US 11,920,200 B2
Epigenetic markers and related methods and means for the detection and management of certain cancers
Martin Widschwendter, Wildermieming (AT); Allison Jones, London (GB); Iona Evans, London (GB); Harri Lempiäinen, Binningen (CH); Johannes Eichner, Lörrach (DE); Tamas Rujan, Oberweil (CH); Timo Wittenberger, Constance (DE); Tobias Paprotka, Leipzig (DE); and Benjamin Lindner, Leipzig (DE)
Assigned to Eurofins Genomics Europe Sequencing GMBH, (DE); Genedata AG, (CH); and UCL Business LTD., (GB)
Appl. No. 16/469,963
Filed by EUROFINS GENOMICS EUROPE SEQUENCING GMBH, Constance (DE); GENEDATA AG, Basel (CH); and UCL BUSINESS LTD., London (GB)
PCT Filed Dec. 15, 2017, PCT No. PCT/EP2017/083170
§ 371(c)(1), (2) Date Jun. 14, 2019,
PCT Pub. No. WO2018/109217, PCT Pub. Date Jun. 21, 2018.
Claims priority of application No. 16204822 (EP), filed on Dec. 16, 2016.
Prior Publication US 2019/0330703 A1, Oct. 31, 2019
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); G16B 20/00 (2019.01); G16B 40/10 (2019.01); G16H 20/00 (2018.01); G16H 50/20 (2018.01)
CPC C12Q 1/6886 (2013.01) [G16B 20/00 (2019.02); G16B 40/10 (2019.02); G16H 20/00 (2018.01); G16H 50/20 (2018.01); C12Q 2600/106 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/154 (2013.01)] 18 Claims
 
1. A method of determining the presence of a cancer in a human individual, said method comprising:
providing a serum or plasma sample from said human individual, said sample comprising cell-free DNA;
determining, in at least one molecule of said cell-free DNA, the methylation status at 16 CpGs located at positions 28, 31, 33, 45, 52, 58, 60, 62, 69, 104, 107, 110, 116, 121, 124 and 126 within the nucleotide sequence of SEQ ID NO: 2 or a 100% complementary sequence to said nucleotide sequence;
determining the presence of cancer in said human individual when at least one molecule of said cell-free DNA is methylated at each of said 16 CpGs; and
treating the cancer in said human individual by (i) administering a chemotherapeutic agent selected from the group consisting of paclitaxel, docetaxel, cisplatin, liposomal doxorubicin, gemcitabine, trabectedin, etoposide, cyclophosphamide, an angiogenesis inhibitor and a PARP inhibitor, or (ii) by performing tumor de-baulking surgery;
wherein (a) when the human individual is a woman the cancer is selected from the group consisting of: breast cancer, lung squamous cell carcinoma, colon cancer, pancreatic cancer, uterine (endometrial) cancer, and ovarian cancer; or (b) when the human individual is a man the cancer is selected from the group consisting of: lung squamous cell carcinoma, colon cancer, pancreatic cancer and prostate cancer.