Analysis of twelve polymorphic markers in the DNA of a population sample from the Costa Rican Central Valley

Authors

  • Eugenia Rojas Perkin Elmer
  • Jorge Lobo Universidad de Costa Rica
  • Pedro León Universidad de Costa Rica

DOI:

https://doi.org/10.51481/amc.v41i3.516

Keywords:

micro y minisatélites del ADN, PCR de polimorfismos humanos, identificación humana

Abstract

Aim: To establish databases of allele frequencies in a Costa Rican Central Valley population sample.

Methods: Peripheral blood samples from more than 40 individuals were used to isolate DNA and analyze each simple with 10 dinucleotide repeat genetic markers and with 2 minisatellite repeats, using the polymerase chain reaction.

Alleles were identified by comparision with DNA from CEPH family members. Genotypes were determined by labelling one of the two PCR primers with 32 P before amplification, electrophoresis in sequencing gels and autoradiography.

Results and Conclusions: Analysis of this data set indicates that this sample is in Hardy-Weinberg equilibrium and shows no evidence of linkage disequilibrium between markers. These data are compared with results from other human populations analyzed with the same markers, finding similarities in allele frequencies among them. Notably, the Costa Rican simple presents the lowest heterozygosity value, with 4 of the 10 dinucleotide markers tested, followed by a Cerdenian sample. In contrast, the two African samples presented the highest heterozygosity indexes with a larger number of alleles.

Downloads

Download data is not yet available.

References

I. JeffreysAJ, BrookfieldJFY, SemenoffR. Positive identification of an immigration test-case using human DNA fingerprints. Nature 1985; 317:818-819.

Nakamuray, LeppertM, O'Connell P, WolffR, Holm T, Culver M, Martin C, Fujimoto E, HoffM, Kumiin E, White R. Variable number of tandem repeat (VNTR) markers fon human gene mapping. Science 1987; 235: 1616-1622.

Nanda I, Zischler H, Epplen C, GuttenbachM, Schmid M. Chromosomal organization of simple repeated DNA sequences used for DNA fingerprinting. Electrophoresis 1991 ; 12: 193-203.

TautzD. Hypervariability ofsimple sequences as a general source for polymorphic DNA markers . Nucleic Acids Research, 1989.

Edwards A, Civitello A, Hammond H, Caskey T. DNA Typing and

Genetic Mapping with Trimeric and Tetrameric Tandem Repeats. Am J Hum Genet 1991; 49:746-756.

Flint J , Boyce AJ, Martinson JJ , Clegg JB. Population Bottlenecks in Polynesia revealed by minisatellites. Hum Genet 1989; 83:257263.

Weissenbach J, Gyapay G, Dib C, Vignal A, Morisette J, Millasseau P, Lathrop M. 1992; A second-generation linkage map of the human genome. Nature 359:794-801.

Gyapay G, Morissette J, Vignal A, Dib C, Fizames C, Millasseau, P, Marc S. et al. The 1993-94 Généthon human genetic linkage map. Nature Genet. 1994; 7:246-339.

Armour JAL, Patel I, Thein SL, Fey MF, Jeffreys AJ. Analysis of somatic mutations at human minisatellite loci in tumours and cell lines. Genomics 1989; 4:328-334.

McKusick VA. Mendelian Inheritance in Man (8th edition), the John Hopkins University Press, Baltimore and London, vol. I and 2, 1994.

Alford RL, Hammond HA, Coto I, Caskey CT. Rapid and Efficient

Resolution Of Parentage by Amplification of Short Tandem Repeats. Am J Hum Genet 1994; 55 190-195.

Amos W, Barrett JA, Pemberton JM. DNA fingerprinting: parentage studies in natural populations and the importance of linkage analysis Proc R Soc Lond B 1992; 249:157-162.

Baird M, Balazs I, Giusti A, Miyazaki L, Nicholas L, Wexler K, Kanter E, Glassberg J, Allen F, Rubinstein P, Sussman L. 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 1986; 39:489-501.

Budowle B, Chakraborty R, Giusti AM, Eisenberg AJ, Aliens RC.

Analysis of the VNTR Locus ms80 by the PCR followed by High-Resolution PAGE. Am J Hum Genet 1991 ; 48: 137-144.

Gill P, Werrett DJ. Exclusion of a man charged with murder by DNA fingerprinting. Foren. Sci. International 1987; 35: 145-148.

Hagelberg E, Gray IC, Jeffreys AJ. Identification of the skeletal remains of a murder victim by DNA analysis. Nature 1991; 352: 427-429.

Hammond HA, Jin L, Zhong Y, Caskey CT, Chakraborty R. Evaluation of 13 Short Tandem Repeat Loci for use in PersonalIdentification Applications. Am J Hum Genet 1994; 55 (1): 175-189.

Trabetti E, Galavotti R, Pignatti PF. Genetic Variation in the Italian population at Five Tandem Repeat Loci Amplified in vitro: use in patenity testing. Molec and Cell Probes 1993; 7: 81-87.

Utah Marker Development Group. A collection of ordered tetranucleotide-repeat markers from the human genome. Am J Hum Genet 1995; 57: 619-628.

Jeffreys AJ, Pena SDJ. Brief introduction to human DNA fingerprinting. In DNA Fingerprinting: State of the Science ed Pena SDJ , Chackaborty R, Eppien JT, Jeffreys AJ, Birkhauser Verlag Basel/SwitzerIand, 1993.

Jeffreys AJ, Royle V, Patel V, Armour JAL, MacLeod A, CollickA, Gray IC, Neumann R, Gibbs M, Crosier M, Hill M, Signer E, Monckton D. Principles and Recent Advances in Human DNA Fingerprinting. In DNA Fingerprinting: Approaches and Aplications. ed. Burke T, DolfG, JeffreysAJ, Wolff R, BirkhauserVerlag Basel/Switzerland. 1991.

Mullis K, Faloona F, Scharf SJ, Saiki R, Horn G, Erlich HA. Specific enzymatic amplification of DNA in vitro: The polymerase chain reaction. Cold Spring Harbor Symp. Quant Biol 1986; 5 1: 263-273.

Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988; 239: 487-491.

SajantillaA, Strom M, Budowle B, Karhunen PJ, Peltonen L. The polymerase chain reaction and post-mortem forensic identity testing: application of amplified DIS80 and HLA-DQa loci to the identification of fire victims. Foren Sci International. 199; 51: 23-34.

Barrantes R. , Smouse PE, Mohrenweiser H, Gershowitz H, Azofeifa J , Arias TD, Neel JV. Microevolution in Lower Central America: Genetic characterization of the Chibcha-speaking groups of Costa Rica and Panama, and a consensus taxonomy based on genetic and linguistic affinity. Am J Hum Genet 1990; 46: 63-84.

Deka R, Jin L, Shriver MD, Yu LM, Saha N, Barrantes R, Chakraborty R, Ferrell RE. Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations. Genome Research 1996; 6: 1177-1184.

Deka R, Majumder P O, Shriver MD, Stivers DN, Zhong Y, Yu LM, Barrantes R, Yin SJ, Miki T, Hundrieser J, Bunker CH. McGarvery ST, sakallah S, Ferrel RE, Chakraborty R. Distribution and evolution of CTG repeats at the myotinin protein kinase gene in human populations. Genome Research 1996; 6:142-154.

Rojas E. Estudio de una muestra poblacional costarricense con marcadores de ADN. Tesis de Maestrfa, Universidad de Costa Rica. 1995.

Di Rienzo A, Peterson AC, Garza JC, Valdés AM, Slatkin M, Freimer NB. Mutational processes of simple-sequence repeat loci in human populations. Proc. Natl. Acad. Sci. USA 1994; 91 : 31663170.

León PE, Raventos H, Lynch E, Morrow J, King MC. Agene for an inherited form of deafness maps to chromosome 5q31. Proc. Natl. Acad. Sci. USA 1992; 89: 5181-5184.

Freimer NB, Reus VI, Escamilla M, McInnes A, Spesny M, Leon PE, Service S, Smith L, Silva S, Rojas E, Gallegos A, Meza L, Fournier E, Baharloo S, Blankenship K, Tyler D, Batki S, Vinogradov S, WeissenbachJ, Barondes S, Sandkuijl LA. Genetic mapping using haplotypes, association and linkage methods suggests a locus for severe bipolar disorder (BPI) at 18q22-q23. Nature Genet 1996; 12:436-441.

Swofford DL. Phylognetic analysis using parsimony, version 3.0. University of Illinois, Urbana; 1990. Nei M. Molecular Evolutionary Genetics. Columbia University Press. New York. 1987; 512pp.

cosso S, Reynolds R. Validation of the AmpliFLP DI S80 PCR amplification kit for forensic casework analysis according to TWGDAM guidelines. J. Forensic Sci. 1991 ; 40: 424-434.

Escamilla MA, Spesny M, Reus VI, Gallegos A, Meza L, Molina J, Sandkuijl L, Fournier E, Le6n PE, Smith L, Freimer NB. Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population. Am J Med Genet 1996; 67: 244-253.

Valdés AM, Slatkin M, Freimer NB. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 1993; 133: 737-749.

Downloads

Published

1999-09-01

How to Cite

Analysis of twelve polymorphic markers in the DNA of a population sample from the Costa Rican Central Valley. (1999). Acta Médica Costarricense , 41(3), 9-14. https://doi.org/10.51481/amc.v41i3.516