NIAID Clinical Genomics Tools

Authors

• A Oler
• S Xirasagar
• Z Li
• K Huang
• D Veltri
• D Kaminsky
• M Simuluk
• Y Zhang
• J Johnson
• C Hong
• J Milner

Abstract

The National Institute of Allergy and Infectious Diseases (NIAID) Intramural Clinical Genomics Program was started in 2014 with the goal of using state-of-the-art genomics technologies to improve diagnosis and treatment of rare or novel immunological disorders. To facilitate their goal, we have developed an integrative, scalable, collaborative, and secure web application called Genomic Research Integration System (GRIS). GRIS enables the capture of patient data with standardized phenotype and genotype data in a family- or individual-based context and importantly, enables genetic analysis utilizing high quality annotations. The system leverages existing open source tools, ontologies, and genomic annotation databases. A customized version of PhenoTips®, along with a user-friendly pedigree editor interface and Human Phenotype Ontology (HPO), has been implemented to enable patient data capture. Standardized analysis pipelines use open source tools including BWA, GATK/Queue, and GEMINI to process sequencing and variant data, and to perform quality control at various stages of data processing. The resulting variant report – enriched with genomic annotations from ClinVar, OMIM, ExAC, gnomAD, dbNSFP, and other high-quality annotation databases – is displayed in an interactive web-based tool, GeminiViewer, to aid researchers in identifying candidate causal variants in Mendelian disorders.

Scientific Focus Area: Computational Biology

This page was last updated on Friday, March 26, 2021