US 11,913,072 B2
Detection of MET exon 14 deletions and associated therapies
Cindy Cheung, Fremont, CA (US); Grantland Hillman, Oakland, CA (US); Xiaoju Max Ma, San Carlos, CA (US); Chitra Manohar, San Ramon, CA (US); and Lily Wong, San Mateo, CA (US)
Assigned to Roche Molecular Systems, Inc., Pleasanton, CA (US)
Filed by Roche Molecular Systems, Inc., Pleasanton, CA (US)
Filed on May 11, 2017, as Appl. No. 15/592,475.
Claims priority of provisional application 62/336,362, filed on May 13, 2016.
Prior Publication US 2017/0327887 A1, Nov. 16, 2017
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/686 (2018.01); C12Q 1/6876 (2018.01); C12Q 1/6886 (2018.01)
CPC C12Q 1/6876 (2013.01) [C12Q 1/686 (2013.01); C12Q 1/6886 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/158 (2013.01); C12Q 2600/16 (2013.01)] 9 Claims
 
1. A method of providing treatment for an individual with cancer comprising:
(a) obtaining a plasma or formalin fix paraffin embedded tissue (FFPET) sample comprising RNA from the individual;
(b) carrying out a reverse transcription reaction on the RNA to produce cDNA;
(c) carrying out an amplification reaction comprising contacting the cDNA with (i) a primer set and a first probe labeled with a first label that specifically amplify and detect MET exon 13-14 junction, (ii) a primer set and a second probe labeled with a second label that specifically amplify and detect MET exon 14-15 junction, and (iii) a primer set and a third probe labeled with a third label that specifically amplify and detect MET exon 13-15 junction;
(d) detecting the presence of a MET exon 14 deletion if an amplification product is formed and detected by the primer set and the third probe of (iii); and
(e) providing treatment for the individual with a MET inhibitor if a MET exon 14 deletion is present;
wherein steps (b) and (c) are carried out in the same vessel, wherein the first probe is specific for the junction point of the MET exon 13-14 junction, the second probe is specific for the junction point of the MET exon 14-15 junction, and the third probe is specific for the junction point of the MET exon 13-15 junction, and wherein the third probe comprises a sequence selected from the group consisting of SEQ ID NOs: 53-55.