Result of SNP-chip analysis. (A) Results of normal and abnormal chromosomes visualized by CNAG software. Blue lines above each chromosome show total gene dosage; level 2 indicates diploid (2N) amount of DNA, which is normal. Green bars under each chromosome indicate the SNP sites showing heterozygosity in leukemic cells. When heterozygosity is not detected in the leukemic cells but is detected in matched normal controls, the result suggests that the leukemic cells have allelic imbalance (AI) in that region. Pink bars that replaced green ones suggest AI. The bottom lines (green and red lines) in each panel show allele-specific gene dosage levels (one indicates the gene dosage of paternal allele, the other indicates the gene dosage of maternal allele). Level 1 is normal for each gene dosage. (i) Pattern of normal chromosome 9. Blue line is at level 2 (2N DNA). Large number of SNP sites shows normal heterozygosity (green bars under the chromosomes), and no pink bars are detected. Allele-specific gene dosage is at level 1. Panel ii shows the pattern of whole chromosome 9 uniparental disomy (UPD) detected by SNP-chip. Total gene dosage (blue line) is normal (level 2). A number of pink bars (AI) are detected. Allele-specific gene dosage data show that one allele is deleted (level 0) and the other allele is duplicated (level 2). Panel iii shows the pattern of partial UPD. Left half shows the pattern of UPD as described above. Right half shows the pattern of a normal chromosome as described above. This case also has homozygous deletion of p16INK4A gene (see that both allele-specific dosage lines [green and red lines] and total gene dosage line [blue line] are at zero). Panel iv shows nondominant UPD. Total gene dosage (blue line) indicates 2N. Allele-specific gene dosage lines (arrows, green and red lines) on left half show that one allele (green line) is lower than normal, and the other allele (red line) is higher than normal. Allele-specific gene dosage on right half show that each allele has same level. (B-D) Validation of SNP-chip data by direct nucleotide sequencing of SNP sites and qPCR. Top panels: direct nucleotide sequencing of SNP sites in ALL samples with matched controls. ALL indicates leukemic samples; N, matched control samples. Heterozygous SNP sites are indicated by arrows. Middle panels: results of SNP-chip data (see Figure 1 legend). Bottom panels: qPCR at each chromosome location. Gene dosage levels were examined using qPCR at indicated chromosomal region. Gene dosage was determined relative to the levels at the 2p21 region. Gene dosage in leukemic cells (ALL) was compared with the matched normal control DNA (N). (B) ALL with 9p hemizygous deletion; homozygous deletion of 9p21 is also detected. (C) ALL with whole chromosome UPD. (D) ALL with 9p UPD.