As presented earlier11 (link), each sample was preprocessed using the PennCNV pipeline for Affymetrix arrays35 (link). Genotyping calls were obtained with Affymetrix Power Tools software using the Birdseed algorithm. Each array was wave-corrected using the built-in algorithm in ASCAT v.2.236 (link) and copy numbers were called with ASCAT v2.2 using information from the matched normal when available. The samples were classified into the 10 integrative clusters from METABRIC using the iC10 package37 (link). We applied ADMIRE21 (link) to identify recurrent alterations.
Michaut M., Chin S.F., Majewski I., Severson T.M., Bismeijer T., de Koning L., Peeters J.K., Schouten P.C., Rueda O.M., Bosma A.J., Tarrant F., Fan Y., He B., Xue Z., Mittempergher L., Kluin R.J., Heijmans J., Snel M., Pereira B., Schlicker A., Provenzano E., Ali H.R., Gaber A., O’Hurley G., Lehn S., Muris J.J., Wesseling J., Kay E., Sammut S.J., Bardwell H.A., Barbet A.S., Bard F., Lecerf C., O’Connor D.P., Vis D.J., Benes C.H., McDermott U., Garnett M.J., Simon I.M., Jirström K., Dubois T., Linn S.C., Gallagher W.M., Wessels L.F., Caldas C, & Bernards R. (2016). Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer. Scientific Reports, 6, 18517.
Other organizations :
The Netherlands Cancer Institute, Cancer Research UK, University of Cambridge, Institut Curie, Agendia (Netherlands), University College Dublin, Cambridge University Hospitals NHS Foundation Trust, Lund University, OncoMark (Ireland), Beaumont Hospital, Massachusetts General Hospital, Harvard University, Wellcome Sanger Institute, Delft University of Technology, Cancer Genomics Centre
Affymetrix Power Tools software using the Birdseed algorithm
ASCAT v.2.2 for wave-correction and copy number calling
IC10 package for sample classification into 10 integrative clusters
ADMIRE for identification of recurrent alterations
dependent variables
Genotyping calls
Copy number calls
Identification of recurrent alterations
Classification of samples into 10 integrative clusters
control variables
Matched normal samples when available for copy number calling with ASCAT v2.2
Annotations
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