Population Data on the STR Loci D7S820, D8S1179, and D12S391 in a Sample Population of Rio De Janeiro, Brazil
Gomes, Giselle G., Marsillac, Sylvia M., Moura-Neto, Rodrigo S., Silva, Rosane, Forensic Science Communications
Allelic distribution for three tetrameric short tandem repeat (STR) loci, D7S820, D8S1179, and D12S391, were determined in a Rio de Janeiro, Brazil, sample population. There were no detectable departures from Hardy-Weinberg expectations in any of the three loci, and there was little evidence for associations of alleles between loci in the database. Departures from expectation of independence were observed at D8S1179/D12S391 (p=0,0488).
Brazil was colonized by the Portuguese at the beginning of the 16th century. Until the end of the 19th century, an official government population survey indicated that the people were miscegeneous: 44 percent Caucasians, 14.6 percent African descendants, and 41.4 percent mulattos (IBGE 2000). After that, other ethnogeographic populations migrated to Brazil from Europe, mainly Spain, Italy, and Germany, and from Japan. Due to highly ethnical miscegenation, it is difficult to identify and study the genetic composition of any given group. Using restricted fragment length polymorphorism genotyping of nine variable number tandem repeat loci, previous work (Moura-Neto and Budowle 1997; Silva and Moura-Neto 1998) had shown no detectable population substructure in a Rio de Janeiro sample population, when compared to United States ethnic groups. Recently, using Y-chromosome single-nucleotide polymorphism haplotyping, it has been demonstrated that the majority of the paternal lineages of Brazilian population descendants originated from Europe (Carvalho-Silva et al. 2001). Also, Y-chromosome STR haplotyping of a Rio de Janeiro sample population has shown a haplotype primarily found in the Europeanlike profile (Costa et al. 2002). Rio de Janeiro is the most representative site of the "melting pot" of Brazilian culture. The aim of this work is to introduce new data about three commonly used STRs in a sample population of Rio de Janeiro, Brazil, that can be used in match probabilities calculations, substructure population analysis, and genetic distance.
Materials and Methods
Samples and DNA Extraction
DNA samples were extracted from peripheral blood samples from 97 unrelated individuals from Rio de Janeiro's population. The considered population structure for Rio de Janeiro is comprised of European-derived Brazilians. African-derived and native Brazilian descendants have been excluded. For this study DNA was extracted according to Miller et al. (1988).
PCR amplification for the loci D7S820 (GenBank: G08616), D8S1179 (GenBank: G08710), and D12S391 (GenBank: G08921) was carried out as described with minor modifications.
* Initial denaturation of 5 minutes at 92[degrees]C
* 27 cycles of 30 seconds at 94[degrees]C
* 75 seconds at 55[degrees]C
* 15 seconds at 72[degrees]C
* Final extension step of 6 minutes at 72[degrees]C
In a volume of 25 ml, 200mM of dNTPs; 50ng of genomic DNA; 1,5U of Taq DNA polymerase; 10 mM Tris-HCl pH 8.3; 1,5mM of MgCl2 ; 50 mM KCl and 1uM of the primers as listed.
* D8S1179, F: 5'TTTTTGTATTTCATGTGT ACATTCG3', R: 5'CGTAGCTATAATTAGTTCATTTTCA3'
* D7S820, F: 5'TGTCATAGTTTAGAACGAACTAACG3', R: 5'CTGAG GTATCAAAAACTCAGAGG3'
* D12S391, F: 5'CCAGAGAGAAAGAATCAACA3', R:5'TGCCTT TTAGACCTGGACTG3'
STR Typing and Sequencing
Different allele sizes were determined through the analysis of PCR product on 6 percent denaturing polyacrylamide gel electrophoresis and visualized with silver nitrate staining. Alleles under homozygous suspicion, after the amplification, were sequenced by dideoxy termination using the Big Dye Terminator Cycle Sequence in an ABI Prism[R] 3100 Genetic Analyzer with separation medium POP-6[TM](Applied Biosystems, Foster City, California).
Frequency of alleles, Hardy-Weinberg equilibrium, and other population parameters were calculated using Genetic Data Analysis Software V1-d16 (Lewis and Zaykin 2001). …