Katy Hanlon, Lorna W. Harries, Sian Ellard, Claudius E. Rudin

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Presentation transcript:

Evaluation of 13q14 Status in Multiple Myeloma by Digital Single Nucleotide Polymorphism Technology Katy Hanlon, Lorna W. Harries, Sian Ellard, Claudius E. Rudin The Journal of Molecular Diagnostics Volume 11, Issue 5, Pages 450-457 (September 2009) DOI: 10.2353/jmoldx.2009.090027 Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Illustration of digital single nucleotide polymorphism (dSNP) analysis. A: Schematic of dSNP results for a theoretical sample with no allelic imbalance. Wells scoring as allele 1 are marked in light gray, wells scoring as allele 2 are marked in dark gray. Wells containing both alleles 1 and 2 are hatched while those with no signal are blank. The total number of informative alleles is 36 (18 allele 1 and 18 allele 2). The allele frequency of both alleles is thus 0.50. B: Schematic of dSNP results for a theoretical sample showing allelic imbalance. Wells scoring as allele 1are marked in light gray, wells scoring as allele 2 are marked in dark gray. Wells containing both alleles 1 and 2 are hatched while those with no signal are blank. The total number of informative alleles is 36 (32 allele 1 and 4 allele 2). The major allele is thus allele 1, with an allele frequency of 0.89. The Journal of Molecular Diagnostics 2009 11, 450-457DOI: (10.2353/jmoldx.2009.090027) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Sequential Probability analysis for detection of loss of heterozygosity (LOH) at 13q. The statistical evidence that an observed skew in allele frequency represents LOH is assessed by plotting the major allele frequency on the y axis against the number of alleles tested on the x axis. Threshold curves are calculated for a given tumor load based on the likelihood ratio of 8. Points plotted above the upper curve represent LOH, while those below the lower curve represent no LOH (see text for further explanation). The different curves represent different ratios of non-neoplastic to neoplastic cells as follows. (A) = 50:50 mixture; (B) = 60:40 mixture; (C) = 70:30 mixture; (D) = 80:20 mixture. The Journal of Molecular Diagnostics 2009 11, 450-457DOI: (10.2353/jmoldx.2009.090027) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Schematic representation of partial and interstitial loss of heterozygosity (LOH) observed at 13q. The sample number is given at the left side of the figure and the markers tested are shown at the top. Markers colored in black represent loci with LOH determined by dSNP analysis, while those in white represent loci with no LOH. A: Patients with partial LOH at 13q. B: Patients with interstitial patterns of LOH/heterozygosity at 13q. In these cases, large regions of LOH were disrupted by small, interstitial patterns of heterozygosity. The Journal of Molecular Diagnostics 2009 11, 450-457DOI: (10.2353/jmoldx.2009.090027) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Schematic representation of cases with discrepant dSNP and FISH results. The sample number is given at the left side of the figure and the markers tested are shown at the top. Markers colored in black represent loci with LOH determined by dSNP analysis, while those in white represent loci with no LOH. The boxes denoted RB1 and D13S319 illustrate the loci of the FISH probes. Each case showed evidence of LOH by dSNP occurring beyond the boundaries of the FISH probes. In four cases (MM01, MM10, MM18, and MM21) heterozygous SNPs at the specific loci targeted by the FISH probes did not show LOH by dSNP analysis, consistent with the FISH result. The Journal of Molecular Diagnostics 2009 11, 450-457DOI: (10.2353/jmoldx.2009.090027) Copyright © 2009 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions