MABBI – Research conducted by Ivan William Harsono, Yulia Ariani, Beben Benyamin, Fadilah Fadilah, Dwi Ari Pujianto, and Cut Nurul Hafifah from UI and Konsultan Transformasi Digital Profesional entitled IDeRare: a lightweight and extensible open-source phenotype and exome analysis pipeline for germline rare disease diagnosis.
Diagnosing rare diseases is challenging and has a debilitating impact if diagnosed late. The lack of national clinical guidelines, advanced omics laboratories, and an integrated phenotype-genotype bioinformatic pipeline forces clinicians, especially in developing countries, to manually curate patient phenotypes and annotate patient genotype variants. Recently, efforts to standardize clinical data collection have used ICD-10, SNOMED-CT, and LOINC terminologies through national programs such as the SATUSEHAT ecosystem in Indonesia. However, OMIM and HPO are more specialized for rare diseases and are not commonly collected in standard medical records. Automatic conversion of these common terminologies to OMIM and HPO, along with linkage analysis and phenotype-based recommendations, can benefit clinicians and geneticists in diagnosing rare diseases. To ease their burden, we built IDeRare, a lightweight, extensible phenotyping and variant analysis pipeline. This pipeline integrates existing tools and runs on a mid-tier personal computer with NVIDIA 8GB GPU memory. The IDeRare pipeline is available on GitHub under the BSD-3 license. (Tri/MABBI)
Read more: https://doi.org/10.1093/jamiaopen/ooae052
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