metodos para selecionar se administrar um agente terapeutico antiangiogenico a um sujeito inclui etapas de medir os niveis de expressao de um ou mais biomarcadores selecionados a partir da tabela 2 ou tabela 3 em uma amostras a partir do sujeito; avaliar a partir dos niveis de expressao de um ou mais biomarcadores se a amostrar a partir do sujeito e positiva ou negativa para uma assinatura de biomarcador, em que se a amostra e positiva para a assinatura do biomarcador, um agente terapeutico antiangiogenico e contraindicado. metodos de prognostico e metodos de tratamento relatados sao tambem fornecidos. a invencao e particularmente aplicavel em cânceres de ovario e colorretal.

teste de diagnostico molecular para câncer. metodos e composicoes sao fornecidos para identificacao de um teste de diagnostico molecular para câncer. o teste define um novo subtipo molecular deficiente de reparo de dna e permite a classificacao de um paciente dentro deste suptipo. a presente invencao pode ser usada para determinar se os pacientes com câncer sao clinicamente responsivos ou nao responsivos a um regime terapeutico antes da administracao de qualquer quimioterapia. este teste pode ser usado em tipos diferentes de câncer com diferentes drogas que afetam direta ou indiretamente dano ou reparo de dna, tal como muitas das drogas quimioterapicas citotoxicas padrao atualmente em uso. em particular, a presente invencao e dirigida ao uso de certas combinacoes de marcadores preditivos, em que a expressao dos marcadores preditivos se correlaciona com responsividade ou nao responsividade a um regime terapeutico.

Abstract BACKGROUND: We previously defined 3 molecular subgroups of High Grade Serous Ovarian Cancer (HGSOC), using gene expression data from 265 FFPE samples obtained from treatment naive patients, who received platinum based treatment following surgical resection. The 3 molecular subgroups were Angio: characterised by upregulation of angiogenesis genes; Immune: characterised by upregulation of immune genes and AngioImmune: characterised by upregulation of angiogenesis and immune genes. Patients within these 3 subgroups respond differently to standard of care treatment The Immune subgroup have the best prognosis and the Angio and AngioImmune subgroups have similar worse prognosis. A weighted gene signature to identify each of the molecular subgroups was developed. This dataset was used as a reference to investigate the effect of chemotherapy on molecular subgroup designation. METHODS: To investigate the effect of chemotherapy on predefined molecular subgroups, we analysed 35 matched pre- and post- chemotherapy samples by gene expression. The molecular subgroup assignment for each of the paired samples was determined using the gene expression signatures for each subgroup. Novel cisplatin resistant HGSOC cell lines were generated to study the mechanisms of acquired cisplatin resistance. RESULTS: 40% of the treatment naive samples that were aligned with the AngioImmune subgroup and this increased to 67.5% post-chemotherapy. 10/15 (67%) treatment naïve tumours that were initially assigned to the good prognostic Immune molecular subgroup shifted to the bad prognostic AngioImmune molecular subgroup post chemotherapy. Hence platinum chemotherapy selects for the AngioImmune subgroup, suggesting that this subgroup represents tumours which are innately platinum resistant but also provides a mechanism of acquired resistance. Additionally we demonstrate that the AngioImmune subgroup is driven by activation of the MAPK pathway and shows that cisplatin resistant HGSOC cell lines are specifically sensitive to MEK inhibitors. CONCLUSIONS: The MAPK pathway is a mechanism of innate and acquired platinum resistance in HGSOC. Furthermore the data suggests that original pre-treatment surgical/biopsy samples may fall within a different molecular subgroup to samples taken post-platinum therapy. Citation Format: Aya El-Helali, Nuala McCabe, Charlie Gourley, Andrena McCavigan, Caroline O. Michie, Bethanie Price, Niamh McGivern, Michael Churchman, Aya El-Helai, Eamonn J. O'Brien, Laura Hill, Timothy S Davison, Alistair Williams, W Glenn McCluggage, Katherine E Keating, Denis P Harkin, and Richard Kennedy. IDENTIFICATION OF A MOLECULAR SUBTYPE OF HIGH GRADE SEROUS OVARIAN CANCER REPRESENTING MAPK PATHWAY ACTIVATION AND PLATINUM RESISTANCE [abstract]. In: Proceedings of the 11th Biennial Ovarian Cancer Research Symposium; Sep 12-13, 2016; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(11 Suppl):Abstract nr MIP-055.

The present invention relates to a cancer sub-type. Provided are methods for determining clinical prognosis of a subject with cancer, selecting whether to administer an anti-angiogenic therapeutic agent to a subject with cancer and predicting responsiveness of a subject with cancer to an anti-angiogenic therapeutic agent. The methods are based on assessing from the expression level of biomarkers disclosed herein whether the cancer belongs to the sub- type. Companion methods of treating cancer and agents for use in treating cancer are also provided.

A 15-gene prognostic signature for early-stage, completely resected, non small-cell lung carcinoma, (which distinguishes between patients with good and poor prognoses) was clinically validated in prior studies. To achieve operational efficiencies, this study was designed to evaluate the assay's performance in RNA-stabilized tissue as an alternative to the fresh-frozen tissue format originally used to develop the assay. The percent concordance between matched tissue formats was 84010 (95% Wilson CI, 700%-92%), a level of agreement comparable to the inherent reproducibility of the assay observed within biological replicates of fresh-frozen tissue. Furthermore, the analytical performance of the assay using the RNA-stabilized tissue format was evaluated. When compared to an accredited reference Laboratory, the clinical laboratory achieved a concordance of 94% (95% Wilson CI, 81%-98%), and there was no evidence of bias between the laboratories. The lower limit of quantitation for the target RNA concentration was confirmed to be, at most, 12.5 ng/mu L. The assay reportable range defined in terms of risk score units was determined to be -4.295 to 4.210. In a large-scale precision study, the assay showed high reproducibility and repeatability. When subjected to a maximal amount of genomic DNA, a potential contaminant, the assay still produced the expected results. The 15-gene signature was confirmed to produce reliable results and, thus, is suitable for its intended use.

La presente invention concerne un sous-type de cancer. L'invention concerne des procedes permettant de determiner le pronostic clinique d'un sujet atteint d'un cancer, de choisir s'il convient d'administrer un agent therapeutique anti-angiogenique a un sujet atteint d'un cancer et de predire la faculte de reponse d'un sujet atteint d'un cancer a un agent therapeutique anti-angiogenique. Les procedes sont bases sur l'evaluation a partir du niveau d'expression des biomarqueurs decrits ci-inclus du fait que le cancer appartient au sous-type. Des procedes paralleles de traitement du cancer et des agents destines a etre utilises dans le traitement du cancer sont egalement decrits.

The invention relates to methods for selecting whether to administer an anti-angiogenic therapeutic agent and determining clinical prognosis of a subject having cancer. The methods are based on assessing the expression level of biomarkers disclosed herein and determining the presence or absence of a biomarker signature. Companion methods of treating cancer and agents for use in treating cancer are also provided.

Abstract Objectives Copy number (CN) and somatic mutation (SM) analysis in tumors is rapidly gaining importance in cancer management as a tool for differential diagnosis, determination of prognosis, and selection of therapeutic. Genome-wide copy number and LOH detection as well as a panel of frequently tested somatic mutations can be detected with OncoScan® FFPE Assay Kit. We report on a validation study of OncoScan FFPE Assay Kit CN and SM data by orthogonal technologies (FISH and NGS, respectively) to estimate the sensitivity and specificity parameters of the platform. In addition, we assessed the reproducibility of the platform across three different sites in the UK: Leeds Institute of Cancer and Pathology (LICP), West Midlands Regional Genetics Laboratory (WMRGL), and Almac Diagnostics (Almac). Methods Validation of CN data was performed on a cohort of cancer samples identified as Her2 positive/ambiguous by FISH. The panel of SMs available was validated by a custom targeted amplicon NGS panel on a diverse collection of samples derived from multiple cohorts across several tumor types sourced from both LICP and WMRGL. For the reproducibility study, 162 samples encompassing six different tumor types (breast, colorectal, lung, melanoma, prostate, and ovarian) were collected from LICP and WMRGL. DNA was extracted and plated in triplicate and distributed to the three testing sites: LICP, WMRGL, and Almac. Data from all sites was analyzed for reproducibility of genome-wide CN/LOH calls and SM calls. Results Cross-site comparisons of genome-wide CN and LOH profiles on 162 FFPE solid tumor samples showed greater than 95% average agreement between three sites (LICP, WMGRL, and Almac), while SM classification concordance between the sites averaged 97%. Initial orthogonal validation of Her2 amplification by FISH showed greater than 90% concordance, as did initial test samples used for validating OncoScan SM calls by a targeted amplicon NGS panel. Conclusion In this study we validated both CN and SM calls using OncoScan FFPE Assay Kit and demonstrated a high degree of agreement with orthogonal methods in all aspects. Reproducibility of whole-genome CN, LOH, and SM data using OncoScan FFPE Assay Kit has also been demonstrated for a range of FFPE samples, including highly degraded samples. This study is a step forward in evaluating the potential clinical utility of a platform combining genome-wide copy number and somatic mutation calls within the national health service of the UK. Citation Format: Joseph M. Foster, Assa Oumie, Fiona S. Togneri, Morag Taylor, Sofia Alyas, Paula Wojtowicz, Henry Wood, Emma Tinkler-Hundal, Katie Southward, Dominic McMullan, Phil Quirke, Katherine E. Keating, Mike Griffiths, Karen G. Spink, Fiona Brew, Eric Fung, Jeanette Schmidt. Cross-site reproducibility and orthogonal validation of copy number and somatic mutation calls of OncoScan® FFPE Assay Kit in solid tumors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 626. doi:10.1158/1538-7445.AM2015-626

BACKGROUND:Adoption of new technology in both basic research and clinical settings requires rigorous validation of analytical performance. The OncoScan® FFPE Assay is a multiplexing tool that offers genome-wide copy number and loss of heterozygosity detection, as well as identification of frequently tested somatic mutations. METHODS:In this study, 162 formalin fixed paraffin embedded samples, representing six different tumour types, were profiled in triplicate across three independent laboratories. OncoScan® formalin fixed paraffin embedded assay data was then analysed for reproducibility of genome-wide copy number, loss of heterozygosity and somatic mutations. Where available, somatic mutation data was compared to data from orthogonal technologies (pyro/sanger sequencing). RESULTS:Cross site comparisons of genome-wide copy number and loss of heterozygosity profiles showed greater than 95% average agreement between sites. Somatic mutations pre-validated by orthogonal technologies showed greater than 90% agreement with OncoScan® somatic mutation calls and somatic mutation concordance between sites averaged 97%. CONCLUSIONS:Reproducibility of whole-genome copy number, loss of heterozygosity and somatic mutation data using the OncoScan® assay has been demonstrated with comparatively low DNA inputs from a range of highly degraded formalin fixed paraffin embedded samples. In addition, our data shows examples of clinically-relevant aberrations that demonstrate the potential utility of the OncoScan® assay as a robust clinical tool for guiding tumour therapy.

5502 Background: HGSOC is a histopathological diagnosis and may represent multiple diseases at a molecular level. We investigated whether distinct molecular subgroups may influence treatment choice. Methods: mRNA was extracted from 265 macrodissected formalin fixed paraffin embedded HGSOCs from Scottish patients (pts) treated with primary debulking then platinum based chemotherapy. Transcriptional analysis was performed using the Ovarian DSA microarray. This was repeated using 283 UK samples from the ICON7 study [first line paclitaxel/carboplatin +/- concomitant and maintenance bevacizumab (bev) for 12 months]. Results: Unsupervised hierarchical clustering (Scottish tumours) identified three major subgroups, two with angiogenic gene upregulation and one with angiogenic gene repression and immune gene upregulation. This latter ‘immune’ subgroup had a superior overall survival (OS) compared to the other two subgroups combined [HR = 0.66 (0.46-0.94)]. A 63-gene expression signature to prospectively identify this subgroup was generated and validated as prognostic for OS in an independent dataset [HR = 0.32 (0.19-0.54)]. As the immune subgroup had repressed angiogenesis-related gene expression we hypothesised that these pts would benefit less from bev [power to detect interaction > 2 in predicted direction for progression free survival (PFS) in ICON7 was 88% (α=0.1, one-tail)]. In ICON7 the gene signature showed a difference in impact of bev on PFS between the immune and proangiogenic subgroups (1-sided test for interaction, p=0.016). For the immune group (41% of cases), the addition of bev conferred a worse PFS [HR = 1.73 (1.12-2.68)] and OS [HR = 2.00 (1.11-3.61)] compared to chemotherapy alone. In the proangiogenic group there was a non-significant trend to improved PFS for the addition of bev (median 17.4 vs 12.3 months in controls). Conclusions: An immune molecular subgroup of HGSOC has superior survival to other HGSOC. The addition of bev appears to significantly reduce PFS and OS in this subgroup. Patients in the proangiogenic subgroups have a trend towards a PFS benefit from bev. These data suggest a mechanism for stratification of bev therapy and should be validated in additional datasets.

BACKGROUND:There is no method routinely used to predict response to anthracycline and cyclophosphamide-based chemotherapy in the clinic; therefore patients often receive treatment for breast cancer with no benefit. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA damage response (DDR) pathway occurs in approximately 25% of breast cancer patients through several mechanisms and results in sensitization to DNA-damaging agents. The aim of this study was to develop an assay to detect DDR-deficient tumors associated with loss of the FA/BRCA pathway, for the purpose of treatment selection. METHODS:DNA microarray data from 21 FA patients and 11 control subjects were analyzed to identify genetic processes associated with a deficiency in DDR. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples, and a molecular subgroup was identified that was defined by the molecular processes represented within FA patients. A 44-gene microarray-based assay (the DDR deficiency assay) was developed to prospectively identify this subgroup from formalin-fixed, paraffin-embedded samples. All statistical tests were two-sided. RESULTS:In a publicly available independent cohort of 203 patients, the assay predicted complete pathologic response vs residual disease after neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline, and cyclophosphamide) with an odds ratio of 3.96 (95% confidence interval [Cl] =1.67 to 9.41; P = .002). In a new independent cohort of 191 breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin, and cyclophosphamide, a positive assay result predicted 5-year relapse-free survival with a hazard ratio of 0.37 (95% Cl = 0.15 to 0.88; P = .03) compared with the assay negative population. CONCLUSIONS:A formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.

TPS11120 Background: Currently there is no biomarker to predict specific benefit from DNA-damaging anthracycline and cyclophosphamide-based chemotherapy in the clinic. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA-damage response pathway occurs in approximately 25% of breast cancer and results in sensitivity to DNA-damaging agents. We therefore developed an assay to detect loss of the FA/BRCA pathway, for the purpose of predicting benefit from chemotherapy. Methods: 21 FA patient samples were analyzed to identify genetic processes associated with loss of the FA/BRCA pathway. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples and a molecular subgroup was identified that was defined by the molecular processes representing loss of the FA/BRCA pathway. A 44-gene DNA Damage response deficient (DDRD) assay was developed that could identify this subgroup from formalin fixed, paraffin embedded (FFPE) samples in the clinic. Results: In a publicly available independent cohort of 204 patients, the assay predicted response to neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline and cyclophosphamide) with an odds ratio of 4.01, (95% Cl:1.69-9.54). We also analysed samples from an independent cohort of 114 node-negative breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin and cyclophosphamide treatment at the Northern Ireland Cancer Centre. The DDRD assay significantly predicted 5-year relapse free survival with a hazard ratio of 0.27 (95% Cl:0.10-0.83). The assay was not predictive of survival in patients who did not receive chemotherapy. Conclusions: An FFPE tissue-based assay that detects loss of the FA/BRCA pathway has been developed and independently validated as a predictor of response and prognosis following DNA damaging anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings.

7532 Background: Recent clinical studies have demonstrated the benefit of adjuvant chemotherapy (ACT) in some early-stage non-small cell lung cancer (NSCLC) patients. A 15-gene signature, developed using fresh frozen (FF) tissue, has been shown to be an independent prognostic marker that identifies high risk patients who may benefit from ACT. Use of this signature in tissue preserved in an RNA stabilization reagent is desired for easier access to tumor tissue in the clinical setting. Methods: Matched FF and RNAlater-preserved (RNAL) tissues were obtained from 43 NSCLC patients. Patients provided written consent for the collection of tumor tissue at the time of surgery under an IRB approved protocol. Each tissue sample was split into 2 pieces, creating biological replicates for each tissue format. For each patient, RNA was extracted from 4 tissue pieces (2 FF, 2 RNAL), followed by microarray-based genomic profiling (Affymetrix U133 Plus 2.0). The 15-gene signature was applied to each profile, generating a numerical risk score and a risk category (high, low) using methods previously established (Zhu 2010 J Clin Oncol). The level of agreement was evaluated within biological replicates of each tissue format, as well as between the averaged biological replicates of matched FF and RNAL tissues. Results: The concordance in risk category between averaged biological replicates of matched FF and RNAL tissues was 84%, with a Pearson correlation of 0.74. This level of agreement is comparable to the inherent reproducibility of the assay observed within biological replicates of FF tissue, which demonstrated concordance of 79% and Pearson correlation of 0.83. In addition, a statistical in silico simulation was used to demonstrate that if the risk scores in this study had spanned the full dynamic range of the assay while maintaining the same level of inherent reproducibility observed in the current study, the level of concordance would be 89% with a Pearson correlation of 0.93. Conclusions: The level of agreement between matched FF and RNAL tissues is not inferior to that seen within FF biological replicates. Therefore, the 15-gene signature maintains its performance when used in RNAlater-preserved NSCLC tissues.

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Epithelial ovarian cancer (EOC) is the leading cause of death from gynecological malignancies in the Western World. The aim of this study was to identify ovarian cancer subtypes related to biological pathways which are currently being targeted by novel therapeutics. SRC (sarcoma) is a tyrosine kinase which plays critical roles in mediating many cellular pathways such as proliferation, adhesion, survival, differentiation and cell motility. SRC activity is increased in many human cancers including EOC. Furthermore, up-regulation of the SRC pathway has been shown to be associated with cisplatin resistance and patient overall survival in EOC. We therefore hypothesised that up-regulation of the SRC pathway may represent a subtype of EOC which could be therapeutically exploited. We used a semi-supervised analysis approach to perform hierarchical clustering analysis of 198 serous, stage III and IV EOC using a 917 public gene list generated by the differentially expressed genes, after DNA microarray profiling, in MCF10A cells with normal expression and over-expression of the SRC gene. A number of gene clusters were identified upon hierarchical clustering which segregated the patient samples. To examine which of the genes from these clusters represented SRC activation we used a series of in vitro assays including phospho-SRC expression, sensitivity to SRC siRNA, and sensitivity to the SRC inhibitors Saracatinib and Dasatinib in 16 ovarian cancer cell lines. The ovarian cell lines were scored individually with the probesets representing the genes of interest from each of the individual gene clusters and the cell line in vitro data. Two gene clusters were selected for further investigation. A panel of 15 breast cancer cell lines were next investigated for SRC activation using the same in vitro assays described above. Correlation of SRC activation, by the scoring of the in vitro assays and the scoring of probesets from the individual gene clusters, demonstrated one gene cluster which showed good correlation and which potentially represented a metagene of SRC activation. The gene cluster consists of 16 genes, some of which are already known components of the SRC pathway. Furthermore, using the probesets representing the genes from this gene cluster to score public DNA microarray profiling data we were able to predict response to Dasatinib in two independent datasets of prostate and breast cancer cell lines (p=<0.05). In summary we have used a SRC activation transcriptional profile to cluster ovarian cancer samples and selected a metagene comprised of 16 genes which correlates to SRC activation in vitro using a panel of assays in ovarian and breast cancer cell lines. This has been shown to be predictive of response to Dasatinib in 2 independent datasets. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4820. doi:1538-7445.AM2012-4820

10511 Background: Loss of a functional DNA-damage response (DDR) sensitizes tumors to DNA-damaging as well as targeted therapeutics such as PARP-1 inhibitors. However, there is no assay to detect DDR proficiency and guide therapeutic choice. Although abrogation of the DDR can result from multiple mechanisms, including loss of components of the BRCA/Fanconi anemia pathway, the resultant DNA-damage may activate common molecular pathways. We hypothesized that these pathways could define a molecular subgroup and form the basis of a diagnostic test for sensitivity to DNA-damaging and targeted therapies. METHODS Using DNA-microarray technology, we profiled a cohort of BRCA mutant enriched and thus DDR-deficient (DDRD) primary breast tumor samples. Hierarchical agglomerative clustering analysis was performed and identified a molecular subtype in breast cancer characterized by activation of pathways known to respond to DNA damage. Computational classification was performed resulting in the generation of a gene signature that could identify this DDRD molecular subgroup. RESULTS A subset of tumors was identified as displaying biology associated with DDRD. Computational classification was performed based upon expression of this DDRD-related biology resulting in the generation of a 44-gene signature. Retrospective validation in independent breast cancer datasets indicated that the DDRD signature was predictive of response to anthracycline-based chemotherapy with an odds ratio of 15.02 (CI 3.51 - 63.49). In addition, the signature could accurately identify non-responding patients with a negative predictive value of 0.96 (CI 0.88-0.99). CONCLUSIONS We report the identification of a novel molecular subgroup associated with a deficiency in DDR that can be identified in both ER-positive and ER-negative breast cancer using a 44-gene signature. This subgroup is enriched for BRCA1/2 mutant tumors and demonstrates sensitivity to DNA-damaging agents. We propose that the DDRD signature could be used as a patient stratification tool for existing chemotherapy or as a clinical trial enrichment tool for DNA-damaging or repair targeted drugs in development.