Use of Single Nucleotide Polymorphisms (SNP) and Real-Time Polymerase Chain Reaction for Bone Marrow Engraftment Analysis Dwight H. Oliver, Richard E.

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Use of Single Nucleotide Polymorphisms (SNP) and Real-Time Polymerase Chain Reaction for Bone Marrow Engraftment Analysis Dwight H. Oliver, Richard E. Thompson, Constance A. Griffin, James R. Eshleman The Journal of Molecular Diagnostics Volume 2, Issue 4, Pages 202-208 (November 2000) DOI: 10.1016/S1525-1578(10)60638-1 Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 CYP2C9 SNP structure and sample characterization/genotyping.A: A single nucleotide polymorphism (SNP) in the CYP2C9 gene contains a C (allele 1) or T (allele 2) at the locus. The C→T alteration destroys an AvaII (GGACC) site.B: A 190-bp fragment containing the SNP was PCR-amplified, digested by AvaII, and run on a polyacrylamide electrophoresis gel. The allele 1 sequence contains an AvaII site and is digested into 75-bp and 115-bp fragments; the site is lost in allele 2, so this amplicon remains 190-bp after digestion. Heterozygous DNA produces 190-, 115-, and 75-bp fragments. Examples from three different individuals are shown before and after cutting with AvaII. The Journal of Molecular Diagnostics 2000 2, 202-208DOI: (10.1016/S1525-1578(10)60638-1) Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Real-time PCR allelic discrimination of the CYP2C9 SNP. SNPs affect fluorescent probe binding to complementary DNA, allowing discrimination of two alleles. Probes that are a perfect complement to the target DNA hybridize and are digested by the 5′→ 3′ exonuclease activity of Taq polymerase, separating VIC or FAM reporter from the quencher. Single base mismatched probes do not bind at this relatively high annealing temperature (non-hybridize), remain intact, and do not report, due to quenching of FAM or VIC fluorescence. The Journal of Molecular Diagnostics 2000 2, 202-208DOI: (10.1016/S1525-1578(10)60638-1) Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Fluorophore emission after real-time PCR amplification of DNA mixes. Standard curves were generated by mixing DNA from two allele 2 heterozygotes into an allele 1 homozygote in varying proportions, and then performing real-time PCR. The calculated FAM/VIC ratio was plotted with respect to the known percentage of allele 2/percentage of allele 1 in the corresponding mix. Error bars indicate 1 SD for triplicate runs. The standard curves allow extrapolation of % allele 2/% allele 1 (x-axis) in unknown specimens using the measured FAM/VIC ratio (y-axis). The Journal of Molecular Diagnostics 2000 2, 202-208DOI: (10.1016/S1525-1578(10)60638-1) Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Validation of the real-time PCR SNP assay with the Southern blot assay. The real-time PCR SNP assay (TaqMan) is compared to Southern blot by running mock chimeric mixes of 100, 74, 62, 43, 28, 9, and 0% heterozygous DNA using both techniques, evaluated in a blinded fashion. The correlation coefficient between the two assays is 0.971, and the slope of the regression line is 1.004. The Journal of Molecular Diagnostics 2000 2, 202-208DOI: (10.1016/S1525-1578(10)60638-1) Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 5 Variation in allele frequency alters the number of SNPs required in a panel. The allele frequency of p was varied from 50% to 2% with a corresponding increase in q. The number of SNP loci that must be tested in each donor and recipient sample in order to be more than 95% certain of finding at least one informative SNP is indicated for various frequencies of the p allele in a population. Data are calculated and graphed using both method A and method B (see Materials and Methods). The Journal of Molecular Diagnostics 2000 2, 202-208DOI: (10.1016/S1525-1578(10)60638-1) Copyright © 2000 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions