AI-MARRVEL (AIM) is an AI system for rare genetic disease diagnosis.
It takes as input patient VCF and phenotype (formatted with HPO) to predict the causal variant(s).
In making prediction, it takes variant annotation from MARRVEL database and more,
and generates prediction score + confidence score as output.
You can use AI-MARRVEL from our website or follow the documentation to run locally.
:new: Our paper is now published in NEJM AI!
AIM utilizes various databases for variant annotation, all of which have been compiled and are available for download. We use AWS S3 for data access, and the data can be downloaded by following these steps:
cd <desired/folder/path>
aws s3 sync s3://aim-data-dependencies-public . --no-sign-request
### Get the software
AIM is released as a Docker image for easy distribution. To get it:
docker pull chaozhongliu/aim-lite:latest
docker run -v <Path to VCF File>:/input/vcf.gz \
-v <Path to HPO file>:/input/hpo.txt \
-v <Path to downloaded database>:/run/data_dependencies \
-v <Path to output folder>:/out \
chaozhongliu/aim-lite /run/proc.sh [Sample ID] [Reference genome: hg19/hg38] [Memory Limit (G)]
AI-MARRVEL is licensed under GPL-3.0. You are welcomed to use it for research purpose.
For business purpose, please contact us for licensing.
@article{doi:10.1056/AIoa2300009,
author = {Dongxue Mao and Chaozhong Liu and Linhua Wang and Rami AI-Ouran and Cole Deisseroth and Sasidhar Pasupuleti and Seon Young Kim and Lucian Li and Jill A. Rosenfeld and Linyan Meng and Lindsay C. Burrage and Michael F. Wangler and Shinya Yamamoto and Michael Santana and Victor Perez and Priyank Shukla and Christine M. Eng and Brendan Lee and Bo Yuan and Fan Xia and Hugo J. Bellen and Pengfei Liu and Zhandong Liu },
title = {AI-MARRVEL — A Knowledge-Driven AI System for Diagnosing Mendelian Disorders},
journal = {NEJM AI},
volume = {1},
number = {5},
pages = {AIoa2300009},
year = {2024},
doi = {10.1056/AIoa2300009},
URL = {https://ai.nejm.org/doi/abs/10.1056/AIoa2300009},
eprint = {https://ai.nejm.org/doi/pdf/10.1056/AIoa2300009}
,
abstract = { AI-MARRVEL is an AI system for genetic diagnosis that improves diagnostic accuracy, surpassing state-of-the-art benchmarked methods. }
}