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Elmadawy MA, Abdullah OA, El Gazzar WB, Ahmad ES, Ameen SG, Abdelkader A. Telomere length and signal joint T-cell receptor rearrangement excision circles as biomarkers for chronological age estimation. Biomarkers 2021; 26:168-173. [PMID: 33401959 DOI: 10.1080/1354750x.2020.1871412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Chronological age estimation is a challenging marker in the field of forensic medicine. The current study aimed to investigate the accuracy of signal joint T-cell receptor rearrangement excision circles (sjTRECs) quantification and telomere length measurement as methods for estimating chronological age. METHODS Telomere length was estimated in the DNA derived from the buccal cells through estimating the telomeric restriction fragment (TRF) length using TeloTTAGGG Telomere Length Assay while the sjTRECs quantification was carried out on DNA isolated from the blood samples using qPCR. RESULTS The TRF length was shortened with increased age (r = -0.722, p < 0.001). The sjTRECs were also decreased with increased age (r = -0.831, p < 0.001). Stronger coefficient and lower standard error of the estimate was obtained when multiple regression analysis for age prediction based on the values of both methods was applied (r = -0.876, p < 0.001).
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Affiliation(s)
- Mostafa Ali Elmadawy
- Faculty of Veterinary Medicine, Department of Forensic Medicine and Toxicology, Kafrelsheikh University, Kafrelsheikh, Egypt.,Department of Legal Medicine, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Omnia A Abdullah
- Faculty of Medicine, Department of Medical Biochemistry and Molecular Biology, Benha University, Benha, Egypt
| | - Walaa Bayoumie El Gazzar
- Faculty of Medicine, Department of Medical Biochemistry and Molecular Biology, Benha University, Benha, Egypt.,Faculty of Medicine, Department of Basic Medical Sciences, Hashemite University, Zarqa, Jordan
| | - Enas Sebaey Ahmad
- Faculty of Medicine, Department of Clinical & Chemical Pathology, Benha University, Benha, Egypt
| | - Seham Gouda Ameen
- Faculty of Medicine, Department of Clinical & Chemical Pathology, Benha University, Benha, Egypt
| | - Afaf Abdelkader
- Faculty of Medicine, Department of Forensic Medicine and Clinical Toxicology, Benha University, Benha, Egypt
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Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Allele frequencies of mitochondrial DNA HVR III 514–524 (CA)n dinucleotide repeats in the Urali Kuruman tribal population of South India. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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3
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Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM. Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago. BMC Evol Biol 2018; 18:98. [PMID: 29921229 PMCID: PMC6009813 DOI: 10.1186/s12862-018-1211-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 06/05/2018] [Indexed: 11/15/2022] Open
Abstract
Background The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya. Results The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers. Conclusions These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis. Electronic supplementary material The online version of this article (10.1186/s12862-018-1211-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
| | - Patricia Marrero
- Research Support General Service, E-38271, La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Ophthalmology and Visual Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
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Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA. Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. Genes (Basel) 2018; 9:genes9030135. [PMID: 29494531 PMCID: PMC5867856 DOI: 10.3390/genes9030135] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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Affiliation(s)
- Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Shashikala Ratnayake
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Timothy B Stockwell
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Nadin Rohland
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Swapan Mallick
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Philip L F Johnson
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, 4094 Campus Drive, College Park, MD 20742, USA.
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
| | - Anthony J Onorato
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - David Reich
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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Yasmin M, Rakha A, Noreen S, Salahuddin Z. Mitochondrial control region diversity in Sindhi ethnic group of Pakistan. Leg Med (Tokyo) 2017; 26:11-13. [PMID: 28549541 DOI: 10.1016/j.legalmed.2017.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 02/02/2017] [Indexed: 12/19/2022]
Abstract
The entire mitochondrial DNA control region (nt 16024-576) of 88 unrelated individuals of Sindhi ethnic group residing in different parts of Sindh province of Pakistan was sequenced. Out of 66 different observed haplotypes 50 were unique and 16 were shared by more than one individual. Results showed admixture of mtDNA pool constituting the haplogroups derived mainly from South Asia (47.6%) and West Eurasian (35.7%) whereas the contribution of the African haplogroup was very small (2.4%). High values of genetic diversity (0.992), power of discrimination (0.981) and low value of random match probability (0.018) indicates that mtDNA analysis for this population can effectively be used for forensic casework. The results are valuable contribution towards building mtDNA population variation database for this particular ethnic group from Pakistan.
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Affiliation(s)
- Memona Yasmin
- University of Health Sciences, Khayaban-e-Jamia Punjab, Lahore 54600, Pakistan.
| | - Allah Rakha
- University of Health Sciences, Khayaban-e-Jamia Punjab, Lahore 54600, Pakistan.
| | - Saadia Noreen
- University of Health Sciences, Khayaban-e-Jamia Punjab, Lahore 54600, Pakistan.
| | - Zeenat Salahuddin
- University of Health Sciences, Khayaban-e-Jamia Punjab, Lahore 54600, Pakistan.
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Hayat S, Akhtar T, Siddiqi MH, Rakha A, Haider N, Tayyab M, Abbas G, Ali A, Bokhari SYA, Tariq MA, Khan FM. Mitochondrial DNA control region sequences study in Saraiki population from Pakistan. Leg Med (Tokyo) 2014; 17:140-4. [PMID: 25465675 DOI: 10.1016/j.legalmed.2014.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/01/2014] [Accepted: 10/30/2014] [Indexed: 11/27/2022]
Abstract
The analysis of mitochondrial DNA (mtDNA) control region was carried in 85 unrelated Sariki individuals living in the different provinces of Pakistan. DNA was extracted from blood preserved in EDTA vacutainers. Hypervariable regions (HV1, HV2 & HV3) were PCR amplified and sequenced. Sequencing results were aligned and compared with revised Cambridge reference sequence (rCRS). The sequencing results showed presence of total 63 different haplotypes, 58 of them are unique and 05 are common haplotypes shared by more than one individual. The most common haplotype observed was (W6) with a frequency 12.9% of population sample. The Saraiki population was detected with genetic diversity (0.9570) and power of discrimination (0.9458). This study will be beneficial for forensic casework.
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Affiliation(s)
- Sikandar Hayat
- Department of Zoology, University of the Punjab, Lahore, Pakistan.
| | - Tanveer Akhtar
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | | | - Allah Rakha
- Department of Forensic Medicine, University of Health Sciences, Lahore, Pakistan
| | - Naeem Haider
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Ghazanfar Abbas
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Azam Ali
- Department of Forensic Science, Institute of Molecular Biology & Biotechnology, University of Lahore, Pakistan
| | | | - Muhammad Akram Tariq
- Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal, Pakistan
| | - Fazle Majid Khan
- Department of Zoology, University of the Punjab, Lahore, Pakistan
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Genetic characterization of the Makrani people of Pakistan from mitochondrial DNA control-region data. Leg Med (Tokyo) 2014; 17:134-9. [PMID: 25454536 DOI: 10.1016/j.legalmed.2014.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 11/20/2022]
Abstract
To estimate genetic and forensic parameters, the entire mitochondrial DNA control region of 100 unrelated Makrani individuals (males, n=96; females, n=4) living in Pakistan (Turbat, Panjgur, Awaran, Kharan, Nasirabad, Gwadar, Buleda, Karachi and Burewala) was sequenced. We observed a total of 70 different haplotypes of which 54 were unique and 16 were shared by more than one individual. The Makrani population showed a high genetic diversity (0.9688) and, consequently, a high power of discrimination (0.9592). Our results revealed a strongly admixed mtDNA pool composed of African haplogroups (28%), West Eurasian haplogroups (26%), South Asian haplogroups (24%), and East Asian haplogroups (2%), while the origin of the remaining individuals (20%) could not be confidently assigned. The results of this study are a valuable contribution to build a database of mtDNA variation in Pakistan.
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