Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has become cost-effective, interpreting these variants-particularly collecting Show more
Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has become cost-effective, interpreting these variants-particularly collecting literature-based evidence like ACMG/AMP PM3-remains complex and time-consuming. Show less
2025 · Bioinformatics · Oxford University Press · added 2026-04-21
Motivation: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has be come cost-effective, interpreting these variants—particular Show more
Motivation: Rare diseases affect over 300 million people worldwide and are often caused by genetic variants. While variant detection has be come cost-effective, interpreting these variants—particularly collecting literature-based evidence like ACMG/AMP PM3—remains complex and time-consuming. Results: We present AutoPM3, a method that automates PM3 evidence extraction from literatures using open-source large language models (LLMs). AutoPM3 combines a Text2SQL-based variant extractor and a retrieval-augmented generation (RAG) module, enhanced by a variantspecific retriever and fine-tuned LLM, to separately process tables and text. We curated PM3-Bench, a dataset of 1027 variant-publication Show less
2025 · Nucleic acids research · Oxford University Press · added 2026-04-21
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation fr Show more
One of the major challenges in precision oncology is the identification of pathogenic, actionable variants and the selection of personalized treatments. We present Onkopus, a variant interpretation framework based on a modular architecture, for interpreting and prioritizing genetic alterations in cancer patients. A multitude of tools and databases are integrated into Onkopus to provide a comprehensive overview about the consequences of a variant, each with its own semantic, including pathogenicity predictions, allele frequency, biochemical and protein features, Show less