FIGURE 2. Mutations in NF1 tumour suppressor gene and EGFR family members.

a, NF1 somatic mutations in 91 glioblastoma tumours. Both missense mutations and truncating nonsense, frameshift and splice site mutations were observed. Splice positions are given in number of bases to the closest exon (e#) numbered according to the NF1 reference transcript in the Human Gene Mutation Database; positive indicates 3' of exon, negative indicates 5' of exon. Asterisk indicates a stop codon. fs, frameshift. b, Correlation of copy number and mutation status at the NF1 locus with level of expression (y axis). Mutation events predicted to result in fewer expressed copies (including deletion, nonsense, splice site and frameshift mutations) generally have lower observed expression. HomoDel, homozygous deletion; HemiDel, single-copy loss; Neutral, no change in copy number (presumed diploid); Amp, increased copy number. Copy number status of the NF1 locus in each sample was determined as described in the Supplementary Information. c, DNA copy number and mRNA expression profiles for TCGA samples TCGA-08-0356 (red), TCGA-02-0064 (blue) and TCGA-02-0529 (green) at the EGFR locus. The upper panel shows the segmented DNA copy number (based on Affymetrix SNP6.0 data) versus genomic coordinates on chromosome 7. The lower panel shows relative exon expression levels across the known EGFR exons from the Affymetrix Exon array ordered by genomic position, where relative expression is the median-centred difference in exon intensity and gene intensity. The EGFR gene model lies between the two plots. Black lines map the genomic positions of exons 2 through to 7 and 26 through to 28. Note that structural deletions cause the relatively lower expression of exons 2–7 in the green and blue samples and exons 26–28 in the red sample. d, ERBB2 somatic mutations in 91 glioblastoma tumours. Mutations cluster in the extracellular domain in both genes. Splice site mutation position is given in number of bases to the closest exon (e#); positive indicates 3' of exon.

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