Rapid extraction of genomic data from these diseases
INTRODUCTION
Navigating the landscape of genomic data can be a challenging endeavor without adequate computational expertise and knowledge of several different databases. An extra layer of difficulty is added when looking for accessible genomic data for rare and neglected diseases because data is often scarce and dispersed among different databases. Some of the most popular databases for genomic data include the Sequence Read Archive (SRA) and the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI), The Cancer Genome Atlas (TCGA) of the National Cancer Institute and the Genetic and Rare Diseases Information Center (GARD) of the National Center for Advancing Translational Sciences (NCATS). To make the process of identifying available data for rare and neglected diseases easier, we developed , RDGREx: Rare Disease Genome Data Extractor, a user- friendly tool for quick and streamlined identification of available genomic data in several common databases. This software, available at , can be utilized to interrogate the availability of genomic data for a range of rare and neglected diseases in several publicly available databases. The tool can identify a range of different omics data types including Whole genome sequencing, whole exome sequencing, RNA-sequencing, ChIP-sequencing data and many more, streamline the downloading process and also provide options for visualization. The input for the RDGREx search is a disease of interest. Additionally, the number of studies to be included in the query can be specified. Ancestry information can be specificed in your search to limit your query to samples from yoru ethnic group of interest. After submission of the query, the user will be able to explore the meta-data associated with the search including a quick summary of the experiment associated with the data. Additional tabs include the location of the data from where it originated, the sequencing platforms associated with it, the Raw data, a summary and supplementary files.
Rare and Neglected Diseases The current version of the RDGREx contains data on the following diseases:
Acute lymphoblastic leukemia
Acute promyelocytic leukemia
Adrenocortical carcinoma
Beta thalassemia
Ehlers-Danlos syndrome
Friedreich ataxia
Glioblastoma
Hodgkin lymphoma
Huntington's disease
Klienefelter Syndrome
Leigh Syndrome
Mantle cell pymphoma
Multiple myeloma
Pituitary Cancer
Prader-Willi syndrome
Retinoblastoma
Sjogren's syndrome
Small cell lung cancer
Spinal muscular atrophy
Turner Syndrome
Williams syndrome
Xeroderma pigmentosum
RDGREx: Rare Disease Genome Data Extractor
Structure of RDGREx
RDGREx consists of a web interface.
PREREQUISITIES
R
Future Directions
This software has the potential to be improved by:
-expanding upon the diseases in the database
-allowing the user to filter search results based on data method (RNAseq, microarray, etc.)
Codeathon Team Members: Agaz Wani, Jan Dahrendorff, Xochitl Diaz, and Hyacinth Burrowes