Articles de revues : « Haplotype analysi »

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Kesik, Harun Kaya, Figen Celik, Seyma Gunyakti Kilinc, Sami Simsek, Haroon Ahmed, Yujuan Shen et Jianping Cao. « Genetic Diversity and Haplotype Analysis of Cattle Hydatid Cyst Isolates Using Mitochondrial Markers in Turkey ». Pathogens 11, n^o 5 (28 avril 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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Epifanio, John M., Bonnie L. Brown, Peter E. Smouse et 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, n^o 8 (1 août 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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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 et 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, n^o 4 (3 octobre 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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Kaul, Noyonika, Prem Lal Kashyap, Sudheer Kumar, Deepti Singh et 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, n^o 8 (5 août 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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Bhattacharyya, Nitai Pada, Priyadarshi Basu, Madhusudan Das, Srimanta Pramanik, Rajat Banerjee, Bidyut Roy, Susanta Roychoudhury et Partha P. Majumder. « Negligible Male Gene Flow Across Ethnic Boundaries in India, Revealed by Analysis of Y-Chromosomal DNA Polymorphisms ». Genome Research 9, n^o 8 (1 août 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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Vathipadiekal, Vinod, Abdulrahman Alsultan, John Farrell, A. M. Al-Rubaish, Fahad Al-Muhanna, Z. Naserullah, A. Alsuliman et al. « Polymorphisms Associated with the Arab-Indian Haplotype of Sickle Cell Anemia Are Candidate Fetal Hemoglobin Gene Modulators ». Blood 126, n^o 23 (3 décembre 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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Tjensvoll, Kjersti, Ove Bruland, Ylva Floderus, Øyvind Skadberg, Sverre Sandberg et Jaran Apold. « Haplotype Analysis of Norwegian and Swedish Patients with Acute Intermittent Porphyria (AIP) : Extreme Haplotype Heterogeneity for the Mutation R116W ». Disease Markers 19, n^o 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 single nucleotide polymorphisms (SNPs) to see if the high frequency of these two mutations is due to a founder effect. Twelve intragenic SNPs were determined by a method based on fluorescent restriction enzyme fingerprinting single-strand conformation polymorphism (F-REF-SSCP).W198X occurred exclusively on one haplotype in both Norwegian and Swedish patients, showing that it has originated from a common gene source. In contrast, R116W was found on three different haplotypes in three Norwegian families, and in five Swedish families on four or five haplotypes. This extreme haplotype heterogeneity indicates that R116W is a recurrent mutation, maybe explained by the high mutability of CpG dinucleotides. This can also explain why it is the only AIP mutation reported to occur in seven different populations (Norway, Sweden, Finland, Netherlands, France, Spain and South Africa).

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TAN, QIHUA, LENE CHRISTIANSEN, KAARE CHRISTENSEN, LISE BATHUM, SHUXIA LI, JING HUA ZHAO et TORBEN A. KRUSE. « Haplotype association analysis of human disease traits using genotype data of unrelated individuals ». Genetical Research 86, n^o 3 (25 novembre 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. Based on the popular logistic regression model, we present a new approach for haplotype association analysis of human disease traits. Using haplotype-based parameterization, our model infers the effects of specific haplotypes (point estimation) and constructs confidence interval for the risks of haplotypes (interval estimation). Based on the estimated parameters, the model calculates haplotype frequency conditional on the trait value for both discrete and continuous traits. Moreover, our model provides an overall significance level for the association between the disease trait and a group or all of the haplotypes. Featured by the direct maximization in haplotype estimation, our method also facilitates a computer simulation approach for correcting the significance level of individual haplotype to adjust for multiple testing. We show, by applying the model to an empirical data set, that our method based on the well-known logistic regression model is a useful tool for haplotype association analysis of human disease traits.

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Anantaphruti, Malinee, Urusa Thaenkham, Teera Kusolsuk, Wanna Maipanich, Surapol Saguankiat, Somjit Pubampen et 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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Pae, C. U. « Association Analysis of Heat Shock Protein 70 Gene Polymorphisms in Schizophrenia ». European Psychiatry 24, S1 (janvier 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 schizophrenia than in controls (Chi-sq=8.23, d.f.=1, p=0.0041). Haplotype based associations were also detected (global p value 0.000003); the T-A-C-C-G haplotype was more prevalent among the patients (odds ratio, OR 5.95). Sliding windows analysis revealed a major contribution from rs2227956 and rs2075799 (global-p value 0.0075), with T-A haplotype significantly associated with schizophrenia. There was no evidence of an association between the clinical variables and schizophrenia across the genotypes.Conclusion:Our results raise the possibility that HSP70 gene (i.e., haplotypes of rs2075799) might be implicated in the development of schizophrenia, although limited by rare haplotypic association with the disease. Hence further studies from different ethnics should be performed to confirm these results.

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Excoffier, L., P. E. Smouse et J. M. Quattro. « Analysis of molecular variance inferred from metric distances among DNA haplotypes : application to human mitochondrial DNA restriction data. » Genetics 131, n^o 2 (1 juin 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, corresponding to different types of molecular data, as well as different types of evolutionary assumptions, without modifying the basic structure of the analysis. The significance of the variance components and phi-statistics is tested using a permutational approach, eliminating the normality assumption that is conventional for analysis of variance but inappropriate for molecular data. Application of AMOVA to human mitochondrial DNA haplotype data shows that population subdivisions are better resolved when some measure of molecular differences among haplotypes is introduced into the analysis. At the intraspecific level, however, the additional information provided by knowing the exact phylogenetic relations among haplotypes or by a nonlinear translation of restriction-site change into nucleotide diversity does not significantly modify the inferred population genetic structure. Monte Carlo studies show that site sampling does not fundamentally affect the significance of the molecular variance components. The AMOVA treatment is easily extended in several different directions and it constitutes a coherent and flexible framework for the statistical analysis of molecular data.

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Adabale, Abosede, Samira Batista Lobo Makanjuola, Akinsegun Akinbami, Adedoyin Dosunmu, Alani Akanmu, Farideh A. Javid et Louis C. Ajonuma. « Frequency of beta S globin gene haplotypes among sickle cell patients in Nigeria ». Journal of International Medical Research 49, n^o 6 (juin 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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Sebastiani, Paola, John J. Farrell, Shuai Wang, Heather L. Edward, Heather M. Shappell, Harold T. Bae, Clinton T. Baldwin 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, n^o 21 (6 décembre 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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Sugiura, Nami, Dingqin Tang, Hiroyuki Kurokochi, Yoko Saito et Yuji Ide. « Genetic structure of Quercus gilva Blume in Japan as revealed by chloroplast DNA sequences ». Botany 93, n^o 12 (décembre 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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Dumaidi, Kamal, Hayah Qaraqe, Amer Al-Jawabreh, Rasmi Abu-Helu, Fekri Samarah et 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, n^o 12 (11 décembre 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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Yuliwulandari, Rika, et Katsushi Tokunaga. « Nasopharyngeal Carcinoma (NPC) Related Human Leukocyte Antigen (HLA) Haplotype Sharing among Southern East Asian Population ». Global Medical & ; Health Communication (GMHC) 5, n^o 1 (27 février 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 2005 to 2015. Haplotype frequencies were estimated using the maximum likelihood method based on an expectation maximization algorithm with ARLEQUIN v.2.0 software. We also calculated the genetic distance among 19 Southern East Asians based on HLA allele frequency using modified Cavalli-Sforza (DA) distance method. Then, a phylogenetic tree was constructed using DISPAN software and principal component analysis (PCA) was performed using XLSTAT-PRO software. A33-B58-DR3 haplotype, tightly linked to NPC, was commonly observed in all populations, supporting the high incidence of NPC in the populations. In addition, A2-B46 haplotype also associated with NPC, was also commonly found in several population that may also have a role in the disease development. The conclusion is the HLA haplotype sharing has an important role than the HLA allele sharing. The A33-B58-DR3 haplotype and A2-B46-DR9 haplotype in this study could be related to NPC in the Southern East Asian populations. The observed haplotype needs to be tested in the real patients to confirm the assumption.AbstrakHuman leukocyte antigens (HLAs) berperan penting dalam sistem imun untuk merespons berbagai patogen dan penyakit di antara individu yang berbeda. Tujuan penelitian ini menganalisis frekuensi alel dan haplotipe HLA populasi Southern East Asia yang menunjukkan insidensi yang tinggi terhadap nasopharyngeal carcinoma (NPC) untuk mengevaluasi kerentanan NPC bagi individu. Informasi haplotipe HLA dikumpulkan dari studi sebelumnya, publikasi jurnal internasional, dan database HLA pada 19 populasi dalam periode tahun 2005–2015. Frekuensi haplotipe dihitung menggunakan metode maximum likelihood berdasarkan expectation maximization algorithm menggunakan piranti lunak ARLEQUIN v.2.0. Jarak genetik di antara 19 populasi Southern East Asians dihitung menggunakan metode modified Cavalli-Sforza (DA) distance. Kemudian, pohon filogenetik dikonstruksi dengan metode neighbor-joining (NJ) menggunakan piranti lunak DISPAN. Principal component analysis (PCA) dilakukan menggunakan piranti lunak XLSTAT-PRO. Haplotipe A33-B58-DR3 terkait erat dengan NPC yang biasa terlihat di semua populasi mendukung tingginya insidensi penyakit dalam populasi. Selain itu, haplotipe A2-B46 juga terkait dengan NPC yang juga ditemukan pada beberapa populasi sehingga kemungkinan memiliki peran dalam perkembangan penyakit. Pada kasus NPC, haplotipe HLA lebih berperan dibanding dengan alel HLA. Haplotipe A33-B58-DR3 dan haplotipe A2-B46-DR9 yang ditemukan terkait dengan NPC pada populasi Southern East Asia. Haplotipe yang diamati tersebut perlu diuji pada pasien nyata untuk mengonfirmasi simpulan.

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Damen, Manon, Mascha Schijvenaars, Marlies Schimmel-Naber, Johanne Groothuismink, Marieke Coenen et Alide Tieleman. « Ancestral Origin of the First Indian Families with Myotonic Dystrophy Type 2 ». Journal of Neuromuscular Diseases 8, n^o 4 (30 juillet 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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Sehgal, D., et S. Dreisigacker. « Haplotypes-based genetic analysis : benefits and challenges ». Vavilov Journal of Genetics and Breeding 23, n^o 7 (24 novembre 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 be a powerful complement to improve efficiency of marker-assisted and genomic selection. This review describes in brief the commonly used approaches to construct haplotype blocks and some examples in animals and crops are cited where haplotype-based dissection of traits were proven beneficial. Some important considerations and facts while working with haplotypes in crops are reviewed at the end.

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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 et G. A. Romanovskaya. « Analysis of nuclear families with two and more diabetic siblings with insulin dependent condition ». Problems of Endocrinology 40, n^o 5 (15 décembre 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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Martin, F. N., et M. D. Coffey. « Mitochondrial Haplotype Analysis for Differentiation of Isolates of Phytophthora cinnamomi ». Phytopathology® 102, n^o 2 (février 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 with A1 and A2 mating type. Three of the regions were primarily intergenic regions between trnG and rns, rns and nad3, and nad6 and cox1, while the remaining loci spanned cox2, nad9, rps10, and secY coding regions and some of the flanking spacer regions. In total, 45 mitochondrial haplotypes were identified (75% of the total isolates examined) with differences due to single-nucleotide polymorphisms (SNPs, totaling 152 bp) and length mutations (17 indels >2 bp representing a total of 910 bp in length). SNPs were the predominate mutation in the four coding regions and their flanking intergenic regions, while both SNPs and length mutations were observed in the three primarily intergenic regions. Some of the length mutations in these regions were due to addition or loss of unique sequences while others were due to variable numbers of subrepeats (in the trnG-rns region, there were 3 to 12 copies of a 24-bp subrepeat sequence that differentiated 17 haplotypes). Network analysis of the haplotypes identified eight primary clades, with the most divergent clade representing primarily A1 isolates collected from Papua New Guinea. The isolate grouping in the network corresponded to mating type and previously published isozyme classifications, with three exceptions: a haplotype representing an A1 mating type (H29) was placed well within the A2 mating type haplotype grouping, one haplotype (H26) had isolates with two isozyme classifications, and one isozyme group was represented on separate network clades, suggesting that recombination has occurred in the past. Among the 62 isolates examined, several examples were identified of isolates recovered from different geographic regions having the same mitochondrial haplotype, suggesting movement of isolates via plant material. Analysis of the data set to determine whether fewer loci could be sequenced to classify haplotypes indicated that the trnG-rns and rns-nad6 loci would classify 87% of the haplotypes identified in this study, while additional sequencing of the nad9 or secY loci would further differentiate the remaining six haplotypes. Based on conservation of gene order in Phytophthora spp., the trnG-rns locus should be useful for mitochondrial haplotype classification in other species, as should the cox2, nad9, rps10, and secY loci. However, the rns-nad3 and nad6-cox1 loci span regions that can have a different gene order in some Phytophthora spp.

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Vadva, Larsen, Propp, Trautwein, Alford et Alper. « A New Pedigree-Based SNP Haplotype Method for Genomic Polymorphism and Genetic Studies ». Cells 8, n^o 8 (5 août 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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Subagiyo, Subagiyo, Retna Handayani et Rahayu Rahayu. « Identifikasi dan Analisis Filogenetik Portunus trituberculatus Dari Perairan Cirebon Menggunakan Barkode Gen COI Mitokondrial ». Jurnal Kelautan Tropis 21, n^o 2 (7 décembre 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 haplotipe from the others. The results of phylogenetic analysis showed that the 25 specimens were clustered into 3 clusters in 2 different lineages with percentages genetic distance were 12.76%, 14.24% and 14.33% respectively. The genetic distance within each cluster ranges from 0 - 2.92%. The Cirebon crab specimen is in the same cluster as the Philippine specimen with 1% genetic distance. Spesimen rajungan Portunus trituberculatus dari perairan Cirebon berhasil diidentifikasi menggunakan gen mitochondrial DNA cytochrome c oxidase subunit I (COI). Analisis distribusi haplotipe dengan data P trituberculatus yang berasal dari China, Korea, India dan Filipina yang diperoleh dari data genebank NCBI didapatkan 17 haplotipe dari 25 spesimen, dengan keragaman haploid 0,943 +0.031 dan keragaman nukleotida 0,04821+0.0139. Spesimen Cirebon merupakan haplotipe yang terpisah dari yang lainnya. Hasil kajian filogenetik menunjukkan 25 spesimen mengelompok ke dalam 3 kluster dari 2 garis keturunan yang berbeda dengan jarak genetik berturut turut 12,76 %, 14,24 % dan 14,33 %. Jarak genetik di dalam masing-masing kluster berkisar antara 0 – 2,92 %. Spesimen rajungan Cirebon berada pada garis keturunan dan kluster yang sama dengan spesimen Filipina dengan jarak genetik 1%.

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Emam, Ahmed Mostafa, Sandra Afonso, Pedro González-Redondo, G. M. K. Mehaisen, A. A. A. Azoz, N. A. Ahmed et N. Fernand. « Status and origin of Egyptian local rabbits in comparison with Spanish common rabbits using mitochondrial DNA sequence analysis ». World Rabbit Science 28, n^o 2 (30 juin 2020) : 93. http://dx.doi.org/10.4995/wrs.2020.12219.

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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 (P<0.05) for Tajima’s D were defined in this study. Haplotype A mostly occurred in 83.3% of Egyptian rabbits and 11.7% of EWR, while haplotype B occurred in 63.8% of Spanish rabbits and 36.2% of the EGS breed. A total of 47 domestic and wild Oryctolagus cuniculus published sequences were used to investigate the origin and relation among the rabbit breeds tested in this study. The most common haplotype (A) was combined with 44.7% of published sequences. However, haplotype B was combined with 8.5%. Haplotypes of Egyptian, SCR and EWR were scattered in cluster 1, while we found only one EGS haplotype with two haplotypes of EWR in cluster 2. Our results assumed that genetic diversity for ERB, EBB and SCR was very low. Egyptian breeds and SCR were introduced from European rabbits. We found that ERB and EBB belong to one breed.

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Kang, Won Sub, Su Kang Kim et Hae Jeong Park. « Association of the Promoter Haplotype of IFN-γ-Inducible Protein 16 Gene with Schizophrenia in a Korean Population ». Psychiatry Investigation 17, n^o 2 (25 février 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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Strucken, E. M., S. Rahmatalla, D. J. De Koning et G. A. Brockmann. « Haplotype analysis and linkage disequilibrium for DGAT1 ; ». Archives Animal Breeding 53, n^o 3 (10 octobre 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 allele 3 with five repeats of the promoter VNTR showed negative effects on protein content when paternally inherited, whereas the haplotype with the A allele and VNTR allele 2 (with six repeats) increased the protein content. Significant differences between these two haplotypes occurred for protein yield as well, pointing to a linked effect that is picked up by the haplotypes rather than a direct effect of the VNTR. The linkage disequilibrium, estimated by D', showed values between 0.29 and 0.59 which is unexpectedly low for a distance of ~10 kb. Only a very low correlation between the two loci was observed due to the almost similar frequencies of haplotypes containing the A or K allele of the K232A locus.

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Hurley, C. K., P. Gregersen, N. Steiner, J. Bell, R. Hartzman, G. Nepom, J. Silver et A. H. Johnson. « Polymorphism of the HLA-D region in American blacks. A DR3 haplotype generated by recombination. » Journal of Immunology 140, n^o 3 (1 février 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.

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Cao, Chang-Chang, et Xiao Sun. « Ehapp2 : Estimate haplotype frequencies from pooled sequencing data with prior database information ». Journal of Bioinformatics and Computational Biology 14, n^o 04 (août 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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Vojvodić, Svetlana, et D. Ademović-Sazdanić. « KIR And HLA Haplotype Analysis in a Family Lacking The KIR 2DL1-2DP1 Genes ». Balkan Journal of Medical Genetics 18, n^o 1 (1 juin 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-specific oligonucleotide (SSO) method and haplotype assignment was done by gene content analysis. Both parents and the maternal grandfather, shared the same Cen-B2 KIR haplotype, containing KIR 3DL3, -2DS2, -2DL2 and -3DP1 genes. The second haplotype in the KIR genotype of the mother and grandfather was Tel-A1 with KIR 2DL4 (normal and deleted variant), -3DL1, -22 bp deletion variant of the 2DS4 gene and -3DL2, while the second haplotype in the KIR genotype of the father was Tel-B1 with 2DL4 (normal variant), -3DS1, -2DL5, -2DS5, -2DS1 and 3DL2 genes. Haplotype analysis in all three offsprings revealed that the children inherited the Cen-B2 haplotype with the same gene content but two of the children inherited a deleted variant of the 2DL4 gene, while the third child inherited a normal one. The second haplotype of all three offspring contained KIR 2DL4, -2DL5, -2DS1, -2DS4 (del 22bp variant), -2DS5, -3DL1 and -3DL2 genes, which was the basis of the assumption that there is a hybrid haplotype and that the present 3DL1 gene is a variant of the 3DS1 gene. Due to consanguinity among the ancestors, the results of KIR segregation analysis showed the existence of a very rare KIR genotype in the offspring. The family who is the subject of this case is even more interesting because the father was 10/10 human leukocyte antigen (HLA)-matched to his daughter, all members of the family have the “best” donor KIR-B content and the presence of a rare KIR genotype with KIR 2DP1-2DL1 genes absence.

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Barnekow, Elin, Wen Liu, Hafdis T. Helgadottir, Kyriaki Michailidou, Joe Dennis, Patrick Bryant, Jessada Thutkawkorapin 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, n^o 5 (25 février 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 window sizes 1–25 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls. (3) Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 × 10−8), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2–25 and 113 risk haplotypes of window size 50 at p < 5 × 10−8 on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68. (4) Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.

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Gtari, Maher, Daniele Daffonchio et 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, n^o 3 (mars 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 isolated by a plant-capturing assay in 1998 from soil collected in the same locality, qualifying it to be the most competitive haplotype in the edapho-climatic condition of the studied desertic date-palm oasis. nifD-K sequences of the three haplotypes formed a closely related phylogenetic subgroup. These results suggest that Frankia variability is constrained by severe edapho-climatic conditions of retreated desert in Tunisian area.

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Rund, Deborah G., Adir Shaulov et 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, n^o 11 (16 novembre 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 genetic mechanism(s) responsible for this high frequency of α-thal, we performed α-globin haplotype analysis on 170 chromosomes (chromos) of 85 homozygotes for -α3.7. We compared chromos of several ethnic groups: Jews (Ashkenazim: 54 chromos, Yemenites: 54 chromos, Iraqis: 14 chromos, others: 14 chromos), Arabs (28 chromos), and Druze (6 chromos). Using PCR and digestion with ApaI and RsaI, it was determined that all but three of the chromos are of the -α3.7I type. Haplotype analysis was performed for polymorphic sites identified by Higgs (1986), using PCR and restriction enzyme digestion. Altogether, 13 haplotypes were found. Unexpectedly, at least 5 haplotypes were found among the Ashkenazim with a large number of chromos carrying unknown haplotypes. Interestingly, 26/54 of Ashkenazi chromos carried haplotype IIIb which is found rarely in Europe and Saudi Arabia but most commonly in Melanesia and Papua New Guinea (Flint, 1992). In contrast, only 3/116 nonAshkenazi chromos carried haplotype IIIb. Interestingly there was little overlap in haplotypes between Ashkenazim and the various ethnic groups studied including the other Jewish groups, with 2 exceptions. First, Arabs and Yemenite Jews each were found to have around 50% chromos which carried haplotype Ia. Additionally, 10% of Ashkenazim and 20% of Yemenites had chromos carrying haplotype IIh, which is a haplotype originally described in an Australiam Aboriginal tribe (Roberts-Thomson, 1996). There was no overlap between Arabs and Druze. In conclusion, α-globin haplotype analysis demonstrates diversity within an apparently homogeneous ethnic group (Ashkenazim homozygous for -α3.7) and demonstrates founder effects in Ashkenazim carrying α-globin gene rearrangements.

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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., n^o 3 (25 septembre 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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Martin, Frank N. « Mitochondrial Haplotype Analysis as a Tool for Differentiating Isolates of Verticillium dahliae ». Phytopathology® 100, n^o 11 (novembre 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 nucleotide polymorphisms, different numbers of bases in specific homopolymeric regions, and copies of subrepeated sequences. When the differences observed for each locus were totaled there were 28 total groupings; when the results of each locus for individual isolates were combined there were 15 mitochondrial haplotypes. Some of the observed groupings correlated with VCG. For example, five VCG-1A and VCG-1B isolates from California, Spain, and Greece had identical haplotypes; however, this was not observed for VCG-2 or VCG-4 isolates. While some VCG-2 isolates also were identical and fell into a single haplotype, five haplotypes were found for this group (five other haplotypes were observed for other isolates that had not been characterized to VCG but grouped with VCG-2 isolates in the phylogenetic analysis). Likewise, five VCG-4 isolates fell into four mitochondrial haplotypes, one of which was identical to the largest VCG-2 grouping. A heterokaryon self-incompatible isolate that was reported in the literature to cluster with VCG-2 isolates by amplified fragment length polymorphism analysis was identical with VCG-1 isolates for four of the five loci, but was intermediate between VCG-1 and VCG-2 in the haplotype analysis. Phylogenetic analysis with these regions revealed the mitochondrial background of VCG-1 and VCG2-B to be monophyletic but VCG-2A and VCG-4 could not be separated. The results obtained indicate that there is variation in mitochondrial haplotypes and this type of analysis may be a useful for characterization of isolates. While data from all five regions was used for the haplotype separation in this study, depending on the VCG or the level of variability observed within a population it is possible to use fewer loci.

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Koseniuk, Anna, et Ewa Słota. « Mitochondrial control region diversity in Polish sheep breeds ». Archives Animal Breeding 59, n^o 2 (30 mai 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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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, n^o 3 (25 octobre 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 remaining 12 are rare (the proportion of occurrence varies from 1 to 3 %, totalling 15 %). Phylogenetic trees constructed using the nearest neighbour and maximum likelihood methods show the presence of two groups (branches) of haplotypes. One of it comprises 8 variants including 2 dominant haplotypes and the other comprises 9 variants including 3 dominant haplotypes. PCR-RFLP analysis of chloroplast DNA showed that the pedunculate oak in Belarus originates from the Balkan refugium. Haplotype No. 1 (µdt189, µdt3123, µdt4142, µcd494, µcd574, µkk4109) is found almost everywhere in Belarus with the exception of the southwest and northeast, while haplotype No. 8 (µdt189, µdt3121, µdt4142, µcd494, µcd574, µkk4109) is mainly localised in the southwest and northeast. Haplotypes No. 3 (µdt189, µdt3120, µdt4141, µcd494, µcd575, µkk4109) and No. 7 (µdt189, µdt3122, µdt4142, µcd494, µcd574, µkk4109) predominantly found in the west of the country. Haplotype No. 2 (µdt190, µdt3120, µdt4141, µcd495, µcd574, µkk4109) is typical for the southeast.

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Ushijima, Koichiro, Hidenori Sassa, Mihoko Tamura, Makoto Kusaba, Ryutaro Tao, Thomas M. Gradziel, Abhaya M. Dandekar et Hisashi Hirano. « 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, n^o 1 (1 mai 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 the Sd haplotype. To analyze the extent of the deletion in Jeffries and gain insight into the physical limit of the S locus region, ∼200 kbp of a cosmid contig for the Sc haplotype was constructed. Genomic Southern blot analyses showed that the deletion in Jeffries extends beyond the region covered by the contig. Most cosmid end probes, except those near the Sc-RNase gene, cross-hybridized with DNA fragments from different S haplotypes. This suggests that regions away from the Sc-RNase gene can recombine between different S haplotypes, implying that the cosmid contig extends to the borders of the S locus.

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Honjo, Masanori, Sono Kataoka, Susumu Yui, Masami Morishita, Miyuki Kunihisa, Takayoshi Yano, Megumi Hamano et Hiromichi Yamazaki. « Maternal Lineages of the Cultivated Strawberry, Fragaria ×ananassa, Revealed by Chloroplast DNA Variation ». HortScience 44, n^o 6 (octobre 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 and was detected mainly in Japanese cultivars. Haplotype X was found in only two English cultivars. This haplotype was positioned as intermediate between haplotypes V and C in a median-joining network and was considered to be representative of the process of differentiation between F. virginiana and F. chiloensis. Results of controlled crosses indicate that cpDNA haplotypes of F. ×ananassa are maternally inherited. These results verify that F. ×ananassa is an interspecific hybrid between F. virginiana and F. chiloensis and indicate that traditional cultivars of F. ×ananassa have been derived from at least three maternal lineages. We demonstrate that the cpDNA variation detected in this study can be used to verify parentage and for extending hypotheses about June yellows, a leaf variegation disorder in strawberry.

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Kao, H. T., P. K. Gregersen, J. C. Tang, T. Takahashi, C. Y. Wang et J. Silver. « Molecular analysis of the HLA class II genes in two DRw6-related haplotypes, DRw13 DQw1 and DRw14 DQw3. » Journal of Immunology 142, n^o 5 (1 mars 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 to have arisen by means of a recombination event between the DR and DQ subregions. Thus, multiple genetic mechanisms, including point mutation, gene conversion, and recombination, have generated diversity among DRw6 haplotypes.

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Baker, Peter R., Erin E. Baschal, Pam R. Fain, Taylor M. Triolo, Priyaanka Nanduri, Janet C. Siebert, Taylor K. Armstrong et al. « Haplotype Analysis Discriminates Genetic Risk for DR3-Associated Endocrine Autoimmunity and Helps Define Extreme Risk for Addison’s Disease ». Journal of Clinical Endocrinology & ; Metabolism 95, n^o 10 (1 octobre 2010) : E263—E270. http://dx.doi.org/10.1210/jc.2010-0508.

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Context: Multiple autoimmune disorders (e.g. Addison’s disease, type 1 diabetes, celiac disease) are associated with HLA-DR3, but it is likely that alleles of additional genes in linkage disequilibrium with HLA-DRB1 contribute to disease. Objective: The objective of the study was to characterize major histocompatability complex (MHC) haplotypes conferring extreme risk for autoimmune Addison’s disease (AD). Design, Setting, and Participants: Eighty-six 21-hydroxylase autoantibody-positive, nonautoimmune polyendocrine syndrome type 1, Caucasian individuals collected from 1992 to 2009 with clinical AD from 68 families (12 multiplex and 56 simplex) were genotyped for HLA-DRB1, HLA-DQB1, MICA, HLA-B, and HLA-A as well as high density MHC single-nucleotide polymorphism (SNP) analysis for 34. Main Outcome Measures: AD and genotype were measured. Result: Ninety-seven percent of the multiplex individuals had both HLA-DR3 and HLA-B8 vs. 60% of simplex AD patients (P = 9.72 × 10−4) and 13% of general population controls (P = 3.00 × 10−19). The genotype DR3/DR4 with B8 was present in 85% of AD multiplex patients, 24% of simplex patients, and 1.5% of control individuals (P = 4.92 × 10−191). The DR3-B8 haplotype of AD patients had HLA-A1 less often (47%) than controls (81%, P = 7.00 × 10−5) and type 1 diabetes patients (73%, P = 1.93 × 10−3). Analysis of 1228 SNPs across the MHC for individuals with AD revealed a shorter conserved haplotype (3.8) with the loss of the extended conserved 3.8.1 haplotype approximately halfway between HLA-B and HLA-A. Conclusion: Extreme risk for AD, especially in multiplex families, is associated with haplotypic DR3 variants, in particular a portion (3.8) but not all of the conserved 3.8.1 haplotype.

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Thomson, Glenys, et William Klitz. « Disequilibrium Pattern Analysis. I. Theory ». Genetics 116, n^o 4 (1 août 1987) : 623–32. http://dx.doi.org/10.1093/genetics/116.4.623.

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ABSTRACT We have developed a method, disequilibrium pattern analysis, for examining the disequilibrium distribution of the entire array of two locus multiallelic haplotypes in a population. It is shown that a selected haplotype will produce a distinct pattern of linkage disequilibrium values for all generations while the selection is acting. This pattern will also presumably be maintained for many generations after the selection event, until the disequilibrium pattern is eventually broken down by genetic drift and recombination. Related haplotypes, sharing an allele with a selected haplotype, assume a value of linkage disequilibrium proportional to the frequency of the unshared allele and have a single negative value of the normalized linkage disequilibrium. The analysis assumes zero linkage disequilibrium for all allelic combinations initially. The same basic results continue to apply if the selection involves a new mutant, the occurrence of which creates linkage disequilibrium for some haplotypes. The disequilibrium pattern predicted under selection is robust with respect to the influence of migration and random genetic drift. This method is applicable to population data having linked polymorphic loci including that determined from protein or DNA sequencing.

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Popoola, Omoniyi Michael. « Genetic Differentiation and Molecular Phylogenetics of North African Catfish from Three Distinct Waterbodies ». Croatian Journal of Fisheries 80, n^o 3 (1 septembre 2022) : 123–32. http://dx.doi.org/10.2478/cjf-2022-0013.

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Abstract The population structure and genetic variability of North African catfish Clarias gariepinus (Burchell 1822) were investigated using partial mitochondrial DNA cytochrome b region sequences. Fifty-four (54) samples were investigated from three geographically isolated rivers in Nigeria. The analysis of 53 haplotypes revealed greater haplotype diversity (0.99930) and nucleotide diversity (p) (0.07270). According to an analysis of molecular variance (AMOVA), the genetic diversity of North African catfish within populations is significantly higher than the genetic diversity across populations. The FST scores (0.75000, 0.94792 and 0.95699) indicated that North African catfish populations in three Nigerian freshwater bodies had a strong genetic structure. The phylogenetic reconstruction of unique haplotypes revealed the placement of a haplotype (Ogbese) linked by others from all three groups with a point mutation ranging from 1 to 24 nucleotides. North African catfish populations in the Asejire and Ureje are genetically diverse, as evidenced by a high level of haplotype diversity of 1.0000, low nucleotide diversity spanning from 0.05101 to 0.07889, and high FST values (within-population genetic variation). The common haplotypes between some populations and mixes of haplotypes from different populations within the same genetic cluster demonstrate that the population genetic structure is not distinct.

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Smart, Utpal, Jennifer Churchill Cihlar, Sammed N. Mandape, Melissa Muenzler, Jonathan L. King, Bruce Budowle et August E. Woerner. « A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures ». Genes 12, n^o 2 (20 janvier 2021) : 128. http://dx.doi.org/10.3390/genes12020128.

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Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture’s genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.

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Zhou, Ren, Mengying Wang, Wenyong Li, Siyue Wang, Hongchen Zheng, Zhibo Zhou, Yonghua Hu et al. « Haplotype and Haplotype-Environment Interaction Analysis Revealed Roles of SPRY2 for NSCL/P among Chinese Populations ». International Journal of Environmental Research and Public Health 16, n^o 4 (15 février 2019) : 557. http://dx.doi.org/10.3390/ijerph16040557.

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Non-syndromic cleft lip with or without cleft palate (NSCL/P) is one of common birth defects in China, with genetic and environmental components contributing to the etiology. Genome wide association studies (GWASs) have identified SPRY1 and SPRY2 to be associated with NSCL/P among Chinese populations. This study aimed to further explore potential genetic effect and gene—environment interaction among SPRY genes based on haplotype analysis, using 806 Chinese case—parent NSCL/P trios drawn from an international consortium which conducted a genome-wide association study. After the process of quality control, 190 single nucleotide polymorphisms (SNPs) of SPRY genes were included for analyses. Haplotype and haplotype—environment interaction analyses were conducted in Population-Based Association Test (PBAT) software. A 2-SNP haplotype and three 3-SNP haplotypes showed a significant association with the risk of NSCL/P after Bonferroni correction (corrected significance level = 2.6 × 10−4). Moreover, haplotype—environment interaction analysis identified these haplotypes respectively showing statistically significant interactions with maternal multivitamin supplementation or maternal environmental tobacco smoke. This study showed SPRY2 to be associated with NSCL/P among the Chinese population through not only gene effects, but also a gene—environment interaction, highlighting the importance of considering environmental exposures in the genetic etiological study of NSCL/P.

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Howard, C. A., G. R. Gummere, M. F. Lyon, D. Bennett et 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, n^o 4 (1 décembre 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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Haapalainen, Minna, Satu Latvala, Annika Wickström, Jinhui Wang, Minna Pirhonen et Anne I. Nissinen. « A novel haplotype of ‘Candidatus Liberibacter solanacearum’ found in Apiaceae and Polygonaceae family plants ». European Journal of Plant Pathology 156, n^o 2 (28 novembre 2019) : 413–23. http://dx.doi.org/10.1007/s10658-019-01890-0.

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AbstractA previously unknown haplotype of the plant pathogen ‘Candidatus Liberibacter solanacearum’ (Lso) was found in cultivated carrots and parsnips in eastern Finland. That same haplotype was found in western Finland, over 300 km away, in the family Polygonaceae, the species Fallopia convolvulus (wild buckwheat) and Persicaria lapathifolia (pale persicaria) growing as weeds within carrot and parsnip fields. The infected plants, both apiaceous and polygonaceous, showed symptoms of foliar discolouration. This is the first report of Lso bacteria in plants of the family Polygonaceae. The finding that the polygonaceous plants infected with a previously unknown haplotype of Lso were growing among the apiaceous plants infected with Lso haplotype C suggests that these two haplotypes might be transmitted by different vectors. Phylogenetic analyses showed that the new haplotype, called haplotype H, is distinct from the previously characterized haplotypes and appears to have diverged early from their common ancestor. Multi-locus sequence analysis revealed four different sequence types (strains) within the haplotype H. These findings suggest that the haplotype H is likely to be endemic in northern Europe and that the genetic diversity within the Lso species is higher than previously assumed.

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Nadeau, J. H., D. Varnum et D. Burkart. « Genetic evidence for two t complex tail interaction (tct) loci in t haplotypes. » Genetics 122, n^o 4 (1 août 1989) : 895–903. http://dx.doi.org/10.1093/genetics/122.4.895.

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Abstract The t complex on chromosome 17 of the house mouse is an exceptional model for studying the genetic control of transmission ratio, gametogenesis, and embryogenesis. Partial haplotypes derived through rare recombination between a t haplotype and its wild-type homolog have been essential in the genetic analysis of these various properties of the t complex. A new partial t haplotype, which was derived from the complete tw71 haplotype and which is called tw71Jr1, was shown to have unexpected effects on tail length and unique recombination breakpoints. This haplotype, either when homozygous or when heterozygous with the progenitor tw71 haplotype, produced short-tailed rather than normal-tailed mice on certain genetic backgrounds. Genetic analysis of this exceptional haplotype showed that the recombination breakpoints were different from those leading to any other partial t haplotype. Based on this haplotype, a model is proposed that accounts for genetic interactions between the brachyury locus (T), the t complex tail interaction (tct) locus, and their wild-type homolog(s) that determine tail length. An important part of this model is the hypothesis that the tct locus, which enhances the tail-shortening effect of T mutations, is in fact at least two, genetically separable genes with different genetic activities. Genetic analysis of parental and recombinant haplotypes also suggests that intrachromosomal recombination involving an inverted duplicated segment can account for the variable orientation of loci within an inverted duplication on wild-type homologs of the t haplotype.

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Cronin, Matthew A., William J. Spearman, Richard L. Wilmot, John C. Patton et 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, n^o 4 (1 avril 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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Wang, Liu, et Pengfeng Xiao. « Haplotype-Contained PCR Products Analysis by Sequencing with Selective Restriction of Primer Extension ». BioMed Research International 2017 (2017) : 1–9. http://dx.doi.org/10.1155/2017/1397902.

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We develop a strategy for haplotype analysis of PCR products that contained two adjacent heterozygous loci using sequencing with specific primers, allele-specific primers, and ddNTP-blocked primers. To validate its feasibility, two sets of PCR products, including two adjacent heterozygous SNPs, UGT1A1⁎6 (rs4148323) and UGT1A1⁎28 (rs8175347), and two adjacent heterozygous SNPs, K1637K (rs11176013) and S1647T (rs11564148), were analyzed. Haplotypes of PCR products, including UGT1A1⁎6 and UGT1A1⁎28, were successfully analyzed by Sanger sequencing with allele-specific primers. Also, haplotypes of PCR products, including K1637K and S1647T, could not be determined by Sanger sequencing with allele-specific primers but were successfully analyzed by pyrosequencing with ddNTP-blocked primers. As a result, this method is able to effectively haplotype two adjacent heterozygous PCR products. It is simple, fast, and irrespective of short read length of pyrosequencing. Overall, we fully hope it will provide a new promising technology to identify haplotypes of conventional PCR products in clinical samples.

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Khanal, Laxman, Mukesh Kumar Chalise, Xue-Long Jiang et Randall C. Kyes. « Mitochondrial Genetic Diversity and Structure of the Langur Population in a Complex Landscape of the Nepal Himalaya ». Diversity 14, n^o 2 (21 janvier 2022) : 69. http://dx.doi.org/10.3390/d14020069.

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Heterogenous landscape features of the Himalayan region shape the genetic structure of animal populations by delimiting spatial patterns of dispersal and reproduction. Integrating population genetic analysis with landscape features could yield results that shed light on the evolutionary diversity of the taxa therein. This study assessed the population genetic structure of the Nepal Himalayan langurs (Semnopithecus spp.) across almost their entire distribution range in the complex landscape of the Nepal Himalaya using the mitochondrial cytochrome b (CYTB, 1140 bp), cytochrome c oxidase I (COI, 676 bp), and control region (1088 bp) sequences. Sequences were successfully retrieved from 52 samples belonging to 17 troops of wild Himalayan langurs in Nepal. The concatenated alignment of the three loci (2904 bp) defined 35 unique haplotypes with haplotype and nucleotide diversities of 0.961 ± 0.017 and 0.0204 ± 0.004, respectively. The results of a median joining haplotype network and of inter-haplotypic phylogenetic analyses revealed five major clades across the country: one from the eastern, two from the central, and two from the western region of Nepal. No haplotypes were shared among the regions. The Mantel test results indicated that the landscape heterogeneity of the Himalaya has shaped the population genetic structure of the Himalayan langurs due to the combined effects of isolation by resistance and isolation by distance phenomena. The strong population genetic structure and deep mtDNA divergence warrants a detailed taxonomic assessment of the Himalayan langurs across their entire range.

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Kalaycı, Gökhan. « Pliocene-Pleistocene dispersal bring along low inter species diversity between Vimba species based on multilocus analysis ». Zoosystematics and Evolution 98, n^o 1 (25 février 2022) : 65–75. http://dx.doi.org/10.3897/zse.98.76937.

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This study investigates phylogenetic and phylogeographic relationships of Vimba species using mitochondrial cytochrome b (cyt b) (1023 bp) and cytochrome c oxidase subunit I (COI) barcoding region (652 bp) genes. Ninety-one samples from 36 populations for the cyt b gene and 67 samples from 20 populations for the COI were analyzed. We identified 29 haplotypes and calculated overall haplotype diversity as Hd: 0.907 ± 0.015 for cyt b. We also identified 13 COI haplotypes and calculated overall haplotype diversity as 0.826 ± 0.026 for this marker. The phylogenetic analysis of Vimba species reveals the presence of four clades, based on concatenated cyt b and COI sequences. The first and second clade consist of Vimba vimba Western lineage, and Vimba vimba Caspian lineage, while the third and fourth clade consist of Vimba mirabilis and Vimba melanops. Based on haplotype network analyses and phylogeographic inferences, the Vimba genus is monophyletic, and its species dispersed in the Pleistocene era.

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