Welcome to the ICMM toolbox

In order to find innovative solutions for South African and global health challenges, the research landscape must first be thoroughly understood. This was the inception of the first research tool made available by the ICMM - the COHG-SA database - which catalogues current literature on host genetic susceptibility and severity of SARS-CoV-2 infection, the causative agent behind COVID-19 disease. As new tools are published and become available for researchers outside the ICMM, they will be posted here in the spirit of global scientific collaboration.

Here we list various tools created by members of the ICMM and its various research groups. These range from databases to bioinformatics tools. These tools are available on the ICMM GitHub page which is available at https://github.com/Tuks-ICMM/

COHG-SA database

Database link: COHG-SA database (available at http://covgene.bi.up.ac.za) 

Description:

The SARS-CoV-2 virus is responsible for the COVID-19 global public health emergency, and the disease it causes is highly variable in its clinical presentation. Clinical phenotypes are heterogeneous both in terms of presentation of symptoms in the host and response to therapy. Several studies and initiatives have been established to analyse and review host genetic epidemiology associated with COVID-19. Our research group curated these articles into a web-based database using the python application-server framework Django. The database provides a searchable research tool describing current literature surrounding COVID-19 host genetic factors associated with disease outcome. 

Article reference: under review

NESHIE-DB

Database link: Under construction

Description: Neonatal encephalopathy (NE) is a condition occurring in neonates at or greater than 35 weeks gestation, characterised by altered neurological function.  NE with suspected hypoxic ischaemic encephalopathy (NESHIE) is a subcategory of NE that occurs due to oxygen deprivation and lack of blood flow. An underlying genetic predisposition to NESHIE may influence neurological outcomes, development, and severity of NESHIE. Recent studies suggest that genetic variants may play a role in NESHIE pathogenesis; however, limited data has been published to date. In contrast, many studies have identified genetic variants associated with cerebral palsy (CP), a non-progressive neurological condition that can develop from moderate to severe NESHIE amongst other causes. Our research group has created a public database of the gene and variant information on NESHIE and CP.

Article Reference: to be added