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readme.md

CancerVar & OPAI detailed document

CancerVar

CancerVar is a bioinformatics software tool for clinical interpretation of somatic variants by the AMP/ASCO/CAP 2017 guidelines. The input to CancerVar is an annotated file generated from ANNOVAR, while the output of CancerVar is the classification of variants into "Tier_I_strong","Tier_II_potential","Tier_IV_benign" and "Tier_III_Uncertain", together with detailed evidence code. CancerVar can have automated interpretation and manual interpretation.

  • Automated interpretation: The standards and guidelines for the clinical interpretation of sequence variants in cancer, based on 12 criteria. The CancerVar can generate automated interpretation on 10 criteria: (CBP1,CBP2,CBP3,CBP4,CBP7,CBP8,CBP9,CBP10,CBP11,CBP12)

  • Manual interpretation: The rest of criteria (CBP5, CBP6) requires user input in the manual adjustment step. The user can provide these criteria or other criteria in the evidence file.

OPAI

OPAI is a python script for oncogenic prioritization by artificial intelligence (OPAI). Based on deep learning-based approach, OPAI predict the oncogenicity of a variant, using 12 clinical evidence features from CancerVar and 19 in silico functional features with scoring metrics predicted by computational tools.

Pipeline

Check here to see what is new in CancerVar & OPAI.

new 2019Dec: The OPAI is online now here.

new 2018Nov: The web server of CancerVar is online now here.

new 2018Jan: The GitHub repository for CancerVar is created.

Reference

  • Quan Li, Zilin Ren, Kajia Cao, Marilyn M. Li, Yunyun Zhou and Kai Wang. CancerVar: an Artificial Intelligence empowered platform for clinical interpretation of somatic mutations in cancer. (Under Review,2022)BioRxiv

  • Li MM, Datto M, Duncavage EJ, Kulkarni S, Lindeman NI, Roy S, Tsimberidou AM, Vnencak-Jones CL, Wolff DJ, Younes A, Nikiforova MN. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.

  • Li Q, Wang K. InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines. American Journal of Human Genetics, 2:267-280, 2017