Jennifer Lea Busby

US Patent:

20230041030, Feb 9, 2023

Filed:

May 13, 2022

Appl. No.:

17/744354

Inventors:

- Emeryville CA, US
Aleksandra Katarzyna Nowicka - Watertown MA, US
Abubakar Jalloh - Somerville MA, US
Roman Yelensky - Newton MA, US
James Xin Sun - Newton MA, US
Jennifer Busby - Burlington MA, US
Matthew Joseph Davis - Scituate MA, US

International Classification:

C07K 16/28
C12N 5/0783
C12N 15/85
A61P 35/00

Abstract:

Provided herein are target HLA-PEPTIDE antigens, e.g., HLA-PEPTIDE neoantigens and shared tumor HLA-PEPTIDE antigens, and antigen binding proteins (ABPs) that bind the target HLA-PEPTIDE antigens. Also disclosed are methods for identifying target HLA-PEPTIDE antigens as well as identifying one or more antigen binding proteins that bind a given HLA-PEPTIDE target antigen.

US Patent:

20210166784, Jun 3, 2021

Filed:

Nov 23, 2020

Appl. No.:

17/101522

Inventors:

- Emeryville CA, US
Adnan Derti - Dedham MA, US
Jennifer Busby - Burlington MA, US

International Classification:

G16B 30/00
A61K 39/00

Abstract:

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

US Patent:

20210113673, Apr 22, 2021

Filed:

Apr 19, 2018

Appl. No.:

16/606577

Inventors:

- Emeryville CA, US
Jennifer Busby - Burlington MA, US
Roman Yelensky - Newton MA, US

International Classification:

A61K 39/00
A61K 35/17
G16B 20/20
C12Q 1/6886
G16B 20/30
G16B 40/00

Abstract:

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

US Patent:

20210098077, Apr 1, 2021

Filed:

Nov 23, 2020

Appl. No.:

17/101518

Inventors:

- Emeryville CA, US
Adnan Derti - Dedham MA, US
Jennifer Busby - Burlington MA, US

International Classification:

G16B 30/00
A61K 39/00

Abstract:

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.

US Patent:

20210011026, Jan 14, 2021

Filed:

Nov 21, 2018

Appl. No.:

16/766627

Inventors:

- Emeryville CA, US
Thomas Francis Boucher - Boston MA, US
Roman Yelensky - Newton MA, US
Jennifer Busby - Burlington MA, US

International Classification:

G01N 33/68
C40B 30/04
G01N 33/574
G16B 30/00
G16B 40/00

Abstract:

Given a set of therapeutic epitopes, a cassette sequence is designed to reduce the likelihood that junction epitopes are presented in the patient. The cassette sequence is designed by taking into account presentation of junction epitopes that span the junction between a pair of therapeutic epitopes in the cassette. The cassette sequence may be designed based on a set of distance metrics each associated with a junction of the cassette. The distance metric may specify a likelihood that one or more of the junction epitopes spanning between a pair of adjacent epitopes will be presented.

US Patent:

20200363414, Nov 19, 2020

Filed:

Sep 5, 2018

Appl. No.:

16/644934

Inventors:

- EMERYVILLE CA, US
Jennifer Busby - Burlington MA, US
Matthew Joseph Davis - Scituate MA, US
Lauren Elizabeth Young - Boston MA, US
Joshua Michael Francis - Weymouth MA, US
Christine Palmer - Cambridge MA, US
Mojca Skoberne - Cambridge MA, US

International Classification:

G01N 33/569
G16B 30/00
G16B 40/00
C12N 5/0783
G06N 20/00
G06N 5/04

Abstract:

A method for identifying T-cells that are antigen-specific for at least one neoantigen that is likely to be presented on surfaces of tumor cells of a subject. Peptide sequences of tumor neoantigens are obtained by sequencing the tumor cells of the subject. The peptide sequences are input into a machine-learned presentation model to generate presentation likelihoods for the tumor neoantigens, each presentation likelihood representing the likelihood that a neoantigen is presented by an MHC allele on the surfaces of the tumor cells of the subject. A subset of the neoantigens is selected based on the presentation likelihoods. T-cells that are antigen-specific for at least one of the neoantigens in the subset are identified. These T-cells can be expanded for use in T-cell therapy. TCRs of these identified T-cells can also be sequenced and cloned into new T-cells for use in T-cell therapy.

US Patent:

20200010849, Jan 9, 2020

Filed:

Nov 22, 2017

Appl. No.:

16/463787

Inventors:

- Emeryville CA, US
Jennifer Busby - Burlington MA, US
Adnan Derti - Dedham MA, US
Leonid Gitlin - Foster City CA, US
Gijsbert Grotenbreg - Berkeley CA, US
Karin Jooss - Emeryville CA, US
Ciaran Daniel Scallan - San Francisco CA, US
Roman Yelensky - Newton MA, US

International Classification:

C12N 15/86
C12N 7/00
A61K 35/761
A61P 35/00
C07K 14/74
A61K 39/00
A61K 39/395
C07K 16/28

Abstract:

Disclosed herein are chimpanzee adenoviral vectors that include neoantigen-encoding nucleic acid sequences derived from a tumor of a subject. Also disclosed are nucleotides, cells, and methods associated with the vectors including their use as vaccines.

US Patent:

20190065675, Feb 28, 2019

Filed:

Jun 6, 2018

Appl. No.:

16/001569

Inventors:

- Emeryville CA, US
Adnan Derti - Dedham MA, US
Jennifer Busby - Burlington MA, US

International Classification:

G06F 19/22
A61K 39/00
A61K 35/15

Abstract:

Disclosed herein is a system and methods for determining the alleles, neoantigens, and vaccine composition as determined on the basis of an individual's tumor mutations. Also disclosed are systems and methods for obtaining high quality sequencing data from a tumor. Further, described herein are systems and methods for identifying somatic changes in polymorphic genome data. Finally, described herein are unique cancer vaccines.