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(19) United States (12) Patent Application Publication (10) Pub US 20140288116A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0288116 A1 BANDLA et al. (43) Pub. Date: Sep. 25, 2014 (54) CLASSIFICATION AND ACTIONABILITY Publication Classi?cation INDICES FOR LUNG CANCER (51) Int. Cl. (71) Applicant: LIFE TECHNOLOGIES C12Q 1/68 (2006.01) CORPORATION, Carlsbad, CA (US) (52) US, Cl, CPC .................................. .. C12Q 1/6886 (2013.01) (72) InventorSI Santhoshi BANDLA, Northville, MI USPC ......................... .. 514/300; 514/318; 435/6.11 (US); Douglas Ross, Burlingame, CA (US); Seth Sadis, AnnArbor, MI (US); Peter Wyngaard, Ann Arbor, MI (US) (57) ABSTRACT (73) Assignee: LIFE TECHNOLOGIES CORPORATION Ca?Sbad’ CA (Us) The disclosure provides compositions, kits, and methods for (21) Appl_ No; 14/212,115 detecting a plurality of genes and associated variants in a sample from a subject With lung cancer. The compositions, (22) Filed: M31? 14, 2014 kits, and methods include a set of oligonucleotides, typically . primers and/or probes that can hybridize to identify a gene Related U's' Apphcatlon Data variant. The methods disclosed herein provide for a mutation (60) Provisional application No. 61/799,399, ?led on Mar. status of a tumor to be determined and subsequently associ 15, 2013. ated With an actionable treatment recommendation. US 2014/0288116 A1 Sep. 25, 2014 CLASSIFICATION AND ACTIONABILITY set of probes that hybridize to and amplify EGFR, ALK, INDICES FOR LUNG CANCER ROSl, KRAS, BRAF, ERBB2, ERRBB4, MET, RET, FGFRl, FGFR2, FGFR3, DDR2, NRAS, PTEN, MAP2K1, BACKGROUND TP53, STKl l, CTNNBl, SMAD4, FBXW7, NOTCH l, KIT/PGDFRA, PIK3CA,AKT1, BRAF, and HRAS genes to [0001] Lung cancer is the leading cause of cancer deaths detect at least one variant; determining, based on the at least among both men and women. It is a fast growing and highly one variant detected, an actionable treatment recommenda fatal disease. Nearly 60% of people diagnosed with lung tion for the subject. cancer die within one year of diagnosis and approximately 75% die within 2 years. There are two major types of lung [0007] In another embodiment, the disclosure provides a method to determine an actionable treatment recommenda cancer: small cell lung cancer (SCLC) and non-small cell lung cancer (N SCLC). Approximately 85% of lung cancers tion for a subject diagnosed with lung cancer, comprising: detecting in a sample from a subject, at least one variant using are NSCLC. There are 3 sub-types of NSCLC, which differ in size, shape, and biochemical make-up. Approximately a set of probes that hybridize to and amplify ALK, ROSl, 25-30% of all lung cancers are squamous cell carcinomas. KRAS, BRAF, ERBB2, MET, RET, FGFRl, and KIT/PDG Adenocarcinomas (e.g., bronchioloalveolar carcinoma) FRA genes to detect at least one variant, and determining, account for approximately 40% of lung cancers, and are based on the at least one variant detected, an actionable treat usually found in the outer region of the lung. Large-cell ment recommendation for the subject. undifferentiated carcinoma accounts for approximately [0008] In yet other embodiments, a method to determine 10-15% of all lung cancers. the likelihood of a response to a treatment in an individual [0002] SCLC and NSCLC are treated very differently. af?icted with lung cancer is provided. The method comprises: SCLC is mainly treated with chemotherapy, either alone or in determining the presence or absence of at least one gene combination with radiation. In contrast with treatment for variant in a sample obtained from the individual, wherein the SCLC, surgery is the only reliable method to cure NSCLC. at least one variant is in EGFR, ALK, ROSl, KRAS, BRAF, Lymph nodes are also removed to assess the spread of cancer. ERBB2, ERRBB4, MET, RET, FGFRl, FGFR2, FGFR3, In addition to surgery, chemotherapy can be used to treat DDR2, NRAS, PTEN, MAP2K1, TP53, STKl l, CTNNBl, NSCLC. SMAD4, FBXW7, NOTCH l, KIT/PGDFRA, PIK3CA, AKTl, and HRAS genes, wherein the presence of at least one [0003] A growing number of treatment regimens are becoming available for lung adenocarcinomas. However, the variant indicates the individual is likely or unlikely to respond to the treatment, wherein the treatment is selected from: cri treatment regimes in many cases are each only effective zotinib when the variant detected is an ALK fusion; ROSl against lung cancers that have a particular genetic variation. fusion (EZR, SLC34A2, CD74, and/or SDC4); MET gene Therefore, a test that could detect many different speci?c ampli?cation; EGFR tyrosine kinase inhibitor (TKI) when actionable genetic variations would have signi?cant value to the variant detected is EGFR (L858R, Exon 19 del, and/or lung cancer patients. However, the tissue required for cur rently available multiple genetic variance assays far exceeds G719X); a non-EGFR TKI treatment when the variant detected is EGFR T790M; a MEK inhibitor when the variant what is available from a typical tumor biopsy or resection. detected is KRAS Gl2CN/D/A/S/R/F, G13C, G13D and/or Furthermore, tests are not available for many of the genetic Gl2F; vermurafenib when the variant detected is BRAF variations, and there is no tool that can recommend a treat V600E; an irreversible pan-erb inhibitor when the variant ment based on a comprehensive scan of many known, action able genetic variations. detected is ERBB2 exon 20 ins; and a PIC3CA inhibitor when the variant detected is PIK3CA (E545K, E545G, E545a, [0004] The disclosed compositions, kits and methods pro H1047R, E542K and/or H1047L). vide comprehensive genetic variance screening of a lung cancer in a single panel utilizing a single lung cancer sample. [0009] In another embodiment, the disclosure provides a method of detecting a nucleic acid variant in a sample, com The genetic variants screened have actionable treatments or prising obtaining a biological sample, amplifying at least one are known to not respond well to certain treatments. This forms the basis of an actionable treatment recommendation gene selected from EGFR, ALK, ROSl, KRAS, BRAF, framework provided herein. ERBB2, ERRBB4, MET, RET, FGFRl, FGFR2, FGFR3, DDR2, NRAS, PTEN, MAP2K1, TP53, STKl l, CTNNBl, BRIEF SUMMARY SMAD4, FBXW7, NOTCH l, KIT/PGDFRA, PIK3CA, AKTl, and HRAS genes, using primers that (a) amplifying at [0005] The disclosure provides methods, compositions and least one variant selected from EGFR (L858R, Exon 19 del, kits. In one embodiment, a method to determine an actionable G719X and/or T790M), KRAS (Gl2C/V/D/A/S/R/F, G13C, treatment recommendation for a subject diagnosed with lung G13D and/or Gl2F), BRAF (L597R, D594H/N, V600E), cancer is provided. The method comprises: obtaining a bio ERBB2 exon 20 ins, PIK3CA (E545K, E545G, E545a, logical sample from the subject; detecting at least one variant H1047R, and/or H1047L); and (b) detecting at least one using a set of probes that hybridize to and amplify EGFR, nucleic acid variant present in the sample. ALK, ROSl, KRAS, BRAF, ERBB2, ERRBB4, MET, RET, [001 0] In yet embodiment, a method of treating lung adeno FGFRl, FGFR2, FGFR3, DDR2, NRAS, PTEN, MAP2K1, carcinoma in a patient is disclosed. The method comprises: TP53, STKl l, CTNNBl, SMAD4, FBXW7, NOTCH l, testing for the presence of variants in at least one of ALK, KIT/PGDFRA, PIK3CA,AKT1, and HRAS genes to detect ROSl, KRAS, BRAF, ERBB2, MET, RET, FGFRl, and KIT/ at least one variant; determining, based on the at least one PDGFRA genes in a lung tumor sample from the patient and variant detected, an actionable treatment recommendation for administering a therapeutically effective amount a treatment the subject. to the patient, wherein the treatment is: Crizotinib when the [0006] The method comprises: contacting a biological variant detected is an ALK fusion, ROSl fusion (EZR, sample from a subject; detecting at least one variant using a SLC34A2, CD74, and/ or SDC4), or MET gene ampli?cation; US 2014/0288116 A1 Sep. 25, 2014 EGFR tyrosine kinase inhibitor (TKI) When the variant of gene variations, the methods provide an actionable treat detected is EGFR (L858R, Exon 19 del, and/or G719X); a ment recommendation for greater than 50% of lung adeno MEK inhibitor When the variant detected is KRAS G12CN/ carcinoma subjects. This comprehensive screening is per D/A/S/R/F, G13C, G13D and/or G12F; Vermurafenib When formed in a single panel and therefore can be performed the variant detected is BRAF V600E; and an irreversible utilizing a single biological sample, thus preserving valuable pan-erb inhibitor When the variant detected is ERBB2 exon sample. 20 ins. [0011] In yet another embodiment, the disclosure provides DEFINITIONS a method of identifying patients With lung cancer eligible for [0016] “Lung cancer” refers generally to two main types of treatment With crizotnib, an EGFR TKI, or a treatment other lung cancer categorized by the size and appearance of the than an EGFR TKI, a MEK inhibitor, verrnurafenib, or an malignant cells: non-small cell (approximately 80% of cases) irreversible pan-erb inhibitor, comprising testing a lung and small-cell (roughly 20% of cases) lung cancer. Lung tumor sample from the patient for the presence of a variant adenocarcinoma is the most common subtype of non-small comprising an ALK fusion, ROSl fusion (EZR, SLC34A2, cell lung cancer (NSCLC); other subtypes include squamous CD74, and/or SDC4), EGFR (L858R, Exon 19 del, and/or cell lung carcinoma, bronchioloalveolar carcinoma, large cell T790M), KRAS (G12C/V/D/A), Wherein the presence of at carcinoma, carcinoid, adenoid cystic carcinoma, cylindroma, least one of said variants indicates the patient is eligible for and mucoepidermoid carcinoma. In one embodiment, lung treatment With at least one of said treatments. cancers are staged according to stages I-IV, With I being an [0012] The disclosure, in certain embodiments, also pro early stage and IV being the most advanced.
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