Methods for evaluating COPD status
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Publication Number
US-10526655-B2
Publication Date
2020-01-07
Expiration Date
Abstract
The invention in some aspects provides methods of determining the likelihood that a subject has COPD based on the expression of informative-genes. In other aspects, the invention provides methods for determining an appropriate diagnostic intervention plan for a subject based on the expression of informative-genes. Related compositions and kits are provided in other aspects of the invention.
Core Innovation
The invention provides a method for processing a biological sample of a subject that includes obtaining the biological sample from bronchial epithelium. A first portion of the sample is subjected to histological or cytological testing, where the testing indicates that the first portion is free of detectable cancer cells. After identifying that the first portion is free of detectable cancer cells, a second portion is used for nucleic acid hybridization, amplification, or sequencing to generate data on gene expression products.
The generated data includes gene expression products of a plurality of genes comprising PCDH7 and PTPRH. The gene expression products are differentially expressed as compared to a reference. The first data set is processed to obtain a second data set that comprises a COPD risk-score for the biological sample, based on the differential gene expression.
The method outputs a report having the COPD risk-score. The described approach further includes processing the report in a way that is compatible with implementation using probes with sequence complementarity, and generating the COPD risk-score from expression product levels. The method is supported by refinement options including expanding the plurality of genes and specifying how the COPD risk-score is computed, such as as a sum of weighted expression product levels.
Claims Coverage
The independent claim is clm-00001. The claim set centers on cancer-free verification of a bronchial epithelium sample portion, differential expression of a gene plurality comprising PCDH7 and PTPRH, and processing the resulting data into a COPD risk-score report.
Cancer-free verification before COPD gene-expression measurement
Subjecting a first portion of the biological sample to histological or cytological testing indicating that the first portion is free of detectable cancer cells, and then, upon identifying that the first portion is free of detectable cancer cells, proceeding with nucleic-acid-based measurement on a second portion.
Differential gene expression using PCDH7 and PTPRH
Generating a first data set using nucleic acid hybridization, amplification, or sequencing to produce gene expression products of a plurality of genes comprising PCDH7 and PTPRH, wherein the gene expression products are differentially expressed as compared to a reference.
Processing differential expression into a COPD risk-score report
Processing the first data set to obtain a second data set comprising a COPD risk-score for the biological sample and outputting a report having the COPD risk-score.
Probe sequence complementarity for nucleic acid measurement
Using probes having sequence complementarity with gene expression products of the plurality of genes comprising PCDH7 and PTPRH.
Bronchial epithelium sample obtained by named collection methods
Obtaining the biological sample by bronchial brushing, broncho-alveolar lavage, or a bronchial biopsy.
COPD risk-score computed as sum of weighted expression product levels
Calculating the COPD risk-score as the sum of weighted gene expression product levels.
Weights tied to relative contribution for increased COPD likelihood
Weighting the weighted expression levels according to their relative contribution to predicting increased likelihood of having COPD.
Expanded gene plurality for the risk-score
Using a plurality of genes comprising at least 3 additional genes selected from a specified set of named genes.
Overall, the claim set centers on verifying a bronchial epithelium sample portion as free of detectable cancer cells, measuring differential gene expression for a plurality of genes comprising PCDH7 and PTPRH via nucleic-acid hybridization, amplification, or sequencing, and processing the resulting data into a COPD risk-score reported to the subject. Dependent claims refine probe complementarity, sample collection method, gene set size, and specific computation and weighting of the COPD risk-score.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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