US 12,391,752 B2
Methods of enriching or amplifying nucleic acids in a sample from a patient with inflammatory bowel disease
Laurens Kruidenier, San Diego, CA (US); Mahyar Sabripour, San Diego, CA (US); Janine Bilsborough, Adelaide (AU); 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 Feb. 13, 2023, as Appl. No. 18/168,519.
Application 18/168,519 is a division of application No. 17/409,639, filed on Aug. 23, 2021, granted, now 12,215,147.
Application 17/409,639 is a continuation of application No. 17/118,441, filed on Dec. 10, 2020, granted, now 11,136,386, issued on Oct. 5, 2021.
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 2023/0272061 A1, Aug. 31, 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)] 34 Claims
 
1. A method of enriching a plurality of target nucleic acids in a biological sample from a subject with an inflammatory bowel disease (IBD), the method comprising:
(a) contacting a plurality of synthetic oligonucleotide molecules with the plurality of target nucleic acids, wherein each of the target nucleic acids in the plurality of target nucleic acids is complementary to at least one of the plurality of synthetic oligonucleotide molecules;
(b) hybridizing the plurality target nucleic acids to the at least one of the plurality of the synthetic oligonucleotide molecules;
(c) amplifying the plurality of target nucleic acids hybridized to the at least one of the plurality of synthetic oligonucleotide molecules in (b), thereby producing enriched target nucleic acids; and
(d) detecting the enriched target nucleic acids, wherein the detecting is predictive of a positive therapeutic response to an inhibitor of tumor necrosis factor-like cytokine 1A (TL1A) activity or expression with a positive predictive value (PPV) of at least about 70%.