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
2010
Prognostic and Therapeutic Implications of Distinct Kinase Expression Patterns in Different Subtypes of Breast Cancer
Bianchini G, Iwamoto T, Qi Y, Coutant C, Shiang CY, Wang B, Santarpia L, Valero V, Hortobagyi GN, Symmans WF, Gianni L, Pusztai L. Prognostic and Therapeutic Implications of Distinct Kinase Expression Patterns in Different Subtypes of Breast Cancer. Cancer Research 2010, 70: 8852-8862. PMID: 20959472, DOI: 10.1158/0008-5472.can-10-1039.Peer-Reviewed Original ResearchConceptsPathologic complete responseBreast cancerClinical subtypesPredictive valueHigher pathologic complete responseHuman epidermal growth factor receptor 2Epidermal growth factor receptor 2Different clinical subsetsDistinct prognostic informationNode-negative patientsGrowth factor receptor 2Different clinical subtypesBreast cancer cell linesFactor receptor 2Subtype-specific inhibitionCancer cell linesNeoadjuvant chemotherapyAdjuvant therapyComplete responseClinical subsetsWorse prognosisPrognostic valuePrognostic informationClinical subgroupsExpression patterns