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Publication Number
US-9994907-B2
Publication Date
2018-06-12
Expiration Date
Abstract
Disclosed herein, in certain instances, are methods for the diagnosis, prognosis and determination of cancer progression of a cancer in a subject. Further disclosed herein, in certain instances, are methods for determining the treatment modality of a cancer in a subject. The methods comprise expression-based analysis of targets. Further disclosed herein, in certain instances, are probe sets for use in assessing a cancer status in a subject.
Core Innovation
The disclosure relates to cancer diagnosis, prognosis, and treatment-modality determination using expression-based analysis of a plurality of targets. The plurality of targets includes coding targets and non-coding or non-exonic nucleic-acid targets, including targets defined by SEQ ID NOs and complements or reverse complements.
A sample is obtained from a subject with thyroid, leukemia, breast, pancreatic, prostate, or lung cancer, and expression levels are detected for a plurality of targets comprising at least two targets selected from specific SEQ ID NOs, including complements, reverse complements, or combinations thereof. The resulting expression measurements are used to determine cancer status and treatment.
In embodiments, expression levels are assayed by sequencing, array hybridization, or nucleic acid amplification. A programmed computer classifies a sample as malignant when there is an increase in expression of the at least two targets relative to a control sample, and the classification is linked to administering a chemotherapeutic agent or radiation treatment.
The disclosure further describes probe sets or arrays with labeled probes, classifiers or algorithms including machine learning, and computational analyses such as PCA, clustering, and MDS. The expression signatures are correlated with cancer status including malignancy, stage, and recurrence risk.
Claims Coverage
The consolidated content identifies three independent claims. Across the claims, the inventive coverage centers on detecting expression levels of a plurality of nucleic-acid targets defined by specific SEQ ID NOs, including complements and reverse complements, and using the result to determine treatment or classify malignant status relative to a control sample.
Treatment selection based on expression levels of SEQ ID NO-defined targets
Obtaining a sample from a subject with thyroid, leukemia, breast, pancreatic, prostate, or lung cancer; detecting expression level in the sample for a plurality of targets comprising at least two targets having a sequence selected from specified SEQ ID NOs, or a complement or reverse complement of such a sequence, or a combination; and administering a chemotherapeutic agent or radiation treatment to the subject.
Treatment determination by expression-level detection of SEQ ID NO-defined targets
Determining a treatment for thyroid, leukemia, breast, pancreatic, prostate, or lung cancer by obtaining a sample, detecting expression level in the sample for a plurality of targets comprising at least two targets having a sequence selected from specified SEQ ID NOs, or a complement or reverse complement of such a sequence, or a combination, and administering a chemotherapeutic agent or radiation treatment to the subject.
Malignant classification from fine needle aspirate expression increase relative to a control
Assaying by sequencing, array hybridization, or nucleic acid amplification the expression level of at least two targets in a fine needle aspirate thyroid, leukemia, breast, pancreatic, prostate, or lung sample, classifying the sample as malignant by a programmed computer if there is an increase in expression of the at least two targets relative to a control sample, and administering a chemotherapeutic agent or radiation treatment to the subject.
The independent claims share a common structure: detect expression levels of at least two targets defined by specific SEQ ID NO sequences with optional complement and reverse-complement relationships, and use the result to support administering a chemotherapeutic agent or radiation treatment. One claim further requires programmed malignant classification based on increased expression relative to a control sample, using fine needle aspirate samples and sequencing, array hybridization, or nucleic acid amplification.
Stated Advantages
Enables classification of a sample as malignant based on increased expression of at least two SEQ ID NO-defined targets relative to a control sample.
Supports selecting or determining administration of a chemotherapeutic agent or radiation treatment based on detected expression levels.
Correlates expression signatures with cancer status, including malignancy, stage, and recurrence risk.
Documented Applications
Cancer diagnostics, prognostics, and treatment-modality determination for thyroid cancer, leukemia, breast cancer, pancreatic cancer, prostate cancer, and lung cancer using expression-based analysis of coding and non-coding or non-exonic nucleic-acid targets.
Malignancy classification and treatment administration based on fine needle aspirate samples from thyroid, leukemia, breast, pancreatic, prostate, or lung cancer patients using sequencing, array hybridization, or nucleic acid amplification.
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