2023
Genomics of ERBB2-Positive Breast Cancer in Young Women Before and After Exposure to Chemotherapy Plus Trastuzumab.
Lipsyc-Sharf M, Jain E, Collins L, Rosenberg S, Ruddy K, Tamimi R, Schapira L, Come S, Peppercorn J, Borges V, Warner E, Snow C, Krop I, Kim D, Weiss J, Zanudo J, Partridge A, Wagle N, Waks A. Genomics of ERBB2-Positive Breast Cancer in Young Women Before and After Exposure to Chemotherapy Plus Trastuzumab. JCO Precision Oncology 2023, 7: e2300076. PMID: 37364233, DOI: 10.1200/po.23.00076.Peer-Reviewed Original ResearchConceptsPositive breast cancerWhole-exome sequencingBreast cancerYoung womenWomen age 40 yearsErbB2-positive breast cancerErb-b2 receptor tyrosine kinase 2Half of patientsTime pointsLarge prospective cohortAge 40 yearsPost-treatment tumorsReceptor tyrosine kinase 2Post-treatment specimensPost-treatment samplesProspective cohortPositive tumorsTyrosine kinase 2Cancer-related genesPatientsTumor-normal pairsTherapeutic resistanceTumor tissueCNS changesHotspot mutations
2022
Clinical Efficacy and Whole-Exome Sequencing of Liquid Biopsies in a Phase IB/II Study of Bazedoxifene and Palbociclib in Advanced Hormone Receptor-Positive Breast Cancer.
Tsuji J, Li T, Grinshpun A, Coorens T, Russo D, Anderson L, Rees R, Nardone A, Patterson C, Lennon NJ, Cibulskis C, Leshchiner I, Tayob N, Tolaney SM, Tung N, McDonnell DP, Krop IE, Winer EP, Stewart C, Getz G, Jeselsohn R. Clinical Efficacy and Whole-Exome Sequencing of Liquid Biopsies in a Phase IB/II Study of Bazedoxifene and Palbociclib in Advanced Hormone Receptor-Positive Breast Cancer. Clinical Cancer Research 2022, 28: 5066-5078. PMID: 36215125, PMCID: PMC9722539, DOI: 10.1158/1078-0432.ccr-22-2305.Peer-Reviewed Original ResearchConceptsProgression-free survivalPhase Ib/II studyCombination of palbociclibBreast cancerWhole-exome sequencingESR1 mutationsII studyClinical efficacySafety profileHormone receptor-positive/HER2-negative advanced breast cancerAdvanced hormone receptor-positive breast cancerHER2-negative advanced breast cancerHormone receptor-positive breast cancerThird-generation selective estrogen receptor modulatorMedian progression-free survivalEndocrine-resistant breast cancerReceptor-positive breast cancerShorter progression-free survivalSelective estrogen receptor modulatorsClinical benefit rateAcceptable safety profileAdvanced breast cancerEstrogen receptor modulatorsSelective ER degraderDNA whole-exome sequencingCirculating Tumor DNA and Late Recurrence in High-Risk Hormone Receptor–Positive, Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer
Lipsyc-Sharf M, de Bruin EC, Santos K, McEwen R, Stetson D, Patel A, Kirkner GJ, Hughes ME, Tolaney SM, Partridge AH, Krop IE, Knape C, Feger U, Marsico G, Howarth K, Winer EP, Lin NU, Parsons HA. Circulating Tumor DNA and Late Recurrence in High-Risk Hormone Receptor–Positive, Human Epidermal Growth Factor Receptor 2–Negative Breast Cancer. Journal Of Clinical Oncology 2022, 40: 2408-2419. PMID: 35658506, PMCID: PMC9467679, DOI: 10.1200/jco.22.00908.Peer-Reviewed Original ResearchConceptsMinimal residual diseaseWhole-exome sequencingClinical recurrenceMetastatic recurrenceBreast cancerEarly-stage hormone receptor-positive breast cancerHormone receptor-positive breast cancerTumor tissueHigh-risk stage IIReceptor-positive breast cancerTumor DNAHuman epidermal growth factor receptorDistant metastatic recurrenceHormone receptor positiveMRD-positive patientsPlasma samplesTime of consentPrimary tumor tissuesSufficient tumor tissueEpidermal growth factor receptorAdjuvant settingGrowth factor receptorLocal recurrenceClinical outcomesDistant metastasisLongitudinal circulating tumor DNA (ctDNA) whole-exome sequencing (WES) in the phase Ib/II trial of palbociclib and bazedoxifene reveals genomic dynamics and clonal evolution with the acquisition of treatment resistance in hormone receptor-positive, HER2-negative (HR+ HER2-), advanced breast cancer (ABC).
Grinshpun A, Tsuji J, Li T, Russo D, Anderson L, Rees R, Cibulskis C, Leshchiner I, Stewart C, Tung N, Krop I, Winer E, Tolaney S, Getz G, Jeselsohn R. Longitudinal circulating tumor DNA (ctDNA) whole-exome sequencing (WES) in the phase Ib/II trial of palbociclib and bazedoxifene reveals genomic dynamics and clonal evolution with the acquisition of treatment resistance in hormone receptor-positive, HER2-negative (HR+ HER2-), advanced breast cancer (ABC). Journal Of Clinical Oncology 2022, 40: 1058-1058. DOI: 10.1200/jco.2022.40.16_suppl.1058.Peer-Reviewed Original ResearchCirculating tumor DNA (ctDNA) and late recurrence in high-risk, hormone receptor–positive, HER2-negative breast cancer (CHiRP).
Lipsyc-Sharf M, De Bruin E, Santos K, McEwen R, Stetson D, Patel A, Kirkner G, Hughes M, Tolaney S, Krop I, Knape C, Feger U, Marsico G, Howarth K, Winer E, Lin N, Parsons H. Circulating tumor DNA (ctDNA) and late recurrence in high-risk, hormone receptor–positive, HER2-negative breast cancer (CHiRP). Journal Of Clinical Oncology 2022, 40: 103-103. DOI: 10.1200/jco.2022.40.16_suppl.103.Peer-Reviewed Original ResearchMinimal residual diseaseDistant metastatic recurrenceAdjuvant endocrine therapyWhole-exome sequencingEndocrine therapyMetastatic recurrenceClinical outcomesBreast cancerHormone receptor-positive breast cancerPlasma samplesTumor tissueHER2-negative breast cancerReceptor-positive breast cancerTumor DNACtDNA detectionRegular surveillance imagingStage 3 diseaseCurative intent chemotherapyTime of consentPrimary tumor tissuesCurrent practice standardsSufficient tumor tissueLiquid biopsy testsAdjuvant settingCtDNA dynamicsMassively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth
Gydush G, Nguyen E, Bae JH, Blewett T, Rhoades J, Reed SC, Shea D, Xiong K, Liu R, Yu F, Leong KW, Choudhury AD, Stover DG, Tolaney SM, Krop IE, Christopher Love J, Parsons HA, Mike Makrigiorgos G, Golub TR, Adalsteinsson VA. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nature Biomedical Engineering 2022, 6: 257-266. PMID: 35301450, PMCID: PMC9089460, DOI: 10.1038/s41551-022-00855-9.Peer-Reviewed Original ResearchConceptsLow-frequency mutationsDuplex SequencingNumber of lociLow-frequency allelesWhole-genome sequencingHuman cell linesSingle nucleotide polymorphismsGenomic DNAWhole-exome sequencingMutation enrichmentParallel enrichmentBreast tumor samplesSequencingLociMutationsDistinct mutationsCell linesDNADetection of mutationsReads
2021
A phase II study of efficacy, toxicity, and the potential impact of genomic alterations on response to eribulin mesylate in combination with trastuzumab and pertuzumab in women with human epidermal growth factor receptor 2 (HER2)+ metastatic breast cancer
Balch SM, Vaz-Luis I, Li T, Tayob N, Jain E, Helvie K, Buendia-Buendia JE, Shannon E, Isakoff SJ, Tung NM, Krop IE, Lin NU, Wagle N, Freedman RA. A phase II study of efficacy, toxicity, and the potential impact of genomic alterations on response to eribulin mesylate in combination with trastuzumab and pertuzumab in women with human epidermal growth factor receptor 2 (HER2)+ metastatic breast cancer. Breast Cancer Research And Treatment 2021, 189: 411-423. PMID: 34302589, DOI: 10.1007/s10549-021-06329-x.Peer-Reviewed Original ResearchConceptsHuman epidermal growth factor receptor 2Objective response ratePhase II studyWhole-exome sequencingEribulin 1.4II studyTreatment landscapeCohort AEribulin mesylateDay 1Genomic alterationsMetastatic breast cancer settingEpidermal growth factor receptor 2More frequent alterationsBreast cancer settingModest clinical activityGrowth factor receptor 2Metastatic breast cancerResponse/resistanceFactor receptor 2Manageable toxicityPertuzumab exposurePrimary endpointSix patientsCohort B
2020
Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer
Parsons HA, Rhoades J, Reed SC, Gydush G, Ram P, Exman P, Xiong K, Lo CC, Li T, Fleharty M, Kirkner GJ, Rotem D, Cohen O, Yu F, Fitarelli-Kiehl M, Leong KW, Hughes ME, Rosenberg SM, Collins LC, Miller KD, Blumenstiel B, Trippa L, Cibulskis C, Neuberg DS, DeFelice M, Freeman SS, Lennon NJ, Wagle N, Ha G, Stover DG, Choudhury AD, Getz G, Winer EP, Meyerson M, Lin NU, Krop I, Love JC, Makrigiorgos GM, Partridge AH, Mayer EL, Golub TR, Adalsteinsson VA. Sensitive Detection of Minimal Residual Disease in Patients Treated for Early-Stage Breast Cancer. Clinical Cancer Research 2020, 26: 2556-2564. PMID: 32170028, PMCID: PMC7654718, DOI: 10.1158/1078-0432.ccr-19-3005.Peer-Reviewed Original ResearchConceptsMinimal residual diseaseMetastatic breast cancerDigital droplet PCRBreast cancerTumor mutationsResidual diseaseMRD detectionEarly-stage breast cancerCurative-intent treatmentCohort of patientsEarly-stage diseaseMedian lead timeClinical data collectionWhole-exome sequencingMRD testFirst positive sampleDistant recurrenceMost patientsMetastatic diagnosisStage 0PatientsPlasma samplingClinical sensitivityPatient-specific mutationsCfDNA samplesReversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer
Waks AG, Cohen O, Kochupurakkal B, Kim D, Dunn CE, Buendia J, Wander S, Helvie K, Lloyd MR, Marini L, Hughes ME, Freeman SS, Ivy SP, Geradts J, Isakoff S, LoRusso P, Adalsteinsson VA, Tolaney SM, Matulonis U, Krop IE, D’Andrea A, Winer EP, Lin NU, Shapiro GI, Wagle N. Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer. Annals Of Oncology 2020, 31: 590-598. PMID: 32245699, PMCID: PMC7946408, DOI: 10.1016/j.annonc.2020.02.008.Peer-Reviewed Original ResearchConceptsMetastatic breast cancerPlatinum chemotherapyDNA-damaging therapyMechanisms of resistanceBreast cancerMetastatic breast cancer patientsBreast cancer patientsTumor DNA sequencingNovel sequence alterationsWhole-exome sequencingDNA-damaging therapiesTreatment failureCancer patientsFunctional statusDisease progressionTumor biopsiesClinical cohortImmunohistochemical stainingSubsequent linesBRCA1/2 mutationsTherapeutic benefitPatientsUseful biomarkerFunctional assessmentTumor sections
2019
Reversion and non-reversion mechanisms of resistance (MoR) to PARP inhibitor (PARPi) or platinum chemotherapy (chemotx) in patients (pts) with BRCA1/2 -mutant metastatic breast cancer (MBC).
Waks A, Cohen O, Kochupurakkal B, Kim D, Wander S, Buendia-Buendia J, Helvie K, Matulonis U, Krop I, Tolaney S, Winer E, D'Andrea A, Shapiro G, Lin N, Wagle N. Reversion and non-reversion mechanisms of resistance (MoR) to PARP inhibitor (PARPi) or platinum chemotherapy (chemotx) in patients (pts) with BRCA1/2 -mutant metastatic breast cancer (MBC). Journal Of Clinical Oncology 2019, 37: 1085-1085. DOI: 10.1200/jco.2019.37.15_suppl.1085.Peer-Reviewed Original ResearchFork protectionRAD51 fociHomologous recombinationWhole-exome sequencingReplication fork protectionDNA end resectionPARP inhibitorsReversion mutationsIntact homologous recombinationEnd resectionGenomic dataBRCA1/2 proteinsMetastatic tumor biopsiesExome sequencingMutationsGenesResponse/resistanceGermline DNAWES analysisIntrinsic resistanceReversionSequencingProteinDNAAlterations
2015
Whole exome sequencing (WES) in HER2+ metastatic breast cancer (MBC) patients (pts) with extraordinary responses to trastuzumab (T).
Luis I, Oh C, Wang Z, Dipiro P, Macrae E, Painter C, Kryukov G, Krop I, Winer E, Lin N, Wagle N. Whole exome sequencing (WES) in HER2+ metastatic breast cancer (MBC) patients (pts) with extraordinary responses to trastuzumab (T). Journal Of Clinical Oncology 2015, 33: 611-611. DOI: 10.1200/jco.2015.33.15_suppl.611.Peer-Reviewed Original Research
2014
Whole-exome sequencing (WES) of HER2+ metastatic breast cancer (MBC) from patients (pts) treated with prior trastuzumab (T): A correlative analysis of TBCRC003.
Wagle N, Lin N, Richardson A, Leshchiner I, Mayer I, Forero-Torres A, Hobday T, Dees E, Nanda R, Rimawi M, Guo H, Barry W, Wolff A, Gabriel S, Garraway L, Winer E, Krop I. Whole-exome sequencing (WES) of HER2+ metastatic breast cancer (MBC) from patients (pts) treated with prior trastuzumab (T): A correlative analysis of TBCRC003. Journal Of Clinical Oncology 2014, 32: 536-536. DOI: 10.1200/jco.2014.32.15_suppl.536.Peer-Reviewed Original Research