Volume 5, Issue 4 , Pages 354-355, August 2011
Allele frequencies of six non-CODIS miniSTR loci (D1S1627, D3S4529, D5S2500, D6S1017, D8S1115 and D9S2157) in three South African populations
Article Outline
Abstract
The allele frequency of six non-CODIS miniSTR loci: D1S1627, D3S4529, D5S2500, D6S1017, D8S1115 and D9S2157 were investigated in three South African populations (Afrikaner, Asian Indian and Mixed Ancestry). Deviation from Hardy–Weinberg equilibrium was observed in the Mixed Ancestry population for the locus D9S2157. All loci showed a moderate degree of polymorphism with heterozygosity values >0.6 for all populations. The combined power of discrimination was: 0.999997723, 0.999997163 and 0.99999961 for Afrikaner, Asian Indian and Mixed Ancestry populations, respectively. The respective values for the combined power of exclusion in these populations were: 0.99, 0.99 and 0.98.
Keywords: Allele frequencies, MiniSTR, DNA typing, Population data, South Africa
Dear Editor,
The allele frequencies and statistical forensic parameters were determined for six non-CODIS miniSTR loci (D1S1627, D3S4529, D5S2500, D6S1017, D8S1115 and D9S2157) in three South African populations.
Samples were collected from healthy unrelated males; 105 Caucasian individuals of Afrikaner descent and 115 individuals of Mixed Ancestry [1] living in the Cape Town metropolitan area, and 112 Asian Indians [2] living in KwaZulu Natal, South Africa. The term Afrikaner is used to describe individuals from the Afrikaans-speaking community of European descent, and mainly of Dutch origin. The term Mixed Ancestry is being used to denote a complex community which was established with contributions from Asians, Caucasians and indigenous populations. The Asian Indian community can trace their ancestry to Indian labourers who came to South Africa during the late 1800s.
Ethical clearance for the study was obtained from the Senate Research Committee of the University of the Western Cape, South Africa. Samples were collected as whole blood or buccal swab samples. DNA was extracted as previously described by Leat and co-investigators [3]. DNA samples were quantified using a Nanodrop ND 1000 UV–vis spectrophotometer.
Primer sets used in the study were those previously designed and used by Hill et al. [4]. PCR amplifications were performed as described by Coble and Butler [5], with minor modifications. Amplified DNA fragments were analyzed on an ABI 377 Genetic Analyzer (Applied Biosystems). Allele designations were assigned according to recommendations of the DNA Commission of the ISFG [6], [7] with the aid of allelic ladders. Allelic ladders were designed by combining products of varying length representative of the common alleles present.
Hardy–Weinberg equilibrium and the significance of population differentiation were determined by an exact test using GENEPOP (Version 4.0.7) software package designed by Raymond and Rousset [8]. The Bonferroni correction was applied to test for deviations from the Hardy–Weinberg equilibrium [9]. Forensic parameters: matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), power of exclusion (PE) and typical paternity index (TPI) were calculated using PowerStats v1.2 software package (Promega) [10].
The observed allele frequencies and statistical parameters for forensic testing based on the six non-CODIS loci in South African populations are summarized in supplementary Tables 1–3. Population differentiation test for each population per locus are presented in supplementary Table 4.
Across the six loci tested for Hardy–Weinberg equilibrium (HWE), loci: D3S4529 and D5S2500, as well as the locus D9S2157 showed p values below 0.05 in the Asian Indian population and the Mixed Ancestry population, respectively (see supplementary Table 3). This suggested a possible deviation from HWE. After the application of the Bonferroni correction [9], only p values below 0.0027777 (0.05/18) would be considered significant. Thus in this study deviation from HWE was shown by the Mixed Ancestry population for the locus D9S2157. The observed heterozygosity values were similar across all three populations (shown in supplementary Table 3). The observed heterozygosity values ranged from: 0.620 to 0.800, 0.607 to 0.808 and 0.696 to 0.843 for Afrikaner, Asian Indian and Mixed Ancestry populations, respectively. D1S1627 was the least polymorphic marker across all three populations but still achieved heterozygosity values >0.6. The combined power of discrimination for the six loci was: 0.999997723, 0.999997163 and 0.99999961 for Afrikaner, Asian Indian and Mixed Ancestry populations, respectively. The respective values for the combined power of exclusion in these three populations were: 0.99, 0.99 and 0.98.
Loci D1S1627 and D9S2157 showed significant differentiation for all three populations. Locus D3S4529 showed no significant differentiation for the Afrikaner-Mixed Ancestry pair. Loci D5S2500 and D6S1017 showed no significant differentiation for the Asian Indian-Afrikaner pair. Locus D8S1115 showed no significant differentiation for the Asian Indian-Afrikaner and the Asian Indian-Mixed Ancestry pairs.
For the six loci investigated in this study, no South African population data has been published. Allele frequency distribution within the studied South African populations was compared to American [11], Lithuanian [13] and Singaporean [12] populations. The Afrikaner and the American Caucasian populations shared the most common alleles for loci D1S1627, D8S1115 and D9S2157. The Asian Indians (South Africa) and the Singaporean Indians shared the most common alleles for loci D3S4529 and D9S2157. The Mixed Ancestry population and the African American population shared the most common alleles in most loci (D1S1627, D5S2500, D8S1115 and D9S2157). For loci D1S1627 and D5S2500, these most common alleles were observed at similar frequencies within the two populations.
One microvariant allele was observed in this study, i.e. allele 9.1 of locus D9S2157, which was found in 9 Mixed Ancestry samples. This microvariant allele has been previously reported in all the American populations investigated by Hill et al. [11] and in the Indian population of Singapore [12]. The microvariant allele was confirmed by sequencing with flanking primer pairs that included the miniSTR amplicon.
This paper follows the guidelines for publication of population data as requested by the journal.
Appendix A. Supplementary data
References
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PII: S1872-4973(10)00027-X
doi:10.1016/j.fsigen.2010.01.019
© 2010 Elsevier Ireland Ltd. All rights reserved.
Volume 5, Issue 4 , Pages 354-355, August 2011
