公开(公告)号：US20200308651A1

公开(公告)日：2020-10-01

申请号：US16630299

申请日：2018-07-11

Applicant: UNIVERSITY HEALTH NETWORK ,  SINAI HEALTH SYSTEM

Inventor： Daniel Diniz DE CARVALHO ,  Scott Victor BRATMAN ,  Rajat SINGHANIA ,  Ankur Ravinarayana CHAKRAVARTHY ,  Shu Yi SHEN

IPC: C12Q1/6886 ,  C12Q1/6827

Abstract: There is described herein a method of detecting the presence of DNA from cancer cells in a subject comprising: providing a sample of cell-free DNA from a subject; subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated, then optionally denaturing the sample; capturing cell-free methylated DNA using a binder selective for methylated polynucleotides; sequencing the captured cell-free methylated DNA; comparing the sequences of the captured cell-free methylated DNA to control cell-free methylated DNAs sequences from healthy and cancerous individuals and from individuals with distinct cancer types and subtypes; identifying the presence of DNA from cancer cells if there is a statistically significant similarity between one or more sequences of the captured cell-free methylated DNA and cell-free methylated DNAs sequences from cancerous individuals.

公开(公告)号：US20210156863A1

公开(公告)日：2021-05-27

申请号：US16760522

申请日：2018-11-01

Applicant: UNIVERSITY HEALTH NETWORK ,  SINAI HEALTH SYSTEM

Inventor： Daniel DINZ DE CARVALHO ,  Scott Victor BRATMAN ,  Ankur RAVINARAYANA CHAKRAVARTHY ,  Rajat SINGHANIA ,  Justin Matthew BURGENER ,  Shu Yi SHEN

IPC: G01N33/574 ,  G16B40/00

Abstract: There is described herein a method of detecting the presence of DNA from cancer cells in a subject comprising: providing a sample of cell-free DNA from a subject; subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; optionally denaturing the sample; capturing cell-free methylated DNA using a binder selective for methylated polynucleotides; sequencing the captured cell-free methylated DNA; comparing the sequences of the captured cell-free methylated DNA to control cell-free methylated DNAs sequences from healthy and cancerous individuals; identifying the presence of DNA from cancer cells if there is a statistically significant similarity between one or more sequences of the captured cell-free methylated DNA and cell-free methylated DNAs sequences from cancerous individuals.

公开(公告)号：US20230203473A1

公开(公告)日：2023-06-29

申请号：US18061273

申请日：2022-12-02

Applicant: University Health Network ,  Sinai Health System

Inventor： Daniel DINIZ DE CARVALHO ,  Shu Yi SHEN ,  Rajat SINGHANIA ,  Scott Victor BRATMAN ,  Ankur RAVINARAYANA CHAKRAVARTHY

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6804 ,  G01N33/53

CPC classification number: C12N15/1003 ,  C12N15/1093 ,  C12N15/10 ,  C12Q1/6806 ,  C12Q1/6804 ,  G01N33/5308 ,  C12Q1/6886

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.

公开(公告)号：US20220251665A1

公开(公告)日：2022-08-11

申请号：US17668314

申请日：2022-02-09

Applicant: UNIVERSITY HEALTH NETWORK ,  SINAI HEALTH SYSTEM

Inventor： Daniel DINIZ DE CARVALHO ,  Scott Victor BRATMAN ,  Rajat SINGHANIA ,  Ankur RAVINARAYANA CHAKRAVARTHY ,  Shu Yi SHEN

IPC: C12Q1/6886 ,  C12Q1/6827

Abstract: There is described herein a method of detecting the presence of DNA from cancer cells in a subject comprising: providing a sample of cell-free DNA from a subject; subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated, then optionally denaturing the sample; capturing cell-free methylated DNA using a binder selective for methylated polynucleotides; sequencing the captured cell-free methylated DNA; comparing the sequences of the captured cell-free methylated DNA to control cell-free methylated DNAs sequences from healthy and cancerous individuals and from individuals with distinct cancer types and subtypes; identifying the presence of DNA from cancer cells if there is a statistically significant similarity between one or more sequences of the captured cell-free methylated DNA and cell-free methylated DNAs sequences from cancerous individuals.

公开(公告)号：US20230287384A1

公开(公告)日：2023-09-14

申请号：US18059370

申请日：2022-11-28

Applicant: University Health Network ,  Sinai Health System

Inventor： Daniel DINIZ DE CARVALHO ,  Shu Yi SHEN ,  Rajat SINGHANIA

IPC: C12N15/10 ,  C12Q1/6806 ,  C12Q1/6804 ,  G01N33/53

CPC classification number: C12N15/1003 ,  C12N15/10 ,  C12N15/1093 ,  C12Q1/6804 ,  C12Q1/6806 ,  G01N33/5308 ,  C12Q1/6886

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.

公开(公告)号：US20190144848A1

公开(公告)日：2019-05-16

申请号：US16098620

申请日：2017-05-03

Applicant: UNIVERSITY HEALTH NETWORK

Inventor： Daniel Diniz DE CARVALHO ,  Shu Yi SHEN ,  Rajat SINGHANIA

IPC: C12N15/10

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 mg of cell-free DNA, comprising the steps of: subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated; denaturing the sample; and capturing cell-free methylated DNA using a binder selective for methylated polynucleotides.

公开(公告)号：US20230024827A1

公开(公告)日：2023-01-26

申请号：US17736570

申请日：2022-05-04

Applicant: UNIVERSITY HEALTH NETWORK ,  VAN ANDEL RESEARCH INSTITUTE

Inventor： Samantha L. WILSON ,  Shu Yi SHEN ,  Daniel DINIZ DE CARVALHO ,  Michael M. HOFFMAN ,  Timothy J. TRICHE

IPC: C12Q1/6858

Abstract: There is described herein, a method of capturing and analyzing cell-free methylated DNA in a sample. The method involves subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA. A predetermined amount of control synthetic DNA fragments are added to the sample. The control synthetic DNA fragments each have a known nucleic acid sequence that does not align to a target genome sequence, and at least some of the control synthetic DNA fragments are methylated. The sample is denatured, and cell-free methylated DNA and the control synthetic DNA fragments are captured using a binder selective for methylated polynucleotides. The captured DNA is amplified and sequenced.