2018
TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options
Gershkovich P, Platt J, Knopf J, Tasoulis MK, Shi W, Pusztai L, Hatzis C. TQuest, A Web-Based Platform to Enable Precision Medicine by Linking a Tumor’s Genetic Defects to Therapeutic Options. JCO Clinical Cancer Informatics 2018, 2: 1-13. PMID: 30652574, DOI: 10.1200/cci.17.00120.Peer-Reviewed Original ResearchConceptsData acquisition layerFull-text indexAcquisition layerUser interfaceData layersPrototype web applicationWeb-based platformWeb applicationRelevance scoresSearch enginesSource codeSoftware toolsSearch resultsInterventional clinical trialsLabel dataClinical trialsTherapeutic optionsPlatformUS FoodMolecular abnormalitiesMetastatic breast cancerPotential therapeutic optionPotential treatment optionTumor DNA sequencingWeb-based modules
2016
Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools
Patel JM, Knopf J, Reiner E, Bossuyt V, Epstein L, DiGiovanna M, Chung G, Silber A, Sanft T, Hofstatter E, Mougalian S, Abu-Khalaf M, Platt J, Shi W, Gershkovich P, Hatzis C, Pusztai L. Mutation based treatment recommendations from next generation sequencing data: a comparison of web tools. Oncotarget 2016, 7: 22064-22076. PMID: 26980737, PMCID: PMC5008344, DOI: 10.18632/oncotarget.8017.Peer-Reviewed Original ResearchConceptsWeb toolArtificial intelligence toolsApplicable software toolsReal-time statusDifferent web toolsIntelligence toolsSoftware toolsRecommendation toolGeneration sequencing dataNext-generation sequencing dataData acquisitionInteraction databasesGenomic dataRecommendation sourcesCancer genome dataProfiling resultsToolDrug-gene interaction databaseMore sourcesGenome dataAlgorithmPlatformPersonalized cancer therapy
2011
Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems
Hess KR, Wei C, Qi Y, Iwamoto T, Symmans WF, Pusztai L. Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems. BMC Bioinformatics 2011, 12: 463. PMID: 22132775, PMCID: PMC3245512, DOI: 10.1186/1471-2105-12-463.Peer-Reviewed Original ResearchConceptsPrediction problemCurrent statistical methodsClinical prediction problemsReal data setsMonte Carlo cross validationStatistical methodsData setsAccurate modelPerturbedInformative featuresPrediction modelCancer data setsPredictor performanceGene expression dataProblemBreast cancer data setsClassification problemSuch featuresMean expression valuesSet
2010
Utility of oncotype DX risk estimates in clinically intermediate risk hormone receptor‐positive, HER2‐normal, grade II, lymph node‐negative breast cancers
Kelly CM, Krishnamurthy S, Bianchini G, Litton JK, Gonzalez‐Angulo A, Hortobagyi GN, Pusztai L. Utility of oncotype DX risk estimates in clinically intermediate risk hormone receptor‐positive, HER2‐normal, grade II, lymph node‐negative breast cancers. Cancer 2010, 116: 5161-5167. PMID: 20665886, DOI: 10.1002/cncr.25269.Peer-Reviewed Original ResearchConceptsTrial Assigning Individualized OptionsRisk of recurrenceOncotype DXRecurrence scoreBreast cancerIntermediate riskGrade I/II tumorsLymph node-negative breast cancerNode-negative breast cancerStage I/IID. Anderson Cancer CenterOncotype DX breast cancerRisk estimatesIntermediate-risk populationEarly breast cancerRoutine clinical variablesHigh-risk groupOncotype DX testingAnderson Cancer CenterAdjuvant chemotherapyDistant recurrenceConsecutive patientsII tumorsClinicopathological variablesLobular carcinoma
2006
Development and validation of nomograms for predicting residual tumor size and the probability of successful conservative surgery with neoadjuvant chemotherapy for breast cancer
Rouzier R, Pusztai L, Garbay J, Delaloge S, Hunt KK, Hortobagyi GN, Berry D, Kuerer HM. Development and validation of nomograms for predicting residual tumor size and the probability of successful conservative surgery with neoadjuvant chemotherapy for breast cancer. Cancer 2006, 107: 1459-1466. PMID: 16948128, DOI: 10.1002/cncr.22177.Peer-Reviewed Original ResearchConceptsResidual tumor sizeBreast conservation therapyNeoadjuvant chemotherapyBreast conservation surgeryBreast cancer patientsTumor sizeConservation therapyBreast conservationConservation surgeryCancer patientsAnthracycline-based neoadjuvant chemotherapyD. Anderson Cancer CenterPaclitaxel neoadjuvant chemotherapyPreoperative chemotherapy regimenPreoperative chemotherapy regimensSuccessful conservative surgeryValidation of nomogramsInstitut Gustave RoussyAnderson Cancer CenterLogistic regression modelsChemotherapy regimenChemotherapy regimensConservative surgeryClinicopathologic dataCancer Center