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1.
Int J Immunogenet ; 42(5): 346-58, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26119888

RESUMEN

Human leucocyte antigens (HLA) typing has been a challenge due to extreme polymorphism of the HLA genes and limitations of the current technologies and protocols used for their characterization. Recently, next-generation sequencing techniques have been shown to be a well-suited technology for the complete characterization of the HLA genes. However, a comprehensive assessment of the different platforms for HLA typing, describing the limitations and advantages of each of them, has not been presented. We have compared the Ion Torrent Personal Genome Machine (PGM) and Illumina MiSeq, currently the two most frequently used platforms for diagnostic applications, for a number of metrics including total output, quality score per position across the reads and error rates after alignment which can all affect the accuracy of HLA genotyping. For this purpose, we have used one homozygous and three heterozygous well-characterized samples, at HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1. The total output of bases produced by the MiSeq was higher, and they have higher quality scores and a lower overall error rate than the PGM. The MiSeq also has a higher fidelity when sequencing through homopolymer regions up to 9 bp in length. The need to set phase between distant polymorphic sites was more readily achieved with MiSeq using paired-end sequencing of fragments that are longer than those obtained with PGM. Additionally, we have assessed the workflows of the different platforms for complexity of sample preparation, sequencer operation and turnaround time. The effects of data quality and quantity can impact the genotyping results; having an adequate amount of good quality data to analyse will be imperative for confident HLA genotyping. The overall turnaround time can be very comparable between the two platforms; however, the complexity of sample preparation is higher with PGM, while the actual sequencing time is longer with MiSeq.


Asunto(s)
Alelos , Genoma Humano , Técnicas de Genotipaje/métodos , Antígenos HLA/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Secuencia de Bases , Línea Celular , Sitios Genéticos , Homocigoto , Humanos , Alineación de Secuencia
2.
Genetika ; 42(1): 89-97, 2006 Jan.
Artículo en Ruso | MEDLINE | ID: mdl-16523671

RESUMEN

The results of clinical, genealogical and molecular investigation of eighteen families with Leber hereditary optic neuropathy (LHON), identified on the territory of Siberia during the period from 1997 to 2005, are presented. Comprehensive analysis of mitochondrial genome variations in probands and their matrilineal relatives revealed the presence of relatively frequent (G11778A, G3460A, and T14484C), as well as rare and new mutations with the established or presumptive pathological effect (T10663C, G363A, C4640T, and A14619G). The G11778A mutation was detected in nine pedigrees (50%), mostly in the families of ethnic Russians. In eight of these families G11778A was found in preferred association with the coding-region substitutions, typical of western Eurasian mtDNA lineage (haplogroup) TJ. On the contrary, the G3460A mutation was detected in the three families belonging to the indigenous Siberian populations (Tuvinians, Altaians, and Buryats). It was associated with clearly different haplotypes of eastern Eurasian haplogroups, C3, D5, and D8. Unexpectedly, the G3460A de novo mutation was found in a large Tuvinian pedigree. At the same time, in eleven out of fourteen families of Caucasoid origin pathogenic mutations in the ND genes were associated with the T4216C and C1542A coding-region mutations, marking the root motif of haplogoup TJ. It is suggested that phylogenetically ancient mutations could have provided their carriers with the adaptive advantages upon the development of Central and Northern Europe at the end of the last glaciation (10 000 to 9 000 years ago), thereby, contributing to the preservation of weekly pathogenic LHON mutations, appearing at specific genetic background.


Asunto(s)
ADN Mitocondrial/genética , Mutación , Atrofia Óptica Hereditaria de Leber/genética , Adolescente , Adulto , Niño , Femenino , Haplotipos , Humanos , Masculino , Linaje , Siberia
3.
Eur J Immunogenet ; 31(1): 43-51, 2004 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-15009181

RESUMEN

Allelic frequencies at the three most polymorphic loci of the HLA class II region (DRB1, DQA1 and DQB1) were determined in the Nganasan and Ket, the remnants of the two most ancient groups in the Lower Yenisey River/Taimyr Peninsula region in northern Siberia. By single-stranded conformational polymorphism typing, verified by sequencing, 19 HLA-DRB1-DQA1-DQB1 haplotypes and 15 HLA-DRB1, seven DQA1 and 11 DQB1 alleles were found. The most frequent alleles were DRB1*1301 (23.5%), DQA1*0103 (29.4%), *0501/03/05 (29.4%), and DQB1*0301/09 (32.4%) in the Ket, and DRB1*0901 (25%), DQA1*0301 (39.6%), and DQB1*0301/09 (37.5%) in the Nganasan. The distribution patterns and comprehensive phylogenic analysis based on the haplotype frequencies of 17 Siberian populations suggest that the founders of both the Ket and the Nganasan came from Palaeolithic populations in the Altai-Sayan Upland.


Asunto(s)
Genes MHC Clase II , Variación Genética , Alelos , Pueblo Asiatico , Clima , Clonación Molecular , ADN/química , Frecuencia de los Genes , Antígenos HLA-DQ/genética , Cadenas beta de HLA-DQ , Antígenos HLA-DR/genética , Cadenas HLA-DRB1 , Haplotipos , Humanos , Modelos Estadísticos , Filogenia , Reacción en Cadena de la Polimerasa , Polimorfismo Conformacional Retorcido-Simple , Siberia , Población Blanca
4.
Genetika ; 39(12): 1710-8, 2003 Dec.
Artículo en Ruso | MEDLINE | ID: mdl-14964841

RESUMEN

Variability of the HLA class II genes (alleles of the DRB1, DQA1, and DQB1 loci) was investigated in a sample of Aleuts of the Commanders (n = 31), whose ancestors inhabited the Commander Islands for many thousand years. Among 19 haplotypes revealed in Aleuts of the Commanders, at most eight were inherited from the native inhabitants of the Commander Islands. Five of these haplotypes (DRB1*0401-DQA1*0301-DQB1*0301, DRB1*1401-DQA1*0101-DQB1*0503, DRB1*0802-DQA1*0401-DQB1*0402, DRB1*1101-DQA1*0501-DQB1*0301, and DRB1*1201-DQA1*0501-DQB1*0301) were typical of Beringian Mongoloids, i.e., Coastal Chukchi and Koryaks, as well as Siberian and Alaskan Eskimos. Genetic contribution of the immigrants to the genetic pool of proper Aleuts constituted about 52%. Phylogenetic analysis based on Transberingian distribution of the DRB1 allele frequencies favored the hypothesis on the common origin of Paleo-Aleuts, Paleo-Eskimos, and the Indians from the northwestern North America, whose direct ancestors survived in Beringian/southwestern Alaskan coastal refugia during the late Ice Age.


Asunto(s)
Genes MHC Clase II , Variación Genética , Inuk/genética , Alelos , Frecuencia de los Genes , Haplotipos , Humanos , Filogenia , Federación de Rusia
5.
Genetika ; 38(11): 1554-60, 2002 Nov.
Artículo en Ruso | MEDLINE | ID: mdl-12500682

RESUMEN

Mitochondrial DNA (mtDNA) variation was studied in 38 Kets and 24 Nganasans, the indigenous inhabitants of the north of the Yenisey River Basin and the Taimyr Peninsula. The results were compared with the analogous data obtained for 59 Kondinski and 39 Sos'vinski Mansi. As a whole, mitochondrial gene pool of Mansi, Nganasans, and Kets was characterized by unique combination of European-specific (H, H2, H3, H8, U2, U4, U5, U7, J2, and W) and Asian-specific (A, C, D, and Z) mtDNA haplogroups. Specific features of the haplogroup geographical distribution along with the results of phylogenetic reconstruction favor the hypothesis of the genetic trace left in Eastern Cis-Urals and the adjacent Siberian territories by early migrations from the Near East.


Asunto(s)
ADN Mitocondrial , Variación Genética , Emigración e Inmigración , Haplotipos/genética , Humanos , Matrimonio , Mutación , Filogenia , Siberia/etnología
6.
Genetika ; 38(2): 161-70, 2002 Feb.
Artículo en Ruso | MEDLINE | ID: mdl-11898607

RESUMEN

To date, more than 100 point mutations and several hundreds of structural rearrangements of mitochondrial DNA (mtDNA) are known too be connected with characteristic neuromuscular and other mitochondrial syndromes varying form those causing death at the neonatal stage to diseases with late ages of onset. The immediate cause of mitochondrial disorders is a defective oxidative phosphorylation. Wide phenotypic variation and the heteroplasmy phenomenon, which some authors include in mutation load, are characteristic of human mitochondrial diseases. As the numbers of cases identified and pedigrees described increase, data on the genotype--phenotype interaction and the structure and frequency of pathogenic and conditionally pathogenic mtDNA mutations in human populations are rapidly accumulated. The data on the genetics and epidemiology of mitochondrial diseases are not only important for differential diagnosis and genetic counseling. Since both neutral and mildly pathogenic mutations of mtDNA are progressively accumulated in maternal phyletic lines, molecular analysis of these mutations permits not only reconstruction of the genealogical tree of modern humans, but also estimation of the role that these mutations play in natural selection.


Asunto(s)
ADN Mitocondrial , Enfermedades Mitocondriales/genética , Mutación , Genética de Población , Genoma Humano , Humanos , Biosíntesis de Proteínas , Proteínas/genética
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