Artykuły w czasopismach na temat „Haplotypes”
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Pegueroles, Cinta, Verónica Mixão, Laia Carreté, Manu Molina i Toni Gabaldón. "HaploTypo: a variant-calling pipeline for phased genomes". Bioinformatics 36, nr 8 (13.12.2019): 2569–71. http://dx.doi.org/10.1093/bioinformatics/btz933.
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Abstract Summary An increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, the most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haplotype correspondence for each heterozygous variant called on a phased reference genome. Availability and implementation HaploTypo is implemented in Python 2.7 and Python 3.5, and is freely available at https://github.com/gabaldonlab/haplotypo, and as a Docker image. Supplementary information Supplementary data are available at Bioinformatics online.
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Li, Ruidong, Han Qu, Jinfeng Chen, Shibo Wang, John M. Chater, Le Zhang, Julong Wei i in. "Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes". Molecular Biology and Evolution 37, nr 12 (15.07.2020): 3684–98. http://dx.doi.org/10.1093/molbev/msaa176.
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Abstract Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor’s chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.
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Kaufman, Letícia, Francisco R. Carnese, Alicia Goicoechea, Cristina Dejean, Francisco M. Salzano i Mara H. Hutz. "Beta-globin gene cluster haplotypes in the Mapuche Indians of Argentina". Genetics and Molecular Biology 21, nr 4 (grudzień 1998): 435–37. http://dx.doi.org/10.1590/s1415-47571998000400003.
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Haplotypes derived from five polymorphic restriction sites in the beta-globin gene cluster were investigated in 86 chromosomes from the Argentinian Mapuche. These results were integrated with those previously obtained for ten Brazilian Indian tribes. Eight haplotypes were identified, the most frequent being 2 (57%) and 6 (27%). The presence of haplotype 3 in 2% of the Mapuche chromosomes is probably an evidence of admixture with individuals of African ancestry. Due to the high number of haplotypes observed, heterozygosity as measured by the Gini-Simpson index was higher in the Mapuche than in Brazilian Indians. The haplotypic distribution in the Mapuche was also significantly different from those of all Brazilian tribes investigated. This heterogeneity could be at least partially explained by admixture with non-Indian populations.
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Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, Sami Simsek, Haroon Ahmed, Yujuan Shen i Jianping Cao. "Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey". Pathogens 11, nr 5 (28.04.2022): 519. http://dx.doi.org/10.3390/pathogens11050519.
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Echinococcus granulosus sensu lato (s.l.) causes cystic echinococcosis in ungulates and humans. The current study was designed to find the genetic diversity and haplotypic profiles of hydatid cysts from the lungs of cattle in three provinces in eastern Turkey. Individual cyst isolates (n = 60) were collected from infected cattle lungs after slaughter and then samples were stored in ethanol (70%) until further use. From each isolate, total gDNA was extracted from the cysts’ germinal layers. A partial (875 bp) mt-CO1 gene was amplified by PCR and sequenced unidirectionally. The final size of the trimmed sequences was 530 bp for 60 sequences. Sequence and haplotype analyses were performed, followed by phylogenetic analyses. According to BLAST searches, all sequences were detected as E. granulosus s.s. (G1 and G3 strains). Forty-nine point mutations were identified. In addition, five conserved fragments were detected in all sequences. The haplotype analysis diagram showed E. granulosus s.s. haplotypes organized in a star-like configuration. The haplotypes were characterized by 1–17 mutations compared with the fundamental focal haplotype. Thirty-three haplotypes were determined in 60 samples of which 17 (28.3%) belonged to the main haplotype (Hap_06). The mt-CO1 sequences revealed 49 polymorphic sites, 34.5% (20/49) of which were informative according to parsimony analysis.
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Roberts, Amity R., Louise H. Appleton, Adrian Cortes, Matteo Vecellio, Jonathan Lau, Laura Watts, Matthew A. Brown i Paul Wordsworth. "ERAP1 association with ankylosing spondylitis is attributable to common genotypes rather than rare haplotype combinations". Proceedings of the National Academy of Sciences 114, nr 3 (3.01.2017): 558–61. http://dx.doi.org/10.1073/pnas.1618856114.
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We investigated the proposal that ankylosing spondylitis (AS) is associated with unusual ERAP1 genotypes. ERAP1 haplotypes were constructed for 213 AS cases and 46 rheumatoid arthritis controls using family data. Haplotypes were generated from five common ERAP1 single nucleotide polymorphisms (SNPs)—rs2287987 (M349V), rs30187 (K528R), rs10050860 (D575N), rs17482078 (R725Q), and rs27044 (Q730E). Haplotype frequencies were compared using Fisher’s exact test. ERAP1 haplotypes imputed from the International Genetics of AS Consortium (IGAS) Immunochip study were also studied. In the family study, we identified only four common ERAP1 haplotypes (“VRNQE,” “MKDRQ,” “MRDRE,” and “MKDRE”) in both AS cases and controls apart from two rare (<0.5%) previously unreported haplotypes. There were no examples of the unusual ERAP1 haplotype combination (“*001/*005”) previously reported by others in 53% of AS cases. As expected, K528-bearing haplotypes were increased in the AS family study (AS 43% vs. control 35%), due particularly to an increase in the MKDRQ haplotype (AS 35% vs. control 25%, P = 0.01). This trend was replicated in the imputed Immunochip data for the two K528-bearing haplotypes MKDRQ (AS 33% vs. controls 27%, P = 1.2 × 10–24) and MKDRE (AS 8% vs. controls 7%, P = 0.004). The ERAP1 association with AS is therefore predominantly attributable to common ERAP1 haplotypes and haplotype combinations.
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Sugiura, Nami, Dingqin Tang, Hiroyuki Kurokochi, Yoko Saito i Yuji Ide. "Genetic structure of Quercus gilva Blume in Japan as revealed by chloroplast DNA sequences". Botany 93, nr 12 (grudzień 2015): 873–80. http://dx.doi.org/10.1139/cjb-2015-0025.
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Quercus gilva (Blume) is an evergreen oak species that is native to Japan, China, and Taiwan. Because of a long history of human impact, this species is threatened with extinction in several regions of Japan. The objective of this study was to identify the genetic structure of Q. gilva based on chloroplast DNA (cpDNA) sequencing analysis. We collected 123 samples from 25 populations in Japan, 8 samples from 1 population in China, and 46 samples from 5 populations in Taiwan. Approximately 1815 bp of cpDNA was sequenced for each of the 177 samples. Thirteen haplotypes were detected, with no cross-region distribution of haplotypes among the three geographically separated countries. There were large genetic differences among populations (GST = 0.824, [Formula: see text] = 0.937). Six haplotypes (haplotypes 1, 2, 3, 4a, 4b, and 5) were detected in Japan; haplotype 4a was the most common, detected from 20 populations, and the other rare haplotypes, except for haplotype 4b, occurred at the edge of the species’ distribution. In addition, four haplotypes (haplotypes 1, 2, 3, and 5) were quite different from the predominant haplotype (haplotype 4a), with more than four cpDNA mutations except for a mononucleotide repeat, suggesting that populations with these rare haplotypes should be conserved separately.
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Vathipadiekal, Vinod, Abdulrahman Alsultan, John Farrell, A. M. Al-Rubaish, Fahad Al-Muhanna, Z. Naserullah, A. Alsuliman i in. "Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators". Blood 126, nr 23 (3.12.2015): 3388. http://dx.doi.org/10.1182/blood.v126.23.3388.3388.
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Abstract Fetal hemoglobin (HbF) inhibits HbS polymerization. Because of this, sufficient HbF in most sickle erythrocytes can lead to a milder disease phenotype. HbF levels differ amongst the β-globin gene (HBB) cluster haplotypes of sickle cell anemia. In the Arab-Indian (AI) haplotype, HbF was about 20% compared with 5-10% in the Bantu, Benin, and Senegal haplotypes. Functional elements linked to the HBB haplotype are likely to regulate the expression of HbF in addition to the effects of trans-acting modulators. To identify cis-acting SNPs in the HBB gene cluster that differentiate the AI haplotype from all others, including the Senegal haplotype-the Senegal haplotype shares some SNPs with the AI haplotype but its carriers have lower HbF-we studied patients with sickle cell anemia who were homozygous for HBB haplotypes by genome-wide SNP association analysis (GWAS; Table). First, we compared the results of GWAS of 42 Saudi AI haplotype homozygotes with GWAS in 71 Saudi Benin haplotype homozygotes. The only variants distinguishing these 2 populations with genome-wide significance (p-values between 9.6E-07 and 2.7E-45) were 223 SNPs in chromosome 11p15 from positions 3.5 to 6.5 mb. This region included the HBB gene cluster, its locus control region (LCR) and the upstream and downstream olfactory receptor gene clusters. The minor allele frequency of SNPs in MYB (chr 6q23), BCL11A (chr 2p16) and KLF1 (chr 19), trans-acting loci that affect expression of the HbF genes, were similar in these 2 cohorts. A novel candidate trans-acting locus was not found, however our power to detect such an association was low. We followed-up these observations by comparing allele frequencies in 303 African American cases homozygous for the haplotypes shown in the Table. Thirteen GWAS-significant SNPs, in addition to rs7482144 and rs10128556, were present in all AI haplotype cases but not in 83 Senegal haplotype chromosomes. The allele frequency of these SNPs was replicated in 62 independent AI haplotype cases. Rs2472530 is in the coding region of OR52A5; rs16912979, rs4910743 and rs4601817 are in the HBB gene cluster LCR; rs16912979 in DNase I hypersensitive site-4 altered motifs for POLR2A, GATA1, and GATA2 binding.The minor allele of rs10837771 causes a missense mutation in OR51B4 an upstream olfactory receptor gene. To see if any of these or other alleles might sometimes be associated with HbF in the Bantu and Benin haplotyes, we selected homozygotes and compound heterozygous for these haplotypes who had unexplained and uncharacteristically high HbF. Thirty-one African Americans, aged ≥5 yrs. who had a HbF of 21% were compared with 350 similar cases who had a mean HbF of 3%. Four additional SNPs on chromosome 11, from positions ranging from 5536415 to 5543705 in the UBQLNL/HBG2, region and present in 45-48% of AI haplotype and 3-13% of other haplotypes, were found at higher frequencies in the high HbF group compared with the low HbF group. These SNPs also altered transcription factor binding motifs. Loci marked by SNPs that distinguish the AI from the Senegal and other HBB haplotypes might contain functionally important polymorphisms and account in part for high HbF in AI haplotype sickle cell anemia, independent of, or in addition to, the effects associated with rs7482144 or rs10128556. They might also be rarely associated with high HbF found in other haplotypes. These observations provide a foundation for mechanistic studies focused on the role of these variants in the expression of their linked HbF genes.Table 1.non-codedallelegenomic locationSaudi AI(n=42)Saudi ben.ben(n=71)AA ben.ben(n=264)AA ban.ban(n=31)AA sen.sen(n=8)HbF (%)1711669rs10837771Gexon OR51B410.020.0200rs4601817GLCR10.020.0400rs4910743CLCR10.010.0100rs16912979CLCR00.960.920.111rs10488675Gintron HBE110.01000rs7482144*AHBG210001rs10128556#TIntron HBBP110001rs7935470COR51V110.020.0300rs10837582GOR51V1100.0200rs11036227TOR51V110000rs10734485COR51A1P00.990.9711rs10837461AOR52A110.01000rs2472522GOR52A110.01000rs2472530Gexon OR52A510.01000rs2499948TOR52A510.020.010.020Allele frequencies in haplotypes of sickle cell anemia. * Xmn1 5' HBG 2 restriction site. This SNP, not present on the SNP microarray, was genotyped independently; # LD with rs7482144; AA designates African Americans; ben-Benin; ban-Bantu; sen-Senegal. Disclosures No relevant conflicts of interest to declare.
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Patel, Suprava, Rachita Nanda, Nighat Hussain, Eli Mohapatra i Pradeep Kumar Patra. "Interactions of Combined Haplotypes of Methylenetetrahydrofolate Reductase on Clinical Events in Children with Sickle Cell Disorder". Journal of Evolution of Medical and Dental Sciences 10, nr 25 (21.06.2021): 1889–94. http://dx.doi.org/10.14260/jemds/2021/390.
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BACKGROUND Methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C variants are considered as potential genetic risk factors for vaso-occlusive complications in sickle cell disorder (SCD). The purpose of the study was to determine the interaction of the combined haplotypes on the clinical presentations in children with sickle cell disorder. METHODS A cross-sectional study was conducted on 249 children, confirmed for sickle cell disorder. Clinical details and frequencies of clinical episodes in the past one year were noted and a severity index number was allotted to each child and evaluated for their relationship with the combined haplotypes of C677T and A1298C single nucleotide polymorphisms genotyped by real-time PCR. RESULTS The frequency for 677T / 1298A haplotype was 46.4 % and that of 677C / 1298C was 12.4 %. The three variant combined haplotypes had higher plasma homocysteine values than the wild 677C / 1298A haplotypes (P < 0.001). Clinical events like vasoocclusive crisis (VOC), homocysteinemia, hospitalization frequency and SI were found significantly related among the children in sickle cell trait (SCT) group (P < 0.001) but not so in SCD group. Chances for anemia was 1.93 times more in presence of dual variant alleles (95 %CI: 0.95 to 3.92, P = 0.07) in SCT. The 677T / 1298C haplotype accounted for higher SI was 7.85 times more than the wild haplotypic children even in SCT children and 1.67 times in SCD children. CONCLUSIONS Presence of the variant haplotypes had significant implication on crisis events in children with sickle cell trait and make them more prone for the clinical severity. A preliminary allelic screening might be helpful in them. KEY WORDS Dual Variant Alleles, Heterozygous, Homozygous, MTHFR, Variant Haplotypes
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Vadva, Larsen, Propp, Trautwein, Alford i Alper. "A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies". Cells 8, nr 8 (5.08.2019): 835. http://dx.doi.org/10.3390/cells8080835.
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Single nucleotide polymorphisms (SNPs) are usually the most frequent genomic variants. Directly pedigree-phased multi-SNP haplotypes provide a more accurate view of polymorphic population genomic structure than individual SNPs. The former are, therefore, more useful in genetic correlation with subject phenotype. We describe a new pedigree-based methodology for generating non-ambiguous SNP haplotypes for genetic study. SNP data for haplotype analysis were extracted from a larger Type 1 Diabetes Genetics Consortium SNP dataset based on minor allele frequency variation and redundancy, coverage rate (the frequency of phased haplotypes in which each SNP is defined) and genomic location. Redundant SNPs were eliminated, overall haplotype polymorphism was optimized and the number of undefined haplotypes was minimized. These edited SNP haplotypes from a region containing HLA-DRB1 (DR) and HLA-DQB1 (DQ) both correlated well with HLA-typed DR,DQ haplotypes and differentiated HLA-DR,DQ fragments shared by three pairs of previously identified megabase-length conserved extended haplotypes. In a pedigree-based genetic association assay for type 1 diabetes, edited SNP haplotypes and HLA-typed HLA-DR,DQ haplotypes from the same families generated essentially identical qualitative and quantitative results. Therefore, this edited SNP haplotype method is useful for both genomic polymorphic architecture and genetic association evaluation using SNP markers with diverse minor allele frequencies.
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Slade, D., Ž. Škvorc, D. Ballian, J. Gračan i D. Papes. "The Chloroplast DNA Polymorphisms of White Oaks of Section Quercus in The Central Balkans". Silvae Genetica 57, nr 1-6 (1.12.2008): 227–34. http://dx.doi.org/10.1515/sg-2008-0035.
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Abstract A total of 444 oak trees from 110 populations from a previously under-sampled area in the central Balkans were analysed using four primer/enzyme combinations which amplified and restricted four, largely non-coding regions of the maternally inherited chloroplast DNA. Using the nomenclature of PETIT et al. (2002 a) to classify the haplotypes and lineages, the seven haplotypes that were found in Croatia, Bosnia and Herzegovina, Montenegro, Albania, Macedonia and southern Kosovo consisted of haplotypes 2, 4, 5, 6, 7, 17, 31, as well as the subtypes of haplotypes 4 (a), 5 (a, b, c), and 17 (a). Five of these haplotypes belong to lineage A. One of these, haplotype 5, is present throughout the sampled area. The distributions of the other haplotypes from this lineage are more geographically structured. The other two haplotypes, haplotype 2 and haplotype 17, belong to lineages C and E, respectively. The data are combined with previous data by PETIT et al. (2002 b) to provide more detailed information of the postglacial routes of colonisation taken by oaks in south-eastern Europe.
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Choi, Mun-Ho, Seung-Ho Kang i Hyeong-Seok Lim. "An improved preprocessing algorithm for haplotype inference by pure parsimony". Journal of Bioinformatics and Computational Biology 12, nr 04 (sierpień 2014): 1450020. http://dx.doi.org/10.1142/s0219720014500206.
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The identification of haplotypes, which encode SNPs in a single chromosome, makes it possible to perform a haplotype-based association test with disease. Given a set of genotypes from a population, the process of recovering the haplotypes, which explain the genotypes, is called haplotype inference (HI). We propose an improved preprocessing method for solving the haplotype inference by pure parsimony (HIPP), which excludes a large amount of redundant haplotypes by detecting some groups of haplotypes that are dispensable for optimal solutions. The method uses only inclusion relations between groups of haplotypes but dramatically reduces the number of candidate haplotypes; therefore, it causes the computational time and memory reduction of real HIPP solvers. The proposed method can be easily coupled with a wide range of optimization methods which consider a set of candidate haplotypes explicitly. For the simulated and well-known benchmark datasets, the experimental results show that our method coupled with a classical exact HIPP solver run much faster than the state-of-the-art solver and can solve a large number of instances that were so far unaffordable in a reasonable time.
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Epifanio, John M., Bonnie L. Brown, Peter E. Smouse i Carol J. Kobak. "Mitochondrial DNA divergence among popylations of American shad (Alosa sapidissima): how much variation is enough for mixed-stock analysis?" Canadian Journal of Fisheries and Aquatic Sciences 52, nr 8 (1.08.1995): 1688–702. http://dx.doi.org/10.1139/f95-761.
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We investigated the geographic distribution of the mitochondrial DNA (mtDNA) diversity of American shad from 15 North American rivers in 1992 with the intent of assessing sampling efficiency for future mixed-stock analysis. We observed 116 haplotypes among the 988 individuals assayed. Because no single or group of haplotypes completely discriminated river stocks or regional complexes, we investigated haplotype frequencies as stock descriptors. Analysis of four unique indices of haplotype divergence indicated that including rather than suppressing restriction site heteroplasmy increased resolution; however, the final results were not overwhelmingly dependent on this choice. A redundancy of variation among restriction enzymes diminished information returns rapidly after considering the six best enzymes, caused by physical linkage of restriction sites on the mtDNA molecule. Stock discriminatory power was tested by computing allocation efficiencies of mtDNA characters. When each individual was temporarily removed from the data set and reallocated to the various candidate populations on the basis of haplotypic similarity, 28% of the reallocations were correct, a fourfold increase over random success. We demonstrate that although the specific stock identity of individuals cannot be confidently established, the haplotypic arrays from baseline stocks can support stock identification and mixed-stock analysis for shad because rivers support stock-specific haplotype frequencies.
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Erhart, M. A., S. J. Phillips, F. Bonhomme, P. Boursot, E. K. Wakeland i J. H. Nadeau. "Haplotypes that are mosaic for wild-type and t complex-specific alleles in wild mice." Genetics 123, nr 2 (1.10.1989): 405–15. http://dx.doi.org/10.1093/genetics/123.2.405.
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Abstract Two outstanding problems pertaining to the population dynamics and evolution of the t complex in mice concern the frequency of t haplotypes in the wild and the degree to which these haplotypes recombine with their wild-type homologs. To address these problems, the frequency and distribution of several t complex-associated restriction fragment variants in wild mice were estimated. Sixty-four versions of chromosome 17 from wild-derived Mus musculus musculus and Mus musculus domesticus were examined with DNA probes for six loci within the t complex that exhibit restriction fragment variation. All six probes detect variants that have heretofore been found exclusively associated with the t complex. Haplotype analysis of wild-derived chromosomes revealed a high frequency (45.3%) of "mosaic" haplotypes with a mixture of t-specific and wild-type variants and only one haplotype with t-specific variants at all six loci. When 12 well-characterized t haplotypes isolated from diverse geographic regions were analyzed, only three had a complete set of t-specific restriction fragments for the six loci examined. The preponderance of mosaic haplotypes in both groups of mice can be explained by any one of the following hypotheses: genetic recombination between t haplotypes and their wild-type homologs, the persistence in wild populations of haplotypes that have descended from ancestral partial t haplotypes, or that the restriction fragment variants fixed in the ancestral t haplotype were also fixed in some wild-type haplotypes. There is evidence to support all three of these hypotheses in our data. The allelic composition of some mosaic haplotypes indicates that they may have been formed by segmental recombination, either double crossing over or gene conversion, rather than by simple single crossovers. The occurrence of indistinguishable mosaic haplotypes in both M. m. musculus and M. m. domesticus suggests that these haplotypes are ancestral rather than recently derived.
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Xiong, Bai, i Thomas D. Kocher. "Intraspecific variation in sibling species of Simulium venustum and Simulium verecundum complexes (Diptera: Simuliidae) revealed by the sequence of the mitochondrial 16S rRNAgene". Canadian Journal of Zoology 71, nr 6 (1.06.1993): 1202–6. http://dx.doi.org/10.1139/z93-164.
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A portion of the mitochondrial large ribosomal RNA gene was amplified and sequenced (460 base pairs) for 10 individuals of each of nine samples of black flies representing three sibling species of the Simulium venustum complex (CC, CC3, and AC(gB)) and two sibling species of the Simulium verecundum complex (ACD = Simulium rostratum and AA). Mitochondrial DNA haplotype heterogeneity was observed in all but the sample of S. verecundum AA from New Hampshire. The sample of S. venustum CC3 had a significantly larger number of haplotypes than other samples. A predominant haplotype was found in most samples except S. venustum CC3 and S. venustum CC from New Hampshire (nine haplotypes in the sample of S. venustum CC3 and two haplotypes with equal frequency in the sample of S. venustum CC from New Hampshire). The predominant haplotype was the same among the three samples of S. verecundum AA. Samples of S. venustum CC also shared haplotypes, but the predominant haplotype was different in each sample. Despite intraspecific variation, haplotypes are usually clustered on a conspecific basis.
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Sebastiani, Paola, John J. Farrell, Shuai Wang, Heather L. Edward, Heather M. Shappell, Harold T. Bae, Clinton T. Baldwin i in. "BCL11A enhancer Haplotypes Are Associated with the Distribution of HbF in Arab-Indian and African Haplotype Sickle Cell Anemia but Not the Different Population Levels of HbF". Blood 124, nr 21 (6.12.2014): 4066. http://dx.doi.org/10.1182/blood.v124.21.4066.4066.
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Abstract Fetal hemoglobin (HbF) modulates the phenotype of sickle cell anemia. In the Middle East and India the HbS gene is often on an Arab-Indian HBB haplotype that is associated with high HbF levels. HbF is “normally” distributed in this population with a mean ~20%. In African HbS haplotypes, HbF levels are much lower (mean value ~6%) with a highly skewed distribution. BCL11A is an important modulator of γ-globin gene (HBG2 and HBG1) expression and BCL11A is regulated by erythroid specific enhancers in its 2nd intron. The enhancers consist of 3 DNase hypersensitive sites (HS) +62, +58 and +55 kb from the transcription initiation site of this gene. Polymorphisms (SNPs) in these enhancers are associated with HbF. The strongest association with HbF levels in African Americans with sickle cell anemia was with rs1427407 in HS +62 and to a lesser extent, rs7606173 in HS+55. Using the results of whole genome sequencing of 14 AI haplotype patients—half with HbF <10%, half with HbF >20%—6 SNPs in the BCL11A enhancer region, rs1427407, rs7599488, rs6706648, rs6738440, rs7565301, rs7606173 and 2 indels rs3028027 and rs142027584 (CCT, CCTCT and AAAAC respectively), were detected as possibly associated with HbF level. There were no novel polymorphisms detected. We genotyped the 6 SNPs and studied their associated haplotypes in 137 Saudi (HbF18.0±7.0%) and 44 Indian patients (HbF23.0±4.8%) with the Arab-Indian HBB haplotype; 50 African Americans with diverse African haplotypes, including 4 Senegal haplotype heterozygotes, (20 with HbF 17.2±4.6% and 30 with HbF 5.0±2.5%) and imputed genotypes for these SNPs in 847 African Americans with sickle cell anemia and diverse haplotypes (HbF 6.6±5.5%). Four SNPs (rs1427407, rs6706648, rs6738440, and rs7606173) in the HS sites showed consistent associations with HbF levels in all 4 cohorts. Haplotype analysis of these 4 SNPs showed that there were 4 common and 10 rare haplotypes. The most common, GCAG, was found in ~54% of Arab-Indian haplotype carriers (HbF, ~20%) and in ~33% of African origin haplotype carriers (HbF, ~5.5%). Two haplotypes, GTAC and GTGC, were carried by ~40% of African American patients and were associated with lower levels of HbF (3.6%-4%). These same haplotypes were carried by 18% of Arab-Indian haplotype carriers and their average HbF level was 17%. These differences were significant. Haplotype TCAG was present in 20% of Arab-Indian and 25% of African haplotype cases, and carriers had on average higher HbF levels (~22% in the Arab-Indian haplotype, ~8% in African Americans). The analysis shows that: BCL11A enhancer haplotypes are differentially distributed among patients with the HbS gene on Arab-Indian or African origin haplotypes; haplotype pairs TCAG/TCAG and GTAC/GTGC are associated with the highest and lowest HbF levels in all the studied groups; the population-specific prevalence of HbF BCL11A enhancer haplotypes are likely to explain the different distributions of HbF in African origin and Arab-Indian haplotypes but do not account for the differences in average population levels of HbF or the high HbF of the Arab-Indian haplotype. Novel SNPs in BCL11A do not explain the high HbF of the Arab-Indian haplotype. Other important loci must have a predominant role in the differential expression of HbF among HbS Arab-Indian haplotype carriers. Disclosures No relevant conflicts of interest to declare.
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Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, Wanna Maipanich, Surapol Saguankiat, Somjit Pubampen i Orawan Phuphisut. "Genetic Variation and Population Genetics ofTaenia saginatain North and Northeast Thailand in relation toTaenia asiatica". Journal of Parasitology Research 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/310605.
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Taenia saginatais the most common humanTaeniain Thailand. Bycox1sequences, 73 isolates from four localities in north and northeast were differentiated into 14 haplotypes, 11 variation sites and haplotype diversity of 0.683. Among 14 haplotypes, haplotype A was the major (52.1%), followed by haplotype B (21.9%). Clustering diagram of Thai and GenBank sequences indicated mixed phylogeny among localities. By MJ analysis, haplotype clustering relationships showed paired-stars-like network, having two main cores surrounded by minor haplotypes. Tajima’sDvalues were significantly negative inT. saginataworld population, suggesting population expansion. Significant Fu’sFsvalues in Thai, as well as world population, also indicate that population is expanding and may be hitchhiking as part of selective sweep. Haplotype B and its dispersion were only found in populations from Thailand. Haplotype B may evolve and ultimately become an ancestor of future populations in Thailand. Haplotype A seems to be dispersion haplotype, not just in Thailand, but worldwide. High geneticT. saginataintraspecies divergence was found, in contrast to its sister species,T. asiatica; among 30 samples from seven countries, its haplotype diversity was 0.067, while only 2 haplotypes were revealed. This extremely low intraspecific variation suggests thatT. asiaticacould be an endangered species.
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Damen, Manon, Mascha Schijvenaars, Marlies Schimmel-Naber, Johanne Groothuismink, Marieke Coenen i Alide Tieleman. "Ancestral Origin of the First Indian Families with Myotonic Dystrophy Type 2". Journal of Neuromuscular Diseases 8, nr 4 (30.07.2021): 715–22. http://dx.doi.org/10.3233/jnd-210671.
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Background: Myotonic dystrophy type 2 (DM2) is caused by a CCTG repeat expansion in intron 1 of the CCHC-Type Zinc Finger Nucleic Acid Binding Protein (CNBP) gene. Previous studies indicated that this repeat expansion originates from separate founders. Objective: This study was set out to determine whether or not patients with DM2 originating from European and non-European countries carry the previously described European founder haplotypes. Methods: Haplotype analysis was performed in 59 DM2 patients from 29 unrelated families. Twenty-three families were from European descent and 6 families originated from non-European countries (India, Suriname and Morocco). Seven short tandem repeats (CL3N122, CL3N99, CL3N59, CL3N117, CL3N119, CL3N19 and CL3N23) and 4 single nucleotide polymorphisms (SNP) (rs1871922, rs1384313, rs4303883 and CGAP_886192) in and around the CNBP gene were used to construct patients’ haplotypes. These haplotypes were compared to the known DM2 haplotypes to determine the ancestral origin of the CNBP repeat expansion. Results: Of 41 patients, the haplotype could be assigned to the previously described Caucasian haplotypes. Three patients from Morocco and Portugal had a haplotype identical to the earlier reported Moroccan haplotype. Twelve patients from India and Suriname, however, carried a haplotype that seems distinct from the previously reported haplotypes. Three individuals could not be assigned to a specific haplotype. Conclusion: The ancestral origin of DM2 in India might be distinct from the Caucasian families and the solely described Japanese patient. However, we were unable to establish this firmly due to the limited genetic variation in the region surrounding the CNBP gene.
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Koks, Sulev, Abigail L. Pfaff, Vivien J. Bubb i John P. Quinn. "Transcript Variants of Genes Involved in Neurodegeneration Are Differentially Regulated by the APOE and MAPT Haplotypes". Genes 12, nr 3 (15.03.2021): 423. http://dx.doi.org/10.3390/genes12030423.
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Genetic variations at the Apolipoprotein E (ApoE) and microtubule-associated protein tau (MAPT) loci have been implicated in multiple neurogenerative diseases, but their exact molecular mechanisms are unclear. In this study, we performed transcript level linear modelling using the blood whole transcriptome data and genotypes of the 570 subjects in the Parkinson’s Progression Markers Initiative (PPMI) cohort. ApoE, MAPT haplotypes and two SNPs at the SNCA locus (rs356181, rs3910105) were used to detect expression quantitative trait loci eQTLs associated with the transcriptome and differential usage of transcript isoforms. As a result, we identified 151 genes associated with the genotypic variations, 29 cis and 122 trans eQTL positions. Profound effect with genome-wide significance of ApoE e4 haplotype on the expression of TOMM40 transcripts was identified. This finding potentially explains in part the frequently established genetic association with the APOE e4 haplotypes in neurodegenerative diseases. Moreover, MAPT haplotypes had significant differential impact on 23 transcripts from the 17q21.31 and 17q24.1 loci. MAPT haplotypes had also the largest up-regulating (256) and the largest down-regulating (−178) effect sizes measured as β values on two different transcripts from the same gene (LRRC37A2). Intronic SNP in the SNCA gene, rs3910105, differentially induced expression of three SNCA isoforms. In conclusion, this study established clear association between well-known haplotypic variance and transcript specific regulation in the blood. APOE e4 and MAPT H1/H2 haplotypic variants are associated with the expression of several genes related to the neurodegeneration.
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Moya, Andrés, Eladio Barrio, David Martínez, Amparo Latorre, Fernando González-Candelas, Misericordia Ramón i José A. Castro. "Molecular characterization and cytonuclear disequilibria of two Drosophila subobscura mitochondrial haplotypes". Genome 36, nr 5 (1.10.1993): 890–98. http://dx.doi.org/10.1139/g93-117.
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According to restriction site analyses of mitochondrial DNA, Drosophila subobscura shows a polymorphism that consists of two frequent haplotypes that are evenly distributed all over the Old World and several rare haplotypes never present in more than one locality. To ascertain the causes responsible for such distribution, three different mtDNA fragments from haplotypes I and II sampled in a population from Zürich have been partially sequenced. Only three silent nucleotide changes have been detected in the ND5 gene. One of them implies the loss of the HaeIII restriction site, which differentiates haplotype I from haplotype II. On the basis of these results as well as on others involving the geographic distribution of haplotypes I and II, they can be considered phenotypically equivalent. The sequencing study has been complemented with the analysis of cytonuclear disequilibria between mitochondrial haplotypes and different nuclear loci in four D. subobscura populations. As expected, no significant cytonuclear disequilibria have been found between haplotypes I and II. Moreover, when haplotypes I and II were pooled and compared with the rare, endemic haplotypes similar results were obtained.Key words: mitochondrial DNA, allozymes, selection, neutrality, cytonuclear disequilibria.
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Nagarajan-Radha, Venkatesh, Ian Aitkenhead, David J. Clancy, Steven L. Chown i Damian K. Dowling. "Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis". Philosophical Transactions of the Royal Society B: Biological Sciences 375, nr 1790 (2.12.2019): 20190178. http://dx.doi.org/10.1098/rstb.2019.0178.
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Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these ‘male-harming’ mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster . Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait—metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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DOD, BARBARA, CATHY LITEL, PATRICK MAKOUNDOU, ANNIE ORTH i PIERRE BOURSOT. "Identification and characterization of t haplotypes in wild mice populations using molecular markers". Genetical Research 81, nr 2 (kwiecień 2003): 103–14. http://dx.doi.org/10.1017/s0016672303006116.
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As part of a population genetics survey of the hybrid zone between mouse subspecies Mus musculus domesticus and M. m. musculus, we identified and characterized the t haplotypes in 1068 mice from 186 different populations in a 2500 km2 area in central Jutland. On the basis of two t-specific PCR markers, 130 mice possessed this haplotype. The allele frequencies at six microsatellites on the third and fourth chromosomal inversions of the t region were sufficiently different between t-bearing and non-t-bearing mice, and linkage disequilibria sufficiently marked on the t haplotype, to be able to reconstitute the genotype of most t haplotypes. A total of three frequent and 15 rarer haplotypes were identified. These haplotypes resemble each other more than they resemble a panel of known haplotypes from a wide range of geographical regions, except for tw73, which was also extracted from Jutland. The patterns of variation at the microsatellite loci suggest that the Jutland haplotypes were derived from a small number of haplotypes, followed by recombination between complementing haplotypes. Further evidence of recombination came from complementation tests that we performed, showing the lack of concordance between the degrees of complementation and of molecular resemblance between haplotypes. This study shows that it is possible to characterize the presence and variation of t haplotypes by a population genetics approach using simple molecular markers. However recombination between t haplotypes has occurred frequently enough to obscure the links between this variation and the biological properties of distortion and lethality of the haplotypes that originally colonized Jutland.
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Padutov, Vladimir E. "THE INFLUENCE OF ENVIRONMENTAL FACTORS ON THE POPULATION GENETIC STRUCTURE OF THE PEDUNCULATE OAK (QUERCUS ROBUR L.) IN BELARUS". Journal of the Belarusian State University. Ecology., nr 3 (25.09.2021): 18–26. http://dx.doi.org/10.46646/2521-683x/2021-3-18-26.
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Pedunculate oak (Quercus robur L.) is one of the main forest forming species in the Republic of Belarus. 18 allelic variants were identified by means of microsatellite loci analysis, which are grouped into 17 different combinations (haplotypes). Twelve of them are rare (the total frequency of occurrence is 15 %) and five are widespread (the proportion of occurrence varies from 7 to 48 %). The last of the named groups includes haplotypes No. 1 (μdt189, μdt3123, μdt4142, μcd494, μcd574, μkk4109), No. 2 (μdt190, μdt3120, μdt4141, μcd495, μcd574, μkk4109), No. 3 (μdt189, μdt3120, μdt4141, μcd494, μcd575, μkk4109), No. 8 (μdt189, μdt3121, μdt4142, μcd494, μcd574, μkk4109). It was found that the geographical distribution of the dominant haplotypes from west to east (along the gradient of climate continentality increasing) has the following order No. 8 – No. 7 – No. 3 – No. 1 – No. 2. It was revealed that haplotype No. 3 is predominantly found in oak forests growing on hills. Haplotype No. 8 prones to form forest stands in depressions, while haplotypes No. 1, No. 2 and No. 7 mainly occupied middle relief elements. The actually observed and theoretically expected frequencies of occurrence in different types of oak forests are close to each other only in the case of haplotype No. 2. For haplotypes No. 1 and No. 8 opposite tendencies of distribution were revealed. In those forest types where for haplotype No. 1 there was an increase in the actual frequency of occurrence compared to the expected one, for haplotype No. 8 there was opposite situation. The reverse trend was also true for this pare of haplotypes. The second pair for which opposite tendencies of distribution were also revealed is haplotypes No. 3 and No. 7.
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Adabale, Abosede, Samira Batista Lobo Makanjuola, Akinsegun Akinbami, Adedoyin Dosunmu, Alani Akanmu, Farideh A. Javid i Louis C. Ajonuma. "Frequency of beta S globin gene haplotypes among sickle cell patients in Nigeria". Journal of International Medical Research 49, nr 6 (czerwiec 2021): 030006052110199. http://dx.doi.org/10.1177/03000605211019918.
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Objective To determine the frequency of beta s globin gene haplotypes in Nigerian patients with sickle cell disease (SCD) and to measure their correlation with clinical and haematological characteristics. Methods This study enrolled patients with SCD and collected their peripheral blood for restriction fragment length polymorphism analysis in order to identify five polymorphic sites in the β-globin gene cluster. Results A total of 245 homozygous SCD patients (490 alleles) were included in the study. Among the analysed alleles, 426 (86.9%) had the Benin (BEN) haplotype; 19 (3.9%) had the Senegal (SEN) haplotype; 31 (6.3%) had the Cameroon haplotype; five (1.0%) had the Bantu/Central African Republic haplotype; and nine 9 (1.8%) had atypical haplotypes. No significant association was observed between the haplotypes and haematological events, although patients with the BEN/SEN haplotype showed improved red blood cell counts, haemoglobin levels and red blood cell width index. No significant association was observed between the haplotypes and the three clinical manifestations, although patients with the BEN/SEN haplotype showed a four-fold lower frequency of painful episodes. Conclusion These findings suggest that the SEN haplotype combined with the BEN haplotype might contribute toward a better haematological profile and milder clinical severity in SCD.
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Cai, Dehan, i Yanni Sun. "Reconstructing viral haplotypes using long reads". Bioinformatics 38, nr 8 (14.02.2022): 2127–34. http://dx.doi.org/10.1093/bioinformatics/btac089.
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Abstract Motivation Most RNA viruses lack strict proofreading during replication. Coupled with a high replication rate, some RNA viruses can form a virus population containing a group of genetically related but different haplotypes. Characterizing the haplotype composition in a virus population is thus important to understand viruses’ evolution. Many attempts have been made to reconstruct viral haplotypes using next-generation sequencing (NGS) reads. However, the short length of NGS reads cannot cover distant single-nucleotide variants, making it difficult to reconstruct complete or near-complete haplotypes. Given the fast developments of third-generation sequencing technologies, a new opportunity has arisen for reconstructing full-length haplotypes with long reads. Results In this work, we developed a new tool, RVHaplo to reconstruct haplotypes for known viruses from long reads. We tested it rigorously on both simulated and real viral sequencing data and compared it against other popular haplotype reconstruction tools. The results demonstrated that RVHaplo outperforms the state-of-the-art tools for viral haplotype reconstruction from long reads. Especially, RVHaplo can reconstruct the rare (1% abundance) haplotypes that other tools usually missed. Availability and implementation The source code and the documentation of RVHaplo are available at https://github.com/dhcai21/RVHaplo. Supplementary information Supplementary data are available at Bioinformatics online.
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Cao, Chang-Chang, i Xiao Sun. "Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information". Journal of Bioinformatics and Computational Biology 14, nr 04 (sierpień 2016): 1650017. http://dx.doi.org/10.1142/s0219720016500177.
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To reduce the cost of large-scale re-sequencing, multiple individuals are pooled together and sequenced called pooled sequencing. Pooled sequencing could provide a cost-effective alternative to sequencing individuals separately. To facilitate the application of pooled sequencing in haplotype-based diseases association analysis, the critical procedure is to accurately estimate haplotype frequencies from pooled samples. Here we present Ehapp2 for estimating haplotype frequencies from pooled sequencing data by utilizing a database which provides prior information of known haplotypes. We first translate the problem of estimating frequency for each haplotype into finding a sparse solution for a system of linear equations, where the NNREG algorithm is employed to achieve the solution. Simulation experiments reveal that Ehapp2 is robust to sequencing errors and able to estimate the frequencies of haplotypes with less than 3% average relative difference for pooled sequencing of mixture of real Drosophila haplotypes with 50× total coverage even when the sequencing error rate is as high as 0.05. Owing to the strategy that proportions for local haplotypes spanning multiple SNPs are accurately calculated first, Ehapp2 retains excellent estimation for recombinant haplotypes resulting from chromosomal crossover. Comparisons with present methods reveal that Ehapp2 is state-of-the-art for many sequencing study designs and more suitable for current massive parallel sequencing.
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Agúndez, José A. G., Klaus Golka, Carmen Martínez, Silvia Selinski, Meinolf Blaszkewicz i Elena García-Martín. "Unraveling Ambiguous NAT2 Genotyping Data". Clinical Chemistry 54, nr 8 (1.08.2008): 1390–94. http://dx.doi.org/10.1373/clinchem.2008.105569.
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Abstract Background: Arylamine N-acetyltransferase 2 (CoASAc; NAT2, EC 2.3.1.5) is a drug-metabolizing enzyme that displays common polymorphisms leading to impaired drug metabolism and adverse drug effects. Determination of the N-acetyltransferase 2 (arylamine N-acetyltransferase) (NAT2) genotype in clinical practice is hampered by the occurrence of ambiguous haplotype combinations that may lead to patient misclassification. We determined the frequencies for ambiguous NAT2 haplotypes and diplotypes in a white population and investigated the use of PHASE v2.1.1, a statistical program for haplotype reconstruction, to clarify this ambiguity and classify individuals according to their acetylation status. Methods: By means of allele-specific haplotype mapping and sequencing, we determined the haplotypes for 7 common single-nucleotide polymorphisms in the NAT2 gene (n = 2624 haplotypes). To test the performance of PHASE, actual genotypes were deconstructed and then reconstructed by haplotype prediction. Results: We identified 21 NAT2 allelic variants, including a new variant allele that combines the single-nucleotide polymorphisms rs1801279, rs1799929, and rs1208. In contrast, the previously described variant alleles *5G, *5J, *6E, *7A, *11A, *11B, and *14B were not identified in the study population. Ambiguous haplotypes were observed in 98 alleles (3.7%), and ambiguous diplotypes were observed in 64 individuals (4.9%). Eleven individuals (0.8%) were misclassified by the use of haplotype prediction. Conclusions: Ambiguous NAT2 genotyping data are common. Actual NAT2 genotypes cannot be fully determined by haplotype prediction techniques. This study provides real haplotype data that can be used as a guide to convert NAT2 haplotypes and diplotypes into actual genotypes in white individuals.
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ABAD-GRAU, MARÍA M., NURIA MEDINA-MEDINA, SERAFÍN MORAL, ROSANA MONTES-SOLDADO, SERGIO TORRES-SÁNCHEZ i FUENCISLA MATESANZ. "INCREASING POWER BY USING HAPLOTYPE SIMILARITY IN A MULTIMARKER TRANSMISSION/DISEQUILIBRIUM TEST". Journal of Bioinformatics and Computational Biology 11, nr 02 (kwiecień 2013): 1250014. http://dx.doi.org/10.1142/s021972001250014x.
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It is already known that power in multimarker transmission/disequilibrium tests may improve with the number of markers as some associations may require several markers to be captured. However, a mechanism such as haplotype grouping must be used to avoid incremental complexity with the number of markers. 2G, a state-of-the-art transmission/disequilibrium test, implements this mechanism to its maximum extent by grouping haplotypes into only two groups, high and low-risk haplotypes, so that the test has only one degree of freedom regardless of the number of markers. The test checks whether those haplotypes more often transmitted from parents to offspring are truly high-risk haplotypes. In this paper we use haplotype similarity as prior knowledge to classify haplotypes as high or low risk ones and start with those haplotypes in which the prior will have lower impact i.e. those with the largest differences between transmission and non-transmission counts. If their counts are very different, the prior knowledge has little effect and haplotypes are classified as low or high risk as 2G does. We show a substantial gain in power achieved by this approach, in both simulation and real data sets.
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Gariepy, Tara D., Dmitry L. Musolin, Aleksandra Konjević, Natalia N. Karpun, Vilena Y. Zakharchenko, Elena N. Zhuravleva, Luciana Tavella, Allison Bruin i Tim Haye. "Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia". NeoBiota 68 (15.09.2021): 53–77. http://dx.doi.org/10.3897/neobiota.68.68915.
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The arrival, establishment and pest status of Halyomorpha halys in Europe and non-native countries in Asia have been well-documented, with thorough characterisation of the genetic diversity and occurrence of cytochrome oxidase I (COI) haplotypes in Switzerland, France, Hungary, Italy and Greece. However, a number of gaps exist in terms of the characterisation of the haplotype diversity and occurrence of H. halys along the invasion front that covers eastern Europe, western and central Asia. To contribute towards filling this gap, the COI haplotype diversity and distribution were investigated for H. halys collected in Serbia, Ukraine, Russia, Georgia and Kazakhstan. A total of 646 specimens were analysed and five haplotypes were found (H1, H3, H8, H33 and H80). Haplotype H1 was present in all five countries investigated and was the only haplotype detected amongst > 500 specimens collected from Ukraine, Russia and Georgia. H1 (82%) was the dominant haplotype found in Kazakhstan, alongside H3 (18%). In contrast to the low or no diversity observed in these four countries, Serbia had higher haplotype diversity and was represented by five haplotypes. Although H3 was dominant (47%) in Serbia, H1 was also prevalent (40%); the remaining haplotypes (H8, H33 and H80) were minor contributors (1–11%) to the haplotype composition. The results are discussed in context with other known populations in neighbouring countries and patterns of haplotype diversity indicate the movement of successful invasive populations in Europe to generate secondary invasions along the eastern front of the invasion in Eurasia. Possible scenarios regarding the spread of particular haplotypes in these regions are discussed, along with suggestions for future research to fill existing gaps.
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Koseniuk, Anna, i Ewa Słota. "Mitochondrial control region diversity in Polish sheep breeds". Archives Animal Breeding 59, nr 2 (30.05.2016): 227–33. http://dx.doi.org/10.5194/aab-59-227-2016.
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Abstract. The aim of the study was to determine the genetic variability of the Polish sheep breeds Świniarka, Wrzosówka, Pomorska, and Wielkopolska based on mitochondrial control region polymorphism. A comprehensive phylogenetic analysis and information about the genetic origin of the breeds were also obtained. The genetic variability of the breeds studied has been assessed based on the number of haplotypes, haplotype diversity, nucleotide diversity, the average number of nucleotide differences, the number of mutations, and phylogenetically informative sites. Sequence divergence between identified haplogroup A (HA) and haplogroup B (HB) was also calculated. Moreover, a neighbour-joining (NJ) haplotype tree was constructed based on Kimura's two-parameter genetic distance calculation. Finally, the history of the population was investigated by mismatch distribution and Fu's F statistics. The 559 bp long mitochondrial DNA (mtDNA) control region (CR) sequences of 143 sheep were analysed. The 65 haplotypes were defined by 45 parsimony informative sites. Among the four Polish breeds, Wrzosówka had the highest while Świniarka the lowest values of haplotype (Hd) and sequence diversity (π) (Hd = 0.9735 and π = 0.0040 for Wrzosówka; Hd = 0.8975 and π = 0.0030 for Świniarka). Five haplotypes were shared between breeds, whereas the remaining 60 were unique. The NJ phylogenetic tree has revealed that 61 haplotypes of all analysed breeds clustered into clade B while the remaining 4 haplotypes representing all but the Świniarka breed pooled together with clade A. None of the other reported mitochondrial haplogroups were identified. The haplotypes representing HB formed a star-like network with the single central haplotype, which in association with extensive haplotype sharing reveals a weak structure of Polish breeds and the existence of gene flow between the breeds studied.
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Kaul, Noyonika, Prem Lal Kashyap, Sudheer Kumar, Deepti Singh i Gyanendra Pratap Singh. "Genetic Diversity and Population Structure of Head Blight Disease Causing Fungus Fusarium graminearum in Northern Wheat Belt of India". Journal of Fungi 8, nr 8 (5.08.2022): 820. http://dx.doi.org/10.3390/jof8080820.
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Head blight or scab caused by Fusarium graminearum (FG), once ranked as a minor disease in wheat, is now emerging as one of the economically important diseases in India. The present study represents the first in-depth population genetic analysis of the FG from the northern wheat belt of India. In this study, multiple conserved gene sequences comprised of β-tubulin (TUB), translation elongation factor 1-α (TEF), and histone-3 (HIS) regions were used for multi-locus phylogenetic analysis of 123 geographically distinct F. graminearum isolates collected from four different states (Haryana (HR), Punjab (PB), Rajasthan (RJ) and West Bengal (WB)) of India. The phylogenetic and haplotype analysis showed the presence of thirty haplotypes in all the analyzed populations. The haplotypic diversity in the RJ population (Hd = 0.981) was higher than in the HR (Hd = 0.972), PB (Hd = 0.965) and WB population (Hd = 0.962). Recombination events (Rm = 12) and mutation events (485) were also detected. Analysis of molecular variance (AMOVA) indicated that genetic diversity was exclusively due to the differences within populations. The haplotype network was widely dispersed and not associated with specific populations, as a single common haplotype was not detected. The PB population contained both unique (H9, H10 and H11) and shared haplotypes (27 haplotypes) in a higher number in comparison to other geographical locations. Except for haplotype H22 (contains highly aggressive isolates), there was no specific linkage noticed between the isolate aggressiveness and haplotype. The concatenated sequences of all the three genes demonstrated a low level of genetic differentiation (Fst = −0.014 to 0.02) in the analyzed population. Positive values for the neutrality tests in PB, HR and RJ reveal a balancing selection mechanism behind the FG population structure. The WB population showed both positive and negative values of neutrality indices, indicating the role of both population expansion as well as balancing selection in structuring the FG population.
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Zheng, Meiyun, Jinyu Yan, Lingling Jiang, Zhenzhen Dai i Xiang Liu. "Association between ANXA5 haplotypes and the risk of recurrent pregnancy loss". Journal of International Medical Research 50, nr 7 (lipiec 2022): 030006052110268. http://dx.doi.org/10.1177/03000605211026809.
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Background Annexin A5 (ANXA5) haplotypes can increase the risk of recurrent pregnancy loss (RPL). This study aimed to investigate the effect of ANXA5 haplotypes on ANXA5 expression in patients with RPL. Methods Female subjects with RPL, parous controls (those who intentionally aborted without medical conditions or complications), and population controls (normal delivery) were studied. Real-time polymerase chain reaction was carried out to evaluate ANXA5 expression in the placenta and peripheral blood. Western blotting and immunohistochemistry were used to assess ANXA5 protein expression. The luciferase assay was performed to detect the effect of M1 and M2 haplotypes on transcription efficiency of the ANXA5 promoter. Results We found that the percentage of the M2 carrier was highest in the RPL group. ANXA5 expression in the placenta and peripheral blood in subjects with RPL was significantly inhibited. Furthermore, ANXA5 expression in subjects carrying the M2 haplotype was remarkably suppressed compared with that in carriers of other haplotypes. Finally, the M2 haplotype decreased the transcription efficiency of the ANXA5 promoter. Conclusion Our findings show that ANXA5 expression is decreased in carriers of the M2 haplotype and that M1/M2 haplotypes in the ANXA5 gene are associated with an increased risk of RPL.
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Adler, Grazyna, Emir Mahmutbegovic, Izabela Uzar, Mateusz Adler i Nevena Mahmutbegovic. "Relationship between H1 and H2 haplotypes of the 17q21 inversion and pregnancy loss in Bosnian population: A case - control study". Genetics & Applications 3, nr 3 (24.12.2019): 33. http://dx.doi.org/10.31383/ga.vol3iss3pp33-37.
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Background: The 17q21.31 band is one of the most structurally complex and evolutionarily dynamic region of the genome. Frequencies of two SNPs: rs9468 and rs1800547 determine worldwide distribution of H1 and H2 haplotypes. Recent studies have demonstrated that H2 haplotype is ancestral in hominoids and under positive selection in European populations. The role of non-inverted orientation (H1 haplotype) and inverted orientation (H2) remains unclear, i.a. it is suggested that mothers who are H1H2 heterozygotes, tend to have more children than H2H2 homozygotes on average. Materials and methods: We investigated the prevalence of haplotypes of the 17q21 inversion in 154 women with pregnancy loss and 154 mothers with at last one live-born child, mean age: 33.0 (±5.4) y/o and 31.4 (±6.7) y/o, respectively. Following DNA extraction from buccal swabs, the genotyping was performed. All tests were performed using the R CRAN statistical software. Haplotypes were compared between groups. Results: In women with and without pregnancy loss we identified: 74.7% and 79.2% H1H1, 24.0% and 17.5% H1H2 and 1.3% and 3.3% H2H2 of haplotypes, respectively. There were no significant differences between the distributions of haplotypes in women with and without pregnancy loss. Statistically significant difference between the average number of children in women with H1H2 haplotype (navg. = 1.54) compared to women with H2H2 haplotype (navg. = 1.29), was not found. Conclusion: Haplotype H2 of the 17q21.31 inversion was not linked to pregnancy loss and number of children in Bosnian women.
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Vojvodic, Svetlana, Stevan Popovic i Lana Macukanovic-Golubovic. "Implications of HLA linkage disequilibrium phenomenon in finding unrelated volunteer bone marrow donors". Medical review 60, nr 3-4 (2007): 178–82. http://dx.doi.org/10.2298/mpns0704178v.
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Introduction. The distribution of HLA genes and haplotypes in the normal population is of considerable importance in disease susceptability studies, population and genetic studies and tissue and organ transplantation. The HLA phenotype frequencies can be used for the estimation of the probability of finding phenotypically identical unrelated volunteer bone marrow donors. It has been presumed that patients with HLA haplotypes in strong linkage disequilibrium, a have higher probability of finding HLA identical unrelated donors than others. Material and methods. HLA gene and haplotype frequencies were calculated, as well as delta values and their significance. The implications of HLA disequilibrium phenomenon in unrelated donor search, was investigated by calculating the correlation coefficient between frequencies of haplotypes showing significant delta values and the linkage disequilibrium coefficient, as well as between the average number of donors necessary for research. Results. Haplotypes showing the highest delta values are at the same time the most frequent haplotypes (A1B8:0,1188 and 0,145; A3B35:0,0722 and 0,1;A2B12:0,055 and 0,105). In patients who have both haplotypes showing significant delta values (e.g. A2B5/A3B35), the number of donors necessary for research is clearly lower than in patients who have only one given haplotype, or have no such haplotypes. Conclusion. Our results showed that patients with HLA haplotypes showing significant delta values have a higher probability of finding HLA identical unrelated donors. .
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Miege, Christine, Véronique Ruffio-Châble, Mikkel H. Schierup, Didier Cabrillac, Christian Dumas, Thierry Gaude i J. Mark Cock. "Intrahaplotype Polymorphism at the Brassica S Locus". Genetics 159, nr 2 (1.10.2001): 811–22. http://dx.doi.org/10.1093/genetics/159.2.811.
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Abstract The S locus receptor kinase and the S locus glycoproteins are encoded by genes located at the S locus, which controls the self-incompatibility response in Brassica. In class II self-incompatibility haplotypes, S locus glycoproteins can be encoded by two different genes, SLGA and SLGB. In this study, we analyzed the sequences of these genes in several independently isolated plants, all of which carry the same S haplotype (S2). Two groups of S2 haplotypes could be distinguished depending on whether SRK was associated with SLGA or SLGB. Surprisingly, SRK alleles from the two groups could be distinguished at the sequence level, suggesting that recombination rarely occurs between haplotypes of the two groups. An analysis of the distribution of polymorphisms along the S domain of SRK showed that hypervariable domains I and II tend to be conserved within haplotypes but to be highly variable between haplotypes. This is consistent with these domains playing a role in the determination of haplotype specificity.
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Budakva, Ye O. "Determination of the genetic structure of pro-maternal pig breeds of Irish selection using mitochondrial DNA markers". Animal Biology 24, nr 2 (czerwiec 2022): 3–8. http://dx.doi.org/10.15407/animbiol24.02.003.
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Traditionally, the mitochondrial genome is characterized as a “molecular clock” for tracking the history of phylogeny along the maternal line. Particular attention is paid to the distribution of mitochondrial DNA haplotypes among commercial pigs (Large White × Landrace) × Maxgro from RPE “Globinsky Pig Farm”, Globyno town, Poltava region, Ukraine. For the study of the genetic structure of the pigs’ hybrid markers of mitochondrial DNA — a maternal type of inheritance was used. DNA markers are a convenient tool for investigating the origin of pro-maternal pig breeds. Application of multiplex analysis PCR-RFLP (Polymerase chain reaction-restriction fragment length polymorphism) when examining the variable area of the D-loop between sites 15558–15917 mitochondrial genome of hybrid pigs made it possible to determine the pro-maternal haplotypes of the experimental sample (n=20). Thus, according to the multisite system developed by Pochernyaev K. F., determination of mitochondrial haplotypes of pigs, which are denoted by Latin letters from A to P allowed to determine the true pro-maternal haplotypes of the experimental sample of pigs (n=20), as evidenced by the presence of the Tas I website in the above-mentioned provisions what actually determine the haplotypes of mitochondrial DNA. According to the results of the study defined haplotypes characterize different breeds, namely 4 animals with haplotype C — Landrace (Ukraine, Poland). 6 pigs have mitochondrial haplotype N — Large White (Asian type) and 7 pigs with mitochondrial haplotype O — Landrace. 1 animal with haplotype G — wild pig and cross-border breed Wales (Italy). 2 representatives of haplotype D — not found among the breeds of domestic pigs. According to the established pro-maternal haplotypes of hybrid pigs, animals-carriers of haplotype O are representatives of Scandinavian female pigs F1 as used in uterine herds in Sweden and Ireland with the participation of the Maxgro terminal parent line in the hybridization system. Identified mitochondrial haplotypes were found to be breed-specific to hybrid pigs of Irish breeding, this is confirmed by the established polymorphism of the mitochondrial genome which is an objective marker even in complex hybridization schemes. The work was done with the support of the National Academy of Agrarian Sciences of Ukraine 31.01.00.07.F. “Investigate the pleiotropic effect gens that the SNP use in marker-associated pig breeding”. DR no. 0121U109838. Following the example of the developed systematization of the combination of restricted fragments by Pochernyaev K. F. in the future, I propose to create a database of reference haplotypes of mitochondrial DNA of pigs’ final hybrid. In the future, it will be used in further research to reconstruct the demographic history of commercial pigs of cross-border breeds.
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Howard, C. A., G. R. Gummere, M. F. Lyon, D. Bennett i K. Artzt. "Genetic and molecular analysis of the proximal region of the mouse t-complex using new molecular probes and partial t-haplotypes." Genetics 126, nr 4 (1.12.1990): 1103–14. http://dx.doi.org/10.1093/genetics/126.4.1103.
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Abstract The t-complex is located on the proximal third of chromosome 17 in the house mouse. Naturally occurring variant forms of the t-complex, known as complete t-haplotypes, are found in wild mouse populations. The t-haplotypes contain at least four nonoverlapping inversions that suppress recombination with the wild-type chromosome, and lock into strong linkage disequilibrium loci affecting normal transmission of the chromosome, male gametogenesis and embryonic development. Partial t-haplotypes derived through rare recombination between t-haplotypes and wild-type homologs have been critical in the analysis of these properties. Utilizing two new DNA probes. Au3 and Au9, and several previously described probes, we have analyzed the genetic structure of several partial t-haplotypes that have arisen in our laboratory, as well as several wild-type chromosomes deleted for loci in this region. With this approach we have been able to further our understanding of the structural and dynamic characteristics of the proximal region of the t-complex. Specifically, we have localized the D17Tul locus as most proximal known in t-haplotypes, achieved a better structural analysis of the partial t-haplotype t6, and defined the structure and lethal gene content of partial t-haplotypes derived from the lethal tw73 haplotype.
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Nejati-Javaremi, Ardeshir, i Charles Smith. "Assigning Linkage Haplotypes From Parent and Progeny Genotypes". Genetics 142, nr 4 (1.04.1996): 1363–67. http://dx.doi.org/10.1093/genetics/142.4.1363.
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Abstract Given the genotypes of parents and progeny, their haplotypes over several or many linked loci can be easily assigned by listing the allele type at each locus along the haplotype known to be from each parent. Only a small number (5-10) of progeny per family is usually needed to assign the parental and progeny haplotypes. Any gaps left in the haplotypes may be filled in from the assigned haplotypes of relatives. The process is facilitated by having multiple alleles at the loci and by using more linked loci in the haplotype and with more progeny from the mating. Crossover haplotypes in the progeny can be identified by their being unique or uncommon, and the crossover point can often be detected if the locus linkage map order is known. The haplotyping method applies to outbreeding populations in plants, animals and man, as well as to traditional experimental crosses of inbred lines. The method also applies to half-sib families, whether the genotypes of the mates are known or unknown. The haplotyping procedure is already used in linkage analysis but does not seem to have been published. It should be useful in teaching and in genetic applications of haplotypes.
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Kang, Won Sub, Su Kang Kim i Hae Jeong Park. "Association of the Promoter Haplotype of IFN-γ-Inducible Protein 16 Gene with Schizophrenia in a Korean Population". Psychiatry Investigation 17, nr 2 (25.02.2020): 140–46. http://dx.doi.org/10.30773/pi.2019.0175.
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Objective Viral infections play an important role in the development of schizophrenia, inducing the faulty immunological responses and aberrant inflammation. IFN-γ-inducible protein 16 (IFI16) is an immunological DNA sensor against viral infections, triggering the inflammatory responses. In this study, we investigated an association between putative promoter single nucleotide polymorphisms (SNPs) and haplotypes of IFI16 and schizophrenia.Methods A total of 280 schizophrenia patients and 427 control subjects were recruited in this study. We genotyped three promoter SNPs (rs1465175, rs3754464, rs1417806) using direct sequencing. Associations of SNPs and haplotypes of IFI16 with schizophrenia were analyzed. The promoter activities on the haplotypes of IFI16 were measured.Results The T allele of rs1465175 and the C allele of rs1417806 were protectively associated with schizophrenia (p=0.021 on rs1465175; p=0.016 on rs1417806), whereas the G allele of rs3754464 was associated with an increased risk of schizophrenia (p=0.019). In haplotype analysis, a significant association between the GGA haplotype and schizophrenia was shown (p=0.013). Moreover, we found that the GGA haplotype elevated the promoter activity compared to the GAA haplotype, whereas the TAC haplotype reduced that.Conclusion The promoter SNPs and haplotypes of IFI16 may contribute to the susceptibility of schizophrenia, affecting the promoter activity of IFI16.
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Dahan, Jennifer, Erik J. Wenninger, Brandon D. Thompson, Sahar Eid, Nora Olsen i Alexander V. Karasev. "Prevalence of ‘CandidatusLiberibacter solanacearum’ Haplotypes in Potato Tubers and Psyllid Vectors in Idaho From 2012 to 2018". Plant Disease 103, nr 10 (październik 2019): 2587–91. http://dx.doi.org/10.1094/pdis-11-18-2113-re.
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‘Candidatus Liberibacter solanacearum’ (Lso) is an uncultured, phloem-associated bacterium causing a severe tuber disease in potato called zebra chip (ZC). Seven haplotypes of Lso have been described in different hosts, with haplotypes A and B found associated with infections in potato and tomato. In the field, Lso is transmitted by the potato psyllid (Bactericera cockerelli), and between 2011 and 2015, a significant change in Lso haplotype prevalence was previously reported in Idaho: from exclusively A haplotype found in tested psyllids in 2012 to mainly B haplotype found in collected psyllids in 2015. However, prevalence of Lso haplotypes in Idaho was not analyzed in potato tubers exhibiting symptoms of ZC. To fill in this knowledge gap, prevalence of Lso haplotypes was investigated in potato tubers harvested in southern Idaho between 2012 and 2018, and it was found to change from exclusively A haplotype in the 2012 season to an almost equal A and B haplotype distribution during the 2016 season. During the same period, haplotype distribution of Lso in psyllid vectors collected using yellow sticky traps also changed, but in psyllids, the shift from A haplotype of Lso to B haplotype was complete, with no A haplotype detected in 2016 to 2018. The changes in the haplotype prevalence of the Lso circulating in potato fields in southern Idaho may be, among other factors, responsible for a decrease in the ZC incidence in Idaho potato fields between an outbreak of the disease in 2012 and a very low level of ZC afterward.
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Bhattacharyya, Nitai Pada, Priyadarshi Basu, Madhusudan Das, Srimanta Pramanik, Rajat Banerjee, Bidyut Roy, Susanta Roychoudhury i Partha P. Majumder. "Negligible Male Gene Flow Across Ethnic Boundaries in India, Revealed by Analysis of Y-Chromosomal DNA Polymorphisms". Genome Research 9, nr 8 (1.08.1999): 711–19. http://dx.doi.org/10.1101/gr.9.8.711.
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From the historically prevalent social structure of Indian populations it may be predicted that there has been very little male gene flow across ethnic boundaries. To test this finding, we have analyzed DNA samples of individuals belonging to 10 ethnic groups, speaking Indo-European or Austroasiatic languages and inhabiting the eastern and northern regions of India. Eight Y-chromosomal markers, two biallelic and six microsatellite, were studied. All populations were monomorphic for the deletion allele at the YAP (DYS287) locus and for the 119-bp allele at the DYS288 locus. Y-chromosomal haplotypes were constructed on the basis of one RFLP locus and five microsatellite loci. The haplotype distribution among the groups showed that different ethnic groups harbor nearly disjoint sets of haplotypes. This indicates that there has been virtually no male gene flow among ethnic groups. Analysis of molecular variance revealed that there was significant haplotypic variation between castes and tribes, but nonsignificant variation among ranked caste clusters. Haplotypic variation attributable to differences in geographical regions of habitat was also nonsignificant.
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Domuschiev, I. P., T. L. Kuraeva, A. S. Sergeyev, V. V. Yazdovsky, L. N. Denisov, V. P. Maximova, O. M. Smirnova i G. A. Romanovskaya. "Analysis of nuclear families with two and more diabetic siblings with insulin dependent condition". Problems of Endocrinology 40, nr 5 (15.12.1994): 11–13. http://dx.doi.org/10.14341/probl12157.
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HLA haplotype distribution was analyzed in nuclear families of patients with insulin-dependent diabetes mellitus. Sixteen families with two or more diabetic siblings were examined, a total of 69 subjects, 33 of these diabetic siblings and 36 normal subjects (siblings and parents). The data were processed using the involved sibling pairs method based on a mixed model making use of a conditional probability approach. The ratio of diabetic sibling pairs concordant by 2 haplotypes, 1 haplotype, and discordant by 2 haplotypes was 9:5:2 vs. 1:2:1 expected according to Mendels accidental distribution (p 0.025). Increased incidence of siblings concordant by 2 haplotypes proves the presence in the HLA domain of one or several genes responsible for the development of diabetes mellitus. Siblings identical by two HLA haplotypes with the diabetic proband are at a higher risk of developing this disease.
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Dimaki, Maria, Anna Hundsdörfer i Uwe Fritz. "Eastern Mediterranean chameleons (Chamaeleo chamaeleon, Ch. africanus) are distinct". Amphibia-Reptilia 29, nr 4 (2008): 535–40. http://dx.doi.org/10.1163/156853808786230415.
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AbstractBased on mitochondrial 16S rRNA sequences, we suggest that the founder individuals of the introduced Greek population of Chamaeleo africanus originated in the Nile Delta region of Egypt. In Ch. chamaeleon, we discovered in the eastern Mediterranean new 16S rRNA haplotypes, being highly distinct from previously published western Mediterranean haplotypes. Eastern Mediterranean haplotypes were found in samples from northern Syria, Cyprus, Crete, Samos, Malta and Tunisia. The occurrence of an eastern Mediterranean haplotype in Tunisia and of distinct haplotypes in Morocco could argue for a phylogeographic break in northwestern Africa.
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Cronin, Matthew A., William J. Spearman, Richard L. Wilmot, John C. Patton i John W. Bickham. "Mitochondrial DNA Variation in Chinook (Oncorhynchus tshawytscha) and Chum Salmon (O. keta) Detected by Restriction Enzyme Analysis of Polymerase Chain Reaction (PCR) Products". Canadian Journal of Fisheries and Aquatic Sciences 50, nr 4 (1.04.1993): 708–15. http://dx.doi.org/10.1139/f93-081.
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We analyzed intraspecific mitochondrial DNA variation in chinook salmon (Oncorhynchus tshawytscha) from drainages in the Yukon River (Alaska and Yukon Territory), the Kenai River (Alaska), and Oregon and California rivers; and chum salmon (O. keta) from the Yukon River and Vancouver Island, and Washington rivers. For each species, three different portions of the mtDNA molecule were amplified separately using the polymerase chain reaction and then digested with at least 19 restriction enzymes. Intraspecific sequence divergences between haplotypes were less than 0.01 base substitution per nucleotide. Nine chum salmon haplotypes were identified. Yukon River chum salmon stocks displayed more haplotypes (eight) than the stocks of Vancouver Island and Washington (two). The most common chum salmon haplotype occurred in all areas. Seven chinook salmon haplotypes were identified. Four haplotypes occurred in the Yukon and Kenai rivers and four occurred in Oregon/California, with only one haplotype shared between the regions. Sample sizes were too small to quantify the degree of stock separation among drainages, but the patterns of variation that we observed suggest utility of the technique in genetic stock identification.
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Dumaidi, Kamal, Hayah Qaraqe, Amer Al-Jawabreh, Rasmi Abu-Helu, Fekri Samarah i Hanan Al-Jawabreh. "Genetic diversity, haplotype analysis, and risk factor assessment of hepatitis A virus isolates from the West Bank, Palestine during the period between 2014 and 2016". PLOS ONE 15, nr 12 (11.12.2020): e0240339. http://dx.doi.org/10.1371/journal.pone.0240339.
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Background Hepatitis A virus (HAV) infection is one of the major causes of acute viral hepatitis. HAV genotypes and its genetic diversity is rarely investigated in our region as well as worldwide. Aims The aims of the present study were to determine the HAV genotypes and its risk factors and to investigate the genetic diversity of the HAV isolates in the West Bank, Palestine. Study design A cohort of 161 clinically and laboratory-confirmed HAV (IgM-positive) cases and 170 apparently healthy controls from all the districts of the West Bank, Palestine during the period of 2014 to 2016 were tested for HAV infection using IgM antibodies, RT-PCR and sequence analysis of the VP3/VP1 junction region of the HAV genome. Phylogenetic analysis, genetic diversity and haplotypes analysis were used to characterize the VP3/VP1 sequences. Results All the 34 sequences of the HAV were found to be of HAV-IB sub-genotype. The phylogenetic analysis showed four main clusters with cluster III exclusively consisting of 18 Palestinian isolates (18/23-78%), but with weak bootstrap values. A high haplotype diversity (Hd) and low nucleotide diversity (π) were observed. Cluster III showed high number of haplotypes (h = 8), but low haplotype (gene) diversity (Hd = 0.69). A total of 28 active haplotypes with some consisting of more than one sequence were observed using haplotype network analysis. The Palestinian haplotypes are characterized by closely related viral haplotypes with one SNV away from each other which ran parallel to cluster III in the phylogenetic tree. A smaller Palestinian haplotype (4 isolates) was three SNVs away from the major haplotype cluster (n = 10) and closer to others haplotypes from Iran, Spain, and South Africa. Young age, low level of parent’s education, infrequent hand washing before meals, and drinking of un-treated water were considered the major HAV risk factors in the present study. Conclusion Haplotype network analysis revealed haplotype variation among the HAV Palestinian sequences despite low genetic variation and nucleotide diversity. In addition, this study reconfirmed that age and parent’s level of education as HAV risk factors, while hand washing and treating drinking water as protective factors.
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Santos, Daniel Wagner C. L., Vania Aparecida Vicente, Vinicius Almir Weiss, G. Sybren de Hoog, Renata R. Gomes, Edith M. M. Batista, Sirlei Garcia Marques, Flávio de Queiroz-Telles, Arnaldo Lopes Colombo i Conceição de Maria Pedrozo e. Silva de Azevedo. "Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network". Journal of Fungi 6, nr 4 (3.10.2020): 204. http://dx.doi.org/10.3390/jof6040204.
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Chromoblastomycosis (CBM) is a neglected implantation mycosis prevalent in tropical climate zones, considered an occupational disease that affects impoverished rural populations. This retrospective study described clinical aspects of CBM in a hyperendemic area in Brazil and constructed a worldwide haplotype network of Fonsecaea spp. strains. The variables were collected from medical records using a standard report form, reporting 191 patients with CBM from Maranhão, Brazil. The mean age was 56.1 years, 168 (88%) patients were male and predominantly farmers (85.8%). The mean time of evolution of the disease until diagnosis was 9.4 years. Lower limbs (81.2%) and upper limbs (14.2%) were the main sites affected. Most patients exhibited verrucous (55%) and infiltrative plaque (48.2%). Fonsecaea spp. were identified in 136 cases and a haplotype network constructed with ITS sequences of 185 global strains revealed a total of 59 haplotypes exhibiting high haplotypic and low nucleotide diversities. No correlation was observed between the different haplotypes of Fonsecaea species and dermatological patterns, severity of disease or geographic distribution inside Maranhão. Data from this area contributed to better understanding the epidemiology of CBM. For the first time, a robust haplotype network with Fonsecaea strains reveals an evolutionary history with a recent population expansion.
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Chen, Wendi, Bin Zhang, Wenjing Ren, Li Chen, Zhiyuan Fang, Limei Yang, Mu Zhuang, Honghao Lv, Yong Wang i Yangyong Zhang. "An Identification System Targeting the SRK Gene for Selecting S-Haplotypes and Self-Compatible Lines in Cabbage". Plants 11, nr 10 (21.05.2022): 1372. http://dx.doi.org/10.3390/plants11101372.
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Cabbage (Brassica oleracea L. var. capitata) self-incompatibility is important for heterosis. However, the seed production of elite hybrid cannot be facilitated by honey bees due to the cross-incompatibility of the two parents. In this study, the self-compatibility of 58 winter cabbage inbred lines was identified by open-flower self-pollination (OS) and molecular techniques. Based on the NCBI database, a new class I S-haplotype-specific marker, PKC6F/PKC6R, was developed. Verification analyses revealed 9 different S-haplotypes in the 58 cabbage inbred lines; of these lines, 46 and 12 belonged to class I (S6, S7, S12, S14, S33, S45, S51, S68) and class II (S15) S-haplotypes, respectively. The coincidence rate between the self-compatibility index and S-haplotype was 91%. This study developed a Tri-Primer-PCR amplification method to rapidly select plants with specific S-haplotypes in biased segregated S-locus populations. Furthermore, it established an S-haplotype identification system based on these nine S-haplotypes. To overcome parental cross-incompatibility (18-503 and 18-512), an inbred line (18-2169) with the S15 haplotype was selected from the sister lines of self-incompatible 18-512 (S68, class I S-haplotype). The inbred line (18-2169) showed self-compatibility and cross-compatibility with 18-503. This study provides guidance for self-compatibility breeding in cabbage and predicts parental cross-incompatibility in elite combinations.
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Eskdale, Joyce, Grant Gallagher, Cor L. Verweij, Vivian Keijsers, Rudi G. J. Westendorp i Tom W. J. Huizinga. "Interleukin 10 secretion in relation to human IL-10 locus haplotypes". Proceedings of the National Academy of Sciences 95, nr 16 (4.08.1998): 9465–70. http://dx.doi.org/10.1073/pnas.95.16.9465.
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Stimulation of human blood cultures with bacterial lipopolysaccharide (LPS) shows large inter-individual variation in interleukin 10 (IL-10) secretion, which has been shown to have a genetic component of over 70%. Alleles at two microsatellite loci in the 4 kb immediately upstream of the human IL-10 transcription initiation site in 132 individuals from 56 Dutch families were defined and assigned as haplotypes. LPS-induced IL-10 secretion was measured by ELISA and related to the IL-10 promoter haplotypes present in 78 unrelated individuals obtained from these families. Analysis showed that LPS-induced IL-10 secretion from unrelated individuals varied with IL-10 promoter haplotypes (P= 0.024; Kruskal-Wallis test). Two observations were made in relation to secreted IL-10 levels and promoter haplotypes; first, those haplotypes containing the allele IL10.R3 were associated with lower IL-10 secretion than haplotypes containing any other IL10.R allele. Second, the haplotype IL10.R2/IL10.G14 was associated with highest IL-10 secretion overall, whereas the haplotype IL10.R3/IL10.G7 was associated with lowest IL-10 secretion. These data demonstrate that the ability to secrete IL-10 can vary in man according to the genetic composition of the IL-10 locus.
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Phillips, D. V., I. Carbone, S. E. Gold i L. M. Kohn. "Phylogeography and Genotype-Symptom Associations in Early and Late Season Infections of Canola by Sclerotinia sclerotiorum". Phytopathology® 92, nr 7 (lipiec 2002): 785–93. http://dx.doi.org/10.1094/phyto.2002.92.7.785.
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Both typical late season stem infections and atypical early season rosette infections of canola, a relatively new crop in the southeastern United States, were caused by Sclerotinia sclerotiorum. The 51 DNA fingerprints (from 71 isolates) did not match any fingerprints from previous studies of canola or other crops. Single locus haplotypes from nuclear DNA sequences included 18 in the intergenic spacer (IGS) of the rRNA repeat, four in 44.11, six in translation elongation factor 1α, three in calmodulin (CAL), and two in chitin synthase 1. Contingency permutation testing for associations of infection type with DNA fingerprint, single- or multilocus haplotype, or hierarchically nested clades based on single locus haplotypes found significant association of haplotype with mycelial compatibility group and DNA fingerprint for all loci except CAL. Significant association of IGS haplotypes with symptom type was detected in one pathogen population. Southeastern U.S. canola was infected by both recently evolved, geographically dispersed pathogen genotypes and older, indigenous genotypes (Carbone and Kohn, 2001. Mol. Ecol. 10:947–964). Indigenous haplotypes are infection-type generalists, and the most frequently isolated from rosette infections. In contrast, haplotypes from the most recently evolved, dispersed population were associated one-to-one with infection type, with only the most recently evolved haplotypes infecting rosettes.
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Shaver, Bradly R., Sergio Marchant, S. Bruce Martin i Paula Agudelo. "18S rRNA and COI haplotype diversity of Trichodorus obtusus from turfgrass in South Carolina". Nematology 18, nr 1 (2016): 53–65. http://dx.doi.org/10.1163/15685411-00002944.
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The stubby-root nematode, Trichodorus obtusus, was recently identified on zoysiagrass in South Carolina, USA. In Florida, T. obtusus causes more damage than other stubby-root nematodes encountered in turfgrass. The objective of this study was to use morphological analysis, mitochondrial DNA (COI: cytochrome oxidase 1) and nuclear (18S rRNA) sequence data to study the genetic structure and haplotype diversity of populations recovered from turfgrasses in South Carolina. Numerous morphological differences were observed among populations. Three 18S haplotypes were shared among South Carolina and Florida populations, and six mitochondrial haplotypes were identified in South Carolina samples. Of the six COI haplotypes, four haplotypes were restricted to one population from St Augustinegrass. The lowest haplotype diversity was found in samples from zoysiagrass. Sequences of the COI mtDNA gene of T. obtusus were published in GenBank and represent the first mtDNA sequences for the genus Trichodorus.
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Hurley, C. K., P. Gregersen, N. Steiner, J. Bell, R. Hartzman, G. Nepom, J. Silver i A. H. Johnson. "Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination." Journal of Immunology 140, nr 3 (1.02.1988): 885–92. http://dx.doi.org/10.4049/jimmunol.140.3.885.
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Abstract The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a serologically undefined DQ allelic product. DNA restriction fragment analysis with the use of several unrelated individuals and an informative family has allowed us to identify unique DQ alpha- and beta-fragments associated with the DR3, DQw- haplotype. Based on fragment size, the DQ alpha genes of the DR3, DQw- and DRw8, DQw- haplotypes are similar as are the DQ beta genes of DR3, DQw-; DRw8, DQw-; and DR4, DQw- haplotypes. In addition, a DX beta gene polymorphism has been identified which is associated with some DR3 haplotypes including the American black DR3, DQw- haplotype. cDNA sequence analysis has revealed a DQw2-like alpha gene and a DQ beta gene which is similar to that previously described for a DR4, DQw- haplotype. It is postulated that recombination between DQ alpha and DQ beta genes and between the DQ and DX subregions has generated the various DR3 haplotypes and has played an important role in creating diversity in the HLA-D region.