Metadata supporting data files in the published article: The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma
Creators: name: Tanjina Kader
name: Kenneth Elder
name: Zethoven, Magnus
name: Semple, Timothy
name: Prue Hill
name: Goode, David L.
name: Thio, Niko
name: Cheasley, Dane
name: Rowley, Simone M.
name: Byrne, David J.
name: Pang, Jia-Min
name: Miligy, Islam M.
name: Green, Andrew R.
name: Rakha, Emad A.
name: Fox, Stephen B.
name: G. Bruce Mann
name: Campbell, Ian G.
name: Gorringe, Kylie L.
Publisher: name: figshare
Year: 2020
Subjects: subject: Cancer
subject: Medicine
subject: 111201 Cancer Cell Biology
subject: FOS: Clinical medicine
subject: FOS: Clinical medicine
subject: 111202 Cancer Diagnosis
subject: 111203 Cancer Genetics
subject: 60405 Gene Expression (incl. Microarray and other genome-wide approaches)
subject: FOS: Biological sciences
subject: FOS: Biological sciences

description: In this study, the authors performed genetic analysis of Intra-ductal papilloma (IDP) cases without carcinoma (“pure” IDP: both benign and atypical IDP) and IDP with co-existing carcinoma of different grades (“synchronous” IDP; ascertained based on cancer diagnosis with IDP being an incidental finding).<br><b>Study approval and patient consent</b>: This study was conducted under ethical approval from the Peter MacCallum Cancer Centre (HREC #12-64), Melbourne Health (HREC# 2012.119) and the North West-Greater Manchester Central Research Ethics Committee 15/NW/0685. This study was performed under a waiver of consent because of difficulty in contacting women whose diagnosis was &gt;10 years prior.<br><b>Data access</b>: The sequencing datasets generated during this study and supporting the conclusions of this article, are publicly available through NCBI Sequence Read Archive: <b>https://identifiers.org/insdc.sra:SRP241968</b>. The molecular inversion probe (MIP) single nucleotide polymorphism (SNP) array datasets generated during this study, are publicly available in Gene Expression Omnibus (GEO): <b>https://identifiers.org/geo:GSE131087</b>. Details of patient samples (de-identified data) are publicly available in supplementary file 1. Data on DNA input and sequencing performance are publicly available in supplementary file 2. <br><b>Study aims and methodology</b>: This study aimed to understand the genetic drivers of IDP, which might provide an insight into the molecular features of progression to malignancy. Understanding the molecular events driving IDP development and genomic features of malignant progression can be used to clinically to identify patients at high risk of progression to carcinoma, and ultimately aid in clinical management.In this study, genome-wide copy number alterations (CNA) and/or targeted mutation analysis was performed on 44 cases of IDP, of which 20 cases had co-existing ductal carcinoma in situ (DCIS), papillary DCIS or invasive ductal carcinoma (IDC).The following techniques are described in more detail in the published article: Tissue micro-dissection and DNA extraction, Sample selection for genetic analysis method, NEBNext® Ultra TM II DNA Library Prep &amp; Low coverage whole genome sequencing (LCWGS), Molecular inversion probe (MIP) SNP arrays, Targeted sequencing library preparation, enrichment and sequencing, immunohistochemistry and data analysis.<br><b>Datasets supporting the figures, tables and supplementary tables in the published article</b>: Dataset names, formats and persistent links to datasets are provided in the file <b>Kader et al.xlsx</b><br><b>Software needed to access data</b>: The software Nexus (Biodiscovery) is required to access the datasets in .OSCHP format. OSCHP files contain analysis results generated by the APT OncoScan analysis pipeline and tools or by the OncoScan Console software. It is recommend that an HDF5 viewing tool, such as HDFView (https://support.hdfgroup.org/products/java/hdfview/index.html) be used to inspect the contents of the files.<br>This document is intended to accompany one or more sample OSCHP files and to provide guidance for interpreting the data in the files: https://media.affymetrix.com/support/developer/powertools/changelog/oschp.html<br>