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Journal articles on the topic 'Haplotype analysi'

Author: Grafiati

Published: 11 March 2023

Last updated: 31 July 2025

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1

Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, et al. "Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey." Pathogens 11, no. 5 (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

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Epifanio, John M., Bonnie L. Brown, Peter E. Smouse, and 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, no. 8 (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 resolut

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Santos, Daniel Wagner C. L., Vania Aparecida Vicente, Vinicius Almir Weiss, et al. "Chromoblastomycosis in an Endemic Area of Brazil: A Clinical-Epidemiological Analysis and a Worldwide Haplotype Network." Journal of Fungi 6, no. 4 (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 o

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Kaul, Noyonika, Prem Lal Kashyap, Sudheer Kumar, Deepti Singh, and 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, no. 8 (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), Pu

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Bhattacharyya, Nitai Pada, Priyadarshi Basu, Madhusudan Das, et al. "Negligible Male Gene Flow Across Ethnic Boundaries in India, Revealed by Analysis of Y-Chromosomal DNA Polymorphisms." Genome Research 9, no. 8 (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 haplot

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Quan Ke Thai, Tuan Thanh Nguyen, and Hien Thi Thanh Pham. "mtDNA haplotype network analysis: Exploring genetic relationships and diversity in dog haplogroups." GSC Biological and Pharmaceutical Sciences 24, no. 1 (2023): 224–32. http://dx.doi.org/10.30574/gscbps.2023.24.1.0284.

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The genetic diversity and relationships of dog haplogroups were studied by analyzing the HV1 region of mitochondrial DNA. Previous studies have found six distinct haplogroups (A, B, C, D, E, and F) in dogs. Haplogroups A, B, and C were widely distributed, while haplogroups D, E, F were rare and distributed in restricted regions. In this study, HV1 sequences from global dog populations were collected, categorized into haplotypes, and used to construct haplotype networks. The results showed that haplogroup A was the most prevalent, comprising approximately 72.34% of dogs worldwide. Haplogroups A

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Quan, Ke Thai, Thanh Nguyen Tuan, and Thi Thanh Pham Hien. "mtDNA haplotype network analysis: Exploring genetic relationships and diversity in dog haplogroups." GSC Biological and Pharmaceutical Sciences 24, no. 1 (2023): 224–32. https://doi.org/10.5281/zenodo.8265409.

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The genetic diversity and relationships of dog haplogroups were studied by analyzing the HV1 region of mitochondrial DNA. Previous studies have found six distinct haplogroups (A, B, C, D, E, and F) in dogs. Haplogroups A, B, and C were widely distributed, while haplogroups D, E, F were rare and distributed in restricted regions. In this study, HV1 sequences from global dog populations were collected, categorized into haplotypes, and used to construct haplotype networks. The results showed that haplogroup A was the most prevalent, comprising approximately 72.34% of dogs worldwide. Haplogroups A

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Vathipadiekal, Vinod, Abdulrahman Alsultan, John Farrell, et al. "Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators." Blood 126, no. 23 (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 hap

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Tjensvoll, Kjersti, Ove Bruland, Ylva Floderus, Øyvind Skadberg, Sverre Sandberg, and Jaran Apold. "Haplotype Analysis of Norwegian and Swedish Patients with Acute Intermittent Porphyria (AIP): Extreme Haplotype Heterogeneity for the Mutation R116W." Disease Markers 19, no. 1 (2003): 41–46. http://dx.doi.org/10.1155/2003/384971.

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Acute intermittent porphyria (AIP), the most common of the acute porphyrias, is caused by mutations in the gene encoding hydroxymethylbilane synthase (HMBS) also called porphobilinogen deaminase (PBGD). The mutation spectrum in the HMBS gene is characterized by a majority of family specific mutations. Among the exceptions are R116W and W198X, with high prevalence in both the Dutch and Swedish populations. These two mutations were also detected in unrelated Norwegian patients. Thus, Norwegian and Swedish patients were haplotyped using closely linked flanking microsatellites and intragenic singl

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TAN, QIHUA, LENE CHRISTIANSEN, KAARE CHRISTENSEN, et al. "Haplotype association analysis of human disease traits using genotype data of unrelated individuals." Genetical Research 86, no. 3 (2005): 223–31. http://dx.doi.org/10.1017/s0016672305007792.

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Haplotype inference has become an important part of human genetic data analysis due to its functional and statistical advantages over the single-locus approach in linkage disequilibrium mapping. Different statistical methods have been proposed for detecting haplotype – disease associations using unphased multi-locus genotype data, ranging from the early approach by the simple gene-counting method to the recent work using the generalized linear model. However, these methods are either confined to case – control design or unable to yield unbiased point and interval estimates of haplotype effects

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Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, et al. "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. sagina

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Pae, C. U. "Association Analysis of Heat Shock Protein 70 Gene Polymorphisms in Schizophrenia." European Psychiatry 24, S1 (2009): 1. http://dx.doi.org/10.1016/s0924-9338(09)71415-4.

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Objectives:This study investigated the association between an enlarged set of SNPs at Heat shock proteins (HSPs) 70 gene and schizophrenia.Methods:Two hundred and ninety four patients with schizophrenia and 287 controls were enrolled in the study. Genotypings of 5 SNPs of HSP70 were performed using pyrosequencing method.Results:Significant association was detected at rs2075799 (allele A, Chi suare =8.03, d.f.=1 p=0.0046), but not at rs2227956 (p=0.28), rs1043618 (p=0.88), rs562047 (p=0.47) or rs539689 (p=0.32). in fact, the rs2075799*G/A genotype was more represented in patients with schizophr

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Excoffier, L., P. E. Smouse, and J. M. Quattro. "Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data." Genetics 131, no. 2 (1992): 479–91. http://dx.doi.org/10.1093/genetics/131.2.479.

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Abstract We present here a framework for the study of molecular variation within a single species. Information on DNA haplotype divergence is incorporated into an analysis of variance format, derived from a matrix of squared-distances among all pairs of haplotypes. This analysis of molecular variance (AMOVA) produces estimates of variance components and F-statistic analogs, designated here as phi-statistics, reflecting the correlation of haplotypic diversity at different levels of hierarchical subdivision. The method is flexible enough to accommodate several alternative input matrices, corresp

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Triandiza, Teddy, Risnita Tri Utami, and Rosmi Nuslah Pesilette. "Karakterisasi Morfometri dan DNA Barcoding Keong Lola Merah (Rochia nilotica Linnaeus, 1767) dari Kepulauan Kei, Maluku." Jurnal Kelautan Tropis 27, no. 3 (2024): 451–65. https://doi.org/10.14710/jkt.v27i3.24411.

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The lola snail (Rochia nilotica) is an herbivorous gastropod that lives in coral reef ecosystems. R. nilotica is an ecologically important species and has high economic value. This study aims to assess morphometric characterization and DNA barcoding. Analysis of growth patterns shows that red lola snails in the Kei Islands show an allometric growth pattern. Analysis of R. nilotica mitochondrial DNA (mtDNA) sequences resulted in 646 base pairs, containing 14 haplotypes with a total of 18 polymorphic sites. The results showed that the genetic diversity of R. nilotica populations in the Kei Islan

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15

Adabale, Abosede, Samira Batista Lobo Makanjuola, Akinsegun Akinbami, et al. "Frequency of beta S globin gene haplotypes among sickle cell patients in Nigeria." Journal of International Medical Research 49, no. 6 (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 Senega

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Sebastiani, Paola, John J. Farrell, Shuai Wang, et al. "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, no. 21 (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 +

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Sugiura, Nami, Dingqin Tang, Hiroyuki Kurokochi, Yoko Saito, and Yuji Ide. "Genetic structure of Quercus gilva Blume in Japan as revealed by chloroplast DNA sequences." Botany 93, no. 12 (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 cros

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Y.P.B.C., Widyatmoko Anthonius, and Susumu Shiraishi. "GEOGRAPHIC VARIATION OF CHLOROPLAST DNA HAPLOTYPES IN Acacia aulacocarpa A. Cunn. ex Benth." JOURNAL OF FORESTRY RESEARCH 10, no. 1 (2013): 43–56. https://doi.org/10.20886/ijfr.2013.10.1.43-56.

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The geographic  variation  of chloroplast  DNA (cpDNA)  haplotypes  of Acacia aulacocar pa was investigated among 18 natural populations. These populations represent the geographical range of the species in New Guinea Island and Queensland. Single strand conformation polymorphism (SSCP) was used for the analysis. Two non-coding regions of cpDNA, the intron region of the trnL gene and the intergenic spacer region between the trnP and trnW genes, were analyzed, and four haplotypes (A, B, C, and D) were recognized. The haplotype distribution corresponded with the geograph

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Dumaidi, Kamal, Hayah Qaraqe, Amer Al-Jawabreh, Rasmi Abu-Helu, Fekri Samarah, and 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, no. 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 teste

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Yuliwulandari, Rika, and Katsushi Tokunaga. "Nasopharyngeal Carcinoma (NPC) Related Human Leukocyte Antigen (HLA) Haplotype Sharing among Southern East Asian Population." Global Medical & Health Communication (GMHC) 5, no. 1 (2017): 1. http://dx.doi.org/10.29313/gmhc.v5i1.1989.

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AbstractThe human leukocyte antigens (HLAs) play important roles in the immune systems to response to various pathogens and disease among individuals. The aim of this study was analyze the HLA allele and haplotype frequencies of Southern East Asian population that show high incidence of nasopharyngeal carcinoma (NPC) to evaluate the shared HLA haplotype contribution to NPC susceptibility among the population and analyses the genetic affinities between the population. We collect information of HLA haplotype from our previous study, other published paper, and HLA database in 19 population during

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Damen, Manon, Mascha Schijvenaars, Marlies Schimmel-Naber, Johanne Groothuismink, Marieke Coenen, and Alide Tieleman. "Ancestral Origin of the First Indian Families with Myotonic Dystrophy Type 2." Journal of Neuromuscular Diseases 8, no. 4 (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 o

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Sehgal, D., and S. Dreisigacker. "Haplotypes-based genetic analysis: benefits and challenges." Vavilov Journal of Genetics and Breeding 23, no. 7 (2019): 803–8. http://dx.doi.org/10.18699/vj19.37-o.

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The increasing availability of Single Nucleotide Polymorphisms (SNPs) discovered by Next Generation Sequencing will enable a range of new genetic analyses in crops, which was not possible before. Concomitantly, researchers will face the challenge of handling large data sets at the whole-genome level. By grouping thousands of SNPs into a few hundred haplotype blocks, complexity of the data can be reduced with fewer statistical tests and a lower probability of spurious associations. Owing to the strong genome structure present in breeding lines of most crops, the deployment of haplotypes could b

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Domuschiev, I. P., T. L. Kuraeva, A. S. Sergeyev, et al. "Analysis of nuclear families with two and more diabetic siblings with insulin dependent condition." Problems of Endocrinology 40, no. 5 (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

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Soberanes-Yepiz, Maritza L., Miriam V. Martín-Manzo, Marcel Martínez-Porchas, et al. "Diversity and genetic structure of <i>Macrobrachium americanum </i>(Bate, 1868) in two geographical areas of Mexico." Revista MVZ Córdoba 30, no. 2 (2025): e3388. https://doi.org/10.21897/rmvz.3388.

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Objetive. Analyze the population genetic with mitochondrial molecular markers (16S mtDNA and COI mtDNA) on the river prawn Macrobrachium americanum, in two different geographic areas of Mexico: Baja California Sur (San Pedro de la Presa and Guamuchil basins) and Guerrero (Aguas Blancas River). Materials and Methods. We calculated the number of haplotypes (H), haplotype diversity (Hd), nucleotide diversity (π), and the number of nucleotide differences (k) for each sampling site using the program Dnasp. To calculate the two phylogenetic networks (COI and 16s rDNA), we used the median-joining imp

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Wang, Dan, Yu Huang, Lu Rui, et al. "Population Genetic Analysis of Paris polyphylla var. yunnanensis Based on cpDNA Fragments." Genes 14, no. 9 (2023): 1754. http://dx.doi.org/10.3390/genes14091754.

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Paris polyphylla var. yunnanensis is a well-known medicinal plant that is mainly distributed in Southwest China; however, its genetic diversity and biodiversity processes are poorly understood. In this study, the sequences of cpDNA trnL-trnF fragments of 15 wild populations and 17 cultivated populations of P. polyphylla var. yunnanensis were amplified, sequenced, and aligned to study the population genetics of this species. Genetic diversity was analyzed based on nucleotide diversity, haplotype diversity, Watterson diversity, population-level diversity, and species-level genetic diversity. Gen

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Martin, F. N., and M. D. Coffey. "Mitochondrial Haplotype Analysis for Differentiation of Isolates of Phytophthora cinnamomi." Phytopathology® 102, no. 2 (2012): 229–39. http://dx.doi.org/10.1094/phyto-04-11-0115.

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Although Phytophthora cinnamomi is heterothallic, there are few instances of successful crossing in laboratory experiments, and analysis of field populations indicates a clonally reproducing population. In the absence of sexual recombination, the ability to monitor mitochondrial haplotypes may provide an additional tool for identification of clonal isolates and analysis of population structure. To determine mitochondrial haplotypes for this species, seven mitochondrial loci spanning a total of 6,961 bp were sequenced for 62 isolates representing a geographically diverse collection of isolates

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Vadva, Larsen, Propp, Trautwein, Alford, and Alper. "A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies." Cells 8, no. 8 (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 ra

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Knoll, Aleš, Lucie Langová, Antonín Přidal, and Tomáš Urban. "Haplotype Diversity in mtDNA of Honeybee in the Czech Republic Confirms Complete Replacement of Autochthonous Population with the C Lineage." Insects 15, no. 7 (2024): 495. http://dx.doi.org/10.3390/insects15070495.

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The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identifie

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Subagiyo, Subagiyo, Retna Handayani, and Rahayu Rahayu. "Identifikasi dan Analisis Filogenetik Portunus trituberculatus Dari Perairan Cirebon Menggunakan Barkode Gen COI Mitokondrial." Jurnal Kelautan Tropis 21, no. 2 (2018): 111. http://dx.doi.org/10.14710/jkt.v21i2.3091.

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Phylogenetic Identification and Analysis Portunus trituberculatus from Cirebon Coast Using the COI Barcode Mitochondrial Portunus trituberculatus spesimen from Cirebon coast were successfully identified using mitochondrial DNA cytochrome c oxydase subunit I (COI) genes. Analysis of haplotype distribution of P. trituberculatus along with the same species from China, Korea, India and the Philippines obtained from NCBI gene banks resulted 17 haplotypes from 25 specimens. Haploid diversity was 0.943 + 0.031 and nucleotide diversity was 0.04821 + 0.0139. The Cirebon specimen is in separated haploti

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Emam, Ahmed Mostafa, Sandra Afonso, Pedro González-Redondo, et al. "Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis." World Rabbit Science 28, no. 2 (2020): 93. http://dx.doi.org/10.4995/wrs.2020.12219.

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<p>Mitochondrial DNA (mtDNA) and cytochrome b (cyt b) gene sequences were used to determine the status of genetic diversity and phylogeny for 132 individuals from local rabbit breeds in Egypt and Spain. The Egyptian local rabbit breeds were Egyptian Red Baladi (ERB), Egyptian Black Baladi (EBB) and Egyptian Gabali Sinai (EGS). However, the Spanish local rabbit breed was Spanish common rabbit (SCR). Previous breeds were compared with European Wild Rabbit taken from Albacete, Spain (EWR). A total of 353 mutations, 290 polymorphic sites, 14 haplotypes, 0.06126 haplotype diversity and -1.900

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Kang, Won Sub, Su Kang Kim та Hae Jeong Park. "Association of the Promoter Haplotype of IFN-γ-Inducible Protein 16 Gene with Schizophrenia in a Korean Population". Psychiatry Investigation 17, № 2 (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, r

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Strucken, E. M., S. Rahmatalla, D. J. De Koning, and G. A. Brockmann. "Haplotype analysis and linkage disequilibrium for <i>DGAT1</i>." Archives Animal Breeding 53, no. 3 (2010): 247–55. http://dx.doi.org/10.5194/aab-53-247-2010.

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Abstract. This study focused on haplotype effects and linkage disequilibrium (LD) for the K232A locus and the promoter VNTR in the DGAT1 gene. Analyses were carried out in three German Holstein Frisian populations (including 492, 305, and 518 animals) for milk yield, milk fat and protein yield, and milk fat and protein content. We found that effects of the promoter VNTR were not significant and explain only a small amount of the variation of the QTL on BTA14. Haplotype effects were less significant than the K232A locus by itself, but the haplotype containing the A allele of the K232A locus and

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Cao, Chang-Chang, and Xiao Sun. "Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information." Journal of Bioinformatics and Computational Biology 14, no. 04 (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 tra

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Hurley, C. K., P. Gregersen, N. Steiner, et al. "Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination." Journal of Immunology 140, no. 3 (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 t

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Vojvodić, Svetlana, and D. Ademović-Sazdanić. "KIR And HLA Haplotype Analysis in a Family Lacking The KIR 2DL1-2DP1 Genes." Balkan Journal of Medical Genetics 18, no. 1 (2015): 55–64. http://dx.doi.org/10.1515/bjmg-2015-0006.

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Abstract The killer cell immunoglobulin-like receptor (KIR) gene cluster exhibits extensive allelic and haplotypic diversity that is observed as presence/absence of genes, resulting in expansion and contraction of KIR haplotypes and by allelic variation of individual KIR genes. We report a case of KIR pseudogene 2DP1 and 2DL1 gene absence in members of one family with the children suffering from acute myelogenous leukemia (AML). Killer cell immunoglo-bulin-like receptor low resolution genotyping was performed by the polymerase chain reaction (PCR)-sequencespecific primers (SSP)/sequence-specif

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Gtari, Maher, Daniele Daffonchio, and Abdellatif Boudabous. "Assessment of the genetic diversity ofFrankiamicrosymbionts ofElaeagnus angustifoliaL. plants growing in a Tunisian date-palm oasis by analysis of PCR amplifiednifD-Kintergenic spacer." Canadian Journal of Microbiology 53, no. 3 (2007): 440–45. http://dx.doi.org/10.1139/w06-139.

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Diversity of Frankia microsymbionts of non-native Elaeagnus angustifolia L. plants spontaneously growing in a Tunisian desertic retreat area, the date-palm oasis of Tozeur, was investigated by polymerase chain reaction – restriction fragment length polymorphism (PCR–RFLP) and PCR-sequencing techniques targeting the nifD-K intergenic spacer. Three PCR–RFLP haplotypes (I, II, and III) were detected among collected nodules. Haplotype I was detected at all five sampling sites and dominated the other haplotypes present at these sites. This haplotype was also exhibited by strain BMG5.10, which was i

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Barnekow, Elin, Wen Liu, Hafdis T. Helgadottir, et al. "A Swedish Genome-Wide Haplotype Association Analysis Identifies a Novel Breast Cancer Susceptibility Locus in 8p21.2 and Characterizes Three Loci on Chromosomes 10, 11 and 16." Cancers 14, no. 5 (2022): 1206. http://dx.doi.org/10.3390/cancers14051206.

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(1) Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility. (2) Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of wi

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Rund, Deborah G., Adir Shaulov та Dvora Filon. "Haplotype Analysis of -α3.7 Chromosomes in Israeli Ethnic Groups Reveals Unexpected Heterogeneity and Demonstrates Ashkenazi Founder Groups in Carriers of α-Thalassemia." Blood 108, № 11 (2006): 1591. http://dx.doi.org/10.1182/blood.v108.11.1591.1591.

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Abstract α-thalassemia (α-thal) is among the world’s most common single gene disorders, whose prevalence in the “malaria belt” is attributed to a selective advantage of carriers. Our previous studies demonstrated a high frequency of deletional α-thal (nearly all heterozygotes or homozygotes for -α3.7) in Ashkenazi Jews (carrier frequency of 7.9%, allele frequency of 0.04) (Rund et al, 2004). Ashkenazim resided in temperate climates for centuries and were not subject to malarial selection pressure, and their carriership for β-thalassemia is very low (estimated <0.1%). To elucidate the geneti

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Liu, Gang, Dongfeng Qiu, Yuxia Lu, et al. "Identification of Superior Haplotypes and Haplotype Combinations for Grain Size- and Weight-Related Genes for Breeding Applications in Rice (Oryza sativa L.)." Genes 14, no. 12 (2023): 2201. http://dx.doi.org/10.3390/genes14122201.

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The identification of superior haplotypes and haplotype combinations is essential for haplotype-based breeding (HBB), which provides selection targets for genomics-assisted breeding. In this study, genotypes of 42 functional genes in rice were analyzed by targeted capture sequencing in a panel of 180 Indica rice accessions. In total, 69 SNPs/Indels in seven genes were detected to be associated with grain length (GL), grain width (GW), ratio of grain length–width (L/W) and thousand-grain weight (TGW) using candidate gene-based association analysis, including BG1 and GS3 for GL, GW5 for GW, BG1

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De Elías-Escribano, Alejandra, Irene Serafín-Pérez, Patricio Artigas, et al. "Wide Variation of Aedes albopictus Genotypes First Introduced into Canary Islands Assessed by rDNA Internal Transcribed Spacer Region and mtDNA cox1 Sequencing and Cloning." Tropical Medicine and Infectious Disease 10, no. 2 (2025): 35. https://doi.org/10.3390/tropicalmed10020035.

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Aedes albopictus, one of the most rapidly spreading invasive mosquito species, has expanded from Asia to establish populations on every continent except Antarctica, showcasing exceptional adaptability, particularly in island environments. This study provides the first molecular characterization of Ae. albopictus in the Canary Islands, Spain. Genotyping was conducted using rDNA 5.8S-ITS2 and mtDNA cox1 sequencing, with haplotype analysis and phylogenetic network assessment. Among 49 sequences, 28 distinct 5.8S-ITS2 haplotypes were identified, with individual specimens containing 5 to 17 haploty

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Alves, Paula D., Paulo Rohan, Rocio Hassan, and Eliana Abdelhay. "Lytic and Latent Genetic Diversity of the Epstein–Barr Virus Reveals Raji-Related Variants from Southeastern Brazil Associated with Recombination Markers." International Journal of Molecular Sciences 25, no. 9 (2024): 5002. http://dx.doi.org/10.3390/ijms25095002.

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Epstein–Barr virus (EBV) is a ubiquitous gammaherpesvirus etiologically associated with benign and malignant diseases. Since the pathogenic mechanisms of EBV are not fully understood, understanding EBV genetic diversity is an ongoing goal. Therefore, the present work describes the genetic diversity of the lytic gene BZLF1 in a sampling of 70 EBV-positive cases from southeastern Brazil. Additionally, together with the genetic regions previously characterized, the aim of the present study was to determine the impact of viral genetic factors that may influence EBV genetic diversity. Accordingly,

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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., no. 3 (September 25, 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,

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Martin, Frank N. "Mitochondrial Haplotype Analysis as a Tool for Differentiating Isolates of Verticillium dahliae." Phytopathology® 100, no. 11 (2010): 1231–39. http://dx.doi.org/10.1094/phyto-12-09-0352.

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The ability to monitor mitochondrial background in Verticillium dahliae may provide an additional tool for population studies and monitoring clonal populations. Published mitochondrial genome sequences of V. dahliae (DQ351941) were used to design primers for amplification of spacer regions for assessment of mitochondrial haplotype differences among isolates. Five regions were examined (5,229 bp, or 19% of the total genome size) for 30 isolates representing a range in vegetative compatibility group (VCG), host, and geographic origin. Observed differences among isolates were due to single nucleo

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Koseniuk, Anna, and Ewa Słota. "Mitochondrial control region diversity in Polish sheep breeds." Archives Animal Breeding 59, no. 2 (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 identi

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Arifin Zein, M. Syamsul, and Sri Sulandari. "Genetic diversity of Lombok chickens based on D-loop mitochondrial DNA sequences." Jurnal Ilmu Ternak dan Veteriner 13, no. 4 (2012): 308–14. https://doi.org/10.14334/jitv.v13i4.575.

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Mitochondrial DNA (mtDNA) displacement (D)-loop sequences were used to study the genetic diversity and relationship of Lombok chickens. A total of 45 individuals were sampled. The D-loop segment was PCR amplified and subsequently sequenced. The sequences of the 785 nucleotides were used for analysis. Twelve haplotypes were identified from 25 polymorphic sites with polymorphism between nucleotides 200 and 400 contributing to 80% of the variation. Fuâ€™s Fs value was - 8.768 (all samples, P = 0), indicating high genetic diversity and population expansion, a conclusion supported by a neighborâ€“

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Arifin Zein, M. Syamsul, and S. Sulandari. "Genetic diversity and haplogroups distributions of Kampung chickens using hypervariable-I mitochondrial DNA control region." Jurnal Ilmu Ternak dan Veteriner 17, no. 2 (2013): 120–31. https://doi.org/10.14334/jitv.v17i2.686.

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Until now no studies evaluating the position of Kampung chickens in chicken clade of Asia. Thus studies based on molecular DNA sequence hipervariable-I on Kampung chicken is needed. Molecular studies based on DNA sequences hyper variable-I of Kampong chicken was done to confirm the results of previous evaluations conducted on 15 families of local chickens of Indonesia. An analysis of 210 individuals Kampung chicken (Aceh, North Sumatra, Lampung, Banten, Central Java, Lombok, Sulawesi, Ternate, Morotai and Halmahera) resulted in 51 haplotypes derived from 62 polymorphic sites. Polymorphic sites

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Ushijima, Koichiro, Hidenori Sassa, Mihoko Tamura, et al. "Characterization of the S-Locus Region of Almond (Prunus dulcis): Analysis of a Somaclonal Mutant and a Cosmid Contig for an S Haplotype." Genetics 158, no. 1 (2001): 379–86. http://dx.doi.org/10.1093/genetics/158.1.379.

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Abstract Almond has a self-incompatibility system that is controlled by an S locus consisting of the S-RNase gene and an unidentified “pollen S gene.” An almond cultivar “Jeffries,” a somaclonal mutant of “Nonpareil” (ScSd), has a dysfunctional Sc haplotype both in pistil and pollen. Immunoblot and genomic Southern blot analyses detected no Sc haplotype-specific signal in Jeffries. Southern blot showed that Jeffries has an extra copy of the Sd haplotype. These results indicate that at least two mutations had occurred to generate Jeffries: (1) deletion of the Sc haplotype and (2) duplication of

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Padutov, Vladimir E. "Population genetic structure of pedunculate oak (Quercus robur L.) in Belarus according to the analysis of chloroplast DNA." Journal of the Belarusian State University. Biology, no. 3 (October 25, 2021): 59–70. http://dx.doi.org/10.33581/2521-1722-2021-3-59-70.

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Pedunculate oak (Quercus robur L.) is one of the main forest forming species in the Republic of Belarus. Its population genetic structure was formed under the influence of various migration processes. Six chloroplast DNA loci (µdt1, µdt3, µdt4, µcd4, µcd5 and µkk4) were used for the genogeographic study. The material for the analysis was collected in 100 oak forest stands (2325 samples); 18 allelic variants were identified, which are grouped into 17 different combinations (haplotypes). Five of them are widespread (the proportion of occurrence varies from 7 to 48 %, totalling 85 %). The remaini

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Honjo, Masanori, Sono Kataoka, Susumu Yui, et al. "Maternal Lineages of the Cultivated Strawberry, Fragaria ×ananassa, Revealed by Chloroplast DNA Variation." HortScience 44, no. 6 (2009): 1562–65. http://dx.doi.org/10.21273/hortsci.44.6.1562.

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We analyzed sequence variation in chloroplast DNA (cpDNA) to investigate the origin of the cultivated strawberry, Fragaria ×ananassa. From analysis of two noncoding regions, trnL–trnF and trnR–rrn5, we found three haplotypes (V, C, and X) in F. ×ananassa. Haplotype V corresponded to the haplotype of F. virginiana and was possessed by cultivars bred over a wide geographic range, including North America, Europe, and Japan. Almost all the North American cultivars analyzed in this study possessed haplotype V, suggesting a founder effect. Haplotype C corresponded to the haplotype of F. chiloensis a

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Kao, H. T., P. K. Gregersen, J. C. Tang, T. Takahashi, C. Y. Wang, and J. Silver. "Molecular analysis of the HLA class II genes in two DRw6-related haplotypes, DRw13 DQw1 and DRw14 DQw3." Journal of Immunology 142, no. 5 (1989): 1743–47. http://dx.doi.org/10.4049/jimmunol.142.5.1743.

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Abstract We have compared the sequence polymorphism of HLA class II genes of two distinct DRw6 haplotypes. cDNA libraries were constructed from two lymphoblastoid cell lines: CB6B (10w9060) which types as DRw13 DQw1, and AMALA (10w9064) which types as DRw14 DQw3. Multiple sequence differences were found at the DR beta I, DQ alpha, and DQ beta loci when these two haplotypes were compared. The DR beta I allele found in the DRw14 DQw3 haplotype appears to have diverged primarily as a result of a gene conversion event with a DR1 allele acting as donor. In contrast, the DRw13 DQw1 haplotype appears

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