Detecting breast cancer
Inventors
Ahlquist, David A. • Taylor, William R. • Mahoney, Douglas W. • Yab, Tracy C. • Kisiel, John B. • Allawi, Hatim T. • Lidgard, Graham P. • Kaiser, Michael W.
Assignees
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Publication Number
US-12325878-B2
Publication Date
2025-06-10
Expiration Date
Abstract
Provided herein is technology for breast cancer screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of breast cancer.
Core Innovation
The invention relates to breast cancer screening based on DNA methylation markers, including identifying differentially methylated regions that distinguish breast cancer tissue from normal tissue. DNA from a sample is treated with a reagent that modifies DNA in a methylation-specific manner, and the treated DNA is analyzed to determine methylation levels using polymerase chain reaction, nucleic acid sequencing, mass spectrometry, a methylation-specific nuclease, mass-based separation, and/or target capture.
A set of primers specific for each of four or more genes is used to amplify the treated DNA, wherein the four or more genes comprise FAM59B, SPHK2, ODC1, and at least one of OSR2_A, OSR2_B, or OSR2_C or any combinations thereof. The methylation level of each gene is determined using polymerase chain reaction and/or other methylation level determination approaches.
The invention further integrates methylation measurement with multi-gene marker sets for classification-related uses, including risk scoring based on multiple differentially methylated region methylation states. The described examples include systems, kits, compositions, and computable approaches that use methylation levels from the selected markers to support screening and diagnostic interpretation.
Claims Coverage
The independent claims cover methylation-specific DNA treatment followed by amplification using gene-specific primers for four or more genes including FAM59B, SPHK2, ODC1, and at least one of OSR2_A, OSR2_B, or OSR2_C, and determining methylation levels for each gene using PCR and/or other specified methylation-analysis modalities. Three inventive features are consistently present across the combined claim coverage.
Methylation-specific DNA treatment with methylation modifier reagent
Treating DNA from a sample with a reagent that modifies DNA in a methylation-specific manner.
Four-or-more gene methylation panel with specified gene primer targets
Amplifying the treated DNA using a set of primers specific for each of four or more genes, wherein the four or more genes comprises FAM59B, SPHK2, ODC1, and at least one of OSR2_A, OSR2_B, or OSR2_C or any combinations thereof.
Determining methylation levels using PCR, sequencing, mass spectrometry, methylation-specific nuclease, mass-based separation, and/or target capture
Determining a methylation level of each of the four or more genes using polymerase chain reaction, nucleic acid sequencing, mass spectrometry, a methylation-specific nuclease, mass-based separation, and/or target capture.
Overall claim coverage is focused on methylation-specific DNA modification followed by amplification of a defined multi-gene methylation panel and determination of per-gene methylation levels using one or more of PCR, sequencing, mass spectrometry, methylation-specific nuclease, mass-based separation, and/or target capture.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Breast cancer screening based on DNA methylation markers, including distinguishing breast cancer tissue from normal tissue.
Distinguishing cancer in breast tissue and in blood/plasma.
Diagnosis/screening, risk/prognosis, and monitoring are described at a high level.
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