Figure 3

<p>LOH and copy number changes on chromosomes 11, 3, 4, 1, 17, and 7. Global view of common areas of LOH (left) and copy number change (right) in 22 primary neuroblastomas. Each sample is depicted as a series of vertical bars in both the LOH and copy number panels. Blue areas represent regions of LOH, while yellow denotes retention of heterozygosity. Copy number is marked by shades of red, with ≤1 copy in light red and ≥3 copies in dark red (see scale at the bottom of the panel).</p

Common regions of LOH in high-risk neuroblastoma and corresponding copy number change (A), and areas of copy number gain (B) identified by 10K SNP array analysis

<p>Common regions of LOH in high-risk neuroblastoma and corresponding copy number change (A), and areas of copy number gain (B) identified by 10K SNP array analysis</p

Figure 1

<p>Frequency of chromosomal aberrations. Fraction of samples with copy number >2.8 (red bars above baseline), copy number <1.2 (grey bars below baseline), and LOH (blue bars below baseline). SNPs are mapped according to their chromosomal position, from chromosome 1 on the left to chromosome X on the right. (Copy number alterations for chromosome X in samples derived from males were counted if copy number was >1.4 or <0.6.)</p

Figure 2

<p>LOH and copy number changes on chromosome 11. SNP array analysis of neuroblastoma tumor samples and matched constitutional DNA showing LOH on the left and copy number on the right of the chromosome 11 ideogram. For each sample, chromosome 11 is depicted as a vertical bar in both the LOH and copy number panels. Blue areas represent regions of LOH, while yellow denotes retention of heterozygosity. Copy number is marked by shades of red, with ≤1 copy in light red and ≥3 copies in dark red (see scale at the bottom of the panel). Both chromosome 11q and 11p LOH, as well as gain of 11p, are shown.</p

Figure 5

<p>Amplifications on chromosome 2p. (A) SNP copy number analysis of a portion of chromosome arm 2p demonstrating amplification (represented by the darker red SNPs) at the <i>MYCN</i> gene locus (2p24.3) in three tumor samples and at the <i>ALK</i> gene locus (2p23.2) in one sample. (B) Individual SNP copy number assessment of the SNPs surrounding the <i>ALK</i> locus. The blue curve in the graph on the right indicates the degree of amplification of each SNP from 0 on the left to 40 on the right. The red vertical line indicates a copy number of 2. (C) FISH of neuroblastoma with the <i>MYCN</i> probe showing multiple copies of <i>MYCN</i> (left panel), and FISH of the same tumor using the <i>ALK</i> break apart probe showing amplification of <i>ALK</i> (right panel).</p

Figure 4

<p>Copy number and LOH analysis of chromosome 17. SNP array analysis of neuroblastoma tumor samples and matched constitutional DNA showing LOH on the left and copy number on the right of the chromosome 17 ideogram. For each sample, chromosome 17 is depicted as a vertical bar in both the LOH and copy number panels. Blue areas represent regions of LOH, while yellow denotes retention of heterozygosity. Copy number is marked by shades of red, with ≤1 copy in light red and ≥3 copies in dark red (see scale at the bottom of the panel). This figure depicts copy number gain of chromosome 17q in 21 out of 22 samples.</p