Resource Spotlight: Ingenuity Variant Analysis
Welcome to Resource Spotlight! The Cushing/Whitney Medical Library provides access to an incredible array of databases, e-book collections, software and more. In this series of posts, we’ll be showcasing highlights from our collection.
In this edition of Resource Spotlight, we’ll be looking at Ingenuity Variant Analysis (IVA). IVA is a web-based tool that combines analytical tools and content from the Ingenuity Knowledge Base to help identify disease variants in human sequencing data.
The product allows you to select multiple samples to analyze together. From there, you can design the forthcoming analysis and add any relevant biological terms to help narrow down the list of variants likely contributing to the disease or phenotype at hand. IVA supports a range of upload formats, including Variant Call Format (VCF), Genome Variation Format (GVF) and Complete Genomics files (Var, MasterVar, High confidence junction, etc.).
After you have set up your data, IVA lets you interact with the data with a series of customizable filters. Some of the filter types include: biological context, genetic analysis, predicted deleterious, cancer driver, pharmacogenetics, and more.
Keep an eye on the library’s class calendar for trainings on IVA and all bioinformatics-related software. In the meantime, Qiagen, the company that produces IVA, has produced webinars, tutorials, and guides to help you get started.
Finally, please note that the library’s license to IVA is for academic and research use only. Results may not be incorporated into a diagnostic product or service.
For questions on how to best use IVA, feel free to contact Rolando Garcia-Milian.
I'm now a master's student at the University of Michigan School of Information, where I've mostly been taking classes relating to libraries, archives, and the preservation of information, but I've also dabbled in data science, programming, and survey research methodology. In addition to my coursework, I work as a research assistant at the University of Michigan College of Engineering, where I'm part of a multidisciplinary group studying engineering education, and in the fall, I'll be a teaching assistant for a master's level introductory course in statistics and data analysis. (I also try to find the time to go out salsa or swing dancing, when I can!) After I finish graduate school next spring, I'm hoping to get a position in an academic library.
Madeline Stanton, who worked as Cushing's secretary, played a major role in the organization and development of the historical collections at the Yale Medical Library (now the Cushing/Whitney Medical Library). As Librarian of the Historical Collections from 1949 until 1968, Stanton maintained an “atmosphere of generous and kindly learning” in the Historical Library. “She always knew,” recalled Gloria Robinson, wife of Yale neurosurgeon Dr. Franklin Robinson. “She had endless special knowledge.” (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.)
Louise Eisenhardt, whom Cushing originally hired as an editorial assistant, obtained a medical degree for herself in 1925 and worked as Cushing's pathologist. A leading expert on tumor diagnosis, Eisenhardt was the first woman president of the American Association of Neurological Surgeons and the first managing editor of the Journal of Neurosurgery, a position she held for 22 years. She was also the curator of the Brain Tumor Registry, Cushing's collection of pathological specimens and patient records, which is now housed in the Cushing Center. (Photograph by Richard U. Light, courtesy of the Harvard Medical School Archives at the Countway Library of Medicine.)
Mildred Codding was a medical illustrator who worked with Cushing from 1928 until his retirement from the Peter Bent Brigham Hospital in 1932. Her surgical drawings and anatomical diagrams grace the pages of many of Cushing's published works. A student and disciple of famed medical illustrator Max Brödel, Codding made masterful use of the carbon dust technique, resulting in wonderfully vivid, detailed, and realistic illustrations of living tissue. After Cushing's retirement, Codding stayed on as an illustrator at the Brigham. Her later illustrations appear in a number of major works, including Zollinger's Atlas of Surgical Operations. (Photograph by Russell B. Harding, courtesy of the Brigham and Women's Hospital Archives.)