1
|
Cheffi K, El Khair A, Dahbi N, Talbi J, Hilali A, El Ossmani H. Genetic analysis based on 15 autosomal short tandem repeats (STRs) in the Chaouia population, western center Morocco, and genetic relationships with worldwide populations. Mol Genet Genomics 2023; 298:931-941. [PMID: 37162566 DOI: 10.1007/s00438-023-02028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/29/2023] [Indexed: 05/11/2023]
Abstract
The complex demographic history of human populations in North Africa has resulted in a high degree of genetic heterogeneity across the region. However, little is known about the pattern of these genetic variations in its current populations. The present study provides new data on the genetic background of Chaouia, an Arabic-speaking North African population in the western center of Morocco. A random sample of 150 unrelated healthy individuals from Chaouia was assessed using the AmpFLSTR Identifiler kit. The most polymorphic markers were D21S11 and D18S51, with 23 and 22 alleles, respectively. After Bonferroni's correction, two loci (TH01 and D18S51) deviated from Hardy-Weinberg equilibrium. The phylogeny analysis separated North African populations into northeastern and northwestern groups. The Chaouia population was clustered with northwestern Africans. It was the closest to the Berbers of Azrou. The Chaouia shared close genetic affinities with populations from North Africa, the Middle East, and Europe, particularly Iberians, and to a lesser extent with sub-Saharan populations. The pattern of genetic admixture varied across North African populations without a clear correlation between their geographic (northeastern or northwestern) or linguistic identities (Arab or Berber), however, genetic heterogeneity among Berbers was observed. These findings suggest that the diversity observed in North African populations extends geographical and linguistic boundaries. It is further linked to each population's unique and complex demographic history. Human North African population genetics seems to present an intriguing landscape for future studies in the region and its surrounding populations to trace the origins of the genetic heterogeneity observed in these populations.
Collapse
Affiliation(s)
- Khadija Cheffi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco.
| | - Abderrazak El Khair
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Noura Dahbi
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Jalal Talbi
- General Directorate of National Security, National Laboratory of the Scientific and Technical Police, Casablanca, Morocco
| | - Abderraouf Hilali
- Hassan First University of Settat, Higher Institute of Health Sciences, Laboratory of Health Sciences and Technologies, Settat, Morocco
| | - Hicham El Ossmani
- Institut de Criminalistique de la Gendarmerie Royale, Rabat, Morocco
| |
Collapse
|
2
|
Muacevic A, Adler JR. The Impact of Leukemia on the Detection of Short Tandem Repeat (STR) Markers. Cureus 2022; 14:e30954. [PMID: 36465210 PMCID: PMC9711926 DOI: 10.7759/cureus.30954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Short tandem repeats (STRs) have been used for various identity typing methods worldwide. They have high discrimination power in human identification in forensics, paternity testing, missed personal identification, genetic diseases, and gene regulatory functions. They have also been used to detect and monitor the stability of diseases, including various types of cancer. This study aimed to investigate the impact of leukemia on the detection and stability of STR markers. METHODS DNA was isolated from 30 participants (15 with chronic myeloid leukemia( CML) and 15 healthy controls) and used to amplify STR markers using specific primers. RESULTS We found that the blood of those with leukemia had more 9.3 and 9 alleles at the tyrosine hydroxylase 1 (TH01) marker than the blood of the healthy control samples. The results of this study will help researchers understand leukemia's effect on the detection and stability of STR markers in leukemic patients compared to healthy individuals. CONCLUSION Our results demonstrate that STR markers could become useful in genetic studies of leukemia cases.
Collapse
|
3
|
Alsafiah HM, Goodwin WH. Population genetic data for 17 non-CODIS STR loci for the Saudi Arabian population using the SureID®23comp Human Identification Kit. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.10.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
4
|
Messaoudi SA, Babu SR, Alsaleh AB, Albujja M, Al-Snan NR, Chaudhary AR, Kassab AC, Assidi M. Population genetic data for 12 X-STR loci in the Central Saudi region using investigator Argus X-12 amplification kit. Ann Hum Biol 2021; 48:321-326. [PMID: 34340612 DOI: 10.1080/03014460.2021.1957147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND X-chromosome short tandem repeat (X-STR) markers are important in forensic identity investigations and kinship analysis. SUBJECT AND METHODS In the current study, the distribution of 12 X-STR loci located in four linkage groups was evaluated using Investigator® Argus X-12 Amplification Kit in 200 unrelated healthy individuals (105 males and 95 females) from the central region of Saudi Arabia in order to develop an allelic frequency database for the markers included in the kit. RESULTS DXS10146 locus was the most informative with 21 alleles, while DXS8378 locus was the least with five alleles. Forensic parameters showed that all X-STRs loci, either as individual markers or as linkage groups, provide genetic information with high discrimination that is appropriate for forensic purposes with polymorphism information content (PIC), power of exclusion (PE), and paternity index (PI) varying from 0.61211 to 0.917979, 0.38722 to 0.842949, and 0.038416 to 0.16367, respectively. The pairwise genetic distance fixation index (Fst) results showed that the Saudi population is genetically closer to the Egyptian and Emirati populations and distant to the Turkish population. CONCLUSION The current study revealed that Investigator® Argus 12 X-STR kit would support the forensic application, kinship testing involving female offspring, and human identification in the Saudi population.
Collapse
Affiliation(s)
- Safia A Messaoudi
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Saranya R Babu
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Abrar B Alsaleh
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mohammed Albujja
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Noora R Al-Snan
- Forensic Science Laboratory, Directorate of Forensic Science, General Directorate of Criminal Investigation and Forensic Science, Ministry of Interior, Manama, Kingdom of Bahrain
| | - Abdul Rauf Chaudhary
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Ahmed Ch Kassab
- Forensic Sciences Department, College of Criminal Justice, Naif Arab University for Security Sciences, Riyadh, Kingdom of Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research (CEGMR), Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| |
Collapse
|
5
|
Muinde JM, Chandra Bhanu DR, Neumann R, Oduor RO, Kanja W, Kimani JK, Mutugi MW, Smith L, Jobling MA, Wetton JH. Geographical and linguistic structure in the people of Kenya demonstrated using 21 autosomal STRs. Forensic Sci Int Genet 2021; 53:102535. [PMID: 34051692 DOI: 10.1016/j.fsigen.2021.102535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/11/2021] [Accepted: 05/16/2021] [Indexed: 11/15/2022]
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.
Collapse
Affiliation(s)
- Jane Mbithe Muinde
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK
| | - Richard Okoth Oduor
- Department of Biochemistry, Microbiology & Biotechnology, Kenyatta University, Nairobi, Kenya
| | | | | | | | - Lisa Smith
- Department of Criminology, University of Leicester, Leicester, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, Leicester, UK.
| |
Collapse
|
6
|
Haidar M, Abbas FA, Alsaleh H, Haddrill PR. Population genetics and forensic utility of 23 autosomal PowerPlex Fusion 6C STR loci in the Kuwaiti population. Sci Rep 2021; 11:1865. [PMID: 33479300 PMCID: PMC7820400 DOI: 10.1038/s41598-021-81425-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/16/2020] [Indexed: 12/02/2022] Open
Abstract
This study evaluates the forensic utility of 23 autosomal short tandem repeat markers in 400 samples from the Kuwaiti population, of which four markers (D10S1248, D22S1045, D2S441 and SE33) are reported for the first time for Kuwait. All the markers were shown to exhibit no deviation from Hardy–Weinberg equilibrium, nor any linkage disequilibrium between and within loci, indicating that these loci are inherited independently, and their allele frequencies can be used to estimate match probabilities in the Kuwaiti population. The low combined match probability of 7.37 × 10–30 and the high paternity indices generated by these loci demonstrate the usefulness of the PowerPlex Fusion 6C kit for human identification in this population, as well as to strengthen the power of paternity testing. Off-ladder alleles were seen at several loci, and these were identified by examining their underlying nucleotide sequences. Principal component analysis (PCA) and STRUCTURE showed no genetic structure within the Kuwaiti population. However, PCA revealed a correlation between geographic and genetic distance. Finally, phylogenetic trees demonstrated a close relationship between Kuwaitis and Middle Easterners at a global level, and a recent common ancestry for Kuwait with its northern neighbours of Iraq and Iran, at a regional level.
Collapse
Affiliation(s)
- Mahdi Haidar
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK. .,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait.
| | - Fatimah A Abbas
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK.,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK.,Kuwait Identification DNA Laboratory (KIDL), General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | - Penelope R Haddrill
- Centre for Forensic Science, Department of Pure and Applied Chemistry, University of Strathclyde, 204 George Street, Glasgow, G1 1XW, Scotland, UK
| |
Collapse
|
7
|
Ch. Kassab A, Alaqeel HFM, Messaoudi SA, Babu SR, Shahid SA, Chaudhary AR. Population data and genetic diversity analysis of 17 Y-STR loci in Saudi population. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2020. [DOI: 10.1186/s41935-020-00205-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The Y chromosome polymorphism has been widely studied for human migrations, population genetics, forensic applications, and paternity analysis. However, studies regarding genetic lineage and population genetic structure of the Y chromosome in different regions of Saudi Arabia are limited.
Aim
This study aimed to analyze the distribution of Y chromosome haplotypes in a sample of 125 native Saudi males from different geographic regions of Saudi Arabia and compare to previously published Y chromosome haplotype data from Saudi Arabia and some neighboring Arab populations.
Materials and methods
Buccal swabs were collected from 125 healthy unrelated native Saudi males from different geographic regions of Saudi Arabia. Genomic DNA was extracted by Chelex®100; 17 Y-STR loci were amplified using the AmpFℓlSTR Yfiler PCR amplification kit and detected on the 3130 Genetic AnalyzerTM. Allele frequency and gene diversity were calculated with online tool STRAF. The Saudi population data were compared with the neighboring populations using pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Website (YHRD) software.
Results and conclusion
One hundred six YSTR haplotypes and 102 YSTR alleles (excluding 4 null alleles) were identified having a discrimination capacity (DC) of 85.8%. The highest haplotype diversity (HD) and gene diversity (GD) were observed at the loci DYS 458 (0.817) and DYS385b (0.807), respectively. According to our results, the Iraqi and Qena (Egypt) populations appeared to have closer relatedness to the Saudi population as compared with Yemen. The UAE and Kuwait populations showed the same degree of relatedness to the Saudi population followed by Bahrain. On the contrary, the Adnanit and Qahtanit populations of Jordan demonstrated low genetic distance from the Saudi population. In short, studying a population sample of pure Saudi ethnicity enabled us to identify a unique set of haplotypes which may help in establishing genetic relatedness between Saudi and the neighboring Arab populations. The present paper, therefore, highlights the importance of ensuring ethnic originality of the study sample while conducting population genetics studies.
Collapse
|
8
|
Khubrani YM, Jobling MA, Wetton JH. Massively parallel sequencing of sex-chromosomal STRs in Saudi Arabia reveals patrilineage-associated sequence variants. Forensic Sci Int Genet 2020; 49:102402. [PMID: 33035796 DOI: 10.1016/j.fsigen.2020.102402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/18/2020] [Accepted: 09/27/2020] [Indexed: 11/27/2022]
Abstract
Massively parallel sequencing (MPS) of forensic STRs has the potential to reveal additional allele diversity compared to conventional capillary electrophoresis (CE) typing strategies, but population studies are currently relatively few in number. The Verogen ForenSeq™ DNA Signature Prep Kit includes both Y-STRs and X-STRs among its targeted loci, and here we report the sequences of these loci, analysed using Verogen's ForenSeq™ Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0, in a representative sample of 89 Saudi Arabian males. We identified 56 length variants (equivalent to CE alleles) and 75 repeat sequence sub-variants across the six X-STRs analysed; equivalent figures for the set of 24 Y-STRs were 147 and 192 respectively. We also observed two flanking sequence variants for the X-, and six for the Y-STRs. Recovery of sequence data and concordance with CE data (where available) across the tested loci was good, though rare flanking variation affected interpretation and allele calling at DYF387S1 and DXS7132. Examination of flanking sequences of the Y-STRs revealed five SNPs (L255, M4790, BY7692, Z16708 and S17543) previously shown to define specific haplogroups by Y-chromosome sequencing. These define Y-haplogroups in 62 % of our sample, a proportion that increases to 91 % when haplogroup-associated repeat-sequence motifs are also considered. A population-level comparison of the Saudi Arabian X-STRs with a global sample showed our dataset to be part of a large cluster of populations of West Eurasian and Middle Eastern origin.
Collapse
Affiliation(s)
- Yahya M Khubrani
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK; Forensic Genetics Laboratory, General Administration of Criminal Evidence, Public Security, Ministry of Interior, Saudi Arabia
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, UK.
| |
Collapse
|
9
|
Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, Haslindawaty ARN, Shamsuddin S, Aziz MY, Chambers GK, Edinur HA. Population dataset for 21 simple tandem repeat loci in the Akan population of Ghana. Data Brief 2020; 31:105746. [PMID: 32490095 PMCID: PMC7262416 DOI: 10.1016/j.dib.2020.105746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 11/29/2022] Open
Abstract
Short tandem repeat (STR) loci are widely used as genetic marker for ancestral and forensic analyses. The latter application includes for paternity testing and DNA profiling of samples collected from scenes of crime and suspects. This survey provides the first dataset for 21 STR loci across the Akan population in Ghana by genotyping of 109 unrelated healthy individuals using Investigator 24plex kit. None of the STR loci screened deviated from Hardy-Weinberg equilibrium after applying Bonferroni correction. Overall, 224 unique alleles were observed with allele frequencies ranging from 0.005 to 0.518. The combined match probability, combined power of exclusion and combined power discrimination were 1 in 4.07 × 10−25, 0.999999999 and 1, respectively. Principal coordinate analysis carried out using 21 STR allele frequency data mapped the Akans with Nigerian subpopulation groups (Hausa, Igbo and Yoruba), but separated from Thais of Thailand, Chechen of Jordan and Tijuana of Mexico.
Collapse
Affiliation(s)
- Abban Edward Kofi
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.,Forensic Science Laboratory, Criminal Investigation Department, Ghana Police Service 233 Accra Ghana
| | - Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 50560, Bukit Aman, Kuala Lumpur, Malaysia
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 50560, Bukit Aman, Kuala Lumpur, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 50560, Bukit Aman, Kuala Lumpur, Malaysia
| | - Anita Ghansah
- Nugochi Memorial Institute of Medical Research, University of Ghana, 233 Accra, Ghana
| | - Abd Rashid Nur Haslindawaty
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Kepala Batas, Penang, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, 6140, New Zealand
| | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.,Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| |
Collapse
|
10
|
Ad'hiah AH, Al-Rikabi AH, Ahmed ZA, Kamil LA. HLA-A, -B, -DRB1 and -DQB1 polymorphisms among Iraqi Arabs. Hum Immunol 2020; 81:191-192. [PMID: 32223986 DOI: 10.1016/j.humimm.2020.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/22/2020] [Accepted: 03/22/2020] [Indexed: 11/25/2022]
Abstract
In this report, HLA polymorphisms (A, B, DRB1 and DQB1 loci) were determined in 149 unrelated Iraqi Arab potential bone marrow and kidney donors. Molecular genotyping was carried out by polymerase chain reaction followed by specific oligonucleotide probe hybridizations. Data were analyzed by Arlequin software. HLA-A, -B and -DRB1 genotype frequencies were significantly deviated from Hardy-Weinberg equilibrium, while HLA-DQB1 frequencies showed no deviation. A*03, B*35, DRB1*11 and DQB1*02 were the most frequent allele groups, while A*02-B*07-DRB1*04-DQB1*03 was the most frequent haplotype. HLA data are available in the Allele Frequencies Net Database (AFND: 3680) under the population name "Iraq Arabs".
Collapse
Affiliation(s)
- Ali H Ad'hiah
- Tropical-Biological Research Unit, College of Science, University of Baghdad, Baghdad, Iraq.
| | - Aaiad H Al-Rikabi
- Department of Biology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Zahra'a A Ahmed
- Department of Biology, College of Science for Women, University of Baghdad, Baghdad, Iraq
| | - Liath A Kamil
- Histocompatibility Centre, Al-Karama Teaching Hospital, Ministry of Health, Baghdad, Iraq
| |
Collapse
|
11
|
Abdeli A, Benhassine T. Genetic diversity of 15 autosomal STRs in a sample of Berbers from Aurès region in the Northeast of Algeria and genetic relationships with other neighbouring samples. Ann Hum Biol 2020; 47:284-293. [PMID: 32183545 DOI: 10.1080/03014460.2020.1736628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Background: The history of the Aurès mountains and neighbouring areas, a large region of the East of Algeria, was part of the history of the ancient independent Berber kingdoms supposed to be the ancestors of the current Berber people. The genetic background of this region has not yet been clarified.Aim: The aims of our study were to investigate the genetic characteristics of 15 autosomal short tandem repeats (STRs) in a sample from these regions, to determine the degree of heterogeneity among Algerian and North African samples and to analyse the genetic relationships with other populations.Subjects and methods: Allele frequencies, forensic parameters and Hardy-Weinberg equilibrium (HWE) of 15 autosomal STRs included in the PowerPlex® ESI 16 System were obtained from 308 individuals. Allele frequencies were used to determine the relationships with other populations.Results: All loci were highly polymorphic and no significant deviation from HWE was detected. Allele frequencies showed that the samples of Aurès region share genetic affinities with other Algerian, North African and Middle Eastern samples, with the exception of samples from Iran and Matmata.Conclusions: These markers revealed a genetic homogeneity between the Algerian and North African samples. The genetic affinities indicate that this sample could share a common ancestor with the Middle Eastern samples.
Collapse
Affiliation(s)
- Amine Abdeli
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria.,Institut National de Criminalistique et de Criminologie de la Gendarmerie Nationale, Alger, Algeria
| | - Traki Benhassine
- Laboratoire de Biologie Cellulaire et Moléculaire, Faculté des Sciences Biologiques, Université des Sciences et de la Technologie Houari Boumediene, Alger, Algeria
| |
Collapse
|
12
|
Massively parallel sequencing of autosomal STRs and identity-informative SNPs highlights consanguinity in Saudi Arabia. Forensic Sci Int Genet 2019; 43:102164. [PMID: 31585345 DOI: 10.1016/j.fsigen.2019.102164] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/19/2019] [Accepted: 09/20/2019] [Indexed: 01/13/2023]
Abstract
While many studies have been undertaken of Middle Eastern populations using autosomal STR profiling by capillary electrophoresis, little has so far been published from this region on the forensic use of massively parallel sequencing (MPS). Here, we carried out MPS of 27 autosomal STRs and 91 identity-informative SNPs (iiSNPs) with the Verogen ForenSeq™ DNA Signature Prep Kit on a representative sample of 89 Saudi Arabian males, and analysed the resulting sequence data using Verogen's ForenSeq Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0. This revealed sequence variation in the composition of complex STR arrays, and SNPs in their flanking regions, which raised the number of STR alleles from 238 distinct length variants to 357 sequence sub-variants. Similarly, between one and three additional polymorphic sites were observed within the amplicons of 37 of the 91 iiSNPs, forming up to six microhaplotypes per locus. These further enhance discrimination compared to the biallelic target SNP data presented by the primary UAS interface. In total, we observed twenty-two STR alleles previously unrecognised in the STRait Razor v3.0 default allele list, along with nine SNPs flanking target iiSNPs that were not highlighted by the UAS. Sequencing reduced the STR-based random match probability (RMP) from 2.62E-30 to 3.49E-34, and analysis of the iiSNP microhaplotypes reduced RMP from 9.97E-37 to 6.83E-40. The lack of significant linkage disequilibrium between STRs and target iiSNPs allowed the two marker types to be combined using the product rule, yielding a RMP of 2.39E-73. Evidence of consanguinity was apparent from both marker types. While TPOX was the only locus displaying a significant deviation from Hardy-Weinberg equilibrium, 23 out of 27 STRs and 63 out of 91 iiSNPs showed fewer than expected heterozygotes, demonstrating an overall homozygote excess probably reflecting the high frequency of first-cousin marriages in Saudi Arabia. We placed our data in a global context by considering the same markers in the Human Genome Diversity Panel (HGDP), revealing that the Saudi sample was typical of Middle Eastern populations, with a higher level of inbreeding than is seen in most European, African and Central/South Asian populations, correlating with known patterns of endogamy. Given reduced levels of diversity within endogamous groups, the ability to combine the discrimination power of both STRs and SNPs offers significant benefits in the analysis of forensic evidence in Saudi Arabia and the Middle East region more generally.
Collapse
|