US 2015 0080239A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0080239 A1 RHODES et al. (43) Pub. Date: Mar. 19, 2015 (54) CLASSIFICATION AND ACTIONABILITY Publication Classification INDICES FOR CANCER (51) Int. Cl. (71) Applicant: LIFE TECHNOLOGIES CI2O I/68 (2006.01) CORPORATION, Carlsbad, CA (US) (52) U.S. Cl. CPC ........ CI2O I/6886 (2013.01); C12O 2600/1 18 (72) Inventors: Daniel RHODES, Ann Arbor, MI (US); (2013.01); C12O 2600/158 (2013.01) Seth SADIS, Ann Arbor, MI (US) USPC .............................................................. SO6/9 (73) Assignee: LIFE TECHNOLOGIES CORPORATION, Carlsbad, CA (US) (57) ABSTRACT (21) Appl. No.: 14/212,717 The disclosure provides compositions, kits, and methods for 1-1. detecting a plurality of genes and associated variants in a (22) Filed: Mar 14, 2014 sample from a subject with cancer. The compositions, kits, O O and methods include a set of oligonucleotides, typically prim Related U.S. Application Data ers and/or probes that can hybridize to identify a gene variant. (60) Provisional application No. 61/877,827, filed on Sep. The methods disclosed herein provide for a mutation status of 13, 2013, provisional application No. 61/891,224, a tumor to be determined and Subsequently associated with a filed on Oct. 15, 2013. report comprising an actionable treatment recommendation. Patent Application Publication Mar. 19, 2015 Sheet 1 of 7 US 2015/0080239 A1 Bulle?d p?AOIdde-WOH 6nup p?AOIdde-WOH XOIO |?In6|- Patent Application Publication Mar. 19, 2015 Sheet 2 of 7 US 2015/0080239 A1 d??O919uol Z?InôH Patent Application Publication Mar. 19, 2015 Sheet 3 of 7 US 2015/0080239 A1 €)NIONE(TOES d??OIIduol £?Inôl JOun1 a?dues <!-- Patent Application Publication Mar. 19, 2015 Sheet 4 of 7 US 2015/0080239 A1 7?In6|- NOISSERHCHXENOIST)– LèJOddf|S Spee. WNO Spee.J WN Patent Application Publication Mar. 19, 2015 Sheet 5 of 7 US 2015/0080239 A1 TO Publish Report Variant Review Read Clinical Select Gene(s) Type Variant Support Driver Evidence SNP V600E 450 / 1203 X SNP R72L 110 | 880 ARID1A INDEL 336 | 662 X AMP 8 copies 1100 X FGFR3, FUSION FGFR3, TACC3 TACC3 120 Figure 5A Patent Application Publication Mar. 19, 2015 Sheet 6 of 7 US 2015/0080239 A1 From Variant Review Publish Report Sample Details Comprehensive Test Results Significant Findings FGFR3-TACC3 Fusion Clinical Research 120 reads 0 approved therapies -1-1 9 Investigational agents Phase III: lenvatinib, dovitinb, Population Statistics briwanib 2% Squamous Cell Lung Carcinoma 2 trial inclusion Criteria <5% Bladder, Glioblastoma, Head & Neck AZD-4547, BGJ-398 BRAF W600E Mutation Clinical Research 2 approved therapies " readsts Veum rafenib, dabrefinb Population Statistics 6 investigational agents 1% Squamous Cell Lung Carcinoma 68 trial inclusion criteria >30% Thyroid, Melanoma, Colorectal Automated report generation Figure 5B Patent Application Publication Mar. 19, 2015 Sheet 7 of 7 US 2015/0080239 A1 9?Inôl US 2015/0080239 A1 Mar. 19, 2015 CLASSIFICATION AND ACTIONABILITY variant detected is EGFRT790M; a MEK inhibitor when the INDICES FOR CANCER variant detected is KRAS G12CN/D/A/S/R/F, G13C, G13D and/or G12F. Vermurafenib when the variant detected is BACKGROUND BRAF V600E; an irreversible pan-erb inhibitor when the variant detected is ERBB2 exon 20 ins; and a PIC3CA inhibi 0001 Cancer is a broad group of diseases involving tor when the variant detected is PIK3CA (E545K, E545G, unregulated cell growth. Although the causes of cancer are E545a, H1047R, E542K and/or H1047L). diverse, our understanding of genetic alterations that are 0007. In another embodiment, the disclosure provides a involved is increasing rapidly. In this regard, a growing num method of detecting a nucleic acid variant in a sample, com ber of treatment regimens are available. However, many treat prising obtaining a biological sample, amplifying at least one ment regimes are only effective against cancers that have a gene selected from EGFR, ALK, ROS1, KRAS, BRAF, particular genetic variation. Therefore, a test that can detect ERBB2, MET, RET, FGFR1, KIT/PGDFRA, PIK3CA, many different specific actionable genetic variations would AKT1, BRAF, and HRAS genes, using primers that (a) have significant value to cancer patients. amplifying at least one variant selected from EGFR (L858R, 0002 The disclosed compositions, kits and methods pro Exon 19 del, G719X and/or T790M), KRAS (G12C/V/D/A/ vide comprehensive genetic variance screening of a cancer in S/R/F, G13C, G13D and/or G12F), BRAF (L597R, D594H/ a single panel utilizing a single cancer sample. The genetic N, V600E), ERBB2 exon 20 ins, PIK3CA (E545K, E545G, variants form the basis of an actionable treatment recommen E545a, H1047R, and/or H1047L); and (b) detecting at least dation framework provided herein. one nucleic acid variant present in the sample. 0008. In yet embodiment, a method of treating lung adeno BRIEF SUMMARY carcinoma in a patient is disclosed. The method comprises: 0003. The disclosure provides methods, compositions and testing for the presence of variants in at least one of ALK, kits. In one embodiment, a method to determine an actionable ROS1, KRAS, BRAF, ERBB2, MET, RET, FGFR1, and KIT/ treatment recommendation for a subject diagnosed with lung PDGFRA genes in a lung tumor sample from the patient and cancer is provided. The method comprises: obtaining a bio administering a therapeutically effective amount a treatment logical sample from the Subject; detecting at least one variant to the patient, wherein the treatment is: Crizotinib when the using a set of probes that hybridize to and amplify EGFR, variant detected is an ALK fusion, ROS 1 fusion (EZR. ALK, ROS1, KRAS, BRAF, ERBB2, MET, RET, FGFR1, SLC34A2, CD74, and/or SDC4), or MET gene amplification; KIT/PGDFRA, PIK3CA, AKT1, BRAF, and HRAS genes to EGFR tyrosine kinase inhibitor (TKI) when the variant detect at least one variant; determining, based on the at least detected is EGFR (L858R, Exon 19 del, and/or G719X): a one variant detected, an actionable treatment recommenda MEK inhibitor when the variant detected is KRAS G12CN/ tion for the subject. D/A/S/R/F, G13C, G13D and/or G12F: Vermurafenib when 0004. The method comprises: contacting a biological the variant detected is BRAF V600E; and an irreversible sample from a subject; detecting at least one variant using a pan-erb inhibitor when the variant detected is ERBB2 exon set of probes that hybridize to and amplify EGFR, ALK, 20 ins. ROS1, KRAS, BRAF, ERBB2, MET, RET, FGFR1, KIT/ 0009. In yet another embodiment, the disclosure provides PGDFRA, PIK3CA, AKT1, BRAF, and HRAS genes to a method of identifying patients with lung cancer eligible for detect at least one variant; determining, based on the at least treatment with crizotnib, an EGFRTKI, or a treatment other one variant detected, an actionable treatment recommenda than an EGFR TKI, a MEK inhibitor, Vermurafenib, or an tion for the subject. irreversible pan-erb inhibitor, comprising testing a lung 0005. In another embodiment, the disclosure provides a tumor sample from the patient for the presence of a variant method to determine an actionable treatment recommenda comprising an ALK fusion, ROS1 fusion (EZR. SLC34A2, tion for a Subject diagnosed with lung cancer, comprising: CD74, and/or SDC4), EGFR (L858R, Exon 19 del, and/or detecting in a sample from a subject, at least one variant using T790M), KRAS (G12C/V/D/A), wherein the presence of at a set of probes that hybridize to and amplify ALK, ROS1, least one of said variants indicates the patient is eligible for KRAS, BRAF, ERBB2, MET, RET, FGFR1, and KIT/PDG treatment with at least one of said treatments. FRA genes to detect at least one variant, and determining, 0010. The disclosure, in certain embodiments, also pro based on the at least one variant detected, an actionable treat vides a kit comprising a set of probes, wherein the set of ment recommendation for the Subject. probes specifically recognize the genes AKT1, ALK, BRAF, 0006. In yet other embodiments, a method to determine ERBB2, EGFR, FGFR1, HRAS, KIT, KRAS, MET, the likelihood of a response to a treatment in an individual PIK3CA, RET and ROS, and wherein the set of probes can afflicted with lung cancer is provided. The method comprises: recognize and distinguish one or more allelic variants of the determining the presence or absence of at least one gene genes AKT1, ALK, BRAF, ERBB2, EGFR, HRAS, KRAS, variant in a sample obtained from the individual, wherein the MET, PIK3CA, RET and ROS. at least one variant is in EGFR, ALK, ROS1, KRAS, BRAF, 0011 Certain embodiments of the disclosure further pro ERBB2, MET, RET, FGFR1, KIT/PGDFRA, PIK3CA, vide a composition comprising a set of probes, wherein the set AKT1, BRAF, and/or HRAS genes, wherein the presence of of probes specifically recognize the genes AKT1, ALK, at least one variant indicates the individual is likely or BRAF, ERBB2, EGFR, FGFR1, HRAS, KIT, KRAS, MET, unlikely to respond to the treatment, wherein the treatment is PIK3CA, RET and ROS, and wherein the set of probes can selected from: crizotinib when the variant detected is an ALK recognize and distinguish one or more allelic variants of the fusion; ROS1 fusion (EZR, SLC34A2, CD74, and/or SDC4): genes AKT1, ALK, BRAF, ERBB2, EGFR, HRAS, KRAS, MET gene amplification; EGFR tyrosine kinase inhibitor MET, PIK3CA, RET and ROS. (TKI) when the variant detected is EGFR (L858R, Exon 19 0012. In certain embodiments of the disclosure, the com del, and/or G719X): a non-EGFRTKI treatment when the positions can comprise a set of probes that specifically rec US 2015/0080239 A1 Mar. 19, 2015 ognize the genes in Tables 11-15 and 17. Further, the methods including driver mutations.