US 12,412,639 B2
Method of characterizing a tumor based on an immune gene expression signature in regulatory T cell (Treg)-enriched tumor samples
Kevin B. Givechian, Irvine, CA (US); Kamil A. Wnuk, Playa Vista, CA (US); Chad Garner, Culver City, CA (US); Stephen Charles Benz, Culver City, CA (US); Hermes J. Garban, Culver City, CA (US); Shahrooz Rabizadeh, Agoura Hills, CA (US); Kayvan Niazi, Culver City, CA (US); and Patrick Soon-Shiong, Culver City, CA (US)
Assigned to NantOmics, LLC, Culver City, CA (US); NantBio, Inc., Culver City, CA (US); and Nant Holdings IP, LLC, Culver City, CA (US)
Filed by Nantomics LLC, Culver City, CA (US); NantBio, Inc., Culver City, CA (US); and Nant Holdings IP, LLC, Culver City, CA (US)
Filed on Jul. 26, 2023, as Appl. No. 18/359,437.
Application 18/359,437 is a division of application No. 16/767,366, granted, now 11,756,651, previously published as PCT/US2018/067319, filed on Dec. 21, 2018.
Claims priority of provisional application 62/613,560, filed on Jan. 4, 2018.
Prior Publication US 2023/0377686 A1, Nov. 23, 2023
This patent is subject to a terminal disclaimer.
Int. Cl. G16B 25/10 (2019.01); C12Q 1/6886 (2018.01)
CPC G16B 25/10 (2019.02) [C12Q 1/6886 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/158 (2013.01)] 16 Claims
 
1. A method of characterizing a tumor, comprising:
quantifying or obtaining expression strength for a plurality of differentially expressed genes, wherein the genes are differentially expressed in an immune competent cell in the tumor, wherein the plurality of differentially expressed genes comprise at least six of PCDHA5, EFNA5, BARX2, DPP4, CEMP1, SSX1, CD70, LTB, LILRA4, TRAV9.2, GZMM, ZAP70, CD3E, SIRPG, CD3D, SIT1, CD27, CTLA4, ICOS, CD5, GPR171, SH2D1A, TRAT1, ITK, CD3G, RYR1, LAIR2, NTN3, PMCH, GPR1, PLCH2, and BCL11B, and wherein the immune competent cell is a regulatory T cell (Treg);
associating the expression strengths with a cluster representative of overall patient survival, immunogenicity of the tumor, and/or chemosensitivity of the tumor; and
using the association to thereby characterize the tumor as being associated with prolonged overall patient survival, immunogenicity of the tumor, and/or chemosensitivity of the tumor.