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Thursday, November 3, 2016

Reference Genomes Should Reflect Population Diversity: An Interview with Valerie Schneider

In a recent Mendelspod interview, host Theral Timpson talked with Valerie Schneider of the National Center for Biotechnology Information about the work of the Genome Reference Consortium (GRC) to bring more ethnic diversity to the latest human reference assembly (GRCh38). Describing the reference genome as something like a Rosetta Stone for scientists working with genomic data, Schneider says it is “really the central piece of data upon which most genomics-based analyses are done, [serving as] the coordinate system for annotations ranging from genes to repeats to epigenomic markers.” As the importance of increasing the representation of population diversity in this…

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Thursday, March 24, 2016

CSHL Scientists Discuss Long-Read Sequencing for More Contiguous Assemblies and Complex Genomes

Much like the “sharpen” tool in Photoshop brings a picture into tighter focus and enhances the fine detail, long-read sequencing offers enhanced resolution of genomic information, according to Cold Spring Harbor Laboratory colleagues Mike Schatz and Maria Nattestad. The scientists spoke with Mendelspod’s Theral Timpson about how long-read sequencing is advancing their research in unique and powerful ways; a brief recap of their conversation follows. Schatz uses PacBio sequencing to establish incredibly accurate assemblies of microbial, crop, animal, and human genomes. Indeed, SMRT technology has significantly improved his work on the flatworm Macrostomum lignano, an organism with regenerative powers. With…

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Tuesday, February 23, 2016

15th Anniversary of the Human Genome Publication; A Conversation with Mike Hunkapiller

This month serves as the 15th anniversary of the first publication of the human genome by both public and private efforts. PacBio CEO Mike Hunkapiller was a central player in both efforts as the leader of Applied Biosystems, the company that developed and supplied the automated Sanger-based sequencing technology that made the projects possible. In honor of the occasion, Mendelspod host Theral Timpson asked Mike to join him in a commemorative conversation to discuss his memories of the project, as well as how genome sequencing technology has developed since. Mike talked about what was happening behind the scenes of these…

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Thursday, January 21, 2016

From Genetic Diagnosis to a Career in Genomics Research: An Interview with Jim Lupski

For Jim Lupski, his long-standing interest in the field of genomics is both personal and professional. His personal interest dates from his teenage years, when he was diagnosed with a rare genetic disease called Charcot-Marie-Tooth (CMT) neuropathy. As a clinician and scientist, he made it his mission to find the genetic basis of CMT, and in 1991 published his discovery of the CMT1A duplication, pioneering the field of structural variation and particularly copy number variation. Today he is a practicing pediatrician and a professor of molecular and human genetics at Baylor College of Medicine, where he is the Principal Investigator…

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Monday, November 9, 2015

Steven Marsh from Anthony Nolan Discusses the Past and Future of Donor Matching

Mendelspod host Theral Timpson recently interviewed Professor Steven Marsh, Director of Bioinformatics at the Anthony Nolan Research Institute, a UK-based organization dedicated to improving the outcomes of bone marrow transplantation and host to the world’s first bone marrow registry. Prof. Marsh and his team have dramatically improved the resolution of HLA typing — one of the methods used for matching compatible donors with transplant recipients — using long, accurate reads from PacBio sequencing. Their fascinating conversation covers the past, present, and future of HLA typing — highlights are below. Short History of HLA Typing — There’s a Lot More Diversity…

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