公开(公告)号：WO2021087615A1

公开(公告)日：2021-05-14

申请号：PCT/CA2020/051507

申请日：2020-11-06

Applicant: UNIVERSITY HEALTH NETWORK ,  VAN ANDEL RESEARCH INSTITUTE

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

IPC: C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6844 ,  C12Q1/6869

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.

公开(公告)号：WO2021203200A1

公开(公告)日：2021-10-14

申请号：PCT/CA2021/050464

申请日：2021-04-07

Applicant: UNIVERSITY HEALTH NETWORK

Inventor： DINIZ DE CARVALHO, Daniel ,  HE, Housheng ,  ETTAYEBI, Ilias ,  SOARES, Fraser ,  LOO YAU, Helen

IPC: C12N5/10 ,  A61K31/7088 ,  A61K31/7105 ,  A61K35/17 ,  A61K38/46 ,  A61P35/00 ,  A61P37/02 ,  C07K19/00 ,  C12N15/113 ,  C12N15/54 ,  C12N15/62 ,  C12N15/63 ,  C12N5/0783 ,  C12N9/22

Abstract: Methods of increasing T cell effector function in a T cell population are provided that involve inhibiting one or more genetic subunits of the SAGA (Spt-Ada-Gcn5-acetyltransferase) gene regulation complex in the T cell population. Also provided are methods of using such T cell populations in the treatment of cancer patients.

公开(公告)号：WO2021253138A1

公开(公告)日：2021-12-23

申请号：PCT/CA2021/050842

申请日：2021-06-18

Applicant: UNIVERSITY HEALTH NETWORK

Inventor： BRATMAN, Scott Victor ,  BURGENER, Justin Matthew ,  DINIZ DE CARVALHO, Daniel

IPC: C12Q1/6809 ,  C12Q1/6886 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/68

Abstract: In an aspect, there is provided a method of detecting the presence of ctDNA from cancer cells in a subject comprising: (a) providing a sample of cell-free DNA from a subject; (b) subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA; (c) optionally adding a first amount of filler DNA to the sample, wherein at least a portion of the filler DNA is methylated, then further optionally denaturing the sample; (d) capturing cell-free methylated DNA using a binder selective for methylated polynucleotides; (e) sequencing the captured cell-free methylated DNA; (f) comparing the sequences of the captured cell-free methylated DNA to control cell-free methylated DNAs sequences from healthy and cancerous individuals; (g) 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; wherein in at least one of the capturing step, the comparing step or the identifying step, the subject cell-free methylated DNA is limited to a sub-population according to a fragment length metric.

公开(公告)号：WO2021243464A1

公开(公告)日：2021-12-09

申请号：PCT/CA2021/050765

申请日：2021-06-03

Applicant: UNIVERSITY HEALTH NETWORK

Inventor： DINIZ DE CARVALHO, Daniel ,  MEHDIPOUR, Parinaz ,  MARHON, Sajid

IPC: C12Q1/6809 ,  A61K45/00 ,  A61P35/00 ,  A61K45/06

Abstract: There is described herein a method of assessing a subject's responsiveness to cancer therapy, comprising: providing a sample from the subject comprising cancers cells or suspected cancer cells; measuring or estimating the expression levels of inverted repeats (IR) Alus in the cells; and determining that the subject would be responsive to 5 cancer therapy if the subject cells exhibit expression levels of inverted repeats (IR) Alus with reference to expression levels in control samples.

公开(公告)号：EP4435118A2

公开(公告)日：2024-09-25

申请号：EP24177800.0

申请日：2020-11-06

Applicant: University Health Network ,  Van Andel Research Institute

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

IPC: C12Q1/6869

CPC classification number: C12Q1/6804 ,  C12Q1/6806 ,  C12N15/1003

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.

公开(公告)号：EP4055183A1

公开(公告)日：2022-09-14

申请号：EP20884272.4

申请日：2020-11-06

Applicant: University Health Network ,  Van Andel Research Institute

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

IPC: C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6844 ,  C12Q1/6869

公开(公告)号：EP4168574A1

公开(公告)日：2023-04-26

申请号：EP21825516.4

申请日：2021-06-18

Applicant: University Health Network

Inventor： BRATMAN, Scott Victor ,  BURGENER, Justin Matthew ,  DINIZ DE CARVALHO, Daniel

IPC: C12Q1/6809 ,  C12Q1/6886 ,  G16B20/00 ,  G16B30/00 ,  C12Q1/68

公开(公告)号：EP4435118A3

公开(公告)日：2025-01-15

申请号：EP24177800.0

申请日：2020-11-06

Applicant: University Health Network ,  Van Andel Research Institute

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

IPC: C12Q1/68 ,  C12Q1/6809 ,  C12Q1/6844 ,  C12Q1/6869

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.

公开(公告)号：EP4425178A2

公开(公告)日：2024-09-04

申请号：EP24176389.5

申请日：2017-05-03

Applicant: University Health Network ,  Sinai Health System

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

IPC: G01N33/53

CPC classification number: C12N15/10 ,  C12N15/1093 ,  C12Q1/6804 ,  C12Q1/6806 ,  C12Q1/6886 ,  G01N33/5308 ,  C12Q2600/15420130101 ,  C12N15/1003

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 ng 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：EP4425178A3

公开(公告)日：2024-12-18

申请号：EP24176389.5

申请日：2017-05-03

Applicant: University Health Network ,  Sinai Health System

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

IPC: C12Q1/68 ,  C12N15/10 ,  C40B30/04 ,  C12Q1/6804 ,  C12Q1/6806 ,  C12Q1/6886 ,  G01N33/53

Abstract: There is described herein, a method of capturing cell-free methylated DNA from a sample having less than 100 ng 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.