of two new projects that include the de novo assembly of a very difficult but important flatworm genome and, secondly, making better variant calls for oncogenes such as HER2.