Developer

This pipeline is developed by BMAP team.

Clinical knowledge base

The medical annotation is based on the Shenzhou Medical’s iCMDB Precision Medicine Knowledge Base, which has been manually checked by at least one researcher.

Workflow

The tumor medication guidance analysis process includes gene annotation of variants in VCF files using Annovar and SnpEff software, medical annotation of variants utilizing Shenzhou Medical’s iCMDB Precision Medicine Knowledge Base, and logical reasoning based on sensitivity and resistance. Ultimately, it provides treatment plans that comply with NCCN guidelines (or FDA, CFDA guidelines) and offers annotations on the molecular mechanisms of each variant.

Background

The patient was initially diagnosed with Stage IV non-small cell lung cancer. After undergoing two cycles of standard pemetrexed combined with cisplatin chemotherapy, the disease progressed, revealing new lesions in the right lung and bilateral pleura. The patient sought new treatment options.

Research Plan

Genomic sequencing was performed on the patient to identify potential sensitive sites for targeted therapies, prognostic sites related to chemotherapy, and ongoing clinical trials. This aimed to provide new treatment strategies.

Results

Genetic sequencing did not identify any known sensitive target sites for existing targeted therapies. However, an EGFR H773L mutation was discovered within the same kinase domain as the known sensitive site L858R. After obtaining informed consent, the patient was treated with the kinase inhibitor osimertinib. The patient's condition significantly improved, suggesting that the H773L site exhibits similar biological and pharmacological responses to L858R. This indicates that H773L is a potential sensitive site for kinase inhibitor therapy.

V1.0 Gene Annotation and Tumor Clinical Treatment Decision Support
The related processes have been published on the code management platform, CRS Hosting ID: CRS1076569736894230528; SRS Hosting ID: SRS1076573619045543936

Reproducibility

The pipeline utilizes code CRS1076569736894230528 and Docker image SRS1076573619045543936, both of which are stored in the BMAP repositories.

Knowledge base

The variants are annotated using a commercial knowledge database (iCMDB).

Usage

1. Select the application 'Precise medication guidance'
2. Click on the 'Analysis' button
3. Click on the 'Clinical annoation'
4. Fill in the request parameters

Note: the vcf file name should include the subfolder name and the extension name (eg. data/tumor.vcf).
5. Upload the compressed data in gz or rar format.

6. View the results