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Kenya

Study statistics

Loci
21 Autosomal STRs
Allele type
Unknown
Sample size
1020
Population
Kenyan (males only)
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Bibliographic information

Date published
May 26, 2021
Title
Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs
Authors
Jane Mbithe Muinde, Devi R Chandra Bhanu, Rita Neumann, Richard Okoth Oduor, Wangu Kanja, Joseph Kagunda Kimani, Marion W Mutugi, Lisa Smith, Mark A Jobling, and Jon H Wetton
Journal
Forensic Science International: Genetics
Abstract

Kenya is a diverse and populous nation that employs DNA evidence in its criminal justice system, and therefore requires reliable information on autosomal STR allele frequency variation across the country and in its many ethnic groups. In order to provide reference data and to assess population structure, we analysed the 21 autosomal STRs in the GlobalFiler multiplex in a sample of 510 indigenous Kenyans representing the country’s eight former provinces, 43 of its 47 counties, three main linguistic families and all 29 ethnic groups that each comprise >0.5% of the 2019 census population. The indigenous population originated from successive migrations of Cushitic, Nilotic and Bantu speaking groups who settled in regions that suited their distinctive sustenance lifestyles. Consequently, they now largely reside in a patchwork of communities with strong associations with particular counties and provinces and limited degrees of inter-group marriage, as shown by DNA donors’ ancestry details. We found significant genetic differentiation between the three Nilotic language sub-families, with Western Nilotes (the Luo ethnic group) showing greater similarity to the Bantu than the Southern and Eastern Nilotes which themselves showed closer affinity to the Cushitic speakers. This concurs with previous genetic, linguistic and social studies. Comparisons with other African populations also showed that linguistic affiliation is a stronger factor than geography. This study revealed several rare off-ladder alleles whose structure was determined by Sanger sequencing. Among the unusual features that could affect profile interpretation were a deletion of Amelogenin Y but no other forensic marker (autosomal or Y-chromosomal), a triallelic pattern at TPOX and an extremely short SE33 allele falling within the expected size range of D7S820. Compared with the currently implemented Identifiler multiplex, Random Match Probabilities decreased from 6.4 × 10–19 to 3.9 × 10–27. The appreciation of local population structure provided by the geographically and ethnically representative sample in this study highlights the structured genetic landscape of Kenya.

Forensic parameters

Forensic parameters for each locus as reported by the authors.
Locus # MP PI Hobs Hexp PIC PD PE HWE
CSF1PO 1020 - 1.947 0.743 - 0.757 0.927 0.498 0.881
D10S1248 1020 - 2.277 0.780 - 0.774 0.932 0.563 0.075
D12S391 1020 - 3.446 0.855 - 0.844 0.963 0.705 0.072
D13S317 1020 - 1.932 0.741 - 0.688 0.880 0.495 0.663
D16S539 1020 - 2.257 0.778 - 0.759 0.924 0.560 0.535
D18S51 1020 - 3.592 0.861 - 0.866 0.972 0.716 0.021
D19S433 1020 - 2.684 0.814 - 0.843 0.966 0.625 0.888
D1S1656 1020 - 3.696 0.865 - 0.851 0.967 0.724 0.784
D21S11 1020 - 3.228 0.845 - 0.832 0.960 0.685 0.889
D22S1045 1020 - 2.318 0.784 - 0.774 0.934 0.570 0.503
D2S1338 1020 - 4.811 0.896 - 0.881 0.976 0.787 0.491
D2S441 1020 - 2.161 0.769 - 0.729 0.901 0.542 0.084
D3S1358 1020 - 1.917 0.739 - 0.686 0.877 0.491 0.062
D5S818 1020 - 2.179 0.771 - 0.704 0.891 0.546 0.294
D7S820 1020 - 1.723 0.710 - 0.732 0.914 0.444 0.104
D8S1179 1020 - 2.383 0.790 - 0.770 0.933 0.581 0.816
FGA 1020 - 4.180 0.880 - 0.868 0.974 0.756 0.646
SE33 1020 - 5.667 0.912 - 0.924 0.989 0.820 0.404
THO1 1020 - 1.783 0.720 - 0.699 0.892 0.459 0.639
TPOX 1020 - 2.073 0.759 - 0.721 0.903 0.525 0.916
vWA 1020 - 2.452 0.796 - 0.806 0.950 0.592 0.456

Allele frequencies

CSF1PO D10S1248 D12S391 D13S317 D16S539 D18S51 D19S433 D1S1656 D21S11 D22S1045 D2S1338 D2S441 D3S1358 D5S818 D7S820 D8S1179 FGA SE33 TH01 TPOX vWA
4.2 0.002
5.2 0.002
6 0.18 0.051
7 0.044 0.006 0.391 0.009
7.1 0.001
7.2 0.001
8 0.044 0.043 0.031 0.068 0.204 0.225 0.291
9 0.08 0.006 0.023 0.211 0.003 0.002 0.028 0.128 0.004 0.149 0.307
9.3 0.001 0.044
10 0.262 0.002 0.03 0.099 0.003 0.013 0.003 0.027 0.046 0.06 0.363 0.016 0.002 0.008 0.072
10.1 0.001
10.2 0.002 0.001 0.002
11 0.21 0.064 0.292 0.289 0.002 0.068 0.047 0.174 0.314 0.001 0.174 0.185 0.055 0.003 0.001 0.227 0.004
11.1 0.002
11.2 0.001 0.01
11.3 0.001 0.044
12 0.294 0.133 0.393 0.232 0.055 0.112 0.062 0.043 0.15 0.002 0.391 0.097 0.145 0.005 0.001 0.039 0.001
12.1 0.001
12.2 0.025 0.008
12.3 0.004
13 0.052 0.258 0.153 0.128 0.043 0.22 0.115 0.009 0.044 0.003 0.256 0.015 0.159 0.015 0.003 0.01
13.2 0.004 0.066 0.011
14 0.011 0.28 0.006 0.064 0.008 0.055 0.233 0.216 0.06 0.325 0.066 0.02 0.312 0.028 0.09
14.2 0.001 0.069 0.009
14.3 0.019 0.001
15 0.002 0.157 0.094 0.001 0.001 0.126 0.095 0.188 0.251 0.002 0.061 0.325 0.003 0.224 0.048 0.001 0.197
15.2 0.005 0.054 0.004
15.3 0.023
16 0.08 0.097 0.175 0.018 0.148 0.274 0.048 0.007 0.312 0.071 0.075 0.249
16.1 0.001
16.2 0.006 0.022 0.001
16.3 0.096
17 0.019 0.175 0.172 0.002 0.026 0.154 0.129 0.239 0.012 0.002 0.102 0.183
17.1 0.002 0.001
17.2 0.005 0.002 0.001 0.002
17.3 0.001 0.036
18 0.001 0.251 0.133 0.004 0.009 0.061 0.047 0.003 0.021 0.143 0.143
18.1 0.001
18.2 0.001 0.002 0.001
18.3 0.012
19 0.137 0.128 0.001 0.155 0.002 0.036 0.125 0.085
19.1 0.005
19.2 0.006
19.3 0.005
20 0.07 0.056 0.108 0.049 0.063 0.028
20.2 0.004
21 0.055 0.02 0.12 0.095 0.051 0.008
21.2 0.009
22 0.031 0.009 0.149 0.201 0.011 0.001
22.2 0.004
23 0.044 0.08 0.165 0.003
23.2 0.006
23.3 0.002 0.002
24 0.015 0.074 0.146 0.001
24.2 0.001 0.022
24.3 0.013
25 0.01 0.041 0.11
25.2 0.001 0.033
25.3 0.002
26 0.004 0.003 0.026 0.063
26.1 0.001
26.2 0.056
27 0.001 0.054 0.007 0.039 0.001
27.2 0.049
28 0.232 0.026 0.003
28.2 0.033
29 0.213 0.015
29.2 0.03
30 0.19 0.007
30.2 0.005 0.002 0.006
31 0.072 0.003
31.2 0.036 0.001 0.006
32 0.014
32.1 0.001
32.2 0.063 0.006
33 0.004 0.001 0.001
33.1 0.002
33.2 0.034 0.003
34 0.015 0.002
34.2 0.003
35 0.024
36 0.014
37 0.004
38 0.002
41.2 0.001
42.2 0.002
43.2 0.002
44.2 0.001

Locus histograms

CSF1PO

D10S1248

D12S391

D13S317

D16S539

D18S51

D19S433

D1S1656

D21S11

D22S1045

D2S1338

D2S441

D3S1358

D5S818

D7S820

D8S1179

FGA

SE33

TH01

TPOX

vWA