Chapter 6: Molecular Tumor Boards & Actionable Biomarker Databases
Chapter 6: Molecular Tumor Boards & Actionable Biomarker Databases
In a Molecular Tumor Board (MTB), medical oncologists, clinical geneticists, pathologists, and bioinformaticians evaluate comprehensive genomic profiling (CGP) reports to formulate individualized treatment strategies for refractory or advanced cancer patients.
The OncoKB Precision Oncology Knowledgebase
Maintained by Memorial Sloan Kettering Cancer Center, OncoKB assigns therapeutic levels of evidence:
- Level 1: FDA-approved companion diagnostic for an FDA-approved drug in this specific cancer indication (e.g. Osimertinib for EGFR T790M NSCLC).
- Level 2: Standard of care biomarker recommended by NCCN guidelines.
- Level 3A: Compelling clinical evidence in this indication, or FDA-approved in another indication (Level 3B).
- Level 4: Compelling biological/preclinical rationale (in vitro/in vivo drug sensitivity).
1. Programmatic Querying with the OncoKB Web API
import requests
import json
def query_oncokb(hugo_symbol: str, alteration: str, tumor_type: str, api_token: str):
url = f"https://www.oncokb.org/api/v1/annotate/mutations/byGenomicChange"
headers = {"Authorization": f"Bearer {api_token}"}
params = {
"hugoSymbol": hugo_symbol,
"alteration": alteration,
"cancerType": tumor_type
}
r = requests.get(url, headers=headers, params=params)
if r.status_code == 200:
data = r.json()
print(f"Oncogenic Status: {data.get('oncogenic')}")
for treatment in data.get('treatments', []):
print(f"Level: {treatment['level']} -> Drugs: {', '.join([d['drugName'] for d in treatment['drugs']])}")
# Example: BRAF V600E in Cutaneous Melanoma
query_oncokb("BRAF", "V600E", "Melanoma", "YOUR_API_TOKEN")