US 12,215,147 B2
Methods of selecting, based on polymorphisms, an inflammatory bowel disease subject for treatment with an anti-TL1A antibody
Laurens Kruidenier, San Diego, CA (US); Mahyar Sabripour, San Diego, CA (US); Janine Bilsborough, Los Angeles, CA (US); Dermot P. McGovern, Los Angeles, CA (US); and Dalin Li, Los Angeles, CA (US)
Assigned to PROMETHEUS BIOSCIENCES, INC., San Diego, CA (US); and CEDARS-SINAI MEDICAL CENTER, Los Angeles, CA (US)
Filed by PROMETHEUS BIOSCIENCES, INC., San Diego, CA (US); and CEDARS-SINAI MEDICAL CENTER, Los Angeles, CA (US)
Filed on Aug. 23, 2021, as Appl. No. 17/409,639.
Application 17/409,639 is a continuation of application No. 17/118,441, filed on Dec. 10, 2020, granted, now 11,136,386.
Application 17/118,441 is a continuation of application No. PCT/US2020/032679, filed on May 13, 2020.
Claims priority of provisional application 62/847,798, filed on May 14, 2019.
Prior Publication US 2023/0018729 A1, Jan. 19, 2023
Int. Cl. C12Q 1/6883 (2018.01); A61P 1/00 (2006.01); A61P 1/04 (2006.01); C07K 16/24 (2006.01); C07K 16/28 (2006.01); A61K 39/00 (2006.01)
CPC C07K 16/241 (2013.01) [A61P 1/00 (2018.01); A61P 1/04 (2018.01); C07K 16/2875 (2013.01); C12Q 1/6883 (2013.01); A61K 2039/505 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01)] 45 Claims
 
1. A method of selecting a subject having inflammatory bowel disease (IBD) for treatment with an anti-tumor necrosis factor-like cytokine 1A (anti-TL1A) antibody or an antigen-binding fragment thereof, the method comprising:
(a) providing a biological sample from a subject having IBD to determine presence of three or more polymorphisms selected from the group consisting of: rs1892231, rs56124762, rs6478109, rs2070558, rs2070561, rs11897732, rs6740739, rs17796285, rs7935393, rs12934476, rs12457255, rs2070557, rs4246905, rs10974900, rs12434976, rs16901748, rs2815844, rs889702, rs2409750, rs1541020, rs4942248, rs2297437, rs41309367, rs10733509, rs10750376, rs10932456, rs1326860, rs1528663, rs951279, rs9806914, rs1690492, rs420726, rs7759385, rs2548147, rs7278257, rs11221332, rs11558819, rs2329718, rs2070559, rs2070560, and any proxy polymorphism in linkage disequilibrium with any of the foregoing as determined with an R2 of at least 0.85;
(b) selecting a subject determined to have the presence of the three or more polymorphisms in (a), wherein the presence of the three or more polymorphisms is indicative of a positive therapeutic response to a treatment with an anti-TL1A antibody or an antigen-binding fragment thereof with a positive predictive value (PPV) of at least about 70%; and
(c) administering a therapeutically effective amount of the anti-TL1A antibody or antigen-binding fragment thereof to the subject selected in (b).