Copy number alteration-based cytogenetic analyses

DM Douglas A. Mata
JB Jamal K. Benhamida
AL Andrew L. Lin
CV Chad M. Vanderbilt
SY Soo-Ryum Yang
LV Liliana B. Villafania
DF Donna C. Ferguson
PJ Philip Jonsson
AM Alexandra M. Miller
VT Viviane Tabar
CB Cameron W. Brennan
NM Nelson S. Moss
MS Martin Sill
RB Ryma Benayed
IM Ingo K. Mellinghoff
MR Marc K. Rosenblum
MA Maria E. Arcila
ML Marc Ladanyi
TB Tejus A. Bale
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In addition to providing data on methylation profiles, the Infinium platform provides high resolution copy-number variant data similar to that provided by conventional whole-genome copy-number microarray. The chromosome- and arm-level cytogenetic profiles of the GBMs with F3T3 fusions were assessed using version 1.20.0 of the conumee-based MNPcnvplot function in the mnp.v11b4 package in R [26]. The overall tumor copy-number alteration burden (TCB), defined as the percentage of the analyzed genome for which the copy number was not equal to two, was also assessed using the larger MSK-IMPACT dataset. Tumor ploidy was also inferred from the tumor and matched germline MSK-IMPACT sequencing data using the previously validated FACETS algorithm [38].

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