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Letteratura scientifica selezionata sul tema "Haplotypage"

Autore: Grafiati

Pubblicato: 25 gennaio 2025

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Articoli di riviste sul tema "Haplotypage"

Kim, Ki-Bong. "Development of Haplotype Reconstruction System Using Public Resources". Journal of the Korea Academia-Industrial cooperation Society 11, n. 2 (28 febbraio 2010): 720–26. http://dx.doi.org/10.5762/kais.2010.11.2.720.

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Xu, Hanli, e Yongtao Guan. "Detecting Local Haplotype Sharing and Haplotype Association". Genetics 197, n. 3 (8 maggio 2014): 823–38. http://dx.doi.org/10.1534/genetics.114.164814.

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Li, Ming, Roberto Romero, Wenjiang J. Fu e Yuehua Cui. "Mapping Haplotype-haplotype Interactions with Adaptive LASSO". BMC Genetics 11, n. 1 (2010): 79. http://dx.doi.org/10.1186/1471-2156-11-79.

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Fellows, M. R., T. Hartman, D. Hermelin, G. M. Landau, F. Rosamond e L. Rozenberg. "Haplotype Inference Constrained by Plausible Haplotype Data". IEEE/ACM Transactions on Computational Biology and Bioinformatics 8, n. 6 (novembre 2011): 1692–99. http://dx.doi.org/10.1109/tcbb.2010.72.

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Salem, M. M. I., G. Thompson, S. Chen, A. Beja-Pereira e J. Carvalheira. "Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle". Czech Journal of Animal Science 63, No. 2 (19 gennaio 2018): 61–69. http://dx.doi.org/10.17221/56/2017-cjas.

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The objectives of this study were to estimate linkage disequilibrium (LD), describe and scan a haplotype block for the presence of genes that may affect milk production traits in Portuguese Holstein cattle. Totally 526 animals were genotyped using the Illumina BovineSNP50 BeadChip, which contained a total of 52 890 single nucleotide polymorphisms (SNPs). The final set of markers remaining after considering quality control standards consisted of 37 031 SNPs located on 29 autosomes. The LD parameters historical recombinations through allelic association (D') and squared correlation coefficient between locus alleles frequencies ( r2) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r2 values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r2 values decreased respectively from 0.815 and 0.283 at the distance of 0–30 kb to 0.578 and 0.090 at the distance of 401–500 kb. The identified total number of blocks was 969 and consisted of 4259 SNPs that covered 159.06 Mb (6.24% of the total genome) on 29 autosomes. Several genes inside the haplotype blocks were detected; CSN1S2 gene in haplotype block 51 on BTA 6, IL6 and B4GALT1 genes in haplotype blocks 6 and 33 on BTA 8, IL1B and ID2 genes in haplotype blocks 19 and 29 on BTA 11, and DGAT1 gene in haplotype block 1 on BTA 14. The extension of LD using BovineSNP50 BeadChip did not exceed 500 kb and its parameters r2 and D’ were less than 0.2 and 0.70, respectively, after 70–100 kb. Consequently, the 50K BeadChip would have a poor power in genome wide association studies at distances between adjacent markers lower than 70 kb.

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Kreisberg, Jason. "Haplotype roundup". Nature Biotechnology 30, n. 8 (agosto 2012): 768. http://dx.doi.org/10.1038/nbt.2337.

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Schwartz, Russell. "Haplotype Parsing". Applied Bioinformatics 3, n. 2 (2004): 181–91. http://dx.doi.org/10.2165/00822942-200403020-00012.

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Weitzman, Jonathan B. "Haplotype blocks". Genome Biology 3 (2002): spotlight—20020524–01. http://dx.doi.org/10.1186/gb-spotlight-20020524-01.

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Boleckova, J., F. Christensen O, P. Sørensen e G. Sahana. "Strategies for haplotype-based association mapping in a complex pedigreed population". Czech Journal of Animal Science 57, No. 1 (27 gennaio 2012): 1–9. http://dx.doi.org/10.17221/5478-cjas.

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In association mapping, haplotype-based methods are generally regarded to provide higher power and increased precision than methods based on single markers. For haplotype-based association mapping most studies use a fixed haplotype effect in the model. However, an increase in haplotype length raises the number of parameters in the model, resulting in low accuracy of the estimates especially for the low-frequency haplotypes. Modeling of haplotype effects can be improved if they are assumed to be random effects, as only one parameter, i.e. haplotype variance, needs to be estimated compared to estimating the effects of all different haplotypes in a fixed haplotype model. Using simulated data, we investigated statistical models where haplotypes were fitted either as a fixed or random effect and we compared them for the power, precision, and type I error. We investigated five haplotype lengths of 2, 4, 6, 10 and 20. The simulated data resembled the Danish Holstein cattle pedigree representing a complex relationship structure and QTL effects of different sizes were simulated. We observed that the random haplotype models had high power and very low type I error rates (after the Bonferroni correction), while the fixed haplotype models had lower power and excessively high type I errors. Haplotype length of 4 to 6 gave the best results for random model in the present study. Though the present study was conducted on data structure more frequent in livestock, our findings on random vs. fixed haplotype effects in association mapping models are applicable to data from other species with a similar pedigree structure.  

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Rustgi, S., R. Bandopadhyay, H. S. Balyan e P. K. Gupta. "EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure". Czech Journal of Genetics and Plant Breeding 45, No. 3 (6 ottobre 2009): 106–16. http://dx.doi.org/10.17221/16/2009-cjgpb.

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The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1–18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

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Tesi sul tema "Haplotypage"

Faure, Roland. "Haplotype assembly from long reads". Electronic Thesis or Diss., Université de Rennes (2023-....), 2024. http://www.theses.fr/2024URENS052.

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Cette thèse propose des solutions pour améliorer l'assemblage des génomes à partir de lectures de séquençage de troisième génération (lectures longues). Plus précisément, elle se concentre sur l'amélioration de l'assemblage des (méta)génomes contenant plusieurs haplotypes, comme des génomes polyploïdes ou des souches bactériennes proches. Les assembleurs actuels ont du mal à séparer les haplotypes très similaires, et fusionnent généralement des (parties d')haplotypes, ce qui entraîne la perte de polymorphismes et d'hétérozygotie dans l'assemblage final. Ce travail présente une série de méthodes et de logiciels pour obtenir des assemblages contenant des haplotypes bien séparés. Plus précisément, GenomeTailor et HairSplitter transforment un assemblage obtenu avec des lectures longues erronées en un assemblage phasé, améliorant considérablement l'état de l'art lorsque de nombreuses souches sont présentes. Le logiciel Alice propose une nouvelle méthode, basée sur des nouveaux sketchs ``MSR'', pour assembler efficacement plusieurs haplotypes séquencés avec des lectures de haute fidélité. Enfin, cette thèse propose une nouvelle stratégie de scaffolding Hi-C basée sur le démêlage des graphes d'assemblage qui améliore considérablement les assemblages finaux, en particulier lorsque plusieurs haplotypes sont présents
This thesis presents solutions to improve genome assembly from third-generation sequencing reads, with a specific focus on improving the assembly of (meta)genomes containing multiple haplotypes, such as polyploid genomes or close bacterial strains. Current assemblers struggle to separate highly similar haplotypes, often collapsing all or parts of the haplotypes into one, thereby discarding polymorphisms and heterozygosity. This work introduces a series of methods and software tools to achieve haplotype-separated assemblies. Specifically, GenomeTailor and HairSplitter transform a collapsed assembly obtained with erroneous long reads into a phased assembly, significantly improving on the state of the art when numerous strains are present. The software Alice introduces a new method based on the new ``MSR'' sketching technique for efficiently assembling multiple haplotypes sequenced with high-fidelity reads. Additionally, this thesis proposes a new Hi-C scaffolding strategy that involves untangling assembly graphs which significantly improves final assemblies, particularly when several haplotypes are present

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Angulo, Rafael Villa. "Computational methods for haplotype inference with application to haplotype block characterization in cattle". Fairfax, VA : George Mason University, 2009. http://hdl.handle.net/1920/4558.

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Thesis (Ph.D.)--George Mason University, 2009.
Vita: p. 123. Thesis director: John J. Grefenstette. Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics and Computational Biology. Title from PDF t.p. (viewed Sept. 8, 2009). Includes bibliographical references (p. 114-122). Also issued in print.

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Beucher, Julie. "Haplotype ancestral AH8.1 dans la mucoviscidose". Phd thesis, Université Pierre et Marie Curie - Paris VI, 2012. http://tel.archives-ouvertes.fr/tel-00827653.

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Rogers, Emma Jayne. "Haplotype evolution and human genetic diversity". Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.342507.

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Xu, Xiao. "Human alpha defensin CNV haplotype diversity". Thesis, University of Nottingham, 2018. http://eprints.nottingham.ac.uk/51262/.

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Humans have highly variable number of alpha defensin genes, with between 3-16 diploid copies. Alpha-defensin genes have important roles in human innate immunity and diseases. Recently, GWAS studies reported this locus associated with IgA nephropathy and periodontitis. However, the underlying mechanism of association is not clear. In this Ph.D. thesis, human alpha defensin CNV flanking haplotype diversity in global populations was studied and the association between diseases and haplotype classes was discussed. Then a novo method to detect variants from inside the DEFA1A3 CNV was developed and a list of potential disease-related mutations for further functional studies was generated. The association between CNV internal variants and flanking haplotype classes was studied. Non-allelic homologous recombination was found to be the major mechanism of CNV formation of alpha defensin CNV. Analysis results were verified by PCR and Sanger sequencing-based methods. Additional to that, the haplotype diversity analysis highlighted an unusual haplotype 5T/7C which is only found in European populations but highly diverged from other human haplotypes. Further evidence was provided to suggest that this is an introgressed haplotype from Neanderthals. Furthermore, we used Oxford Nanopore to reconstruct haplotype structure in DEFA1A3 CNV and discussed its advantages and limitations by our analysis results. In brief, this Ph.D. research greatly improved our understanding of DEFA1A3 global diversity, evolutionary history, diseases and haplotype association.

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Huang, Bevan Emma Lin Danyu. "Statistical aspects of haplotype-based association studies". Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1237.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.
Title from electronic title page (viewed Mar. 26, 2008). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biostatistics, School of Public Health." Discipline: Biostatistics; Department/School: Public Health.

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Zhang, Jun. "Genotype/Haplotype Tagging Methods and their Validation". Digital Archive @ GSU, 2007. http://digitalarchive.gsu.edu/cs_theses/51.

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This study focuses how the MLR-tagging for statistical covering, i.e. either maximizing average R2 for certain number of requested tags or minimizing number of tags such that for any non-tag SNP there exists a highly correlated (squared correlation R2 > 0.8) tag SNP. We compare with tagger, a software for selecting tags in hapMap project. MLR-tagging needs less number of tags than tagger in all 6 cases of the given test sets except 2. Meanwhile, Biologists can detect or collect data only from a small set. So, this will bring a problem for scientists that the estimates accuracy of tag SNPs when constructing the complete human haplotype map. This study investigates how the MLR-tagging for statistically coverage performs under unbias study. The experiment results shows MLR-tagging still select small amount of SNPs very well even without observing the entire SNP in the sample.

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Vijaya, Satya Ravi. "ALGORITHMS FOR HAPLOTYPE INFERENCE AND BLOCK PARTITIONING". Doctoral diss., University of Central Florida, 2006. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/2490.

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The completion of the human genome project in 2003 paved the way for studies to better understand and catalog variation in the human genome. The International HapMap Project was started in 2002 with the aim of identifying genetic variation in the human genome and studying the distribution of genetic variation across populations of individuals. The information collected by the HapMap project will enable researchers in associating genetic variations with phenotypic variations. Single Nucleotide Polymorphisms (SNPs) are loci in the genome where two individuals differ in a single base. It is estimated that there are approximately ten million SNPs in the human genome. These ten million SNPS are not completely independent of each other - blocks (contiguous regions) of neighboring SNPs on the same chromosome are inherited together. The pattern of SNPs on a block of the chromosome is called a haplotype. Each block might contain a large number of SNPs, but a small subset of these SNPs are sufficient to uniquely dentify each haplotype in the block. The haplotype map or HapMap is a map of these haplotype blocks. Haplotypes, rather than individual SNP alleles are expected to effect a disease phenotype. The human genome is diploid, meaning that in each cell there are two copies of each chromosome - i.e., each individual has two haplotypes in any region of the chromosome. With the current technology, the cost associated with empirically collecting haplotype data is prohibitively expensive. Therefore, the un-ordered bi-allelic genotype data is collected experimentally. The genotype data gives the two alleles in each SNP locus in an individual, but does not give information about which allele is on which copy of the chromosome. This necessitates computational techniques for inferring haplotypes from genotype data. This computational problem is called the haplotype inference problem. Many statistical approaches have been developed for the haplotype inference problem. Some of these statistical methods have been shown to be reasonably accurate on real genotype data. However, these techniques are very computation-intensive. With the international HapMap project collecting information from nearly 10 million SNPs, and with association studies involving thousands of individuals being undertaken, there is a need for more efficient methods for haplotype inference. This dissertation is an effort to develop efficient perfect phylogeny based combinatorial algorithms for haplotype inference. The perfect phylogeny haplotyping (PPH) problem is to derive a set of haplotypes for a given set of genotypes with the condition that the haplotypes describe a perfect phylogeny. The perfect phylogeny approach to haplotype inference is applicable to the human genome due to the block structure of the human genome. An important contribution of this dissertation is an optimal O(nm) time algorithm for the PPH problem, where n is the number of genotypes and m is the number of SNPs involved. The complexity of the earlier algorithms for this problem was O(nm^2). The O(nm) complexity was achieved by applying some transformations on the input data and by making use of the FlexTree data structure that has been developed as part of this dissertation work, which represents all the possible PPH solution for a given set of genotypes. Real genotype data does not always admit a perfect phylogeny, even within a block of the human genome. Therefore, it is necessary to extend the perfect phylogeny approach to accommodate deviations from perfect phylogeny. Deviations from perfect phylogeny might occur because of recombination events and repeated or back mutations (also referred to as homoplasy events). Another contribution of this dissertation is a set of fixed-parameter tractable algorithms for constructing near-perfect phylogenies with homoplasy events. For the problem of constructing a near perfect phylogeny with q homoplasy events, the algorithm presented here takes O(nm^2+m^(n+m)) time. Empirical analysis on simulated data shows that this algorithm produces more accurate results than PHASE (a popular haplotype inference program), while being approximately 1000 times faster than phase. Another important problem while dealing real genotype or haplotype data is the presence of missing entries. The Incomplete Perfect Phylogeny (IPP) problem is to construct a perfect phylogeny on a set of haplotypes with missing entries. The Incomplete Perfect Phylogeny Haplotyping (IPPH) problem is to construct a perfect phylogeny on a set of genotypes with missing entries. Both the IPP and IPPH problems have been shown to be NP-hard. The earlier approaches for both of these problems dealt with restricted versions of the problem, where the root is either available or can be trivially re-constructed from the data, or certain assumptions were made about the data. We make some novel observations about these problems, and present efficient algorithms for unrestricted versions of these problems. The algorithms have worst-case exponential time complexity, but have been shown to be very fast on practical instances of the problem.
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Cavalleri, Gianpiero. "Haplotype mapping in epilepsy genetics and pharmacogenetics". Thesis, University College London (University of London), 2006. http://discovery.ucl.ac.uk/1445351/.

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Despite the success achieved in identifying mutations causing Mendelian forms of epilepsy, little progress has been made in illuminating variation contributing to the development of more common forms of the condition. The aim of this thesis was to improve methodology that would aid the detection of variation functional in the development and treatment of common forms of epilepsy. Attempted replication of previous claims of association with common forms of epilepsy allowed resolution of true effects from false positive results and illustrated shortcomings in the application of association based genetic mapping. Where effects looked real, haplotype-based fine mapping techniques were applied to identify candidate causal variation. The tagging SNP method was applied to HapMap data in an attempt to identify variation that might guide the safe prescription of Vigabatrin, an effective antiepileptic drug limited by a serious adverse drug reaction. Results outlined here show all previous claims of association with temporal lobe epilepsy and febrile seizures are likely to be false positives. However, supportive evidence is presented that common genetic variation predisposes to juvenile myoclonic epilepsy in a population specific manner. Evidence is also presented that variation that could be considered clinically relevant for the safe administration of Vigabatrin does not exist in the candidate genes examined here. Finally, a study design is proposed that seeks to significantly increase genetic power of detection through the incorporation of lessons learned from previous studies. In conclusion, epilepsy appears to be as genetically complex as the phenotypic spectrum of the condition would suggest. This work illustrates key areas in study design that require improvement and presents methodological developments in genetic mapping techniques which together provide a solid platform for future success.

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Beucher, Julie. "Haplotype ancestral AH8. 1 dans la mucoviscidose". Paris 6, 2012. http://www.theses.fr/2012PA066142.

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La mucoviscidose est une maladie à transmission autosomique récessive, due à des mutations du gène CFTR. Les patients, partageant de mêmes mutations de CFTR et un même environnement, ont une expression phénotypique variable, suggérant l'influence d’autres gènes modifiant la sévérité de la maladie, appelés gènes modificateurs. L’atteinte respiratoire, caractérisée par une inflammation exacerbée, est un facteur principal de morbi-mortalité. L’haplotype ancestral AH8. 1, impliqué dans la réponse inflammatoire, est constitué de 4 variants : LTa +252A/G, TNF -308G/A, HSPA1B +1267A/G et AGER -429T/C. Ainsi, l’objectif était de rechercher une association entre l’haplotype AH8. 1 et la sévérité de l’atteinte respiratoire. Nous avons montré dans une cohorte de 404 patients européens, porteurs de différentes mutations de CFTR, que AH8. 1 était associé au déclin de la fonction respiratoire. Nous avons taché de répliquer nos résultats dans une cohorte homogène de 1089 patients français, F508del homozygotes, sans succès à ce jour. Nous poursuivons cette étude chez des patients porteurs d’autres mutations de CFTR. Les variants de cet haplotype ont également été étudié séparément. Nous avons ainsi montré que AGER-429T/C, non seulement modulait la sévérité de l’atteinte respiratoire, mais, était également associé in vitro à une plus grande production de la protéine RAGE. L’ensemble de ces résultats suggère à ce jour que l’haplotype AH8. 1 pourrait moduler la sévérité de l’atteinte respiratoire des patients non homozygotes pour la mutation CFTR F508del. De plus, le variant AGER-429T/C seul, modulant la sévérité de l’atteinte respiratoire, la protéine RAGE pourrait être envisagée comme biomarqueur dans la mucoviscidose
Cystic fibrosis is an autosomic recessive disease due to mutations in the gene CFTR. There is a great phenotypic variability among patients with identical mutations and with identical environment. These data suggest that others genes, called modifier genes, may affect the lung phenotype. Lung disease, characterized by airway inflammation, is a key component of morbi-mortality. The ancestral haplotype AH8. 1, involved in the inflammatory response, is composed of 4 variants: LTa +252A/G, TNF -308G/A, HSPA1B +1267A/G and AGER -429T/C. The aim of the study was to test whether this haplotype AH8. 1 was associated with lung disease severity in cystic fibrosis. We showed in a cohort of 404 European patients, carriers of different mutations of CFTR, that AH8. 1 is associated with a greater lung disease severity. We did not succeed to replicate our results in a homogeneous cohort of 1039 French patients F508del homozygotes. We proceed with this study in patients, carriers of other CFTR mutations. Variants of this haplotype were also studied separately. We have shown that AGER-429T/C, not only modulates the severity of lung disease, but was also associated in vitro with a greater production of the protein RAGE. All these results suggest to date that AH8. 1 haplotype could modulate the lung disease severity in patients not homozygous for the F508del CFTR mutation. Moreover, the variant AGER-429T/C modulated the lung disease severity and the protein RAGE may be considered as a biomarker in cystic fibrosis

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Libri sul tema "Haplotypage"

Iliadis, Alexandros. Haplotype Inference through Sequential Monte Carlo. [New York, N.Y.?]: [publisher not identified], 2013.

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Istrail, Sorin, Michael Waterman e Andrew Clark, a cura di. Computational Methods for SNPs and Haplotype Inference. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/b96286.

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Pound, Michelle C. Deletion screening and haplotype analysis in the Fraxe region at Xq28. [Portsmouth]: [University of Portsmouth], 2000.

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Svensson, Ann-Cathrin. Molecular analyses of human endogenous retrovirus ERV9: Marker for HLA-DR haplotype evolution. Uppsala: Sveriges Lantbruksuniversitet, 1996.

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Männikkö, Minna. Congenital nephrotic syndrome of the Finnish type: Refined mapping of the gene locus on chromosome 19q13.1 and haplotype analysis. Oulu: University of Oulu, 1996.

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Sorin, Istrail, Waterman Michael S e Clark Andrew G. 1954-, a cura di. Computational methods for SNPs and Haplotype inference: DIMACS/RECOMB satellite workshop, Piscataway, NJ, USA, November 21-22, 2002 : revised papers. Berlin: Springer-Verlag, 2004.

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Mészáros, Gábor, Marco Milanesi, Paolo Ajmone Marsan e Yuri Tani Utsunomiya, a cura di. Haplotype Analysis Applied to Livestock Genomics. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-968-4.

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(Editor), Sorin Istrail, Michael Waterman (Editor) e Andrew Clark (Editor), a cura di. Computational Methods for SNPs and Haplotype Inference. Springer, 2004.

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The structure of haplotype blocks in the human genome. 2002.

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Sun, Shuying. Haplotype inference using a hidden Markov model with efficient Markov chain sampling. 2007, 2007.

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Capitoli di libri sul tema "Haplotypage"

Bloch, Michael H., Michael H. Bloch, Mark A. Geyer, David C. S. Roberts, Eileen M. Joyce, Jonathan P. Roiser, John H. Halpern et al. "Haplotype". In Encyclopedia of Psychopharmacology, 577. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_1518.

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Choudhury, Shalini Roy. "Haplotype". In Encyclopedia of Animal Cognition and Behavior, 1–3. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-47829-6_21-1.

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Choudhury, Shalini Roy. "Haplotype". In Encyclopedia of Animal Cognition and Behavior, 3045–47. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_21.

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Liu, Jun. "Haplotype Inference and Haplotype Information". In Computational Methods for SNPs and Haplotype Inference, 138. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_18.

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Li, Xin, e Jing Li. "Haplotype Inference". In Methods in Molecular Biology, 411–21. Totowa, NJ: Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-555-8_22.

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Zhang, Yu, e Tianhua Niu. "Haplotype Structure". In Handbook on Analyzing Human Genetic Data, 25–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-69264-5_2.

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Song, Sunah, Xin Li e Jing Li. "Haplotype Inference". In Methods in Molecular Biology, 469–84. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7274-6_23.

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Delaneau, Olivier, e Jean-François Zagury. "Haplotype Inference". In Data Production and Analysis in Population Genomics, 177–96. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-870-2_11.

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Fellows, Michael R., Tzvika Hartman, Danny Hermelin, Gad M. Landau, Frances Rosamond e Liat Rozenberg. "Haplotype Inference Constrained by Plausible Haplotype Data". In Combinatorial Pattern Matching, 339–52. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-642-02441-2_30.

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Epstein, Michael P., e Lydia C. Kwee. "Haplotype Association Analysis". In Handbook on Analyzing Human Genetic Data, 241–76. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-69264-5_8.

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Atti di convegni sul tema "Haplotypage"

Jiang, Yongshuai, Ruijie Zhang, Guiyou Liu, Zhen Wang, Zhiqiang Chen, Peng Sun, Chen Huang e Xuehong Zhang. "Multifactor Dimensionality Reduction for Detecting Haplotype-Haplotype Interaction". In 2009 Sixth International Conference on Fuzzy Systems and Knowledge Discovery. IEEE, 2009. http://dx.doi.org/10.1109/fskd.2009.750.

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Clark, Andrew G. "Haplotype phase inference". In the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640086.

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Bagdat, A., D. Ziyabek, Zh Muslimova e E. Usenbekov. "DIAGNOSTICS OF CARRIERS OF HH2 FERTILITY HAPLOTYPES IN HOLSTIN COWS". In SCIENTIFIC SUPPORT FOR LIVESTOCK BREEDING IN SIBERIA, 356–59. Krasnoyarsk Scientific Research Institute of Agriculture is a separate division of the Federal Research Center KSC SB RAS, 2024. https://doi.org/10.52686/conferencearticle_67597ceef0f045.18547197.

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Abstract (sommario):

The authors of the article used the Tetra-Primer ARMS-PCR reaction method to identify heterozygous carriers of the HH2 fertility haplotype in Holstein cows of foreign selection. A total of 150 DNA samples were tested, of which 8 individuals turned out to be heterozygous carriers of single-nucleotide deletion; the frequency of the harmful mutation was 5.4%. It has been established that the detection of DNA fragments on an electropherogram with sizes of 281 bp, 184 bp. and 145 bp, indicates that the animal is a heterozygous carrier of the HH2 fertility haplotype. It should be noted that to control the spread of harmful mutations, it is necessary to conduct selective genetic monitoring of the cattle population.

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Sadovnychenko, Iurii, e Nataliia Pastukhova. "Open data of molecular genetic research through the prism of global trends". In First International Conference "Open Science and Innovation in Ukraine 2022". State Scientific and Technical Library of Ukraine, 2022. http://dx.doi.org/10.35668/978-966-479-129-5-7-18.

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The availability analysis of genetic databases in the articles of Ukrainian and foreign scientists was performed. Only 6.4 % of articles in domestic journals provided data on the subjects’ genotype and haplotype distribution. Most journals are open access, but their editorial policy does not postulate their commitment to open data sharing.

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Li, Lei, Jong Hyun Kim e Michael S. Waterman. "Haplotype reconstruction from SNP alignment". In the seventh annual international conference. New York, New York, USA: ACM Press, 2003. http://dx.doi.org/10.1145/640075.640102.

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Lin, Shili, e Terence P. Speed. "An algorithm for haplotype analysis". In the first annual international conference. New York, New York, USA: ACM Press, 1997. http://dx.doi.org/10.1145/267521.267548.

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Halperin, Eran, e Richard M. Karp. "Perfect phylogeny and haplotype assignment". In the eighth annual international conference. New York, New York, USA: ACM Press, 2004. http://dx.doi.org/10.1145/974614.974617.

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Si, Hongbo, Haris Vikalo e Sriram Vishwanath. "Haplotype assembly: An information theoretic view". In 2014 IEEE Information Theory Workshop (ITW). IEEE, 2014. http://dx.doi.org/10.1109/itw.2014.6970817.

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Che, Dongsheng, Haibao Tang e Yinglei Song. "Haplotype inference using a genetic algorithm". In 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2009. http://dx.doi.org/10.1109/cibcb.2009.4925704.

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ZHU, X., S. ZHANG, D. KAN e R. COOPER. "HAPLOTYPE BLOCK DEFINITION AND ITS APPLICATION". In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2003. http://dx.doi.org/10.1142/9789812704856_0015.

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Rapporti di organizzazioni sul tema "Haplotypage"

Su, Hailin, James E. Koltes, Mahdi Saatchi, Jungjae Lee, Rohan L. Fernando e Dorian J. Garrick. Characterizing Haplotype Diversity in Ten US Beef Cattle Breeds. Ames (Iowa): Iowa State University, gennaio 2014. http://dx.doi.org/10.31274/ans_air-180814-1132.

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Roecklein, Kathryn A. Haplotype Analysis of the Melanopsin Gene in Seasonal Affective Disorder and Controls. Fort Belvoir, VA: Defense Technical Information Center, maggio 2007. http://dx.doi.org/10.21236/ad1014058.

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Weng, Ziqing, Anna Wolc, Jesus Arango, Petek Settar, Janet E. Fulton, Neil P. O'Sullivan, Rohan L. Fernando, Jack C. M. Dekkers e Dorian J. Garrick. Estimation of Haplotype Diversity and Recombination Rate on Chromosomes 5 and 15 in Layer Chickens. Ames (Iowa): Iowa State University, gennaio 2015. http://dx.doi.org/10.31274/ans_air-180814-1322.

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Sherman, Amir, Rebecca Grumet, Ron Ophir, Nurit Katzir e Yiqun Weng. Whole genome approach for genetic analysis in cucumber: Fruit size as a test case. United States Department of Agriculture, dicembre 2013. http://dx.doi.org/10.32747/2013.7594399.bard.

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Abstract (sommario):

The Cucurbitaceae family includes a broad array of economically and nutritionally important crop species that are consumed as vegetables, staple starches and desserts. Fruit of these species, and types within species, exhibit extensive diversity as evidenced by variation in size, shape, color, flavor, and others. Fruit size and shape are critical quality determinants that delineate uses and market classes and are key traits under selection in breeding programs. However, the underlying genetic bases for variation in fruit size remain to be determined. A few species the Cucurbitaceae family were sequenced during the time of this project (cucumber was already sequenced when the project started watermelon and melon sequence became available during the project) but functional genomic tools are still missing. This research program had three major goals: 1. Develop whole genome cucumber and melon SNP arrays. 2. Develop and characterize cucumber populations segregating for fruit size. 3. Combine genomic tools, segregating populations, and phenotypic characterization to identify loci associated with fruit size. As suggested by the reviewers the work concentrated mostly in cucumber and not both in cucumber and melon. In order to develop a SNP (single nucleotide polymorphism) array for cucumber, available and newly generated sequence from two cucumber cultivars with extreme differences in shape and size, pickling GY14 and Chinese long 9930, were analyzed for variation (SNPs). A large set of high quality SNPs was discovered between the two parents of the RILs population (GY14 and 9930) and used to design a custom SNP array with 35000 SNPs using Agilent technology. The array was validated using 9930, Gy14 and F1 progeny of the two parents. Several mapping populations were developed for linkage mapping of quantitative trait loci (QTL) for fruit size These includes 145 F3 families and 150 recombinant inbred line (RILs F7 or F8 (Gy14 X 9930) and third population contained 450 F2 plants from a cross between Gy14 and a wild plant from India. The main population that was used in this study is the RILs population of Gy14 X 9930. Phenotypic and morphological analyses of 9930, Gy14, and their segregating F2 and RIL progeny indicated that several, likely independent, factors influence cucumber fruit size and shape, including factors that act both pre-anthesis and post-pollination. These include: amount, rate, duration, and plane of cell division pre- and post-anthesis and orientation of cell expansion. Analysis of F2 and RIL progeny indicated that factors influencing fruit length were largely determined pre-anthesis, while fruit diameter was more strongly influenced by environment and growth factors post-anthesis. These results suggest involvement of multiple genetically segregating factors expected to map independently onto the cucumber genome. Using the SNP array and the phenotypic data two major QTLs for fruit size of cucumber were mapped in very high accuracy (around 300 Kb) with large set of markers that should facilitate identification and cloning of major genes that contribute to fruit size in cucumber. In addition, a highly accurate haplotype map of all RILS was created to allow fine mapping of other traits segregating in this population. A detailed cucumber genetic map with 6000 markers was also established (currently the most detailed genetic map of cucumber). The integration of genetics physiology and genomic approaches in this project yielded new major infrastructure tools that can be used for understanding fruit size and many other traits of importance in cucumber. The SNP array and genetic population with an ultra-fine map can be used for future breeding efforts, high resolution mapping and cloning of traits of interest that segregate in this population. The genetic map that was developed can be used for other breeding efforts in other populations. The study of fruit development that was done during this project will be important in dissecting function of genes that that contribute to the fruit size QTLs. The SNP array can be used as tool for mapping different traits in cucumber. The development of the tools and knowledge will thus promote genetic improvement of cucumber and related cucurbits.

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