-
The review is out now
Settling the score: variant prioritization and Mendelian disease Karen Eilbeck, Aaron Quinlan & Mark Yandell Nature Reviews Genetics (2017) doi:10.1038/nrg.2017.52 Published online 14 August 2017 Abstract: When investigating Mendelian disease using exome or genome sequencing, distinguishing disease-causing genetic variants from the multitude of candidate variants is a complex, multidimensional task. Many prioritization tools and online interpretation resources exist, and professional organizations have offered clinical guidelines for review and return of prioritization results. In this Review, we describe the strengths and weaknesses of widely used computational approaches, explain their roles in the diagnostic and discovery process and discuss how they can inform (and misinform)…
-
Lots of Updates
DECART: DATA SCIENCE FOR THE HEALTH SCIENCES July 10-12, 2017 (The python at the end of the galaxy (A play on the restaurant at the end of the universe) Galaxy is an open source, web-based platform for data intensive biomedical research. Thousands of bioinformatics tools have been imported into this graphical user interface. This tool enables biomedical informatics exploration and the building and sharing of reusable workflows. Ipython notebooks are now an integral part of galaxy. Dissertation award entry Recently graduated doctoral students who have published a dissertation may apply for the CGS/ProQuest Distinguished Dissertation Award, which recognizes excellence in dissertation writing. For…
-
Academy of health sciences and other things
As part of my continued interest in the educational needs of the health science community for bioinformatics resources, I have joined the Academy of Health Science Educators at the School of Medicine. MissionThe Academy of Health Science Educators (AHSE) is designed to advance state-of-the-art education at the University of Utah through teaching, research, mentorship and service. The Academy serves as a home for health science educators and a community that advocates for excellence in health science education. Academy AimsThe specific aims of the academy are to: TRIG (Translational Informatics Interest Group) I have also been leading the TRIG – A biomedical…
-
Compute resources for teaching
We (Amy Sheide and myself) were awarded funds to host our Hands-on Bioinformatics Experience teaching material on XSEDE. This is a huge bonus for us and will enable us to develop our Galaxy based teaching material in a friendly environment. Many thanks to the XSEDE Resource Allocations Service. This resource complements our previous funding to update the foundations of bioinformatics course and will facilitate the practice of bioinformatics by our new students.
-
biocuration conference 2017
Nicole Ruiz will be presenting a poster: hgvs-eval: automated evaluation suite to assess HGVS-formatting tools at the biocuration conference at the end of the month. This work is part of a GA4GH initiative. We are grateful to have received a travel fellowship from the conference organizers. The ClinGen clinical domain working group for inborn errors of metabolism will also be presenting: Creation and Implementation of Variant Curation Workflow for the ClinGen Inborn Errors in Metabolism Working Group: Phenylalanine Hydroxylase Deficiency
-
VMC workshop
I attended a productive 2 day GA4GH Variation Modeling Collaboration workshop in Cambridge, to continue development of the model and preliminary spec for the sharing of variation from simple variants to haplotypes and genotypes. The mission of the Variation Modeling Collaboration is to enable organizations to reliably share information associated with variation in biological sequences. Instead of sharing a photo of a conference room white boards, here is a pre-meeting photo of Boston. https://www.instagram.com/p/BMgqIKcD064
-
Teaching grant and galaxy workshop
In late October I was awarded a teaching grant from the University of Utah Teaching Committee, to incorporate the use of Galaxy into the teaching of bioinformatics in the department. Galaxy is an online framework that embeds bioinformatics tools into a user friendly interface. It also enables the sharing of work flows. This will enable students to participate in more hands on activities and explore real data. As we have students entering the department from many backgrounds and disciplines, it can be difficult difficult to hit the right balance. Galaxy will enable the students to gain confidence in by practicing what they…
-
Shale defended thesis
Shale Dames successfully defended his thesis: Development of a Clinical Next generation Sequencing Assay for Mitochondrial Disorders on Wednesday. He described several years of work developing and testing an NGS pipeline for a clinical mitochondrial disorder panel. He touched many pertinent points such as selecting the nuclear genes implicated in mitochondrial disease and issues related to heteroplasmy. Many thanks to the committee for their feedback: Rong Mao, Ram Gouripeddi, Younghee Lee and Robert Schlaberg.
-
GA4GH Variant Modeling Collaboration
I have been virtually attending the GA4GH Variant Modeling Collaboration meeting in Boston, bringing together ClinGen, GA4GH, HL7, FHIR, NCBI and others to find agreement on how we model sequence variation. The Sequence Ontology plays a role here given its history and usage in genomic annotation and variant annotation tools. The outcomes of this group will hopefully be agreed upon terminology, use cases and a shared model.
-
Taxonomer update
The manuscript describing Taxonomer is finally out in Genome Biology:Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling The paper has been picked up by various media outlets including the Deseret News, and KEUR radio. The tool is available here through the iobio platform and here through IDbyDNA’s public interface.