Please use this identifier to cite or link to this item: https://doi.org/10.1186/s13058-016-0692-6
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dc.titleA five-gene reverse transcription-PCR assay for pre-operative classification of breast fibroepithelial lesions
dc.contributor.authorTan, W.J
dc.contributor.authorCima, I
dc.contributor.authorChoudhury, Y
dc.contributor.authorWei, X
dc.contributor.authorLim, J.C.T
dc.contributor.authorThike, A.A
dc.contributor.authorTan, M.-H
dc.contributor.authorTan, P.H
dc.date.accessioned2020-09-14T08:14:30Z
dc.date.available2020-09-14T08:14:30Z
dc.date.issued2016
dc.identifier.citationTan, W.J, Cima, I, Choudhury, Y, Wei, X, Lim, J.C.T, Thike, A.A, Tan, M.-H, Tan, P.H (2016). A five-gene reverse transcription-PCR assay for pre-operative classification of breast fibroepithelial lesions. Breast Cancer Research 18 (1) : 31. ScholarBank@NUS Repository. https://doi.org/10.1186/s13058-016-0692-6
dc.identifier.issn1465-5411
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/176133
dc.description.abstractBackground: Breast fibroepithelial lesions are biphasic tumors and include fibroadenomas and phyllodes tumors. Preoperative distinction between fibroadenomas and phyllodes tumors is pivotal to clinical management. Fibroadenomas are clinically benign while phyllodes tumors are more unpredictable in biological behavior, with potential for recurrence. Differentiating the tumors may be challenging when they have overlapping clinical and histological features especially on core biopsies. Current molecular and immunohistochemical techniques have a limited role in the diagnosis of breast fibroepithelial lesions. We aimed to develop a practical molecular test to aid in distinguishing fibroadenomas from phyllodes tumors in the pre-operative setting. Methods: We profiled the transcriptome of a training set of 48 formalin-fixed, paraffin-embedded fibroadenomas and phyllodes tumors and further designed 43 quantitative polymerase chain reaction (qPCR) assays to verify differentially expressed genes. Using machine learning to build predictive regression models, we selected a five-gene transcript set (ABCA8, APOD, CCL19, FN1, and PRAME) to discriminate between fibroadenomas and phyllodes tumors. We validated our assay in an independent cohort of 230 core biopsies obtained pre-operatively. Results: Overall, the assay accurately classified 92.6% of the samples (AUC = 0.948, 95% CI 0.913-0.983, p = 2.51E-19), with a sensitivity of 82.9% and specificity of 94.7%. Conclusions: We provide a robust assay for classifying breast fibroepithelial lesions into fibroadenomas and phyllodes tumors, which could be a valuable tool in assisting pathologists in differential diagnosis of breast fibroepithelial lesions. © 2016 Tan et al.
dc.sourceUnpaywall 20200831
dc.subjectABC transporter A8
dc.subjectapolipoprotein D
dc.subjectfibronectin
dc.subjectformaldehyde
dc.subjectmacrophage inflammatory protein 3beta
dc.subjectparaffin
dc.subjecttranscriptome
dc.subjectABC transporter
dc.subjectABCA8 protein, human
dc.subjectAPOD protein, human
dc.subjectapolipoprotein D
dc.subjectCCL19 protein, human
dc.subjectfibronectin
dc.subjectFN1 protein, human
dc.subjectmacrophage inflammatory protein 3beta
dc.subjectPRAME protein, human
dc.subjecttranscriptome
dc.subjecttumor antigen
dc.subjectABCA8 gene
dc.subjectadolescent
dc.subjectadult
dc.subjectaged
dc.subjectAPOD gene
dc.subjectarea under the curve
dc.subjectArticle
dc.subjectbreast fibroepithelial lesion
dc.subjectbreast tumor
dc.subjectCCL19 gene
dc.subjectclinical article
dc.subjectclinical feature
dc.subjectcohort analysis
dc.subjectcontrolled study
dc.subjectcystosarcoma phylloides
dc.subjectdiagnostic accuracy
dc.subjectdiagnostic test accuracy study
dc.subjectFN1 gene
dc.subjectgene
dc.subjectgene expression
dc.subjectgene expression profiling
dc.subjectgenetic transcription
dc.subjecthuman
dc.subjecthuman tissue
dc.subjectmachine learning
dc.subjectmolecular diagnosis
dc.subjectmultigene
dc.subjectpolymerase chain reaction
dc.subjectPRAME gene
dc.subjectprediction
dc.subjectpreoperative period
dc.subjectquantitative analysis
dc.subjectreceiver operating characteristic
dc.subjectreverse transcription polymerase chain reaction
dc.subjectsensitivity and specificity
dc.subjecttumor classification
dc.subjectvalidation process
dc.subjectbiopsy
dc.subjectbiosynthesis
dc.subjectBreast Neoplasms
dc.subjectdifferential diagnosis
dc.subjectfemale
dc.subjectfibroadenoma
dc.subjectgene expression regulation
dc.subjectgenetics
dc.subjectmiddle aged
dc.subjectpathology
dc.subjectphyllodes tumor
dc.subjectpreoperative period
dc.subjectprocedures
dc.subjectvery elderly
dc.subjectAdolescent
dc.subjectAdult
dc.subjectAged
dc.subjectAged, 80 and over
dc.subjectAntigens, Neoplasm
dc.subjectApolipoproteins D
dc.subjectATP-Binding Cassette Transporters
dc.subjectBiopsy
dc.subjectBreast Neoplasms
dc.subjectChemokine CCL19
dc.subjectDiagnosis, Differential
dc.subjectFemale
dc.subjectFibroadenoma
dc.subjectFibronectins
dc.subjectGene Expression Regulation, Neoplastic
dc.subjectHumans
dc.subjectMiddle Aged
dc.subjectPhyllodes Tumor
dc.subjectPreoperative Period
dc.subjectReverse Transcriptase Polymerase Chain Reaction
dc.subjectTranscriptome
dc.typeArticle
dc.contributor.departmentDUKE-NUS MEDICAL SCHOOL
dc.description.doi10.1186/s13058-016-0692-6
dc.description.sourcetitleBreast Cancer Research
dc.description.volume18
dc.description.issue1
dc.description.page31
dc.published.statePublished
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