US 12,404,557 B2
Biomarkers predictive of anti-immune checkpoint response
Eliezer Van Allen, Brookline, MA (US); and Diana Miao, Acton, MA (US)
Assigned to Dana-Farber Cancer Institute, Inc., Boston, MA (US)
Filed by Dana-Farber Cancer Institute, Inc., Boston, MA (US)
Filed on May 27, 2022, as Appl. No. 17/826,477.
Application 17/826,477 is a division of application No. 16/475,577, granted, now 11,377,697, previously published as PCT/US2018/012936, filed on Jan. 9, 2018.
Claims priority of provisional application 62/445,105, filed on Jan. 11, 2017.
Prior Publication US 2022/0389519 A1, Dec. 8, 2022
Int. Cl. C12Q 1/6886 (2018.01); G01N 33/50 (2006.01); G01N 33/574 (2006.01)
CPC C12Q 1/6886 (2013.01) [G01N 33/5011 (2013.01); G01N 33/57484 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01)] 18 Claims
 
1. A method of treating melanoma, non-small cell lung cancer (NSCLC), or head and neck squamous cell carcinoma (HNSCC) in a subject likely to be responsive to immune checkpoint therapy against PD-1 or CTLA-4, the method comprising:
i) selecting the subject, the subject having been identified according to:
a) determining the copy number of ARID2 in a sample from the subject having cancer selected from the group consisting of melanoma, non-small cell lung cancer (NSCLC), and head and neck squamous cell carcinoma (HNSCC), wherein the sample comprises nucleic acid molecules from the subject's cancer; and
b) comparing said copy number to that of a control sample,
wherein an increased copy number of ARID2 encoding a loss of function mutation in the subject sample, relative to the control sample identifies the cancer as being more likely to be responsive to the immune checkpoint therapy against PD-1 or CTLA-4; and
ii) administering the immune checkpoint therapy against PD-1 or CTLA-4 to the selected subject.