2024
Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes
Sura G, Tran K, Trevarton A, Marczyk M, Fu C, Du L, Qu J, Lau R, Tasto A, Gould R, Tinnirello A, Sinn B, Pusztai L, Hatzis C, Symmans W. Comparative Analysis of Ficoll-Hypaque and CytoLyt® Techniques for Blood Removal in Breast Cancer Malignant Effusions: Effects on RNA Quality and Sequencing Outcomes. Journal Of The American Society Of Cytopathology 2024 DOI: 10.1016/j.jasc.2024.11.001.Peer-Reviewed Original ResearchRNA integrity numberRNA qualityRNA-seqMeasurement of gene expressionRNA-seq analysisMetastatic breast cancerFicoll-Hypaque methodDensity gradient enrichmentSequence dataRead-basedVariant detectionMalignant effusionsCytospin slidesFresh frozen samplesRNA fragmentsTranscript abundanceSequencing outcomesSequencing methodsBreast cancerRNA sequencingFicoll-HypaqueUMI-basedGene expressionRNAMalignant effusion specimens
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
2011
S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer.
Pusztai L, Qi Y, Shi W, Liu C, Wang B, Liu X, Booser D, Esteva F, Symmans F, Hortobagyi G. S6-4: Protein Kinase Mutation Patterns in Human Breast Cancer. Cancer Research 2011, 71: s6-4-s6-4. DOI: 10.1158/0008-5472.sabcs11-s6-4.Peer-Reviewed Original ResearchGene expression profilingBiological pathwaysExpression profilingHuman protein kinasesImportant regulatory genesCanonical biological pathwaysDNA copy number variationsDNA copy number alterationsArray CGHSOLiD sequencing platformTarget base pairCopy number variationsFunctional impact scoresCopy number alterationsProtein functionAffymetrix U133A chipsMAPK familyRegulatory genesBMP2KEntire genomeProtein kinaseSequence dataGerm-line variantsGenomic dataBiological functions