Molecular Profiling of Pancreatic Precursor Lesions

Our study cohort included 23 isolated HG-PanINs from 21 patients; samples were retrieved from the database of the Department of Pathology of The Johns Hopkins Hospital or collected from the participating institutions after the approval of the Institutional Review Board. Neoplastic cells were isolated from formalin-fixed, paraffin-embedded (FFPE) tissue sections by laser capture microdissection (supplementary material, Figure S1). DNA was extracted and analysed by targeted next-generation sequencing of pancreatic cancer driver genes using Ion AmpliSeq library preparation on an IonTorrent Personal Genome Machine (17 HG-PanINs and 16 LG-PanINs) or by whole-exome sequencing using Agilent SureSelect library preparation on an Illumina HiSeq (five HG-PanINs). In addition, immunohistochemistry for p53 and SMAD4 protein was performed on FFPE sections (18 HG-PanINs). Additional details are provided in the Supplementary materials and methods.

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Hosoda W., Chianchiano P., Griffin J.F., Pittman M.E., Brosens L.A., Noë M., Yu J., Shindo K., Suenaga M., Rezaee N., Yonescu R., Ning Y., Albores-Saavedra J., Yoshizawa N., Harada K., Yoshizawa A., Hanada K., Yonehara S., Shimizu M., Uehara T., Samra J.S., Gill A.J., Wolfgang C.L., Goggins M.G., Hruban R.H, & Wood L.D. (2017). Genetic analyses of isolated high-grade pancreatic intraepithelial neoplasia (HG-PanIN) reveal paucity of alterations in TP53 and SMAD4. The Journal of pathology, 242(1), 16-23.

Publication 2017

Personal Genome Machine SureSelect

Cancer genes Cells Embedded paraffin Formalin Genes Genes cancer Genome library Immunohistochemistry Institutional review board Isolated patients Laser capture microdissection Library Neoplastic Pancreatic Pancreatic cancer Smad4 protein

Corresponding Organization : Cancer Research Center

Other organizations : Cornell University, University Medical Center Utrecht, Hospital Médica Sur, Mie University, Kanazawa University, Kyoto University Hospital, Onomichi General Hospital, Shinshu University, Royal North Shore Hospital, University of Sydney

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Protocol cited in 6 other protocols

Variable analysis

independent variables

Laser capture microdissection

dependent variables

Presence and types of mutations in pancreatic cancer driver genes

control variables

Formalin-fixed, paraffin-embedded (FFPE) tissue sections
Ion AmpliSeq library preparation on an IonTorrent Personal Genome Machine
Agilent SureSelect library preparation on an Illumina HiSeq
Immunohistochemistry for p53 and SMAD4 protein on FFPE sections

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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