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 modulesA framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT)
Mateo J, Chakravarty D, Dienstmann R, Jezdic S, Gonzalez-Perez A, Lopez-Bigas N, Ng CKY, Bedard PL, Tortora G, Douillard J, Van Allen EM, Schultz N, Swanton C, André F, Pusztai L. A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Annals Of Oncology 2018, 29: 1895-1902. PMID: 30137196, PMCID: PMC6158764, DOI: 10.1093/annonc/mdy263.Peer-Reviewed Original ResearchConceptsESMO ScaleMolecular targetsClinical actionabilityPrecision Medicine Working GroupGenomic alterationsPrecision medicineRoutine clinical decisionEvidence-based criteriaMedicine Working GroupLack of evidencePreclinical evidenceClinical benefitClinical evidencePatient populationClassification systemClinical managementCancer precision medicineInvestigational targetsPatient managementMolecular aberrationsTumor typesClinical decisionClinical targetsAvailable evidenceEuropean Society
2016
Is precision medicine ready for use in breast cancer?
Pusztai L. Is precision medicine ready for use in breast cancer? Clinical Advances In Hematology And Oncology 2016, 14: 964-966. PMID: 28212357.Peer-Reviewed Original ResearchMutation 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
2015
Standardization efforts enabling next-generation sequencing and microarray based biomarkers for precision medicine
Zheng Y, Qing T, Song Y, Zhu J, Yu Y, Shi W, Pusztai L, Shi L. Standardization efforts enabling next-generation sequencing and microarray based biomarkers for precision medicine. Biomarkers In Medicine 2015, 9: 1265-1272. PMID: 26502353, DOI: 10.2217/bmm.15.99.Peer-Reviewed Original Research
2014
A Targeted Next‐Generation Sequencing Assay Detects a High Frequency of Therapeutically Targetable Alterations in Primary and Metastatic Breast Cancers: Implications for Clinical Practice
Vasan N, Yelensky R, Wang K, Moulder S, Dzimitrowicz H, Avritscher R, Wang B, Wu Y, Cronin MT, Palmer G, Symmans WF, Miller VA, Stephens P, Pusztai L. A Targeted Next‐Generation Sequencing Assay Detects a High Frequency of Therapeutically Targetable Alterations in Primary and Metastatic Breast Cancers: Implications for Clinical Practice. The Oncologist 2014, 19: 453-458. PMID: 24710307, PMCID: PMC4012963, DOI: 10.1634/theoncologist.2013-0377.Peer-Reviewed Original ResearchConceptsBreast cancerGenomic alterationsV-akt murine thymoma viral oncogene homolog 1Stage IV cancerMetastatic breast cancerActionable genomic alterationsPotential treatment optionOncogene homolog 1Primary tumor biopsiesCancer-related genesClinical Laboratory Improvement AmendmentsDependent kinasesMedian sequencing depthGene fusionsSequencing depthBase substitutionsHER2 mutationsHomolog 1Actionable alterationsTargetable alterationsTreatment optionsClinical trialsHER2 amplificationMetastatic cancerTumor biopsies