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more USTAR media
The USTAR Genetic Discovery Program is has been in the media lately: The Scope: Using Computer Logic to Diagnose Rare Diseases Apr 15, 2014It’s impossible to treat a patient effectively without knowing what’s wrong. Published this month in the American Journal for Human Genetics, computational biologist Dr. Mark Yandell reports a novel method for diagnosing the toughest inherited diseases. Inspired by “Watson,” the computer that won first place on the quiz show Jeopardy, he explains why the approach may soon become a fixture in clinics. Episode Transcript Announcer: Examining the latest research and telling you about the latest breakthroughs, the…
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Reed Gardner Faculty Excellence Award
At the annual BMI awards on Friday I was shocked to win the Reed Gardner award. This is a student driven endeavor and means a lot to me. Link to photo, with the student committee Bob, Jeff, Jingran and Begum.
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SnpEff and SO
We (mostly Nicole) have been quietly working with Pablo Cingolani and Uma Devi Paila on mapping the SnpEff variant effect terms to SO and adding new terms where we were missing concepts. SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). The latest release, 3.6 is fully compatible with SO. These mappings are also available in SO as synonyms.
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CSHL Biology of Genomes
Our abstract The Utah Genome Project has been accepted for a talk at the Biology of Genomes meeting in CSHL, May 6-10th 2014. Mark Yandell will present. The Utah Genome Project (UGP) is an intramural, multi-million dollar effort to improve patient care, and facilitate research into undiagnosed diseases. Unlike the other large-scale sequencing projects currently underway in the US and the UK, the UGP is a pedigree-based sequencing effort, and is centered on the Utah Population Database (UPDB), the world’s largest resource for tracking diseases in families. The UGP’s analysis pipeline features a number of novel tools that enable integrated…
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A few new papers
It seems like years ago since we put together a three site team to participate in the Clarity Challenge. This contest was an incredible learning experience. We just heard that the manuscript detailing this giant effort in clinical genetic analysis has been accepted by Genome Biology: An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. The paper is available here. We also had news yesterday that the Phevor manuscript is in press at the AJMG. This manuscript describes the Phevor tool that combines the output of variant prioritization tools…
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Annotation Jamboree
My lab, in collaboration with the Yandell lab (Human Genetics) will be hosting a cancer themed annotation jamboree next week (Spring Break). Monday March 10 from 3-5pm Tuesday March 11 from 12-3pm Wednesday March 12 from 12-5 pm There will be pizza. Computer lab, office suite 140, Building 421. See you there.
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USTAR Genetic Discovery Program
The USTAR Genetic Discovery Program, an initiative within the University of Utah has announced the first hire: Gabor Marth. I am pleased to Welcome Gabor to Utah, and look forward to working with him as part of the Genetic Discovery Program. I have know Gabor since I moved to the US – and currently we are working together on the CDC’s clinical variant file working group and we have a joint R01 proposal pending.
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2014 Public Health Informatics Conference
We have had our session titled “RCKMS: Delivering Reporting Specifications in the New World!” selected for presentation at the 2014 Public Health Informatics Conference, which will be held April 29-May 1, 2014, at the Westin Peachtree Plaza Hotel in downtown Atlanta, Georgia. Looking forward to the 90 minute learning session with Catherine Staes, Shu McGarvey and others.
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Conference Posters in the next week or so
Jeff Duncan from the Staes lab is presenting a poster at AMIA next week: Using KAoS Ontologies to Model Policy Requirements for a Statewide Master Person Index Jeffrey Duncan, MS, Stephen Clyde, PhD, Scott P. Narus, MD, Leslie Lenert, MD,Karen Eilbeck, PhD, Catherine Staes, BSN, MPH, PhD