Dataset Information

Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.

ABSTRACT: Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28?×?10-19. CPE was highest for the Khoisan Tuu ethnolinguistic group and the Northeast District at 0.9999582029 and 0.9999922652 respectively. CMP ranged from 6.28?×?10-19 (Khoisan Tuu) to 1,02?×?10-18 (Northwest district). Using pairwise genetic distances (FST), analysis of molecular variance (AMOVA), factorial correspondence analysis (FCA), and the unsupervised Bayesian clustering method found in STRUCTURE and TESS, ethno-linguistics were found to have a greater influence on population structure than geography. FCA showed clustering between Bantu and Khoisan, and within the Bantu. This Bantu sub-structuring was not seen with STRUCTURE and TESS, which detected clustering only between Bantu and Khoisan. The patterns of population structure revealed highlight the need for regional reference databases that include ethno-linguistic and geographic location information. These markers have important potential for bio-anthropological studies as well as for forensic applications.

SUBMITTER: Tau T

PROVIDER: S-EPMC5533702 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.

Tau Tiroyamodimo T Wally Anthony A Fanie Thokozile Patricia TP Ngono Goitseone Lorato GL Mpoloka Sununguko Wata SW Davison Sean S D'Amato María Eugenia ME

Scientific reports 20170728 1

Population structure was investigated in 990 Botswana individuals according to ethno-linguistics, Bantu and Khoisan, and geography (the nine administrative districts) using the Identifiler autosomal microsatellite markers. Genetic diversity and forensic parameters were calculated for the overall population, and according to ethno-linguistics and geography. The overall combined power of exclusion (CPE) was 0.9999965412 and the combined match probability 6,28 × 10<sup>-19</sup>. CPE was highest fo ...[more]

PMID: 28754995

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Project description:BackgroundIn the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers.ResultsWe proposed a new dynamic programming based realignment method named STR-realigner that considers repeat patterns in STR regions as prior knowledge. By allowing the size change of repeat patterns with low penalty in STR regions, accurate realignment is expected. For the performance evaluation, publicly available STR variant calling tools were applied to three types of aligned reads: synthetically generated sequencing reads aligned with BWA-MEM, those realigned with STR-realigner, those realigned with ReviSTER, and those realigned with GATK IndelRealigner. From the comparison of root mean squared errors between estimated and true STR region size, the results for the dataset realigned with STR-realigner are better than those for other cases. For real data analysis, we used a real sequencing dataset from Illumina HiSeq 2000 for a parent-offspring trio. RepeatSeq and lobSTR were applied to the sequence reads for these individuals aligned with BWA-MEM, those realigned with STR-realigner, ReviSTER, and GATK IndelRealigner. STR-realigner shows the best performance in terms of consistency of the size of estimated STR regions in Mendelian inheritance. Root mean squared error values were also calculated from the comparison of these estimated results with STR region sizes obtained from high coverage PacBio sequencing data, and the results from the realigned sequencing data with STR-realigner showed the least (the best) root mean squared error value.ConclusionsThe effectiveness of the proposed realignment method for STR regions was verified from the comparison with an existing method on both simulation datasets and real whole genome sequencing dataset.

Project description:Men are more susceptible to impulsive behavior than women. Epidemiological studies revealed that the impulsive aggressive behavior is affected by genetic factors, and the male-specific Y chromosome plays an important role in this behavior. In this study, we investigated the association between the impulsive aggressive behavior and Y-chromosomal short tandem repeats (Y-STRs) loci.The collected biologic samples from 271 offenders with impulsive aggressive behavior and 492 healthy individuals without impulsive aggressive behavior were amplified by PowerPlexRY23 PCR System and the resultant products were separated by electrophoresis and further genotyped. Then, comparisons in allele and haplotype frequencies of the selected 22 Y-STRs were made in the two groups.Our results showed that there were significant differences in allele frequencies at DYS448 and DYS456 between offenders and controls (p < .05). Univariate analysis further revealed significant frequency differences for alleles 18 and 22 at DYS448 (0.18 vs 0.27, compared to the controls, p = .003, OR=0.57,95% CI=0.39-0.82; 0.03 vs 0.01, compared to the controls, p = .003, OR=7.45, 95% CI=1.57-35.35, respectively) and for allele 17 at DYS456 (0.07 vs 0.14, compared to the controls, p = .006, OR=0.48, 95% CI =0.28-0.82) between two groups. Interestingly, the frequency of haploid haplotype 22-15 on the DYS448-DYS456 (DYS448-DYS456-22-15) was significantly higher in offenders than in controls (0.033 vs 0.004, compared to the control, p = .001, OR = 8.42, 95%CI =1.81-39.24). Moreover, there were no significant differences in allele frequencies of other Y-STRs loci between two groups. Furthermore, the unconditional logistic regression analysis confirmed that alleles 18 and 22 at DYS448 and allele 17 at DYS456 are associated with male impulsive aggression. However, the DYS448-DYS456-22-15 is less related to impulsive aggression.Our results suggest a link between Y-chromosomal allele types and male impulsive aggression.

Dataset Information

Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.

Publications

Genetic variation and population structure of Botswana populations as identified with AmpFLSTR Identifiler short tandem repeat (STR) loci.

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