US 12,325,878 B2
Detecting breast cancer
David A. Ahlquist, Rochester, MN (US); William R. Taylor, Lake City, MN (US); Douglas W. Mahoney, Elgin, MN (US); Tracy C. Yab, Rochester, MN (US); John B. Kisiel, Rochester, MN (US); Hatim T. Allawi, Middleton, WI (US); Graham P. Lidgard, Middleton, WI (US); and Michael W. Kaiser, Stoughton, WI (US)
Assigned to Mayo Foundation for Medical Education and Research, Rochester, MN (US); and Exact Sciences Corporation, Madison, WI (US)
Filed by Mayo Foundation for Medical Education and Research, Rochester, MN (US); and Exact Sciences Corporation, Madison, WI (US)
Filed on Mar. 18, 2021, as Appl. No. 17/205,796.
Application 17/205,796 is a continuation of application No. 16/202,935, filed on Nov. 28, 2018, granted, now 10,975,443.
Claims priority of provisional application 62/592,828, filed on Nov. 30, 2017.
Prior Publication US 2021/0207224 A1, Jul. 8, 2021
Int. Cl. C12Q 1/68 (2018.01); C07H 21/04 (2006.01); C12Q 1/6806 (2018.01); C12Q 1/6809 (2018.01); C12Q 1/6811 (2018.01); C12Q 1/682 (2018.01); C12Q 1/6827 (2018.01); C12Q 1/6837 (2018.01); C12Q 1/6853 (2018.01); C12Q 1/6886 (2018.01); G16H 50/30 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6806 (2013.01); C12Q 1/6809 (2013.01); C12Q 1/6811 (2013.01); C12Q 1/682 (2013.01); C12Q 1/6827 (2013.01); C12Q 1/6837 (2013.01); C12Q 1/6853 (2013.01); G16H 50/30 (2018.01); C12Q 2537/143 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/154 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01); C12Q 2600/16 (2013.01)] 9 Claims
 
1. A method, comprising:
treating DNA from a sample with a reagent that modifies DNA in a methylation-specific manner;
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; and
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.