US 12,031,184 B2
Cancer detection and classification using methylome analysis
Daniel Diniz De Carvalho, Toronto (CA); Scott Victor Bratman, Toronto (CA); Rajat Singhania, Toronto (CA); Ankur Ravinarayana Chakravarthy, Toronto (CA); and Shu Yi Shen, Markham (CA)
Assigned to University Health Network, Toronto (CA); and Sinai Health System, Toronto (CA)
Appl. No. 16/630,299
Filed by UNIVERSITY HEALTH NETWORK, Toronto (CA); and SINAI HEALTH SYSTEM, Toronto (CA)
PCT Filed Jul. 11, 2018, PCT No. PCT/CA2018/000141
§ 371(c)(1), (2) Date Jan. 10, 2020,
PCT Pub. No. WO2019/010564, PCT Pub. Date Jan. 17, 2019.
Claims priority of provisional application 62/531,527, filed on Jul. 12, 2017.
Prior Publication US 2020/0308651 A1, Oct. 1, 2020
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01); C12Q 1/6827 (2018.01); G16B 5/20 (2019.01); G16B 40/00 (2019.01); G16B 30/20 (2019.01)
CPC C12Q 1/6886 (2013.01) [C12Q 1/6827 (2013.01); G16B 5/20 (2019.02); G16B 40/00 (2019.02); C12Q 2522/10 (2013.01); C12Q 2537/164 (2013.01); C12Q 2600/154 (2013.01); G16B 30/20 (2019.02)] 22 Claims
 
1. A method comprising:
(a) providing a sample of cell-free DNA from a subject;
(b) adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated, and wherein the first amount of filler DNA is from about 20 nanograms (ng) to about 100 ng;
(c) capturing cell-free methylated DNA using a binder selective for methylated polynucleotides;
(d) sequencing the captured cell-free methylated DNA to generate a plurality of sequencing reads; and
(e) computer processing the plurality of sequencing reads to obtain a methylation profile of the subject.