Ishida et al. Supplementary Figures 1-3 Page 1 Supplementary Fig. 1. Stepwise determination of genomic aberrations on chr-13 in medulloblastomas from Ptch1 +/  mice. (A) Typical data for loss of heterozygosity (LOH) analysis on chr-13 in MBs from Ptch1 +/  mice. An electrophoretogram showing retention of both Ptch1 alleles in DNA from normal tissue from different mouse strains (ear) and loss of the wild-type C3H/He allele in MBs from nonirradiated Ptch1 +/  mice. Loss of the wild-type allele is indicated by arrows. a: ear from C3H/He mouse, b: ear from C57B6/J mouse, c: ear from C3B6F1 mouse (Ptch1 +/+ ), d: tumor from nonirradiated C3B6F1 mouse (Ptch1 +/  ). (B) Sequencing profiles obtained with an automatic sequencer revealed the presence (left panel) and absence (right panel) of a polymorphism (T/C) at position 4016 of the Ptch1 gene, thus demonstrating retention of both Ptch1 alleles in DNAs from normal tissue and loss of the wild-type Ptch1 allele in MBs. (C) Array-CGH profiles for three tumors in which no aberrations were found around the Ptch1 locus, both by LOH analysis and sequencing analysis at the T/C polymorphism at position 4016 of Ptch1. Moving averages of the normalized log 2 Cy5/Cy3 ratio, calculated based on 10 data points, are plotted in the array-CGH profiles. On the left, the position of the neomycin resistance cassette is indicated by a blue box. (D) Schematic diagram representing sequence analysis of deletion breakpoints in tumors (S14964, S14586, S14862). The dotted line indicates the deleted genomic region. Gray boxes indicate the sequences used to locate microhomology at both ends of the deletion in a tumor of S14964, which suggest that a microhomology-mediated rearrangement may have led to the deletion. The position of deleted genomic region is indicated above the dotted line according to mouse genomic build of mm9.

Ishida et al. Supplementary Figures 1-3 Page 2 Supplementary Fig. 2. Association of gene expression in S-type and R-type tumors with normal postnatal cerebellar development. (A, B) Normalized signal intensity values of probes which showed higher values in R-type (A) and S-type (B) tumors, respectively, in three normal cerebellum samples (N1-N3) and twelve MBs. Yellow, light blue, blue, and red bars represent expression levels in different subgroups of tumors as illustrated at the top of Figure 4A. There were six genes, whose probes were classified into both (A) and (B) groups, depending on the corresponding region of the same gene. Affymetrix probe sets corresponding to these six genes were excluded in the following analysis. (C, D) The histograms in (C) and (D) represent the number of probe sets included in (A) and (B) group, respectively, as a function of the day when the probe intensity is maximal. The genes were selected by the significant change (>2 fold in light blue and >1.5 fold in brown in the bar graphs) during development of PN1 to PN21, based on the GEO database by Kho et al (accession no. GSE14514).

Ishida et al. Supplementary Figures 1-3 Page 3 Supplementary Fig. 3. Gene expression levels of many genes on chr-6 reflect aneuploidy of chr-6. (A) The average number of chr-6 copies per genome, which was calculated based on the average values of the log 2 ratios of all probes on chr-6 in array- CGH profiles. (B) Normalized signal intensity values of all probes on chr-6, which were normalized “per gene” to the median expression levels in 12 tumors from 1 to 12, are indicated by the color scale shown at the bottom. The order of tumors was rearranged by the calculated number of chr-6 copies per genome. Color tones changed from blue to red shades in a left-to-right fashion, suggesting that expression levels of many genes on chr-6 reflected aneuploidy of chr-6. (C) Correlation of expression levels of 12 genes on chr-6, as represented by normalized intensity values, and the numbers of chr-6 copies per genome in each MB, which were calculated average values of the log 2 ratios of all probes throughout the entire chr-6 in array-CGH profiles.