Abstract
This work describes the statistical features of a STR database for Cafuzos and Mamelucos, two Brazilian populations descending from Amerindian related to African-Americans and Caucasians, resident in the city of Porto Velho, RO, north of Brazil.
Keywords
1. Materials and methods
1.1 Population groups
Biological samples were collected from 93 unrelated individuals from Porto Velho City, Rondonia State.
1.2 DNA extraction
DNA was extracted by organic extraction methods and ethanol precipitation [
[1]
].1.3 PCR protocol
PCR amplifications were performed by using primer sequences according GeneBank information (http://www.gdb.org) using a GeneAmp PCR System 2400 (Applied Biosystems, Foster City, CA, USA).
1.4 Allele detection
FMBIO II Fluorescent Scanner (Hitachi Software Engineering American Ltd., San Francisco, CA) and reference sequenced ladders (unpublished data).
1.5 Analysis of data
Statistical analyses were performed using trade method by Arlequin 3.01 software [
[2]
].1.6 Access to the data
The complete dataset is available upon request.
2. Results
The estimate of the allelic and genotypic distribution for ten loci studied showed that the population of Porto Velho is in balance with Hardy and Weinberg law (p > 0.05) (Table 1).
Table 1Allele frequencies of 10 STR loci in the Porto Velho City, Rondonia State
| Allele | Penta E | D18S51 | TH01 | D3S1358 | D21S11 | FGA | D16S539 | D7S820 | D13S317 | vWA |
|---|---|---|---|---|---|---|---|---|---|---|
| 5 | 0.022 | – | – | – | – | – | – | – | – | – |
| 6 | 0.011 | – | 0.285 | – | – | – | – | – | – | – |
| 7 | 0.075 | – | 0.274 | – | – | – | – | 0.016 | – | – |
| 8 | 0.042 | – | 0.075 | – | – | – | – | 0.141 | 0.071 | – |
| 9 | 0.011 | 0.011 | 0.108 | – | – | – | 0.195 | 0.047 | 0.179 | – |
| 9.3 | – | – | 0.258 | – | – | – | – | – | – | – |
| 10 | 0.065 | – | 0.011 | – | – | – | 0.148 | 0.297 | 0.117 | – |
| 11 | 0.106 | 0.038 | 0.005 | – | – | – | 0.226 | 0.305 | 0.203 | – |
| 12 | 0.172 | 0.086 | – | – | – | – | 0.242 | 0.172 | 0.25 | – |
| 13 | 0.102 | 0.124 | – | – | – | – | 0.164 | 0.024 | 0.125 | 0.008 |
| 14 | 0.07 | 0.167 | – | 0.1025 | – | – | 0.016 | – | 0.047 | 0.039 |
| 15 | 0.112 | 0.172 | – | 0.355 | – | – | 0.008 | – | 0.008 | 0.125 |
| 16 | 0.042 | 0.129 | – | 0.312 | – | – | – | – | – | 0.336 |
| 17 | 0.052 | 0.124 | – | 0.134 | – | – | – | – | – | 0.281 |
| 18 | 0.022 | 0.059 | – | 0.086 | – | 0.039 | – | – | – | 0.117 |
| 19 | 0.022 | 0.038 | – | 0.011 | – | 0.102 | – | – | – | 0.086 |
| 20 | 0.022 | 0.027 | – | – | – | 0.109 | – | – | – | 0.008 |
| 21 | 0.016 | 0.005 | – | – | – | 0.055 | – | – | – | – |
| 22 | 0.016 | 0.011 | – | – | – | 0.071 | – | – | – | – |
| 23 | – | 0.005 | – | – | – | 0.141 | – | – | – | – |
| 24 | – | – | – | – | – | 0.195 | – | – | – | – |
| 25 | – | – | – | – | – | 0.164 | – | – | – | – |
| 26 | – | – | – | – | – | 0.094 | – | – | – | – |
| 27 | – | – | – | – | 0.005 | 0.016 | – | – | – | – |
| 28 | – | – | – | – | 0.102 | 0.008 | – | – | – | – |
| 29 | – | – | – | – | 0.156 | – | – | – | – | – |
| 29.2 | – | – | – | – | 0.005 | – | – | – | – | – |
| 30 | – | – | – | – | 0.28 | – | – | – | – | – |
| 31 | – | – | – | – | 0.043 | 0.008 | – | – | – | – |
| 31.2 | – | – | – | – | 0.094 | – | – | – | – | – |
| 32 | – | – | – | – | 0.043 | – | – | – | – | – |
| 32.2 | – | – | – | – | 0.075 | – | – | – | – | – |
| 33 | – | – | – | – | 0.005 | – | – | – | – | – |
| 33.2 | – | – | – | – | 0.027 | – | – | – | – | – |
| 33 | – | – | – | – | 0.005 | – | – | – | – | – |
| 33.2 | – | – | – | – | 0.027 | – | – | – | – | – |
| 34 | – | – | – | – | 0.005 | – | – | – | – | – |
| N | 93 | 93 | 93 | 93 | 93 | 64 | 64 | 64 | 64 | 64 |
| N° alleles | 18 | 13 | 7 | 6 | 12 | 12 | 7 | 7 | 8 | 8 |
| HOBS | 0.826 | 0.815 | 0.794 | 0.718 | 0.703 | 0.906 | 0.922 | 0.937 | 0.953 | 0.828 |
| HEXP | 0.935 | 0.924 | 0.805 | 0.688 | 0.795 | 0.875 | 0.804 | 0.768 | 0.826 | 0.78 |
| p | 0.82 | 0.86 | 0.1 | 0.54 | 0.46 | 0.99 | 0.99 | 0.81 | 0.93 | 0.1 |
N: number of typed individuals; N° alleles: number of alleles marker; HEXP: expected heterozygosity; HOBS: observed heterozygosity; p: Hardy–Weinberg equilibrium exact test based in 10.000 shuffling.
3. Other remarkers
The 10 loci belong to effort building a database of Cafuzos and Mamelucos, Amazonian population, for use in parentage testing and forensic identification of individuals in this population. No differences with others Brazilians populations were detected regarding allele frequencies for the respective loci [
3
, 4
, 5
, 6
]. This paper follows the guideline for publication of population data request by the journal.Conflict of interest
None.
Acknowledgement
DNA Program—State University of Rio de Janeiro and Justice Department of Rio de Janeiro State.
References
- A single salting out procedure for extracting DNA from human nucleated cells.Nucl. Acids Res. 1988; 16: 1215
- Arlequin v2000, A Software for Population Genetic Data Analysis.University of Geneva, 2000
- Statistical analyses of 14 short tandem repeat loci in Brazilian populations from Rio de Janeiro and Mato Grosso do Sul states for forensic and identity testing purposes.Forensic Sci. Int. 2004; 139: 173-176
- Population genetic data for the STR loci using the AmpFlSTR® Identifiler™ Kit in Bahia, Brazil.Prog. Forensic Genet. 2004; 10: 219-222
- Populations genetics of nine STR loci in two populations from Brazil.J. Forensic Sci. 2000; 45: 432-435
- Allele frequencies data and statistic parameters for 13 STR loci in a population of the Brazilian Amazon region.Forensic Sci Int. 2006; (June 2, version on line)
Article info
Publication history
Accepted:
October 9,
2007
Received:
August 17,
2007
Identification
Copyright
© 2008 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
