	US 11,981,966 B2
	Methods for screening solid tumors for mutations
Heather Sanders, San Juan Capistrano, CA (US); Kevin Qu, San Juan Capistrano, CA (US); James Prentice, San Juan Capistrano, CA (US); and Frederic Waldman, San Juan Capistrano, CA (US)
Assigned to Quest Diagnostics Investments LLC, Secaucus, NJ (US)
Filed by Quest Diagnostics Investments LLC, Secaucus, NJ (US)
Filed on May 8, 2020, as Appl. No. 16/870,033.
Application 16/870,033 is a continuation of application No. 15/576,219, granted, now 10,689,710, previously published as PCT/US2015/057733, filed on Oct. 28, 2015.
Claims priority of provisional application 62/246,895, filed on Oct. 27, 2015.
Claims priority of provisional application 62/166,996, filed on May 27, 2015.
Prior Publication US 2020/0385817 A1, Dec. 10, 2020
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6886 (2018.01)

CPC C12Q 1/6886 (2013.01) [C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/16 (2013.01)]

12 Claims

1. A method for detecting at least one mutation in a plurality of cancer-related genes in a subject diagnosed with breast cancer or colorectal cancer comprising:

(a) extracting genomic DNA from a formalin fixed paraffin-embedded specimen obtained from the subject;

(b) generating a library comprising amplicons corresponding to each of a plurality of cancer-related genes, said plurality of cancer-related genes comprising AKT1, ERBB2, FOXL2, IDH2, NRAS, RET, ALK, ERBB4, GNA11, KIT, PDGFRA, SMO, BRAF, FBXW7, GNAQ, KRAS, PIK3CA, STK11, CTNNB1, FGFR2, GNAS, MAP2K1, PIK3R1, TP53, DDR2, FGFR3, HRAS, MET, PTCH1, EGFR, FGFR4, IDH1, NOTCH1, and PTEN, wherein the amplicons are generated in a multiplex amplification reaction using primer pairs specific for each of the cancer related genes and wherein at least two of the primer pairs are selected from the group consisting of the primers of SEQ ID NOS: 1-18, 45-54, and 71-274 or the group consisting of the primers of SEQ IN NOS: 19-44, 55-70, and 275-464, wherein:

(i) generating the library proceeds independently of using a bait set comprising nucleic acid sequences that are complementary to at least one of the plurality of amplicons, and

(ii) the quality of the genomic DNA extracted from the formalin fixed paraffin-embedded specimen is not assessed using quantitative PCR prior to generating the library;