Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification

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Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification.

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Measurement of Relative Copy Number of CDKN2A/ARF and CDKN2B in Bladder Cancer by Real-Time Quantitative PCR and Multiplex Ligation-Dependent Probe Amplification Joanne S. Aveyard, Margaret A. Knowles The Journal of Molecular Diagnostics Volume 6, Issue 4, Pages 356-365 (November 2004) DOI: 10.1016/S1525-1578(10)60532-6 Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Genomic organization of the CDKN2A locus showing positions of the Taqman probes. The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 p14ARF and p16 gene dosage ratios relative to ALDOB for a DNA series containing 0 to 100% normal DNA and 0 to 100% DNA from a cell line with homozygous deletion of both targets. The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Pattern of DNA copy number alterations in bladder tumor cell lines. Gene dosage ratios were calculated relative to ALDOB. ▪, homozygous deletion; , under-representation of 9p21 gene; , over-representation of 9p21 gene; □, no copy number change. The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Pattern of DNA copy number changes in primary bladder tumors. Gene dosage ratios were calculated relative to PFKL. ▪, homozygous deletion; , under-representation of 9p21 gene; , over-representation of 9p21 gene; □, no copy number change. Patterns of deletion are shown for 32 tumors with homozygous deletion of one or more genes (a), 23 tumors with under-representation of one or more genes (b), 10 tumors with over-representation of one or more genes (c), 18 tumors with no copy number change (d). The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Relative gene dosage ratios for p16 exon 2 and p14ARF in 83 primary bladder tumors. Gray areas are those scored as homozygous deletion for each gene (ie, GDR ≤0.36). Values are all relative to PFKL control. The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 6 MLPA results for 21 probes on 9p21 for 5 TCC samples. a: Tumor with no copy number change in region. b: Tumor with minimal normal DNA contamination showing clear homozygous deletion with no products for probes encompassing p15, p14ARF, and p16. c: Tumor with homozygous deletion of all three genes but distinct centromeric breakpoint. d: Tumor with homozygous deletion encompassing p14ARF and p16 but not p15. e: Tumor scored as having homozygous deletion of p16 exon 2 alone by RTQ-PCR using PFKL as control. MLPA result indicates under-representation rather than homozygous deletion but confirms small region of deletion involving p16 only. The Journal of Molecular Diagnostics 2004 6, 356-365DOI: (10.1016/S1525-1578(10)60532-6) Copyright © 2004 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions