Additional Supporting Information may be found in the online version of this article.

GCC_20668_sm_SuppInfo.doc2833KSupplementary Methods
GCC_20668_sm_SuppTable1.doc204KTable S1. Higher frequencies for gains and losses in 45MM dataset
GCC_20668_sm_SuppTable2.doc139KTable S2
GCC_20668_sm_SuppTable3.doc219KTable S3. List of the 144 genes at a q-value<0.01 whose expression levels correlate with relative copy number alteration
GCC_20668_sm_SuppTable4.doc102KTable S4. List of the 68 genes at a q-value<0.05 whose downregulation correlates with the occurrence of loss of heterozygosity
GCC_20668_sm_SuppTable.xls48KSupplement Table
GCC_20668_sm_SuppFig6.doc129KFigure S6. Hierarchical clustering (Euclidean distance and Ward linkage metrics) of the 41 MM and 4 PCL samples based on conventional CN calculation procedure (FBN not applied) Vertical axis: primary tumors. Red boxes indicated the unrecognized near-tetraploid samples. Horizontal axis: absolute position. Heatmap of inferred CNs based on MCN: loss: green; normal copy-number: grey; gain: dark-red; amplification: light-red.
GCC_20668_sm_SuppFig7.doc113KFigure S7. Boxplot representation of the 68 genes which significantly correlated with the occurrence of LOH in the 40 MM samples dataset. The gene expression values are grouped according to the presence (LOH) or absence (w/o LOH) of LOH as assessed by Human Mapping arrays (horizontal axis). Vertical axis show absolute linear expression signal.

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