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Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, Behar DM, Gölge M, Hatina J, Al-Gazali L, Bradley DG, Macaulay V, Amorim A. Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale. Forensic Sci Int 2005; 159:43-50. [PMID: 16076538 DOI: 10.1016/j.forsciint.2005.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Revised: 06/17/2005] [Accepted: 06/18/2005] [Indexed: 11/22/2022]
Abstract
The impact of phylogeographic information on mtDNA forensics has been limited to the quality control of published sequences and databases. In this work we use the information already available on Eurasian mtDNA phylogeography to guide the choice of coding-region SNPs for haplogroup H. This sub-typing is particularly important in forensics since, even when sequencing both HVRI and HVRII, the discriminating power is low in some Eurasian populations. We show that a small set (eight) of coding-region SNPs resolves a substantial proportion of the identical haplotypes, as defined by control-region variation alone. Moreover, this SNP set, while substantially increasing the discriminating efficiency in most Eurasian populations by roughly equal amounts, discloses population-specific profiles.
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Affiliation(s)
- Luísa Pereira
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto, R. Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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302
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Zhadanov SI, Atamanov VV, Zhadanov NI, Oleinikov OV, Osipova LP, Schurr TG. A novel mtDNA ND6 gene mutation associated with LHON in a Caucasian family. Biochem Biophys Res Commun 2005; 332:1115-21. [PMID: 15922297 DOI: 10.1016/j.bbrc.2005.05.059] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 05/12/2005] [Indexed: 10/25/2022]
Abstract
Leber's hereditary optic neuropathy (LHON) is a frequent cause of inherited blindness. A routine screening for common mtDNA mutations constitutes an important first in its diagnosis. However, a substantial number of LHON patients do not harbor known variants, both pointing to the genetic heterogeneity of LHON and bringing into question its genetic diagnosis. We report a familial case that exhibited typical features of LHON but lacked any of the common mutations. Genetic analysis revealed a novel pathogenic defect in the ND6 gene at 14279A that was not detected in any haplogroup-matched controls screened for it, nor has it been previously reported. This mutation causes a substantial conformational change in the secondary structure of the polypeptide matrix coil and may explain the LHON expression. Thus, it expands the spectrum of deleterious changes affecting ND6-encoding subunit and further highlights the functional significance of this gene, providing additional clues to the disease pathogenesis.
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Affiliation(s)
- Sergey I Zhadanov
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA, USA.
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303
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Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, Fornarino S, Magri C, Scozzari R, Babudri N, Santachiara-Benerecetti AS, Bandelt HJ, Semino O, Torroni A. Saami and Berbers--an unexpected mitochondrial DNA link. Am J Hum Genet 2005; 76:883-6. [PMID: 15791543 PMCID: PMC1199377 DOI: 10.1086/430073] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Accepted: 03/03/2005] [Indexed: 12/22/2022] Open
Abstract
The sequencing of entire human mitochondrial DNAs belonging to haplogroup U reveals that this clade arose shortly after the "out of Africa" exit and rapidly radiated into numerous regionally distinct subclades. Intriguingly, the Saami of Scandinavia and the Berbers of North Africa were found to share an extremely young branch, aged merely approximately 9,000 years. This unexpected finding not only confirms that the Franco-Cantabrian refuge area of southwestern Europe was the source of late-glacial expansions of hunter-gatherers that repopulated northern Europe after the Last Glacial Maximum but also reveals a direct maternal link between those European hunter-gatherer populations and the Berbers.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Chiara Rengo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Vincenza Battaglia
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Simona Fornarino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Chiara Magri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Rosaria Scozzari
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Nora Babudri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - A. Silvana Santachiara-Benerecetti
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Hans-Jürgen Bandelt
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
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304
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Pereira L, Richards M, Goios A, Alonso A, Albarrán C, Garcia O, Behar DM, Gölge M, Hatina J, Al-Gazali L, Bradley DG, Macaulay V, Amorim A. High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium. Genome Res 2005; 15:19-24. [PMID: 15632086 PMCID: PMC540273 DOI: 10.1101/gr.3182305] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The advent of complete mitochondrial DNA (mtDNA) sequence data has ushered in a new phase of human evolutionary studies. Even quite limited volumes of complete mtDNA sequence data can now be used to identify the critical polymorphisms that define sub-clades within an mtDNA haplogroup, providing a springboard for large-scale high-resolution screening of human mtDNAs. This strategy has in the past been applied to mtDNA haplogroup V, which represents <5% of European mtDNAs. Here we adopted a similar approach to haplogroup H, by far the most common European haplogroup, which at lower resolution displayed a rather uninformative frequency distribution within Europe. Using polymorphism information derived from the growing complete mtDNA sequence database, we sequenced 1580 base pairs of targeted coding-region segments of the mtDNA genome in 649 individuals harboring mtDNA haplogroup H from populations throughout Europe, the Caucasus, and the Near East. The enhanced genealogical resolution clearly shows that sub-clades of haplogroup H have highly distinctive geographical distributions. The patterns of frequency and diversity suggest that haplogroup H entered Europe from the Near East approximately 20,000-25,000 years ago, around the time of the Last Glacial Maximum (LGM), and some sub-clades re-expanded from an Iberian refugium when the glaciers retreated approximately 15,000 years ago. This shows that a large fraction of the maternal ancestry of modern Europeans traces back to the expansion of hunter-gatherer populations at the end of the last Ice Age.
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Affiliation(s)
- Luísa Pereira
- IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), 4200-465 Porto, Portugal
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