Abstract
The amount of genomic DNA obtained from buccal cell methods may be suboptimal for large-scale genetics projects, because the quantity of DNA may be insufficient for the number of analyses proposed. Primer extension preamplification (PEP) methods that can amplify the entire genome 100-fold or more, offer a potential solution to this problem. We compared PEP buccal DNA with genomic buccal DNA from 315 individuals from 97 families of the Colorado Longitudinal Twin Study for three loci: the dopamine transporter, dopamine D4 receptor, and serotonin transporter. A total of 1890 genomic and 1890 PEP alleles were assessed, and 1670 comparisons (88%) agreed after a single determination. Fifty-three individuals had one or more failed initial polymerase chain reactions (PCR), with 81 failed PCRs in total, accounting for 162 missing allele calls. The failed PCRs were repeated once, and 146 of the missing allele calls were recovered. Comparisons between genomic and PEP DNA allele calls showed 37 individuals had one or more discrepancies, for a total of 52 inconsistencies. Of these, the initial PEP result was found to be correct in 18 cases, the initial genomic result was found to be correct in 25 cases, and 9 could not be resolved. Overall, rates of true calls, missing data, and genotyping errors for genomic and PEP DNA samples were nearly identical: of the 1890 genotypes assessed, true calls were found in 1845 genomic and 1840 PEP samples, missing genotypes in 18 genomic and 16 PEP samples, and incorrect assignments in 18 genomic and 25 PEP samples. These results suggest that routine whole-genome preamplification of genomic DNA is an appropriate method for providing DNA to genotype these loci.
References
Don, R. H., Cox, P. T., Wainwright, B. J., Baker, K., and Mattick, J. S. (1992). “Touchdown” PCR to circumvent spurious priming during gene amplification. Nucl. Acids Res. 19:4008.
Doucette-Stamm, L. A., Blakey, D. J., Tian, J., Mockus, S., and Mao, J. I. (1995). Population genetic study of human dopamine transporter gene (DAT1). Genet. Epidemiol. 12:303-308.
Freeman, B., Powell, J., Ball, D., Hill, L., Craig, I., and Plowmin, R. (1997). DNA by mail: An inexpensive and noninvasive method for collecting DNA samples from widely dispersed populations. Behav. Genet. 27:251-257.
Giacalone, J., Xu, L., Lehrach, H., and Francke, U. (1996). High density radiation hybrid map of human chromosome 18 and contig of 18p. Genomics 37:9-18.
Heils, A., Teufel, A., Petri, S., Stober, G., Riederer, P., Bengel, D., and Lesch, K. P. (1996) Allelic variation of the human serotonin transporter gene expression. J. Neurochem. 66:2621-2624.
Heinz, A., Goldman, D., Jones, D. W., Palmour, R., Hommer, D., Gorey, J. G., Lee, K. S., Linnoila, M., and Weinberger, D. R. (2000). Genotype influences in vivo dopamine transporter availability in human striatum. Neuropsychopharmacology 22:133-139.
Krauter, K. S., Hutchinson, J., Hewitt, J. K., Stallings, M., Smolen, A., and Crowley, T. J. (1991). Large-scale marker screening using minute quantities of DNA. Drug Alc. Depend, 63:Suppl. 1:S84.
Lench, N., Stanier, P., and Williamson, R. (1988). Simple noninvasive method to obtain DNA for gene analysis. Lancet i:1356-1358.
Lesch, K. P., Bengel, D., Heils, A., Sabol, S. Z., Greenberg, B. D., Petri, S., Benjamin, J., Muller, C. R., Hamer, D. H., and Murphy, D. L. (1996). Association of anxiety-related traits with a polymorphism in the serotonin transporter gene regulatory region. Science 274:1527-1531.
Lichter, J. B., Barr, C. L., Kennedy, J. L., Van Tol, H. H. M., Kidd, K. K., and Livak, K. J. (1993). A hypervariable segment in the human dopamine receptor D4 (DRD4) gene. Hum. Mol. Genet. 2:767-773.
Meulenbelt, I., Droog, S., Trommelen, G. J., Boomsma, D. I., and Slagboom, P. E. (1995). High-yield noninvasive human genomic DNA isolation method for genetic studies in geographically dispersed families and populations. Am. J. Hum. Genet. 57:1252-1254.
Plomin, R., Campos, J., Corley, R., Emde, R. N., Fulker, D. W., Kagan, J., Reznick, J. S., Robinson, J., Zahn-Waxler, C., and DeFries, J. C. (1990). Individual differences during the second year of life: The MacArthur Longitudinal Twin Study, In: Colombo, J., and Fagan, J. (eds.), Individual Differences in Infancy: Reliability, Stability, Prediction, Lawrence Erlbaum Associates, Hillsdale, NJ, pp. 431-455.
Sander, T., Harms, H., Dufeu, P., Kuhn, S., Rommelspacher, H., and Schmidt, L. G. (1997). Dopamine D4 receptor Exon III alleles and variation of novelty seeking in alcoholics. Am. J. Med. Genet. 74:483-487.
Spitz, E., Moutier, R., Reed, T., Busnel, M. C., Marchaland, C., Roubertoux, P. L., and Carlier, M. (1996). Comparative diagnoses of twin zygosity by SSLP variant analysis, questionnaire, and dermatoglyphic analysis. Behav. Genet. 26:55-64.
Stallings, M. C., Corley, R. P., Hewitt, J. K., Krauter, K. S., Lessem, J. M., Mikulich, S. K., Rhee, S. H., Smolen, A., Young, S. E., and Crowley, T. J. (2002). A genome-wide search for quantitative trait loci influencing substance dependence vulnerability in adolescence, submitted for Publication.
Van Tol, H. H., Wu, C. M., Guan, H. C., Ohara, K., Bunzow, J. R., Civelli, O., Kennedy, J., Seeman, P., Niznik, H. B., and Jovanovic, V. (1992). Multiple dopamine D4 receptor variants in the human population. Nature 358:149-152.
Vandenbergh, D. J., Perisco, A. M., Hawkins, A. L., Griffin, C. A., Li, X., Jabs, E. W., and Uhl, G. R. (1992). Human dopamine transporter gene (DAT1) maps to chromosome 5p15.3 and displays a VNTR. Genomics 14:1104-1106.
Zhang, L., Cui, X., Schmitt, K., Hubert, R., Navidi, W., and Arnheim, N. (1992). Whole genome amplification from a single cell: Implications for genetic analysis. Proc. Nat. Acad. Sci. (USA) 89:5847-5851.
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Anchordoquy, H.C., McGeary, C., Liu, L. et al. Genotyping of Three Candidate Genes After Whole-Genome Preamplification of DNA Collected from Buccal Cells. Behav Genet 33, 73–78 (2003). https://doi.org/10.1023/A:1021007701808
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DOI: https://doi.org/10.1023/A:1021007701808