# US 2012/0074311 A1 · Monitoring treatment of Head and Neck cancer patients with drugs targeting EGFR pathway using mass spectrometry of patient samples

> Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt

- Number: US 2012/0074311 A1
- Document ID: US20120074311A1
- Status: Published application
- Kind: A1
- Application number: 13/313,838
- Filed: 2011-12-07
- Published: 2012-03-29
- Earliest claimed: 2006-03-31
- Assignees: Biodesix, Inc.
- Inventors: Heinrich Röder; Maxim Tsypin; Julia Grigorieva
- Web page: https://patentgrep.com/patent/US20120074311A1

## CPC

- A61K 31/517: ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
- A61K 31/5377: not condensed and containing further heterocyclic rings, e.g. timolol
- G16B 40/00: ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
- G16B 40/10: Signal processing, e.g. from mass spectrometry [MS] or from PCR
- G16B 20/00: ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- Y10T 436/24: Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)
- G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION

## Abstract

Methods using mass spectral data analysis and a classification algorithm provide an ability to determine whether a non-small-cell lung cancer patient, head and neck squamous cell carcinoma or colorectal cancer patient has likely developed a non-responsiveness to treatment with a drug targeting an epidermal growth factor receptor pathway. As the methods of this disclosure require only simple blood samples, the methods enable a fast and non-intrusive way of measuring when drugs targeting the EGFR pathway cease to be effective in certain patients. This discovery represents the first known example of true personalized selection of these types of cancer patients for treatment using these classes of drugs not only initially, but during the course of treatment.

## Claims

### Claim 1

A method of facilitating treatment of a head and neck squamous cell carcinoma cancer (HNSCC) patient, comprising the steps of:
1) assigning a baseline class label for the patient using a classifier operating on integrated intensity values at pre-defined m/z ranges in mass-spectral data obtained from a blood-based sample of the patient and a training set comprising class-labeled spectra from other patients, the baseline class label indicating whether the patient is likely to benefit from administration of a drug targeting an epidermal growth factor receptor pathway, wherein if the baseline class label is “good” (or the equivalent), the drug is administered to the patient; and
2) thereafter, while the patient is being treated with the drug, a) obtaining a mass spectrum of a blood-based sample of the patient, b) performing one or more predefined pre-processing steps on the mass spectrum, c) obtaining integrated intensity values of selected features in said spectrum at said one or more pre-defined m/z ranges after the pre-processing steps on the mass spectrum have been performed, and d) assigning a further class label for the sample using the classifier and the training set, the further class label indicating whether the patient has developed a non-responsiveness to the treatment with the said drug.

### Claim 2 (depends on 1)

The method of claim 1, wherein step 2) including sub-steps a)-d) are performed periodically during the course of treatment of the patient.

### Claim 3 (depends on 1)

The method of claim 1, wherein the one or more pre-defined m/z ranges comprises one or more m/z ranges selected from the group of m/z ranges consisting of:
5732 to 5795
5811 to 5875
6398 to 6469
11376 to 11515
11459 to 11599
11614 to 11756
11687 to 11831
11830 to 11976
12375 to 12529
23183 to 23525
23279 to 23622 and
65902 to 67502.

### Claim 4 (depends on 1)

The method of claim 1, wherein the steps a)-d) are performed at intervals of between 30 and 100 days.