Methods of selecting, based on polymorphisms, an inflammatory bowel disease subject for treatment with an anti-TL1A antibody
AssigneesPrometheus Biosciences, Inc., Cedars-Sinai Medical Center
InventorsLaurens Kruidenier, Mahyar Sabripour, Janine Bilsborough, Dermot P. McGovern, Dalin Li
Life of this patent
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Abstract
Provided are methods, systems, and kits for selecting a patient for treatment with a therapeutic agent based on a presence of a genotype associated with a positive therapeutic response to the therapeutic agent. The therapeutic agent, in some embodiments, is an inhibitor of TL1A activity or expression, such as for example, an anti-TL1A antibody.
Claims45
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).
A method comprising:
- (a) contacting genetic materials in a biological sample obtained from a subject having inflammatory bowel disease (IBD) with one or more nucleic acid primer pairs having forward and reverse primers capable of hybridizing to one or more target nucleic acid sequences, the one or more target nucleic acid sequences collectively comprising chromosome positions 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) amplifying the target nucleic acid sequences by polymerase chain reactions with the nucleic acid primer pairs of (a);
- (c) inputting results from (b) into a computer system;
- and
- (d) analyzing the results of (b) via the computer system to determine the presence in the target nucleic acid sequences of the three or more polymorphisms of step (a),
- wherein the presence of the three or more polymorphisms is indicative of a positive therapeutic response to a treatment with an anti-tumor necrosis factor-like cytoking 1A (anti-TL1A) antibody or an antigen-binding fragment thereof with a positive predictive value (PPV) of at least about 70%, and wherein the computer system comprises a storage unit configured to store the three or more polymorphisms.
Dependencies are inferred from the claim text.