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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