2018
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity
Shi W, Ng CKY, Lim RS, Jiang T, Kumar S, Li X, Wali VB, Piscuoglio S, Gerstein MB, Chagpar AB, Weigelt B, Pusztai L, Reis-Filho JS, Hatzis C. Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity. Cell Reports 2018, 25: 1446-1457. PMID: 30404001, PMCID: PMC6261536, DOI: 10.1016/j.celrep.2018.10.046.Peer-Reviewed Original ResearchExome SequencingFemaleGenetic HeterogeneityHumansINDEL MutationMutationNeoplasmsPloidiesPolymorphism, Single NucleotideReproducibility of Results
2015
Characterization of DNA variants in the human kinome in breast cancer
Agarwal D, Qi Y, Jiang T, Liu X, Shi W, Wali VB, Turk B, Ross JS, Fraser Symmans W, Pusztai L, Hatzis C. Characterization of DNA variants in the human kinome in breast cancer. Scientific Reports 2015, 5: 14736. PMID: 26420498, PMCID: PMC4588561, DOI: 10.1038/srep14736.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overBiomarkers, TumorBreast NeoplasmsFemaleGene Expression Regulation, NeoplasticGenetic Predisposition to DiseaseGenetic VariationHigh-Throughput Nucleotide SequencingHumansMiddle AgedMutationNeoplasm GradingNeoplasm MetastasisNeoplasm StagingPhosphotransferasesPolymorphism, Single NucleotideReproducibility of ResultsTranscriptomeConceptsBreast cancerHuman kinomeKinase geneGreater mutational loadNucleic acid variationPrimary cancer samplesPrimary breast cancerHistologic grade 1Major functional impactSOLiD sequencing platformIndividual breast cancersNon-synonymous variantsFine-needle biopsyGrade 3 casesCancer-related genesNucleotide variationsDNA variantsSequencing platformsMetastatic lesionsMutational loadAcid variationsCancer biologyGenesNeedle biopsyAdditional cancersReproducibility 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 ResearchMeSH KeywordsAllelesArtifactsBreast NeoplasmsDNAFemaleGene FrequencyGenome, HumanHigh-Throughput Nucleotide SequencingHumansPolymorphism, Single NucleotideProtein KinasesReproducibility of ResultsSequence Analysis, DNAConceptsSingle 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
2012
Mutation profiling identifies numerous rare drug targets and distinct mutation patterns in different clinical subtypes of breast cancers
Santarpia L, Qi Y, Stemke-Hale K, Wang B, Young EJ, Booser DJ, Holmes FA, O’Shaughnessy J, Hellerstedt B, Pippen J, Vidaurre T, Gomez H, Valero V, Hortobagyi GN, Symmans WF, Bottai G, Di Leo A, Gonzalez-Angulo AM, Pusztai L. Mutation profiling identifies numerous rare drug targets and distinct mutation patterns in different clinical subtypes of breast cancers. Breast Cancer Research And Treatment 2012, 134: 333-343. PMID: 22538770, PMCID: PMC3885980, DOI: 10.1007/s10549-012-2035-3.Peer-Reviewed Original ResearchConceptsTriple-negative breast cancerBreast cancer subtypesBreast cancerPIK3CA mutationsCancer subtypesEstrogen receptor-positive cancersBreast cancer molecular subtypesMajor breast cancer subtypesSingle needle biopsyProspective clinical trialsReceptor-positive cancersDifferent breast cancer subtypesDifferent clinical subtypesNegative breast cancerCancer molecular subtypesFine-needle aspirationMutation patternsClinical subtypesClinical trialsNeedle biopsyMolecular subtypesNeedle aspirationInvestigational drugsStage IFBXW7 mutations