title: A five-gene reverse transcription-PCR assay for pre-operative classification of breast fibroepithelial lesions.
abstract: BACKGROUND
  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.
authors.affiliation: Division of Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Republic of Singapore. wjtan@ibn.a-star.edu.sg.
authors.forename: Wai Jin
authors.initials: WJ
authors.lastname: Tan
authors.affiliation: Division of Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Republic of Singapore. ilcima@ibn.a-star.edu.sg.
authors.forename: Igor
authors.initials: I
authors.lastname: Cima
authors.affiliation: Division of Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Republic of Singapore. yukti@ibn.a-star.edu.sg.
authors.forename: Yukti
authors.initials: Y
authors.lastname: Choudhury
authors.affiliation: Division of Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Republic of Singapore. xnwei@ibn.a-star.edu.sg.
authors.forename: Xiaona
authors.initials: X
authors.lastname: Wei
authors.affiliation: Department of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Diagnostics Tower, Singapore, 169856, Republic of Singapore. jeffrey.lim.c.t@sgh.com.sg.
authors.forename: Jeffrey Chun Tatt
authors.initials: JC
authors.lastname: Lim
authors.affiliation: Department of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Diagnostics Tower, Singapore, 169856, Republic of Singapore. daw.aye.aye.thike@sgh.com.sg.
authors.forename: Aye Aye
authors.initials: AA
authors.lastname: Thike
authors.affiliation: Division of Biodevices and Diagnostics, Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Republic of Singapore. mhtan@ibn.a-star.edu.sg.
authors.forename: Min-Han
authors.initials: MH
authors.lastname: Tan
authors.affiliation: Department of Pathology, Singapore General Hospital, 20 College Road, Academia, Level 7, Diagnostics Tower, Singapore, 169856, Republic of Singapore. tan.puay.hoon@singhealth.com.sg.|Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Republic of Singapore. tan.puay.hoon@singhealth.com.sg.
authors.forename: Puay Hoon
authors.initials: PH
authors.lastname: Tan
mesh_terms: D018528:ATP-Binding Cassette Transporters / Q000096:biosynthesis / Q000235:genetics; D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000951:Antigens, Neoplasm / Q000096:biosynthesis / Q000235:genetics; D053399:Apolipoproteins D / Q000096:biosynthesis / Q000235:genetics; D001706:Biopsy; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D054415:Chemokine CCL19 / Q000096:biosynthesis / Q000235:genetics; D003937:Diagnosis, Differential; D005260:Female; D018226:Fibroadenoma / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D005353:Fibronectins / Q000096:biosynthesis / Q000235:genetics; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008875:Middle Aged; D003557:Phyllodes Tumor / Q000175:diagnosis* / Q000235:genetics / Q000473:pathology; D057234:Preoperative Period; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D059467:Transcriptome / Q000235:genetics
chemical_list: C582675:ABCA8 protein, human; C024328:APOD protein, human; D018528:ATP-Binding Cassette Transporters; D000951:Antigens, Neoplasm; D053399:Apolipoproteins D; C515460:CCL19 protein, human; D054415:Chemokine CCL19; C067625:FN1 protein, human; D005353:Fibronectins; C404944:PRAME protein, human