IP Library › Granted Patent US 12,540,361
Granted Patent B2
US 12,540,361 · App. 18/752,771 · Granted Feb 3, 2026

Gene signatures for cancer characterization and treatment

Inventor: Maria Jesus Ruiz Echevarria (Edmond, OK)
Assignee: The Board of Regents of the University of Oklahoma
C12Q1/6886C12Q2600/118C12Q2600/158
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,540,361
App. No.
18/752,771
Granted
Feb 3, 2026
Kind
B2
Abstract

An assay system and method for generating quantitative data for a subject and a method for treating prostate cancer in a subject by determining an expression level of a biomarker panel in a sample obtained from the subject, the biomarker panel including the genes CDC45, CENPI, CLSPN, ERCC6L, EXO1, NCAPG, BUB1B, CDK1, NUSAP1, RAD51, and RRM2 and optionally E2F7 and/or GSG2, wherein the expression level is obtained by measuring expression of the biomarker panel in the sample, and wherein the subject has a cancer, or is suspected of having a cancer. The cancer may be, for example, prostate cancer, brain cancer, lung cancer, breast cancer, bladder cancer, or ovarian cancer.

Claims (27)

1 . A method of treating prostate cancer in a subject in need of such treatment, comprising:

(a) providing an assay system for analyzing a sample of prostate gland tissue obtained from the subject, the assay system comprising:

a set of immobilized probes, wherein the probes are selected from a group of probes specific for RNA, proteins, and/or cDNA corresponding to a biomarker panel comprising at least the genes CDC45, CENPI, CLSPN, ERCC6L, EXO1, NCAPG, BUB1B, CDK1, NUSAP1, RAD51, and RRM2, and wherein an expression level of the biomarker panel in the sample is obtainable by measuring expression of each biomarker of the biomarker panel in the sample;

(b) providing the sample;

(c) using the assay system to measure expression of the biomarker panel in the sample;

(d) calculating a test value based on the expression of the biomarker panel;

(e) comparing the test value to a threshold index value; and

(f) administering to the subject one or more prostate cancer treatment therapies selected from the group consisting of prostate cancer hormonal therapy, prostate cancer chemotherapy, prostate cancer immunotherapy, prostate cancer radiation therapy, prostate cancer cryotherapy, and prostate cancer surgery when the test value is equal to or greater than the threshold index value.

2 . The method of claim 1 , wherein the assay system further comprises oligonucleotides specific for one or more housekeeping genes for normalizing the expression level of the biomarker panel.

3 . A method of treating a subject after completion of a surgical procedure to treat prostate cancer in the subject, comprising:

(a) providing an assay system for analyzing a sample of prostate gland tissue obtained from the subject, the assay system comprising:

a set of immobilized probes, wherein the probes are selected from a group of probes specific for RNA, proteins, and/or cDNA corresponding to a biomarker panel comprising at least the genes CDC45, CENPI, CLSPN, ERCC6L, EXO1, NCAPG, BUB1B, CDK1, NUSAP1, RAD51, and RRM2, and wherein an expression level of the biomarker panel in the sample is obtainable by measuring expression of each biomarker of the biomarker panel in the sample;

(b) providing the sample;

(c) using the assay system to measure expression of the biomarker panel in the sample;

(d) calculating a test value based on the expression of the biomarker panel;

(e) comparing the test value to a threshold index value; and

(f) administering to the subject one or more prostate cancer treatment therapies selected from the group consisting of prostate cancer hormonal therapy, prostate cancer chemotherapy, prostate cancer immunotherapy, prostate cancer radiation therapy, prostate cancer cryotherapy, and radical prostatectomy surgery when the test value is equal to or greater than the threshold index value.

4 . The method of claim 3 , wherein the assay system further comprises oligonucleotides specific for one or more housekeeping genes for normalizing the expression level of the biomarker panel.

5 . A method of treating prostate cancer in subject who has had a radical prostatectomy procedure, comprising:

(a) providing an assay system for analyzing a sample of prostate gland tissue obtained from the subject, the assay system comprising:

a set of immobilized probes, wherein the probes are selected from a group of probes specific for RNA, proteins, and/or cDNA corresponding to a biomarker panel comprising at least the genes CDC45, CENPI, CLSPN, ERCC6L, EXO1, NCAPG, BUB1B, CDK1, NUSAP1, RAD51, and RRM2, and wherein an expression level of the biomarker panel in the sample is obtainable by measuring expression of each biomarker of the biomarker panel in the sample;

(b) providing the sample;

(c) using the assay system to measure expression of the biomarker panel in the sample;

(d) calculating a test value based on the expression of the biomarker panel;

(e) comparing the test value to a threshold index value; and

(f) administering to the subject one or more prostate cancer treatment therapies selected from the group consisting of prostate cancer hormonal therapy, prostate cancer chemotherapy, prostate cancer immunotherapy, prostate cancer radiation therapy, and prostate cancer cryotherapy, when the test value is equal to or greater than the threshold index value.

6 . The method of claim 5 , wherein the assay system further comprises oligonucleotides specific for one or more housekeeping genes for normalizing the expression level of the biomarker panel.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Sep 9, 2024
From: RUIZ ECHEVARRIA, MARIA JESUS
To: THE BOARD OF REGENTS OF THE UNIVERSITY OF OKLAHOMA
Reel/Frame 068530/0519 →
Continuity (3)
Continuation 17255375
Provisional Application 62694323 · Jul 5, 2018
Related Publication 20240417808A1 · Dec 19, 2024
References Cited (243)
US 6110678A · Weisburg · 2000 [cited by applicant]
US 8778621B2 · Hoffmann et al. · 2014 [cited by applicant]
US 9410206B2 · Hoon et al. · 2016 [cited by applicant]
US 9605319B2 · Stone et al. · 2017 [cited by applicant]
US 9846158B2 · Mansfield et al. · 2017 [cited by applicant]
US 9976188B2 · Stone et al. · 2018 [cited by applicant]
US 10191056B2 · McNeel et al. · 2019 [cited by applicant]
US 10260105B2 · Goel et al. · 2019 [cited by applicant]
US 10302664B2 · Rolfs et al. · 2019 [cited by applicant]
US 20040166494A1 · Green · 2004 [cited by applicant]
US 20060110744A1 · Sampas · 2006 [cited by applicant]
US 20110033854A1 · Drmanac · 2011 [cited by applicant]
US 20110236903A1 · McClelland et al. · 2011 [cited by applicant]
US 20130302242A1 · Stone · 2013 [cited by applicant]
US 20130344495A1 · Sanders · 2013 [cited by applicant]
US 20140162888A1 · Kuslich et al. · 2014 [cited by applicant]
US 20160090638A1 · Tsai et al. · 2016 [cited by applicant]
US 20160222461A1 · Wilson · 2016 [cited by examiner]
US 20160237505A1 · Nonn et al. · 2016 [cited by applicant]
US 20160312287A1 · Cottrell · 2016 [cited by examiner]
US 20160312296A1 · Laghi et al. · 2016 [cited by applicant]
US 20160333420A1 · Stern et al. · 2016 [cited by applicant]
US 20170096712A1 · Stone et al. · 2017 [cited by applicant]
WO WO200230268A2 · 2002 [cited by applicant]
Siegel, Rebecca L. et al.; “Cancer Statistics, 2015”; CA: A Cancer Journal for Clinicians; vol. 65 No. 1; Jan./Feb. 2015; pp. 5-29. [cited by applicant]
Aizer, Ayal A. et al.; “Initial management of prostate-specific antigen-detected, low-risk prostate cancer and the risk of death from prostate cancer”; BJU International; 113; 2014; pp. 43-50. [cited by applicant]
Gery, Sigal et al.; “Repression of the TMEFF2 Promoter by c-Myc”; Journal of Molecular Biology; 328; 2003; pp. 977-983. [cited by applicant]
Han, Hongchao et al.; “Upregulation of TMEFF2 is involved in the antiproliferative effects of vitamin C and tyrphostin AG490 on GES-1 and AGS cells”; Oncology Letters; 17; 2019; pp. 652-659. [cited by applicant]
Herbst, Andreas et al.; “Methylated free-circulating HPP1 Dna is an early response marker in patients with metastic colorectal cancer”; International Journal of Cancer; 140; 2017; pp. 2134-2144. [cited by applicant]
Ivanauskas, A. et al.; “Distinct TPEF/HPP1 gene methylation patterns in gastric cancer indicate a field effect in gastric carcinogenesis”; Digestive and Liver Disease; 40; 2008; pp. 920-926. [cited by applicant]
Li, Kailiang et al.; “Expression of TMEFF2 in Human Pancreatic Cancer Tissue and the Effects of TMEFF2 Knockdown on Cell, Proliferation, and Apoptosis in Human Pancreatic Cell Lines”; Medical Science Monitor; 25; 2019; … [cited by applicant]
Monteriro-Reis, Sara et al.; “Accurate detection of upper tract urothelial carcinoma in tissue and urine by means of quantitative GDF15, TMEFF2 and VIM promoter methylation”; European Journal of Cancer; 50; 2014; pp. 22… [cited by applicant]
Shaw, Richard J. et al; “Molecular Staging of Surgical Margins in Oral Squamous Cell Carcinoma Using Promoter Methylation of p16INK4A, Cytoglobin, E-cadherin, and TMEFF2”; Annals of Surgical Oncology; 20; 2013; pp. 2796… [cited by applicant]
Sun, Tiantian et al.; “TMEFF2 Deregulation Contributes to Gastric Carcinogenesis and Indicates Poor Survival Outcome”; Clinical Cancer Research; vol. 20 No. 17; Sep. 1, 2014; pp. 4689-4704. [cited by applicant]
Sun, Tian-Tian et al.; “Bidirectional regulation between TMEFFS and STAT3 may contribute to [cited by applicant]
Allera-Moreau et al.; “DNA replication stress response involving PLK1, CDC6, POLQ, RAD51 and CLASPIN upregulation prognoses the outcome of early/mid-stage non-small cell lung cancer patients”; Oncogenesis; 2012; 10 page… [cited by applicant]
Ruijter, Emiel Th et al.; “Histological Grade Heterogeneity In Multifocal Prostate Cancer. Biological And Clinical Implications”; Journal of Pathology; vol. 180; 1996; pp. 295-299. [cited by applicant]
Alshalalfa, Mohammed et al.; “Evolving transcriptomic fingerprint based on genome-wide data as prognostic tools in prostate cancer”; Biology of the Cell; vol. 107; 2015; pp. 232-244. [cited by applicant]
Assié, Guillaume et al.; “Value of Molecular Classification for Prognostic Assessment of Adrenocortical Carcinoma”; JAMA Oncology; Jul. 11, 2019; pages E1-E8. [cited by applicant]
Barbano, Raffaela et al; “High RAD51 mRNA expression characterize estrogen receptor-positive/progesteron receptor-negative breast cancer and is associated with patient's outcome”; International Journal of Cancer; 129; 2… [cited by applicant]
Bie, Li et al; “The Accuracy of Survival Time Prediction for Patients with Glioma Is Improved by Measuring Mitotic Spindle Checkpoint Gene Expression”; PLoS One; vol. 6 Iss. 10; Oct. 2011; 10 pages. [cited by applicant]
Bishoff, Jay T. et al.; “Prognostic Utility of the Cell Cycle Progression Score Generated from Biopsy in Men Treated with Prostatectomy”; The Journal of Urology; vol. 192; Aug. 2014; pp. 409-414. [cited by applicant]
Boström, Peter J. et al.; “Genomic Predictors of Outcome in Prostate Cancer”; European Urology; 68; 2015; pp. 1033-1044. [cited by applicant]
Boukovinas, Ioannis et al.; “Tumor BRCA1, RRM1 and RRMS mRNA Expression Levels and Clinical Response to First-Line Gemcitabine plus Docetaxel in Non-Small-Cell Lung Cancer Patients”; PLoS One; vol. 3 Iss. 11; Nov. 2008;… [cited by applicant]
Castelblanco, Esmeralda et al.; “APLP2, RRMS, and PRC1: New Putative Markers for the Differential Diagnosis of Thyroid Follicular Lesions”; Thyroid; vol. 27 No. 1; Nov. 1, 2017; pp. 59-66. [cited by applicant]
Chang, Wai Hoong et al.; “Transcriptional landscape of DNA repair genes underpins a pan-cancer prognostic signature associated with cell cycle dysregulation and tumor hypoxia”; DNA Repair; 78; 2019; pp. 142-153. [cited by applicant]
Chen, Li et al; “High Levels of Nucleolar Spindle-Associated Protein and Reduced Levels of BRCA1 Expression Predict Poor Prognosis in Triple-Negative Breast Cancer”; PLOS One; Oct. 20, 2015; 14 pages. [cited by applicant]
Boutros, Paul C et al.; “Spatial genomic heterogeneity within localized, multifocal prostate cancer”; Nature Genetics; vol. 47 No. 7; Jul. 2015; pp. 736-745. [cited by applicant]
Chen, Jian et al.; “Novel key genes in triple-negative breast cancer identified by weighted gene co-expression network analysis”; Journal of Cellular Biochemistry; 120; 2019; pp. 16900-16912. [cited by applicant]
Chen, Juan et al.; “Identification of novel biomarkers and small molecule drugs in human colorectal cancer by microarray and bioinformatics analysis”; Molecular Genetics & Genomic Medicine; 2019; 15 pages. [cited by applicant]
Chen, Ru et al.; “Identification of modules and functional analysis in CRC subtypes by integrated bioinformatics analysis”; PLOS One, Aug. 30, 2019; 16 pages. [cited by applicant]
Chen, Wei-xian et al.; “Bioinformatics analysis revealing prognostic significance of RRM2 gene in breast cancer”; Bioscience Reports; 39; 2019; 9 pages. [cited by applicant]
Chen, Fang-Fang et al.; “Integrative genomics analysis of hub genes and their relationship with prognosis and signaling pathways in esophageal squamous cell carcinoma”; Molecular Medicine Reports; 20; 2019; pp. 3649-366… [cited by applicant]
Chistiakov, Dimitry A. et al.; “New biomarkers for diagnosis and prognosis of localized prostate cancer”; Seminars in Cancer Biology; 52; 2018; pp. 9-16. [cited by applicant]
Chu, Junjun et al.; “E2F7 overexpression leads to tamoxifen resistance in breast cancer cells by competing with E2F1 at miR-15a/16 promoter”; Oncotarget; vol. 6 No. 31; 2015; pp. 31944-31957. [cited by applicant]
Cooperberg, Matthew R. et al.; “Validation of a Cell-Cycle Progression Gene Panel to Improve Risk Stratification in a Contemporary”; Journal of Clinical Oncology; vol. 31 No. 11; Apr. 10, 2013; pp. 1428-1434. [cited by applicant]
Cooperberg, Matthew R. et al.; “Combined Value of Validated Clinical and Genomic Risk Stratification Tools for Predicting Prostate Cancer Mortality in a High-risk Prostatectomy Cohort”; European Urology; 67; 2015; pp. 3… [cited by applicant]
Cullen, Jennifer et al.; “A Biopsy-based 17-gene Genomic Prostate Score Predicts Recurrence After Radical Prostatectomy and Adverse Surgical Pathology in a Racially Diverse Population of Men with Clinically Low- and Int… [cited by applicant]
Cyll, Karolina et al.; “Tumour heterogeneity poses a significant challenge to cancer biomarker research”; British Journal of Cancer; 117; 2017; pp. 367-375. [cited by applicant]
Cuzick, J et al.; “Prognostic value of a cell cycle progression signature for prostate cancer death in a conservatively managed needle biopsy cohort”; British Journal of Cancer; 106(6); 2012; pp. 1095-1099. [cited by applicant]
Dancik, Garrett M. et al.; The Prognostic Value of Cell Cycle Gene Expression Signatures in Muscle Invasive High-Grade Bladder Cancer; Bladder Cancer; 1; 2015; pp. 45-63. [cited by applicant]
Deng, Leihong et al.; “Identification and characterization of biomarkers and their functions for docetazel-resistant prostate cancer cells”; Oncology Letters; 18; 2019; pp. 3236-3248. [cited by applicant]
Eure, Gregg et al.; “Use of a 17-Gene Prognostic Assay in Contemporary Urologic Practice: Results of an Interim Analysis in an Observational Cohort”; Genomics in Urologic Health and Disease; 107; 2017; pp. 67-75. [cited by applicant]
Fisher, Sarah B. et al.; “Excision Repair Cross-Complementing Gene-1, Ribonucleotide Reductase Subunit M1, Ribonucleotide Reductase Subunit M2, and Human Equilibrative Nucleoside Transporter-1 Expression and Prognostic … [cited by applicant]
Freedland, Stephen J. et al.; “Prognostic Utility of Cell Cycle Progression Score in Men With Prostate Cancer After Primary External Beam Radiation Therapy”; International Journal of Radiation Oncology Biology Physics; … [cited by applicant]
Fu, Xin et al.; “Overexpression of BUBIB contributes to progression of prostate cancer and predicts poor outcome in patients with prostate cancer”; OncoTargets and Therapy; 9; 2016; pp. 2211-2220. [cited by applicant]
Gachechiladze, Mariam et al.; “Prognostic and predictive value of loss of nuclear RAD51 immunoreactivity in resected non-small cell lung cancer patients”; Lung Cancer; 105; 2017; pp. 31-38. [cited by applicant]
Grolmusz, Vince Kornél et al.; “Cell cycle dependent RRM2 may serve as proliferation marker and pharmaceutical target in adrenocortical cancer”; American Journal of Cancer Research; 6(9); 2016 pp. 2041-2053. [cited by applicant]
Grossi, Francesco et al.; “Expression of Ribonucleotide Reductase Subunit-2 and Thymidylate Synthase Correlates with Poor Prognosis in Patients with Resected Stages I-III Non-Small Cell Lung Cancer”; Disease Markers; vo… [cited by applicant]
Boutros, Paul C. et al.; “Clonality of localized and metastatic prostate cancer”; Current Opinion in Urology; vol. 26 No. 3; May 2016; pp. 219-224. [cited by applicant]
Guo, Ai Ye et al.; “Identification of a Low-Frequency Missense Variant in E2F Transcription Factor 7 Associated with Colorectal Cancer Risk In A Chinese Population”; Asian Pacific Journal of Cancer Prevention; vol. 18; … [cited by applicant]
Haider, Syed et al.; “A multi-gene signature predicts outcome in patients with pancreatic ductal adenocarcinoma”; Genome Medicine; vol. 6 No. 105; 2014; 11 pages. [cited by applicant]
Han, Ping et al.; “Ribonucleotide reductase M2 subunit expression and prognostic value in nasopharyngeal carcinoma”; Molecular Medicine Reports; 12; 2015; pp. 401-409. [cited by applicant]
Han, Guangchun et al.; “Unique protein expression signatures of survival time in kidneynal clear cell carcinoma through a pan-cancer screening”; BMC Genomics; 18; 2017; pp. 80-93. [cited by applicant]
Hansel, Donna E. et al.; “CDC2/CDK1 Expression in Esophageal Adenocarcinoma and Precursor Lesions Serves as a Diagnostic and Cancer Progression Marker and Potential Novel Drug Target”; The American Journal of Surgical P… [cited by applicant]
He, Zhaohui et al.; “Analysis of differentially expressed genes, clinical value and biological pathways in prostate cancer”; The American Journal of Translational Research; 10(5); 2018; pp. 1444-1456. [cited by applicant]
He, Wenwu et al.; “Gene set enrichment analysis and meta-analysis to identify six key genes regulating and controlling the prognosis of esophageal squamous cell carcinoma”; Journal of Thoracic Disease; 10(10); 2018; pp.… [cited by applicant]
Hongo, Fumiya et al.; “CDK1 and CDK2 activity is a strong predictor of renal cell carcinoma recurrence”; Urologic Oncology; 32; 2014; pp. 1240-1246. [cited by applicant]
Huang, Yasheng et al.; “The prognostic value of ribonucleotide reductase small subunit M2 in predicting recurrence for prostate cancers”; Urologic Oncology; 32; 2014; pp. 51.e9-51.e19. [cited by applicant]
Ihara, Keisuke et al.; “Expression of DNA double-strand break repair proteins predicts the response and prognosis of colorectal cancer patients undergoing oxaliplatin-based chemotherapy”; Oncology Reports; 35; 2016; pp.… [cited by applicant]
Tosoian, Jeffrey J. et al.; “Molecular heterogeneity of localized prostate cancer: more different than alike”; Translational Cancer Research; 6; Feb. 2017; 5 pages. [cited by applicant]
Johnston, Wendy L. et al.; “Unbiased data mining identifies cell cycle transcripts that predict non-indolent Gleason score 7 prostate cancer”; BMC Urology; 19:4; 2019; 11 pages. [cited by applicant]
Kessous, Roy et al.; “Distinct homologous recombination gene expression profiles after neoadjuvant chemotherapy associated with clinical outcome in patients with ovarian cancer”; Gynecologic Oncology; 148; 2018; pp. 553… [cited by applicant]
Kobayashi, Go et al.; “Clinicopathological significance of claspin overexpression and its association with spheroid formation in gastric cancer”; Human Pathology; 84; 2019; pp. 8-17. [cited by applicant]
Kori, Medi et al.; “Potential biomarkers and therapeutic targets in cervical cancer: Insights from the meta-analysis of transcriptomics data within network biomedicine perspective”; PLOS One; Jul. 18, 2018; 27 pages. [cited by applicant]
Kretschmer, Céline et al.; “Identification of early molecular markers for breast cancer”; Molecular Cancer; 10:15; 2011; 11 pages. [cited by applicant]
Lee, Boin et al.; “High Expression of Ribonucleotide Reductase Subunit M2 Correlates with Poor Prognosis of Hepatocellular Carcinoma”; Gut and Liver; vol. 8 No. 6; Nov. 2014; pp. 662-668. [cited by applicant]
Leonardi, Simona et al.; “The relevance of prelamin A and RAD51 as molecular biomarkers in cervical cancer”; Oncotarget; vol. 8 No. 55; 2017; pp. 94247-94258. [cited by applicant]
Li, Yong et al.; “Elevated Expression of Rad51 is Correlated With Decreased Survival in Resectable Esophageal Squamous Cell Carcinoma”; Journal of Surgical Oncology; 104; 2011; pp. 617-622. [cited by applicant]
Li, Boxuan et al.; “Identifying novel biomarkers in hepatocellular carcinoma by weighted gene co-expression network analysis”; Journal of Cellular Biochemistry; 120; 2019; pp. 11418-11431. [cited by applicant]
Li, Yunhai et al.; “Expression patterns of E2F transcription factors and their potential prognostic roles in breast cancer”; Oncology Letters; 15; 2018; pp. 9216-9230. [cited by applicant]
Shoag, Jonathan et al.; “Clinical variability and molecular heterogeneity in prostate cancer”; Asian Journal of Andrology; 18; 2016; pp. 543-548. [cited by applicant]
Li, Shicheng et al.; “Identification of an eight-gene prognostic signature for lung adenocarcinoma”; Cancer Management and Research; 10; 2018; pp. 3383-3392. [cited by applicant]
Liao, Xiwen et al.; “Integrated analysis of competing endogenous RNA network revealing potential prognostic biomarkers of hepatocellular carcinoma”; Journal of Cancer; 10(14); 2019; pp. 3267-3283. [cited by applicant]
Liu, Xiyong et al.; “Ribonucleotide reductase small subunit M2 serves as a prognostic biomarker and predicts poor survival of colorectal cancers”; Clinical Science; 124; 2013; pp. 567-578. [cited by applicant]
Liu, Rong et al.; “Network-based approach to identify prognostic biomarkers for estrogen receptor-positive breast cancer treatment with tamoxifen”; Cancer Biology & Therapy; 16:2; Feb. 2015; pp. 317-324. [cited by applicant]
Liu, Wanwei et al.; “Overexpression of non-SMC condensin I complex subunit G serves as a promising prognostic marker and therapeutic target for hepatocellular carcinoma”; International Journal of Molecular Medicine; 40;… [cited by applicant]
Liu, Ze-Long et al.; “Expressions and prognostic values of the E2F transcription factors in human breast carcinoma”; Cancer Management and Research; 10; 2018; pp. 3521-3532. [cited by applicant]
Liu, Zhaoxiu et al.; “High NUSAP1 expression predicts poor prognosis in colon cancer”; Pathology—Research and Practice; 214; 2018; pp. 968-973. [cited by applicant]
Liu, Wan-Ting et al.; “A novel strategy of integrated microarray analysis identifies CENPA, CDK1 and CDC20 as a cluster of diagnostic biomarkers in lung adenocarcinoma”; Cancer Letters; 425; 2018; pp. 43-53. [cited by applicant]
Luo, Fei et al.; “Exonuclease 1 expression is associated with clinical progression, metastasis, and survival prognosis of prostate cancer”; Journal of Cellular Biochemistry; 120; 2019; pp. 11383-11389. [cited by applicant]
Maddalena, Francesca et al.; “TRAP1 protein signature predicts outcome in human metastatic colorectal carcinoma”; Oncotarget; vol. 8 No. 13; 2017; pp. 21229-21240. [cited by applicant]
Cooper et al.; “Nature Genetics”; 47(4); Apr. 2015; 21 pages. [cited by applicant]
Mah, Vei et al.; “Ribonucleotide Reductase Subunit M2 Predicts Survival in Subgroups of Patients with Non-Small Cell Lung Carcinoma: Effects of Gender and Smoking Status”; PLOS One; May 22, 2015; 15 pages. [cited by applicant]
Manicum, Theasha et al.; “Prognostic values of E2F mRNA expression in human gastric cancer”; Bioscience Reports; 38; 2018; 14 pages. [cited by applicant]
Martin, Katherine J. et al.; “Prognostic Breast Cancer Signature Identified from 3D Culture Model Accurately Predicts Clinical Outcome across Independent Datasets”; PLoS One; vol. 3 Iss. 8; Aug. 2008; 9 pages. [cited by applicant]
Matakidou, Athena et al.; “Genetic variation in the DNA repair genes is predictive of outcome in lung cancer”; Human Molecular Genetics; vol. 16 No. 19; 2007; pp. 2333-2340. [cited by applicant]
Mullane, Stephanie A. et al.; “Expression Levels of DNA Damage Repair Proteins Are Associated With Overall Survival in Platinum-Treated Advanced Urothelial Carcinoma”; Clinical Genitourinary Cancer; Aug. 2016; pp. 352-3… [cited by applicant]
Nagathihalli, Nagaraj S. et al.; “RAD51 as a potential biomarker and therapeutic target for pancreatic cancer”; Biochimica et Biophysica Acta; 1816; 2011; pp. 209-218. [cited by applicant]
Nam, Seungyoon et al.; “A pathway-based approach for identifying biomarkers of tumor progression to trastuzumab-resistant breast cancer”; Cancer Letters; 356; 2015; pp. 880-890. [cited by applicant]
Pan, Shen et al.; “Identification of Biomarkers for Controlling Cancer Stem Cell Characteristics in Bladder Cancer by Network Analysis of Transcriptome Data Stemness Indices”; Frontiers in Oncology; vol. 9 Art. 613; Jul… [cited by applicant]
Pataer, Apar et al.; “Major pathologic response and RAD51 predict survival in lung cancer patients receiving neoadjuvant chemotherapy”; Cancer Medicine; 7(6); 2018; pp. 2405-2414. [cited by applicant]
Piao, Junjie et al.; “Target gene screening and evaluation of prognostic values in non-small cell lung cancers by bioinformatics analysis”; Gene; 647; 2018; pp. 306-311. [cited by applicant]
Gundem, Gunes et al.; “The Evolutionary History of Lethal Metastatic Prostate Cancer”; Nature; 520(7547); Apr. 16, 2015; 24 pages. [cited by applicant]
Pu, Shao-Yan et al.; “ERCC6L, a DNA helicase, is involved in cell proliferation and associated with survival and progress in breast and kidney cancers”; Oncotarget; vol. 8 No. 26; 2017; pp. 42116-42124. [cited by applicant]
Putluri, Nagireddy et al.; “Pathway-Centric Integrative Analysis Identifies RRM2 as a Prognostic Marker in Breast Cancer Associated with Poor Survival and Tamoxifen Resistance”; Neoplasia; vol. 16 No. 5; May 2014; pp. 3… [cited by applicant]
Qiao, G-B et al.; “High-level expression of Rad51 is an independent prognostic marker of survival in non-small-cell lung cancer patients”; British Journal of Cancer; 93; 2005; pp. 137-143. [cited by applicant]
Rajan, Prabhakar et al.; “Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer”; BMC Cancer;… [cited by applicant]
Raman, Pichai et al.; “Pancreatic cancer survival analysis defines a signature that predicts outcome”; PLOS One; Aug. 9, 2018; 18 pages. [cited by applicant]
Ramos-Montoya, Antonio et al.; “HES6 drives a critical AR transcriptional programme to induce castration-resistant prostate cancer through activation of an E2F1-mediated cell cycle network”; EMBO Molecular Medicine; vol… [cited by applicant]
Reimer, Daniel et al.; “Clinical Relevance of E2F Family Members in Ovarian Cancer—An Evaluation in a Training Set of 77 Patients”; Clinical Cancer Research; 13(1); Jan. 1, 2007; pp. 144-151. [cited by applicant]
Frio, Thomas Rio et al.; “Homozygous BUB1B Mutation and Susceptibility to Gastrointestinal Neoplasia”; The New England Journal of Medicine; 363:27; Dec. 30, 2010; pp. 2628-2637. [cited by applicant]
Rubicz, Rohina et al.; “Expression of Cell Cycle-Regulated Genes and Prostate Cancer Prognosis in a Population-Based Cohort”; The Prostate; 75; 2015; pp. 1354-1362. [cited by applicant]
Schulten, Hans-Juergen et al.; “Comprehensive molecular biomarker identification in breast cancer brain metastases”; Journal of Translational Medicine; 15:269; 2017; 20 pages. [cited by applicant]
Guiu, S. et al.; “Molecular subclasses of breast cancer: how do we define them? The IMPAKT 2012 Working Group Statement”; Annals of Oncology; 23; 2012; pp. 2997-3006. [cited by applicant]
Shi, Yuan-Xiang et al.; “Prognostic and predictive values of CDK1 and MAD2L1 in lung adenocarcinoma”; Oncotarget; vol. 7 No. 51; 2016; pp. 85235-85243. [cited by applicant]
Söderlund, Karin et al.; “The BRCA1/BRCA2/Rad51 complex is a prognostic and predictive factor in early breast cancer”; Radiotherapy and Oncology; 84; 2007; pp. 242-251. [cited by applicant]
Song, Bin et al.; “Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer”; Biological Research; 51:44; 2018; 12 pages. [cited by applicant]
Song, Ying-Jian et al.; “Integrated analysis reveals key genes with prognostic value in lung adenocarcinoma”; Cancer Management and Research; 10; 2018; pp. 6097-6108. [cited by applicant]
Souglakos, J. et al.; “Ribonucleotide reductase subunits M1 and M2 mRNA expression levels and clinical outcome of lung adenocarcinoma patients treated with docetaxel/gemcitabine”; British Journal of Cancer; 98(10); 2008… [cited by applicant]
Su, Ying-Fang et al.; “The Expression of Ribonucleotide Reductase M2 in the Carcinogenesis of Uterine Cervix and Its Relationship with Clinicopathological Characteristics and Prognosis of Cancer Patients”; PLOS One; vol… [cited by applicant]
Sun, Qian et al.; “Gene co-expression network reveals shared modules predictive of stage and grade in serious ovarian cancers”; Oncotarget; vol. 8 No. 26; 2017; pp. 42983-42996. [cited by applicant]
Tang, Hao et al.; “A 12-Gene Set Predicts Survival Benefits from Adjuvant Chemotherapy in Non-Small Cell Lung Cancer Patients”; Clinical Cancer Research; 19(6); Mar. 15, 2013; pp. 1577-1586. [cited by applicant]
Sung, Wen-Wei et al.; “High nuclear/cytoplasmic ratio of Cdk1 expression predicts poor prognosis in colorectal cancer patients”; BMC Cancer; 14:951; 2014; 7 pages. [cited by applicant]
Taylor, Karen J et al.; “Dynamic changes in gene expression in vivo predict prognosis of tamoxifen-treated patients with breast cancer”; Breast Cancer Research; 12:R39; 2010; 13 pages. [cited by applicant]
Shtivelman, Emma et al.; “Molecular pathways and targets in prostate cancer”; Oncotarget; vol. 5 No. 17; Aug. 2014; pp. 7217-7259. [cited by applicant]
Bertucci, Francois et al.; “Gene Expression Profiling and Clinical Outcome in Breast Cancer”; A Journal of Integrative Biology; vol. 10 No. 4; 2006; pp. 429-443. [cited by applicant]
Thangavelu, Pulari U. et al.; “Overexpression of the E2F target gene CENPI promotes chromosome instability and predicts poor prognosis in estrogen receptor-positive breast cancer”; Oncotarget; vol. 8 No. 37; 2017; pp. 6… [cited by applicant]
Tryfonidis, K et al.; “Association of BRCA1, ERCC1, RAP80, PKM2, RRM1, RRM2, TS, TSP1, and TXR1 mRNA expression levels between primary tumors and infiltrated regional lymph nodes in patients with resectable non-small ce… [cited by applicant]
Uddin, Md. Nazim et al.; “Identification of Transcriptional Signatures of Colon Tumor Stroma by a Meta-Analysis”; Journal of Oncology; vol. 2019; 12 pages. [cited by applicant]
Wang, Xin et al.; “A network-pathway based module identification for predicting the prognosis of ovarian cancer patients”; Journal of Ovarian Research; 9:73; 2016; 8 pages. [cited by applicant]
Xiang, Xiao-Hong et al.; “Seven-senescence-associated gene signature predicts overall survival for Asian patients with hepatocellular carcinoma”; World Journal of Gastroenterology; vol. 25 Iss. 14; Apr. 14, 2019; pp. 17… [cited by applicant]
Xiao, He et al.; “Identification of Five Genes as a Potential Biomarker for Predict Progress and Prognosis in Adrenocortical Carcinoma”; Journal of Cancer; vol. 9; 2018; pp. 4484-4495. [cited by applicant]
Yan, Yongcong et al.; “Identification and validation of a prognostic four-genes signature for hepatocellular carcinoma: integrated ceRNA network analysis”; Hepatology International; 13; 2019; pp. 618-630. [cited by applicant]
Yan, Xin et al.; “Identification of Hub Genes Associated With Progression and Prognosis in Patients With Bladder Cancer”; Frontiers in Genetics; vol. 10 Art. 408; May 2019; 12 pages. [cited by applicant]
Yang, Hui et al.; “A four-gene signature for prognosis in breast cancer patients with hypermethylated IL15RA”; Oncology Letters; 17; 2019; pp. 4245-4254. [cited by applicant]
Yang, Wookyeom et al.; “Accumulation of cytoplasmic Cdk1 is associated with cancer growth and survival rate in epithelial ovarian cancer”; Oncotarget; vol. 17 No. 31; 2016; pp. 49481-49497. [cited by applicant]
Parker, Joel S. et al.; “Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes”; Journal of Clinical Oncology; vol. 27 No. 8; Mar. 10, 2009; pp. 1160-1167. [cited by applicant]
Yin, Xiaomao et al.; “Identification of biomarkers of chromophobe renal cell carcinoma by weighted gene co-expression network analysis”; Cancer Cell International; 18:206; 2018; 12 pages. [cited by applicant]
Zeestraten, ECM et al.; “Specific activity of cyclin-dependent kinase I is a new potential predictor of tumour recurrence in stage II colon cancer”; British Journal of Cancer 106; 2012; pp. 133-140. [cited by applicant]
Zhang, Chunyu et al.; “Loss of Cytoplasmic CDK1 Predicts Poor Survival in Human Lung Cancer and Confers Chemotherapeutic Resistance”; PLOS One; vol. 6 Iss. 8; Aug. 2011; 15 pages. [cited by applicant]
Zhang, Hang et al.; “Prognostic and therapeutic significance of ribonucleotide reductase small subunit M2 in estrogen-negative breast cancers”; BMC Cancer; 14:664; 2014; 16 pages. [cited by applicant]
Zhong, Xiaodan et al.; “Identification of Potential Prognostic Genes for Neuroblastoma”; Frontiers in Genetics; vol. 19 Art. 589; Nov. 2018; 10 pages. [cited by applicant]
Zhuang, Liping et al.; “Upregulation of BUB1B, CCNB1, CDC7, CDC20, and MCM3 in Tumor Tissues Predicted Worse Overall Survival and Disease-Free Survival in Hepatocellular Carcinoma Patients”; BioMed Research Internationa… [cited by applicant]
Stark, Rory; “Checking gene expression signatures against random and known signatures with SigCheck”; Dec. 9, 2015; 17 pages. [cited by applicant]
Moschini, Marco et al.; “Incorporation of tissue-based genomic biomarkers into localized prostate cancer clinics”; BMC Medicine; 14:67; 2016; 7 pages. [cited by applicant]
Cuzick, Jack et al.; “Prognostic value of an RNA expression signature derived from cell cycle proliferation genes in patients with prostate cancer: a retrospective study”; The Lancet Oncology; vol. 12; Mar. 2011; pp. 24… [cited by applicant]
Erho, Nicholas et al.; “Discovery and Validation of a Prostate Cancer Genomic Classifier that Predicts Early Metastasis Following Radical Prostatectomy”; PLOS One; vol. 8 Iss. 6; Jun. 2013; 12 pages. [cited by applicant]
Klein, Eric A. et al.; “A 17-gene Assay to Predict Prostate Cancer Aggressiveness in the Context of Gleason Grade Heterogeneity, Tumor Multifocality, and Biopsy Undersampling”; European Urology; 66; 2014; pp. 550-560. [cited by applicant]
Kaffenberger, Samuel D. et al.; “Molecular subtyping of prostate cancer”; Current Opinion in Urology; vol. 26 No. 3; May 2016; pp. 213-218. [cited by applicant]
Schoenborn, Jamie R. et al.; “Genomic Profiling Defines Subtypes of Prostate Cancer with the Potential for Therapeutic Stratification”; Clinical Cancer Research; 19(15); Aug. 1, 2013; pp. 4058-4066. [cited by applicant]
Demichelis, Francesca et al.; “Molecular Archeology: Unearthing Androgen Induced Structural Rearrangements in Prostate Cancer Genomes”; Cancer Cell .; 23(2); Feb. 11, 2013; 5 pages. [cited by applicant]
Lee, D et al.; “Molecular alterations in prostate cancer and association with MRI features”; Prostate Cancer and Prostatic Diseases; 2017; pp. 430-435. [cited by applicant]
Humphrey, Peter A.; “Gleason grading and prognostic factors in carcinoma of the prostate”; Modern Pathology; 17; 2004; pp. 292-306. [cited by applicant]
Schultz, Nikolaus et al.; “The molecular taxonomy of primary prostate cancer”; Cell.; 163(4); Nov. 5, 2015; 29 pages. [cited by applicant]
Gorlov, Ivan P. et al.; “How to get the most from microarray data: advice from reverse genomics”; BMC Genomics; 15; 2014; 10 pages. [cited by applicant]
Ross-Adams, H. et al.; “Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study”; EBioMedicine; 2; 2015; pp. 1133-1144. [cited by applicant]
Chen, Xiaofei et al.; “The TMEFF2 tumor suppressor modulates integrin expression, RhoA activation and migration of prostate cancer cells”; Biochimica et Biophysica Acta; 1843; 2014; pp. 1216-1224. [cited by applicant]
Chen, Xiaofei et al.; “The Tumor Suppressor Activity of the Transmembrane Protein with Epidermal Growth Factor and Two Follistatin Motifs 2 (TMEFF2) Correlates with Its Ability to Modulate Sarcosine Levels”; The Journal… [cited by applicant]
Corbin, Joshua M. et al.; Analysis of TMEFF2 Allografts and Transgenic Mouse Models Reveals Roles in Prostate Regeneration and Cancer; The Prostate; 76; 2016; pp. 97-113. [cited by applicant]
Green, Thomas et al.; “TMEFF2 and SARDH Cooperate to Modulate One-Carbon Metabolism and Invasion of Prostate Cancer Cells”; The Prostate; 73; 2013; pp. 1561-1575. [cited by applicant]
Afar, Daniel E.H. et al.; “Preclinical validation of anti-TMEFF2-auristatin E-conjugated antibodies in the treatment of prostate cancer”; Molecular Cancer Therapeutics; 3(8); Aug. 2004; pp. 921-932. [cited by applicant]
Glynne-Jones, Eveline et al.; “TENB2, a Proteoglycan Identified in Prostate Cancer That is Associated With Disease Progression and Androgen Independence”; International Journal of Cancer; 94; 2001; pp. 178-184. [cited by applicant]
Lin, Kui et al.; TMEFF2 Is a PDGF-AA Binding Protein with Methylation-Associated Gene Silencing in Multiple Cancer Types Including Glioma; PLOS One; vol. 6 Iss. 4; Apr. 2011; 14 pages. [cited by applicant]
Joniau, Steven et al.; “Stratification of High-risk Prostate Cancer into Prognostic Categories: A European Multi-institutional Study”; European Urology; 67; 2015; pp. 157-164. [cited by applicant]
Taylor, Barry S.et al.; “Integrative Genomic Profiling of Human Prostate Cancer”; Cancer Cell; 18; Jul. 13, 2010; pp. 11-22. [cited by applicant]
Rhodes, Daniel R. et al.; “Oncomine: A Cancer Microarray Database and Integrated Data-Mining Platform”; Neoplasia; vol. 6 No. 1; Jan./Feb. 2004; 6 pages. [cited by applicant]
Grasso, Catherine S. et al.; “The mutational landscape of lethal castration-resistant prostate cancer”; Nature; vol. 487; Jul. 12, 2012; pp. 239-243. [cited by applicant]
Szklarczyk, Damian et al.; “The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible”; Nucleic Acids Research; vol. 45; 2017; pp. D362-D368. [cited by applicant]
Aguirre-Gamboa, Raul et al.; “SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis”; PLOS One; vol. 8 Iss. 9; Sep. 2013; 9 pages. [cited by applicant]
Stark, Rory et al.; “SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata”; Bioconductor; Oct. 10, 2019; 4 pages. [cited by applicant]
Venet, David et al.; “Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome”; PLOS Computational Biology; vol. 7 Iss. 10; Oct. 2011; 8 pages. [cited by applicant]
Roehl, Kimberly A. et al.; “Cancer Progression And Survival Rates Following Anatomical Radical Retropubic Prostatectomy In 3,478 Consecutive Patients: Long-Term Results”; The Journal of Urology; vol. 172; Sep. 2004; pp.… [cited by applicant]
Freedland, Stephen J. et al.; “Risk of Prostate Cancer-Specific Mortality Following Biochemical Recurrence After Radical Prostatectomy”; The Journal of the American Medical Association; vol. 294 No. 4; Jul. 27, 2005; pp… [cited by applicant]
Antonarakis, Emmanuel S. et al.; “The natural history of metastatic progression in men with prostate-specific antigen recurrence after radical prostatectomy: long-term follow-up”; BJU International; 109; 2011; pp. 32-39. [cited by applicant]
Draisma, Gerrit et al.; “Lead Time and Overdiagnosis in Prostate-Specific Antigen Screening: Importance of Methods and Context”; Journal of the National Cancer Institute; vol. 101 Iss. 6; Mar. 18, 2009; pp. 374-383. [cited by applicant]
Paller, Channing J. et al.; “Management of Biochemically Recurrent Prostate Cancer After Local Therapy: Evolving Standards of Care and New Directions”; Clinical Advances in Hematology and Oncology; 11(1); Jan. 2013; 15 … [cited by applicant]
Amling, Christopher L. et al.; “Long-Term Hazard of Progression After Radical Prostatectomy for Clinically Localized Prostate Cancer Continued Risk of Biochemical Failure After 5 Years”; The Journal of Urology; vol. 164… [cited by applicant]
Han, Misop et al.; “Long-Term Biochemical Disease-Free and Cancer-Specific Survival Following Anatomic Radical Retropubic Prostactomy”; Urologic Clinics of North America; vol. 28 No. 3; Aug. 2001; pp. 555-565. [cited by applicant]
Hull, Gerald W. et al.; “Cancer Control With Radical Prostatectomy Alone in 1,000 Consecutive Patients”; The Journal of Urology; vol. 167; Feb. 2002; pp. 528-534. [cited by applicant]
Psutka, Sarah P. et al.; “Men With Organ-confined Prostate Cancer and Positive Surgical Margins Develop Biocheml Failure at a Similar Rate to Men With Extracapsular Extension”; Journal of Urology; 78(1); 2011; pp. 121-1… [cited by applicant]
Loeb, Stacy et al.; “Overdiagnosis and Overtreatment of Prostate Cancer”; European Urology; 65(6); Jun. 2014; 21 pages. [cited by applicant]
Klotz, Laurence; “Prostate cancer overdiagnosis and overtreatment”; Current Opinion in Endocrinology, Diabetes and Obesity; vol. 20 No. 3; Jun. 2013; pp. 204-209. [cited by applicant]
Armenia, Joshua et al.; “The long tail of oncogenic drivers in prostate cancer”; Nature Genetics; 50(5); May 2018; 17 pages. [cited by applicant]
Gery, Sigal et al.; “TMEFF2 is an adrogen-regulated gene exhibiting antiproliferative effects in prostate cancer cells”; Oncogene; 21; 2002; pp. 4739-4746. [cited by applicant]
Hong, Sung Kyu et al.; “Insignificant disease among men with intermediate-risk prostate cancer”; World Journal of Urology; 32(6); Dec. 2014; 10 pages. [cited by applicant]
Overcash, Ryan F. et al.; “Androgen Signaling Promotes Translation of TMEFF2 in Prostate Cancer Cells via Phosphorylation of the α Subunit of the Translation Initiation Factor 2”; PLOS One; vol. 8 Iss. 2; Feb. 2013; 13 … [cited by applicant]
Kim, Jung H. et al.; “Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer”; Genome Research; 21; 2011; pp. 1028-1041. [cited by applicant]
Fournier, Pierrick GJ et al.; “The TGFβ Signaling Regulator PMEPA1 Suppresses Prostate Cancer Metastases to Bone”; Cancer Cell.; 27(6); Jun. 8, 2015; 29 pages. [cited by applicant]
Xu, Youyuan et al.; “Androgens Induce Prostate Cancer Cell Proliferation through Mammalian Target of Rapamycin Activation and Post-transcriptional Increases in Cyclin D Proteins”; Cancer Research; 66(15); Aug. 1, 2006; … [cited by applicant]
McNair, C et al.; “Cell cycle-coupled expansion of AR activity promotes cancer progression”; Oncogene; 36; 2017; pp. 1655-1668. [cited by applicant]
Balk, Steven P. et al.; “AR, the cell cycle, and prostate cancer”; Journal of the Nuclear Receptor Signaling Atlas; vol. 6; 2008; 12 pages. [cited by applicant]
Sivanandam, Arun et al.; “Role of Androgen Receptor in Prostate Cancer Cell Cycle Regulation: Interaction with Cell Cycle Regulatory Proteins and Enzymes of DNA Synthesis”; Current Protein and Peptide Science; vol. 11 N… [cited by applicant]
Koryakina, Yulia et al.; “Cell Cycle Dependent Regulation of Androgen Receptor Function”; Endocrine-Related Cancer; 22(2); Apr. 2015; 25 pages. [cited by applicant]
Paju, Annukka et al.; “Increased Expression of Tumor-Associated Trypsin Inhibitor, TATI, in Prostate Cancer and in Androgen-Independent 22Rv1 Cells”; European Urology; 52; 2007; pp. 1670-1681. [cited by applicant]
Stenman, Ulf-Håkan; SPINK1: A New Therapeutic Target in Cancer?; Clinical Chemistry; 57:11; 2011; pp. 1474-1475. [cited by applicant]
Tomlins, Scott A. et al.; “The Role of SPINK1 in ETS Rearrangement Negative Prostate Cancers”; Cancer Cell.; 13(6); Jun. 2008; 22 pages. [cited by applicant]
Flavin, Richard et al.; “SPINK1 Protein Expression and Prostate Cancer Progression”; Clinical Cancer Research; 20(18); Sep. 15, 2014; pp. 4904-4911. [cited by applicant]
Ateeq, Bushra et al.; “Therapeutic targeting of SPINK1-positive prostate cancer”; Science Translational Medicine; 3(72); Mar. 2, 2011; 18 pages. [cited by applicant]
Bolger, Anthony M. et al.; “Trimmomatic: a flexible trimmer for Illumina sequence data”; Bioinformatics; vol. 30 No. 15; 2014; pp. 2114-2120. [cited by applicant]
Bray, Nicolas L. et al.; “Near-optimal RNA-Seq quantification”; Nat Biotechnol; 34:525-7; 2016; 21 pages. [cited by applicant]
Soneson, Charlotte et al.; “Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences”; F1000Research; 4:1521; 2016; 19 pages. [cited by applicant]
Love, Michael I et al.; “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2”; Genome Biology; 15:550; 2014; 21 pages. [cited by applicant]
Varambally, Sooryanarayana et al.; “Integrative genomic and proteomic analysis of prostate cancer reveals signatures of metastatic progression”; Cancer Cell; vol. 8; Nov. 2005; pp. 393-406. [cited by applicant]
Vanaja, Donkena Krishna et al.; “Transcriptional Silencing of Zinc Finger Protein 185 Identified by Expression Profiling Is Associated with Prostate Cancer Progression”; American Association for Cancer Research; 63; Jul… [cited by applicant]
Cerami, Ethan et al.; “The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data”; Cancer Discovery; 2(5); May 2012; 7 pages. [cited by applicant]
Shao, Yu-Hsuan et al.; “Contemporary Risk Profile of Prostate Cancer in the United States”; Journal of the National Cancer Institute; vol. 101 Iss. 18; Sep. 16, 2009; pp. 1280-1283. [cited by applicant]
Alves de Inda, Marcia et al.; “Validation of Cyclic Adenosine Monophosphate Phosphodiesterase-4D7 for its Independent Contribution to Risk Stratification in a Prostate Cancer Patient Cohort with Longitudinal Biological … [cited by applicant]
Georgescu, Constantin et al.; “A TMEFF2-regulated cell cycle derived gene signature is prognostic of recurrence risk in prostate cancer”; BMC Cancer; 19:423; 2019; 13 pages. [cited by applicant]
Altschul, Stephen F. et al.; “Basic Local Alignment Search Tool”; Journal of Molecular Biology; 215; 1990; pp. 403-410. [cited by applicant]
Gish, Warren et al.; “Identification of protein coding regions by database similarity search”; Nature Genetics; vol. 3; Mar. 1993; pp. 266-272. [cited by applicant]
Karlin, Samuel et al.; “Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes”; Proceedings of the National Academy of Sciences of the USA; vol. 87; Mar. 1990… [cited by applicant]
Karlin, Samuel et al.; “Applications and statistics for multiple high-scoring segments in molecular sequences”; Proceedings of the National Academy of Sciences of the USA; vol. 90; Jun. 1993; pp. 5873-5877. [cited by applicant]
Myers, Eugene W. et al.; Optimal alignments in linear space; CABIOS; vol. 4 No. 1; 1988; pp. 11-17. [cited by applicant]
Pearson, William R. et al.; “Improved tools for biological sequence comparison”; Proceedings of the National Academy of Sciences of the USA; vol. 85; Apr. 1988; pp. 2444-2448. [cited by applicant]
Ali, Nazim et al.; “Phorbol Ester-induced Shedding of the Prostate Cancer Marker Transmembrane Protein with Epidermal Growth Factor and Two Follistatin Motifs 2 Is Mediated by the Disintegrin and Metalloproteinase-17”; … [cited by applicant]
Antunes, Alberto A. et al.; “The Role of Prostate Specific Membrane Antigen and Pepsinogen C Tissue Expression as an Adjunctive Method to Prostate Cancer Diagnosis”; The Journal of Urology; vol. 181; Feb. 2009; pp. 594-… [cited by applicant]
Schröder, Fritz H. et al.; “Prostate-Cancer Mortality at 11 Years of Follow-up”; The New England Journal of Medicine; vol. 366 No. 11; Mar. 15, 2012; pp. 981-990. [cited by applicant]
Chen, Qian et al.; “Gene expression in the LNCaP human prostate cancer progression model: Progression associated expression in vitro corresponds to expression changes associated with prostate cancer progression in vivo”… [cited by applicant]
Chen, Xiaofei et al.; “TMEFF2 modulates the AKT and ERK signaling pathways”; International Journal of Biochemistry and Molecular Biology; 4(2); 2013; pp. 83-94. [cited by applicant]
Chen, Ying-Chieh et al.; “Quantitative DNA methylation analysis of selected genes in endometrial carcinogenesis”; Taiwanese Journal of Obstetrics & Gynecology; 54; 2015; pp. 572-579. [cited by applicant]
Chen, Tian Rui et al.; “Generation and characterization of Tmeff2 mutant mice”; Biochemical and Biophysical Research Communications; 425; 2012; pp. 189-194. [cited by applicant]
Chen, Hua-Yun et al.; “High CpG island methylator phenotype is associated with lymph node metastasis and prognosis in gastric cancer”; Cancer Science; vol. 103 No. 1; Jan. 2012; pp. 73-79. [cited by applicant]
Clarke, Megan A. et al.; “Discovery and validation of candidate host DNA methylation markers for detection of cervical pecancer and cancer”; International Journal of Cancer; 141; 2017; pp. 701-710. [cited by applicant]
Costa, Vera L. et al.; Three Epigenetic Biomarkers, GDF15, TMEFF2, and VIM, Accurately Predict Bladder Cancer from DNA-Based Analyses of Urine Samples; Clinical Cancer Research; 16(23); Dec. 1, 2010; pp. 5842-5851. [cited by applicant]
Ebert, Matthias P.A. et al.; “Hypermethylation of the TPEF/HPP1 Gene in Primary and Metastatic Colorectal Cancers”; Neoplasia; vol. 7 No. 8; Aug. 2005; pp. 771-778. [cited by applicant]
Elahi, Abul et al.; “HPP1-mediated tumor suppression requires activation of STAT1 pathways”; International Journal of Cancer; 122; 2008; pp. 1567-1572. [cited by applicant]
Gawel-Beben, Katarzyna et al.; TMEFF2 shedding is regulated by oxidative stress and mediated by ADAMs and transmembrane serine proteases implicated in prostate cancer; Cell Biology International; 42; 2018; pp. 273-280. [cited by applicant]
Saha, Partha et al.; “The Human Homolog of [cited by applicant]
Agilent. Agilent Whole Human Genome Microarray 4 x 44K. 2015. Available via URL: <ftp.ebi.ac.uk/biostudies/nfs/A-MEXP-/125/A-MEXP-1125/Files/A-MEXP-1125.adf.txt> (Year: 2015). [cited by applicant]
NCBI Gene Expression Omnibus (GEO). Platform GPL29829, Mar. 9, 2021, 194 pages (Year: 2021). [cited by applicant]
Georgescu et al. bioRxiv preprint. Aug. 21, 2018. 32 pages, available via URL: <biorxiv.org/content/10.1101/397331v1 .full.pdf>) (Year: 2018). [cited by applicant]
Corbin et al. AACR Annual Meeting 2019. “A tumor suppressor-regulated cell cycle derived gene signature is prognostic of recurrence risk in prostate cancer” 3152/5, Session PO.CL 11.09, Apr. 2, 2019 (Year: 2019). [cited by applicant]