US 11,053,542 B2
Compositions and methods for screening mutations in thyroid cancer
Shih-Min Cheng, San Juan Capistrano, CA (US); Joseph J. Catanese, San Juan Capistrano, CA (US); Andrew Grupe, San Juan Capistrano, CA (US); Feras Hantash, Mission Viejo, CA (US); Frederic M. Waldman, San Juan Capistrano, CA (US); and Kevin Qu, San Juan Capistrano, CA (US)
Assigned to Quest Diagnostics Investments LLC, Secaucus, NJ (US)
Appl. No. 16/67,189
Filed by Quest Diagnostics Investments LLC, Madison, NJ (US)
PCT Filed Dec. 30, 2016, PCT No. PCT/US2016/069478
§ 371(c)(1), (2) Date Jun. 29, 2018,
PCT Pub. No. WO2017/117523, PCT Pub. Date Jul. 6, 2017.
Claims priority of provisional application 62/439,572, filed on Dec. 28, 2016.
Claims priority of provisional application 62/273,783, filed on Dec. 31, 2015.
Prior Publication US 2019/0112653 A1, Apr. 18, 2019
Int. Cl. C12Q 1/6874 (2018.01); C12Q 1/6886 (2018.01); C12Q 1/6869 (2018.01); C12N 15/10 (2006.01)
CPC C12Q 1/6874 (2013.01) [C12N 15/1068 (2013.01); C12Q 1/6869 (2013.01); C12Q 1/6886 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/156 (2013.01)] 30 Claims
 
1. A method for detecting at least one mutation in a plurality of thyroid cancer-related genes in a subject comprising
(a) extracting DNA from a FFPE thyroid sample or a FNA thyroid sample obtained from the subject;
(b) generating a DNA library of a first plurality of amplicons using a hot start DNA polymerase that substantially lacks 5′-3′ exonuclease activity, wherein at least one amplicon corresponds to each of the plurality of thyroid cancer-related genes, said plurality of thyroid cancer-related genes comprising BRAF, NRAS, HRAS, KRAS, PIK3CA, TP53, CTNNB1, PTEN, TSHR, AKT1, GNAS, RET, EIF1AX, and TERT promoter;
(c) incorporating an adapter sequence on to the ends of the first plurality of amplicons via polymerase chain reaction; and
(d) detecting at least one mutation in at least one of the first plurality of amplicons using high throughput massive parallel sequencing.