Summary
We have analyzed the hypervariable locus D17S5 in four well-defined human populations (Kachari of Northeast India; Dogrib Indian of Canada; New Guinea Highlander of Papua New Guinea; and a relatively homogeneous Caucasian population of North German extraction) using both Southern blot analysis and the polymerase chain reaction (PCR) technique to; (1) compare the efficiency and limitation of Southern blotting versus PCR-based techniques in genotyping variable number of tandem repeat loci, and (2) provide allele frequency data at this locus in these four anthropologically defined populations. Preferential PCR amplification of smaller alleles associated with D17S5 was corrected by lowering the DNA template concentration to 200ng, and by reducing the extension time to 2 min. A perfect correspondence was observed between the results from Southern blot and PCR analysis in all but one sample. A very large allele, of approximately 24 to 25 repeat units, detected by Southern blotting, could not be amplified by PCR, resulting in an incorrect genotyping rate of less than 0.5%. Considering the grave consequences of mistyping in forensic and paternity testing, it is suggested that heterozygous controls consisting of large and small alleles should be employed in each PCR experiment, and PCR-generated homozygotes should be confirmed by Southern blotting. Significant variation in the number and frequency of alleles at this locus was observed in the four examined populations. A total of 15 different alleles were detected. The average heterozygosity varied from 54% in the Dogrib to 89% in the Kachari. No heterozygote deficiency was observed at this locus in any of the examined populations.
Similar content being viewed by others
References
Aldridge J, Kunkel L, Bruns G, Tantaravahi U, Lalande M, Brewster T, Moreau E, Wilson M, Bromley W, Roderick T, Latt SA (1984) A strategy to reveal high-frequency RFLPs along the X chromosome. Am J Hum Genet 36:546–564
Baird M, Balazs I, Giusti A, Miyazaki L, Wexler K, Kanter E, Glassberg J, Rubinstein P, Sussman L (1986) Allele frequency distribution of two highly polymorphic DNA sequences in three ethnic groups and its application to the determination of paternity. Am J Hum Genet 39:489–501
Balazs I, Baird M, Clyne M, Meade E (1989) Human population genetic studies of five hypervariable DNA loci. Am J Hum Genet 44:182–190
Batanian JR, Ledbetter SA, Wolff RK, Nakamura Y, White R, Dobyns WB, Ledbetter DH (1990) Rapid diagnosis of Miller-Dieker syndrome and isolated lissencephaly sequence by the polymerase chain reaction. Hum Genet 85:555–559
Boerwinkle EW, Xiong W, Forrest E, Chan L (1989) Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction: application to the apolipoprotein B 3′ hypervariable region. Proc Natl Acad Sci USA 86:212–216
Chakraborty R, Deka R, Jin L, Ferrell RE (1992) Allele sharing at six VNTR loci and genetic distances among three ethnically defined human populations. Am J Hum Biol 4:387–397
Deka R, Chakraborty R, Ferrell RE (1991) A population genetic study of six VNTR loci in three ethnically defined populations. Genomics 11:83–92
Deka R, Chakraborty R, DeCroo S, Rothhammer F, Barton SA, Ferrell RE (1992) Characteristics of polymorphism at a variable number of tandem repeat (VNTR) locus 3′ to the apolipoprotein B gene in five human populations. Am J Hum Genet (in press)
Flint J, Boyce AJ, Martinson JJ, Clegg JB (1989) Population bottlenecks in Polynesia revealed by minisatellites. Hum Genet 83:257–263
Gasparini P, Trabetti E, Savoia A, Marigo M, Pignatti PF (1990) Frequency distribution of the alleles of several variable number of tandem repeat DNA polymorphisms in the Italian population. Hum Hered 40:61–68
Gécz J (1991) PCR amplification of large VNTR alleles of D17S5 (YNZ22) locus. Nucleic Acids Res 19:5806
Horn GT, Richards B, Klinger KW (1989) Amplification of a highly polymorphic VNTR segment by the polymerase chain reaction. Nucleic Acids Res 17:2140
Kidd JR, Black FL, Weiss KM, Balazs I, Kidd KK (1991) Studies of three Amerindian populations using nuclear DNA polymorphisms. Hum Biol 63:775–794
Lander ES (1991) Research on DNA typing catching up with courtroom application. Am J Hum Genet 48:819–823
Ludwig EH, Friedl W, McCarthy BJ (1989) High-resolution analysis of a hypervariable region in the human apolipoprotein B gene. Am J Hum Genet 45:458–464
Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16:1215
Nakamura Y, Leppert M, O'Connell P, Wolff R, Holm T, Culver M, Martin C, Fujimoto F, Hoff M, Kumlin E, White R (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235:1616–1622
Neel JV (1978) Rare variants, private polymorphisms, and locus heterozygosity in Amerindian populations. Am J Hum Genet 30:465–490
Odelberg SJ, Paltke R, Eldridge JR, Ballard L, O'Connell P, Nakamura Y, Leppert M, Lalouel JM, White R (1989) Characterization of eight VNTR loci by agarose gel electrophoresis. Genomics 5:915–924
Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
Tuinen P van, Dobyns WB, Rich DC, Summers KM, Robinson TJ, Nakamura Y, Ledbetter DH (1988) Molecular detection of microscopic and submicroscopic deletions associated with Miller-Dieker syndrome. Am J Hum Genet 43:587–596
Wolff RK, Nakamura Y, White R (1988) Molecular characterization of a spontaneously generated new allele at a VNTR locus: no exchange of flanking DNA sequence. Genomics 3:347–351
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Deka, R., DeCroo, S., Mei Yu, L. et al. Variable number of tandem repeat (VNTR) polymorphism at locus D17S5 (YNZ22) in four ethnically defined human populations. Hum Genet 90, 86–90 (1992). https://doi.org/10.1007/BF00210749
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF00210749