Figure 1
Figure 1. Comparative analysis of chromosome 17p LOH, copy number estimates, FISH, and p53 mutation analysis. Text files generated through use of the Affymetrix programs GDAS and Copy Number Tool for all patients were imported into the LOH tool, and all individual positions of LOH between buccal DNA and paired tumor DNA were graphed as a blue tick mark across the length of the chromosomes. Copy number estimates for all SNP positions for all patients were generated through dChipSNP, as described, and displayed across the length of the chromosomes. Copy losses are displayed with blue colors, copy gains with red colors. The physical position of SNPs is not linear along the displayed portions of the chromosome. (A) LOH display for chromosome 17p. Each row represents one patient. Vertical solid lines indicate 10-Mb intervals. The location of the commonly used FISH probe spanning the p53 gene at 17p13.1 is marked with a vertical arrow. (B) Chromosome 17 FISH results from all patients with del17p by clinical FISH panel (Mayo Clinic) with the estimated percentage of positive cells in parentheses. (C) Copy number display for chromosome 17p. The location of the commonly used FISH probe spanning the p53 gene at 17p13.1 is marked with a vertical arrow. The estimated copy numbers for all SNP positions for CLL no. 14 are shown below the chromosome 17p display, with the red line indicating the 2N state. (D) p53 Mutation analysis for exons 5 to 9. Sample numbers are indicated in column 1. The nucleotide and amino acid residue for that position in the cDNA NM 000546 or genomic DNA (same result) is shown in column 2. The nucleotide and amino acid residue for that position in FACS-sorted CD3+ cells (somatic control DNA) is shown in column 3, and the nucleotide and amino acid residue for that position in FACS-sorted CD19+ cells is shown in column 4. In panels A and C, patients with CLL with del17p and p53 wild-type status are indicated in green. Patients with CLL without del17p and p53 mutant status are indicated in blue. Patients with CLL with del17p and p53 mutant status are indicated in black.

Comparative analysis of chromosome 17p LOH, copy number estimates, FISH, and p53 mutation analysis. Text files generated through use of the Affymetrix programs GDAS and Copy Number Tool for all patients were imported into the LOH tool, and all individual positions of LOH between buccal DNA and paired tumor DNA were graphed as a blue tick mark across the length of the chromosomes. Copy number estimates for all SNP positions for all patients were generated through dChipSNP, as described, and displayed across the length of the chromosomes. Copy losses are displayed with blue colors, copy gains with red colors. The physical position of SNPs is not linear along the displayed portions of the chromosome. (A) LOH display for chromosome 17p. Each row represents one patient. Vertical solid lines indicate 10-Mb intervals. The location of the commonly used FISH probe spanning the p53 gene at 17p13.1 is marked with a vertical arrow. (B) Chromosome 17 FISH results from all patients with del17p by clinical FISH panel (Mayo Clinic) with the estimated percentage of positive cells in parentheses. (C) Copy number display for chromosome 17p. The location of the commonly used FISH probe spanning the p53 gene at 17p13.1 is marked with a vertical arrow. The estimated copy numbers for all SNP positions for CLL no. 14 are shown below the chromosome 17p display, with the red line indicating the 2N state. (D) p53 Mutation analysis for exons 5 to 9. Sample numbers are indicated in column 1. The nucleotide and amino acid residue for that position in the cDNA NM 000546 or genomic DNA (same result) is shown in column 2. The nucleotide and amino acid residue for that position in FACS-sorted CD3+ cells (somatic control DNA) is shown in column 3, and the nucleotide and amino acid residue for that position in FACS-sorted CD19+ cells is shown in column 4. In panels A and C, patients with CLL with del17p and p53 wild-type status are indicated in green. Patients with CLL without del17p and p53 mutant status are indicated in blue. Patients with CLL with del17p and p53 mutant status are indicated in black.

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