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Archive - Oct 30, 2018

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GangSTR—New Algorithm Applied to Genome-Wide Genotyping of Short Tandem Repeat (STR) Expansions, Such As Those Implicated in Huntington’s Disease, Fragile X Syndrome, & Myotonic Dystrophy

(BY SALLY G. PASION, PhD, Associate Professor of Biology, San Francisco State University). On October 18, at the 2018 American Society for Human Genetics (ASHG) Annual Meeting in San Diego, California (http://www.ashg.org/2018meeting/) (October 16-20), software engineer Nima Mousavi, PhD (@nmmsv), in the Electrical and Computer Engineering Department, University of California San Diego (UCSD), in the laboratory of Dr. Melissa Gymrek (https://gymreklab.github.io/), highlighted GangSTR, a novel algorithm for genome-wide profiling of both normal and expanded tandem repeats (TRs). GangSTR provides a new way to identify short tandem repeats (STRs) from next-generation sequencing (NGS) data. STRs are 1-6 base-pair (bp) sequences, repeated in tandem in the genome. Dr. Mousavi’s presentation was one of six that were delivered in a late-morning meeting session (#51) titled ““What Are We Missing? Identification of Previously Underappreciated Mendelian Variants.” The session is described at the following link: http://www.ashg.org/2018meeting/listing/NumberedSessions.shtml#sess51. Dr. Mousavi’s presentation (#188) was titled “GangSTR: Genome-Wide Genotyping Short Tandem Repeat Expansions” (https://eventpilot.us/web/page.php?page=IntHtml&project=ASHG18&id=180122313). STRs exhibit a higher mutation rate compared to insertion-deletions (indels) or single nucleotide polymorphisms (SNPs). Three percent of the human genome contains STRs, and the presence of the repeats may affect the coding region and thus the protein sequence, or it may occur in the non-coding region and affect gene expression. There are STRs that are implicated in trinucleotide repeat diseases such as Huntington’s disease (HD), fragile X syndrome, Friedreich ataxia, spinocerebellar ataxia, and myotonic dystrophy.

From Pond Hockey to Top of Scientific World--U Minnesota Honors Distinguished Alumnus, World-Class Immunologist Dr. Ronald Faanes

On October 11, 2018, the University of Minnesota College of Biological Sciences (CBS) honored one of its own—eminent immunologist Ronald Faanes, PhD—at the College’s annual Recognition and Appreciation Dinner at Memorial Hall in the McNamara Alumni Center. Dr. Faanes, who received his BS (chemistry) and PhD (microbiology) from U Minnesota, was the keynote speaker at this year’s dinner, which drew a crowd of 300 donors, faculty, and student scholarship winners. Ron was introduced by CBS Dean Dr. Valery Forbes (https://cbs.umn.edu/contacts/valery-forbes), who noted that as a pupil and mentee of longtime CBS faculty member Dr. Palmer Rogers, “Ron brings a wealth of insight, and some really great stories, about the revered scientist and teacher for whom the Palmer Rogers Microbiology Scholar ship is named.” Some of Dr. Rogers family were in the audience and they could not help being moved by the poignant memories of Palmer that Ron would recount in his address. Ron, who had also played hockey for the Gophers, had moved on from U Minnesota to work first as a tumor immunologist at the Sloan-Kettering Institute, the research arm of the renowned Memorial Sloan Kettering Cancer Center, in New York. Legendary U Minnesota physician/scientist Dr. Robert Good, who had led the team that performed the world’s first successful human bone marrow transplant between persons who were not identical twins and is regarded as a founder of modern immunology, had just been named Director of Sloan-Kettering and he brought many of his best scientists, including Ron, along with him to New York.