2018
Increased epigenetic age in normal breast tissue from luminal breast cancer patients
Hofstatter EW, Horvath S, Dalela D, Gupta P, Chagpar AB, Wali VB, Bossuyt V, Storniolo AM, Hatzis C, Patwardhan G, Von Wahlde MK, Butler M, Epstein L, Stavris K, Sturrock T, Au A, Kwei S, Pusztai L. Increased epigenetic age in normal breast tissue from luminal breast cancer patients. Clinical Epigenetics 2018, 10: 112. PMID: 30157950, PMCID: PMC6114717, DOI: 10.1186/s13148-018-0534-8.Peer-Reviewed Original ResearchConceptsNormal breast tissueBreast cancer patientsBreast cancerCancer patientsEpigenetic age accelerationBreast tissueAge accelerationLuminal breast cancer patientsNormal adjacent breast tissueNormal breast tissue samplesIncident breast cancerTissue samplesNon-tumor sitesBreast cancer riskImportant risk factorAdjacent breast tissueKomen Tissue BankChronological ageBreast cancer statusMalignant breast tissueNormal tissue samplesAge-related changesBreast tissue samplesBreast surgeryUnaffected women
2017
Association Between Genomic Metrics and Immune Infiltration in Triple-Negative Breast Cancer
Karn T, Jiang T, Hatzis C, Sänger N, El-Balat A, Rody A, Holtrich U, Becker S, Bianchini G, Pusztai L. Association Between Genomic Metrics and Immune Infiltration in Triple-Negative Breast Cancer. JAMA Oncology 2017, 3: 1707-1711. PMID: 28750120, PMCID: PMC5824276, DOI: 10.1001/jamaoncol.2017.2140.Peer-Reviewed Original ResearchMeSH KeywordsBiomarkers, TumorCohort StudiesGene DosageGene Expression ProfilingGene Expression Regulation, NeoplasticGenetic HeterogeneityHumansImmunologic SurveillanceLymphocyte CountLymphocytes, Tumor-InfiltratingPrognosisSequence Analysis, DNASequence Analysis, RNASurvival AnalysisTriple Negative Breast NeoplasmsConceptsTriple-negative breast cancerImmune infiltrationTNBC cohortBetter prognosisPrognostic categoriesPoor prognosisInverse associationBreast cancerImmune surveillanceImmune checkpoint inhibitor therapyMore effective immunotherapy strategiesSubset of TNBCLow immune cell infiltrationClonal heterogeneityCheckpoint inhibitor therapySelection of patientsImmune cell infiltrationEffective immunotherapy strategiesIndependent validation cohortPatient survival informationLymphocyte countImmunotherapy strategiesInhibitor therapyNeoantigen loadValidation cohort
2015
Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments
Qi Y, Liu X, Liu CG, Wang B, Hess KR, Symmans WF, Shi W, Pusztai L. Reproducibility of Variant Calls in Replicate Next Generation Sequencing Experiments. PLOS ONE 2015, 10: e0119230. PMID: 26136146, PMCID: PMC4489803, DOI: 10.1371/journal.pone.0119230.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsEuropean Genome-phenome ArchiveProtein kinase geneMillions of nucleotidesSame genomic DNANext-generation sequencing experimentsVariant callsGenomic locationNext-generation sequencingSequence dataSNV callsKinase geneGenomic DNANucleotide substitutionsSequencing experimentsHigh stringencyVariant allele frequencyNucleotide variantsTrue biological changeNucleotide alterationsGeneration sequencingAllele countsSequencing errorsBreast cancer samplesAllele frequencies
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
2013
Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
Frampton GM, Fichtenholtz A, Otto GA, Wang K, Downing SR, He J, Schnall-Levin M, White J, Sanford EM, An P, Sun J, Juhn F, Brennan K, Iwanik K, Maillet A, Buell J, White E, Zhao M, Balasubramanian S, Terzic S, Richards T, Banning V, Garcia L, Mahoney K, Zwirko Z, Donahue A, Beltran H, Mosquera JM, Rubin MA, Dogan S, Hedvat CV, Berger MF, Pusztai L, Lechner M, Boshoff C, Jarosz M, Vietz C, Parker A, Miller VA, Ross JS, Curran J, Cronin MT, Stephens PJ, Lipson D, Yelensky R. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nature Biotechnology 2013, 31: 1023-1031. PMID: 24142049, PMCID: PMC5710001, DOI: 10.1038/nbt.2696.Peer-Reviewed Original Research
2011
The Value of Genomic Analysis of Breast Cancer in Drug Development
Szekely B, Pusztai L. The Value of Genomic Analysis of Breast Cancer in Drug Development. JNCI Monographs 2011, 2011: 60-62. PMID: 22043042, DOI: 10.1093/jncimonographs/lgr039.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic AgentsBreast NeoplasmsDNA, NeoplasmDrug DiscoveryFemaleGenomicsHumansSequence Analysis, DNA