2024
Correlation of hormone receptor positive HER2-negative/MammaPrint high-2 breast cancer with triple negative breast cancer: Results from gene expression data from the ISPY2 trial.
Rios-Hoyo A, Xiong K, Marczyk M, García-Millán R, Wolf D, Huppert L, Nanda R, Yau C, Hirst G, van 't Veer L, Esserman L, Pusztai L. Correlation of hormone receptor positive HER2-negative/MammaPrint high-2 breast cancer with triple negative breast cancer: Results from gene expression data from the ISPY2 trial. Journal Of Clinical Oncology 2024, 42: 573-573. DOI: 10.1200/jco.2024.42.16_suppl.573.Peer-Reviewed Original ResearchGene expression dataGene expression analysisExpression dataExpressed genesExpression analysisTriple-negativeDistance analysisPathway analysisDifferential gene expression analysisCell cycle pathwayGene set enrichment analysisBreast cancerIngenuity Pathway AnalysisRate of pathological complete responseHigh-risk stage IIGlucocorticoid receptor signalingTriple negative breast cancerCycle pathwayPathological complete responseDNA repairEnrichment analysisOptimal treatment strategyNegative breast cancerI-SPY2 trialGenes
2022
Investigating Sources of Zeros in 10× Single-Cell RNAseq Data
Slowik H, Zyla J, Marczyk M. Investigating Sources of Zeros in 10× Single-Cell RNAseq Data. Lecture Notes In Computer Science 2022, 13347: 71-80. DOI: 10.1007/978-3-031-07802-6_6.Peer-Reviewed Original ResearchSingle-cell levelSingle-cell RNA sequencingSingle-cell RNAseq dataNumber of transcriptsMulti-omics dataGene expression estimatesRibosomal genesRNA sequencingExpression profilingEnrichment analysisRNAseq dataBiological pathwaysSequencing platformsExpression dataGenesExpression estimatesIndividual cellsBreast cancer cell linesCancer cell linesCell linesSingle experimentLow mappabilityTranscriptsSequencingProfilingPredictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer.
Blenman KRM, Marczyk M, Karn T, Qing T, Li X, Gunasekharan V, Yaghoobi V, Bai Y, Ibrahim EY, Park T, Silber A, Wolf DM, Reisenbichler E, Denkert C, Sinn BV, Rozenblit M, Foldi J, Rimm DL, Loibl S, Pusztai L. Predictive Markers of Response to Neoadjuvant Durvalumab with Nab-Paclitaxel and Dose-Dense Doxorubicin/Cyclophosphamide in Basal-Like Triple-Negative Breast Cancer. Clinical Cancer Research 2022, 28: 2587-2597. PMID: 35377948, PMCID: PMC9464605, DOI: 10.1158/1078-0432.ccr-21-3215.Peer-Reviewed Original ResearchConceptsBasal-like triple-negative breast cancerPathologic complete responseResidual diseaseNeoadjuvant durvalumabDNA damage repairSomatic mutationsBreast cancerWnt/β-cateninHigh expressionTriple-negative breast cancerBasal-Like TripleDoxorubicin/cyclophosphamideDNA repairTumor mutation burdenRNA sequencingEpithelial-mesenchymal transitionFive-gene signatureB-cell markersCancer driversEnrichment analysisNegative breast cancerDamage repairGene expressionJAK-STATCell cycle
2021
Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies
Marczyk M, Macioszek A, Tobiasz J, Polanska J, Zyla J. Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies. Frontiers In Genetics 2021, 12: 767358. PMID: 34956320, PMCID: PMC8696167, DOI: 10.3389/fgene.2021.767358.Peer-Reviewed Original ResearchGenome-wide association studiesOver-Representation AnalysisSingle nucleotide polymorphismsMeta-Analysis Gene-set EnrichmentSame geneTypical genome-wide association studyEnrichment analysisAssociation studiesGene-set analysisLD correctionGene set enrichmentGene expression dataGSEA-SNPCancer Genome Atlas (TCGA) databaseRelevant single nucleotide polymorphismsTranscriptomic levelGene levelExpression dataVariant associationsNonrandom associationGenesAssociation of SNPsMore lociAtlas databaseBreast cancer samples