Relevant bibliographies by topics / Haplotype block

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Academic literature on the topic 'Haplotype block'

Author: Grafiati
Published: 4 June 2021
Last updated: 20 June 2025

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Journal articles on the topic "Haplotype block"

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Batalha, Fernanda de Almeida, Elizangela Farias da Silva, Paula Taquita Serra, et al. "IgM against Merozoite Surface Protein 1-Block 2 Haplotypes as New Tools for Plasmodium vivax Infections." Journal of Global Infectious Diseases 16, no. 4 (2024): 152–59. https://doi.org/10.4103/jgid.jgid_35_24.

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Introduction: The tools to distinguish relapse from reinfection are needed in malaria-endemic areas. We evaluated seroprevalence against sets of specific peptides to the block 2 region of Plasmodium vivax-merozoite surface protein-1 (PvMSP1) to detect parasite clones. Methods: We applied amplicon deep sequencing (ADS) of block 2 region of the MSP-1 gene (pvmsp1) to determine cocirculating parasite clones within eight P. vivax-infected individuals. Based on this, a seroprevalence of IgM and IgG antibodies against sets of peptides of different block-2 haplotypes was validated. After, we evaluated the seroprevalence in plasma of 72 pregnant women, from which 31 had recurrent P. vivax infections. Results: ADS revealed one block 2 haplotype clone infecting five of eight P. vivax-infected individuals. In all, IgM antibodies, not IgG, recognized only a set of peptides specific to the block 2 haplotype determined by ADS. In the other three patients, ADS determined three concurrent block 2 haplotype clones, among whom there was always one haplotype that predominated with more than 95% of high-quality reads and two other smaller haplotypes with up to 5% and the least was <1%. We observed higher IgM levels against haplotype-specific peptides corresponding to the predominant clone. The seroprevalence of pregnant women showed that anti-haplotype-specific IgM detected coinfection with parasite clones per pregnant woman and we also observed levels of anti-haplotype-specific IgM in primary infection increased in some recurrent episodes. Conclusion: IgM against sets of peptides specific to different pvmsp1 haplotypes may be employed as a serological marker for parasite clones in vivax malaria.
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SAZONOVA, NADEZHDA, and E. JAMES HARNER. "HAPLOTYPE INFERENCE AND BLOCK PARTITIONING IN MIXED POPULATION SAMPLES." Journal of Bioinformatics and Computational Biology 06, no. 06 (2008): 1177–92. http://dx.doi.org/10.1142/s0219720008003898.

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Multi-population haplotype inference and block partitioning is a difficult task when dealing with mixed genotype samples. A number of studies have shown that the haplotype block structures, as well as the collections of common haplotypes and their frequencies, vary significantly among world populations. These differences are more extreme when the geographical locations for the populations are more distant. Some of the previous studies performed haplotype inference in multi-population samples with known population assignment. Others developed algorithms for clustering of the mixed haplotype or genotype samples with different block structures or genetic marker profiles. We present a new algorithm that performs haplotype inference and block partitioning in a mixed sample of genotypes from two populations when the population assignments are not known. Given a mixed genotype sample, the proposed algorithm (HAPLOCLUST) extracts two clusters of genotypes with different block structures in addition to performing haplotype inference on each of these clusters. When tested on a set of unrelated individuals, our algorithm provides correct assignments comparable to those of two state-of-the-art algorithms for population stratification. The contribution of HAPLOCLUST consists of performing haplotype/block-based population stratification and simultaneously finding the haplotype resolution and block partitioning for the extracted clusters.
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Salem, M. M. I., G. Thompson, S. Chen, A. Beja-Pereira, and J. Carvalheira. "Linkage disequilibrium and haplotype block structure in Portuguese Holstein cattle." Czech Journal of Animal Science 63, No. 2 (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 ( r<sup>2</sup>) were estimated and haplotype block analyses were performed using the Haploview software. The averages of D' and r<sup>2</sup> values were 0.628 and 0.122, respectively. The LD value decreased with increasing physical distance. The D' and r<sup>2</sup> 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 r<sup>2</sup> 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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Chen, Wen-Pei, Che-Lun Hung, and Yaw-Ling Lin. "Efficient Haplotype Block Partitioning and Tag SNP Selection Algorithms under Various Constraints." BioMed Research International 2013 (2013): 1–13. http://dx.doi.org/10.1155/2013/984014.

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Patterns of linkage disequilibrium plays a central role in genome-wide association studies aimed at identifying genetic variation responsible for common human diseases. These patterns in human chromosomes show a block-like structure, and regions of high linkage disequilibrium are called haplotype blocks. A small subset of SNPs, called tag SNPs, is sufficient to capture the haplotype patterns in each haplotype block. Previously developed algorithms completely partition a haplotype sample into blocks while attempting to minimize the number of tag SNPs. However, when resource limitations prevent genotyping all the tag SNPs, it is desirable to restrict their number. We propose two dynamic programming algorithms, incorporating many diversity evaluation functions, for haplotype block partitioning using a limited number of tag SNPs. We use the proposed algorithms to partition the chromosome 21 haplotype data. When the sample is fully partitioned into blocks by our algorithms, the 2,266 blocks and 3,260 tag SNPs are fewer than those identified by previous studies. We also demonstrate that our algorithms find the optimal solution by exploiting the nonmonotonic property of a common haplotype-evaluation function.
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YUAN, AO, GUANJIE CHEN, CHARLES ROTIMI, and GEORGE E. BONNEY. "A STATISTICAL FRAMEWORK FOR HAPLOTYPE BLOCK INFERENCE." Journal of Bioinformatics and Computational Biology 03, no. 05 (2005): 1021–38. http://dx.doi.org/10.1142/s021972000500151x.

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The existence of haplotype blocks transmitted from parents to offspring has been suggested recently. This has created an interest in the inference of the block structure and length. The motivation is that haplotype blocks that are characterized well will make it relatively easier to quickly map all the genes carrying human diseases. To study the inference of haplotype block systematically, we propose a statistical framework. In this framework, the optimal haplotype block partitioning is formulated as the problem of statistical model selection; missing data can be handled in a standard statistical way; population strata can be implemented; block structure inference/hypothesis testing can be performed; prior knowledge, if present, can be incorporated to perform a Bayesian inference. The algorithm is linear in the number of loci, instead of NP-hard for many such algorithms. We illustrate the applications of our method to both simulated and real data sets.
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Zhang, K., and L. Jin. "HaploBlockFinder: haplotype block analyses." Bioinformatics 19, no. 10 (2003): 1300–1301. http://dx.doi.org/10.1093/bioinformatics/btg142.

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Karkar, Slim, Claire Dandine-Roulland, Jean-François Mangin, et al. "Genome-wide haplotype association study in imaging genetics using whole-brain sulcal openings of 16,304 UK Biobank subjects." European Journal of Human Genetics 29, no. 9 (2021): 1424–37. http://dx.doi.org/10.1038/s41431-021-00827-8.

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AbstractNeuroimaging-genetics cohorts gather two types of data: brain imaging and genetic data. They allow the discovery of associations between genetic variants and brain imaging features. They are invaluable resources to study the influence of genetics and environment in the brain features variance observed in normal and pathological populations. This study presents a genome-wide haplotype analysis for 123 brain sulcus opening value (a measure of sulcal width) across the whole brain that include 16,304 subjects from UK Biobank. Using genetic maps, we defined 119,548 blocks of low recombination rate distributed along the 22 autosomal chromosomes and analyzed 1,051,316 haplotypes. To test associations between haplotypes and complex traits, we designed three statistical approaches. Two of them use a model that includes all the haplotypes for a single block, while the last approach considers each haplotype independently. All the statistics produced were assessed as rigorously as possible. Thanks to the rich imaging dataset at hand, we used resampling techniques to assess False Positive Rate for each statistical approach in a genome-wide and brain-wide context. The results on real data show that genome-wide haplotype analyses are more sensitive than single-SNP approach and account for local complex Linkage Disequilibrium (LD) structure, which makes genome-wide haplotype analysis an interesting and statistically sound alternative to the single-SNP counterpart.
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Bernig, Toralf, Willemijn Breunis, Nannette Brouwer, Dirk Roos, Taco W. Kuijpers, and Stephen J. Chanock. "Functional Consequences of Genetic Variation across the Entire MBL2 Locus: Possible Identification of 3′ SNPs That Could Modify Circulating Levels of MBL." Blood 104, no. 11 (2004): 1330. http://dx.doi.org/10.1182/blood.v104.11.1330.1330.

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Abstract Mannose-binding protein (MBL) is a critical component of innate immunity and provides first-line protection against pathogens by binding to N-acetyl-glucosamine and mannose residues on the surface of microorganisms (bacteria, fungi and parasites). MBL can activate complement by the lectin pathway. Both circulating MBL serum levels and functional activity have been correlated with common genetic variants in the MBL2 gene; decreased levels and activity correlate with 3 nonsynonymous single nucleotide polymorphisms, SNPs, (known as B, C and D) in exon 1 and two linked promoter SNPs (−550 H/L and −221 Y/X) as well as a 5′UTR SNP (+4 P/Q) influence circulating levels. These components form the “secretor haplotypes”, which correlate with circulating levels. A number of studies have reported associations between MBL deficiency and recurrent or severe infections, especially in immuno-incompetent patients (i.e., BMT recipients, cancer patients, and infants) or in auto-immune disorders; however, measured MBL serum levels do not fully correlate with the “secretor haplotypes”. Based on data from a re-sequence analysis across the entire MBL2 locus, in which we revealed a probable recombination hotspot in the 3′ end of the gene dividing MBL2 into two haplotype blocks, we investigated whether the extended block structure might identify additional SNPs that contribute to MBL serum levels and activity. We analysed more than 20 common SNPs across the locus, including haplotype-tagging SNPs (htSNPs) with Taqman assays validated on the SNP500 website (http://snp500cancer.nci.nih.gov); we captured more than 95% of common haplotypes in both the 5′ and 3′ haplotype blocks. Our pilot analysis was performed in 235 DNA samples of healthy Dutch Caucasian blood donors with known MBL serum concentrations measured by ELISA. Haplotypes were deduced by maximization-estimation analysis of unphased genotypes; PHASE 2.0 (http://www.stat.washington.edu/stephens/software.html). The haplotype analysis of the results confirmed the haplotype block structure of MBL2 in the Dutch population. The additional 5′ variants tested in this study were in strong linkage to the elements of the “secretor haplotypes”; functional alleles B, C and D also lie on restricted haplotypes. As reported by others, in our study, the secretor haplotypes predicted levels in roughly 85%. Four variants in the 3′ block (Ex4–1483T>C, Ex4–1067G>A, Ex4–901G>A and Ex4–710G>A) lie in 3 common haplotypes (TAAA, CGGG and TGAA) that strongly correlate with MBL serum concentration (Kruskal-Wallis p < 0.0001); individuals with at least one TAAA allele have a higher serum concentration. Thus, it is also possible that both 5′ and the 3′ haplotypes could contribute to serum levels. This suggests that there could be a selective advantage for diversification of the 3′ region of the gene, perhaps altering expression or stability (to be analyzed in follow-up studies). Our data provide evidence that there are additional SNPs in regulatory elements of MBL2, which could influence circulating levels. These observations could improve the predictive value of locus-wide analysis of MBL2 in genetic association studies.
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Nowak-Göttl, Ulrike, Birgit Fröhlich, Sabine Thedieck, Andreas Huge, and Monika Stoll. "Association of the protein Z ATG haplotype with symptomatic nonvascular stroke or thromboembolism in white children: a family-based cohort study." Blood 113, no. 10 (2009): 2336–41. http://dx.doi.org/10.1182/blood-2008-10-181461.

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Abstract To clarify the role of protein Z (PZ) in children with stroke/thromboembolism (TE), the present haplotype (HT)–based family study was performed. We genotyped 365 pediatric stroke/TE families (stroke n = 216; TE n = 149) for 4 single nucleotide polymorphisms (SNPs; rs3024718, rs3024731, rs3024772, and rs3024778) to assess the association between genetic variation within a conserved block of linkage disequilibrium harboring the PZ gene and pediatric TE. Association was assessed with use of the transmission disequilibrium test (TDT), corrected for multiple testing (permutation testing: HAPLOVIEW). In addition, PZ antigen was determined and correlated with carriership of PZ haplotypes and the FV G1691A mutation. Rs3024718, rs3024731, and rs3024772 are in tight linkage disequilibrium (LD) and define 4 haplotypes, capturing 97% of the genetic variation for this LD block. HT1 (ATG) was significantly overtransmitted from parents to affected offspring (HT frequency 73.5%, T:U 122:80, χ2 = 8.791, P = .003). The ATG risk haplotype was significantly correlated with greater PZ antigen levels. Multivariate analysis adjusted for age, sex, established thrombophilias, smoking, fibrinogen, and PZ levels revealed a significant association of the ATG haplotype and TE in children (odds ratio [OR] 1.4; 95% confidence interval [95% CI] 1.08-1.93). Our results suggest that the ATG haplotype of the PZ gene is a genetic marker for symptomatic TE in white German children.
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ESKIN, ELEAZAR, ERAN HALPERIN, and RICHARD M. KARP. "EFFICIENT RECONSTRUCTION OF HAPLOTYPE STRUCTURE VIA PERFECT PHYLOGENY." Journal of Bioinformatics and Computational Biology 01, no. 01 (2003): 1–20. http://dx.doi.org/10.1142/s0219720003000174.

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Each person's genome contains two copies of each chromosome, one inherited from the father and the other from the mother. A person's genotype specifies the pair of bases at each site, but does not specify which base occurs on which chromosome. The sequence of each chromosome separately is called a haplotype. The determination of the haplotypes within a population is essential for understanding genetic variation and the inheritance of complex diseases. The haplotype mapping project, a successor to the human genome project, seeks to determine the common haplotypes in the human population. Since experimental determination of a person's genotype is less expensive than determining its component haplotypes, algorithms are required for computing haplotypes from genotypes. Two observations aid in this process: first, the human genome contains short blocks within which only a few different haplotypes occur; second, as suggested by Gusfield, it is reasonable to assume that the haplotypes observed within a block have evolved according to a perfect phylogeny, in which at most one mutation event has occurred at any site, and no recombination occurred at the given region. We present a simple and efficient polynomial-time algorithm for inferring haplotypes from the genotypes of a set of individuals assuming a perfect phylogeny. Using a reduction to 2-SAT we extend this algorithm to handle constraints that apply when we have genotypes from both parents and child. We also present a hardness result for the problem of removing the minimum number of individuals from a population to ensure that the genotypes of the remaining individuals are consistent with a perfect phylogeny. Our algorithms have been tested on real data and give biologically meaningful results. Our webserver () is publicly available for predicting haplotypes from genotype data and partitioning genotype data into blocks.
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Dissertations / Theses on the topic "Haplotype block"

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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.<br>Ph.D.<br>Other<br>Engineering and Computer Science<br>Computer Science
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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.<br>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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Sazonova, Nadezhda A. "Parsimony-based genetic algorithm for haplotype resolution and block partitioning." Morgantown, W. Va. : [West Virginia University Libraries], 2007. https://eidr.wvu.edu/etd/documentdata.eTD?documentid=5499.

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Thesis (Ph. D.)--West Virginia University, 2007.<br>Title from document title page. Document formatted into pages; contains xi, 127 p. : ill. Includes abstract. Includes bibliographical references (p. 109-114).
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Zhang, Ruosi. "Simulations of Different P-values Combination Methods Using SNPs on Diverse Biology Levels." Digital WPI, 2019. https://digitalcommons.wpi.edu/etd-theses/1317.

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The method of combination p-values from multiple tests is the foundation for some studies like meta-analysis and detection of signal. There are tremendous methods have been developed and applied like minimum p-values, Cauchy Combination, goodness-of-fit combination and Fisher’s combination. In this paper, I tested their ability to detect signals which is related to real case in biology to find out significant single-nucleotide polymorphisms (SNPs). I simulated p-values for SNPs logistics regression model and test 7 combination methods’ power performance in different setting conditions. I compared sparse or dense signals, dependent or independent and combine them in gene-level or pathway-level. One method based on Fisher’s combination called Omni-TFisher is ideal for most of the situations. Recent years, genome-wide association studies (GWASs) focused on BMD-related SNPs at gene significance level. In this paper I used Omni-TFisher to analyses real data on haplotype blocks. As a result, haplotype blocks can find more SNPs in non-coding and intergeneric regions than gene-based and save computational complexity. It finds out not only known genes, but also other genes need further verification.
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Younkin, Samuel G. "The Linkage Disequilibrium LASSO for SNP Selection in Genetic Association Studies." Case Western Reserve University School of Graduate Studies / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=case1291219489.

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Nothnagel, Michael. "The definition of multilocus haplotype blocks and common diseases." [S.l.] : [s.n.], 2004. http://deposit.ddb.de/cgi-bin/dokserv?idn=973611448.

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Nothnagel, Michael. "The definition of multilocus haplotype blocks and common diseases." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2005. http://dx.doi.org/10.18452/15174.

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Bisherige Methoden der Haplotyp-Block-Definition zielen entweder auf abwesende Rekombinationsereignisse oder eine effiziente Beschreibung genomischer Variation. Die vorliegende Arbeit definiert Blöcke von Single Nucleotide Polymorphisms (SNP) als Gebiete erhöhten Kopplungsungleichgewichtes (LD). Für dieses Ziel wird ein neues, entropie-basiertes Maß für LD zwischen multiplen Markern/Loci (Normalized Entropy Difference) entwickelt und als eine Multilocus-Erweiterung des paarweisen Maßes r2 charakterisiert. Ein zugehöriger Algorithmus für die Block-Definition wird vorgeschlagen. Seine Evaluierung an einem Datensatz des menschlichen Chromosoms 12 vom Internationalen Haplotype Map Projekt zeigt die Nützlichkeit der abgeleiteten Blöcke in Hinblick auf verschiedene Eigenschaften, einschließlich ihrer chromosomalen Coverage und der Anzahl sowie des Anteils der häufigen Block-Haplotypen. Der wesentliche Einfluß der SNP-Dichte auf die zu entdeckenden LD- und Blockstrukturen wird demonstriert. Der Erfolg von Assoziationsstudien in komplexen Erkrankungen mit Block-Haplotypen als multiallelischen Markern wird davon abhängen, ob die Common Variants/Common Diseases (CV/CD) Hypothese für solche Erkrankungen erfüllt ist.<br>Current approaches to haplotype block definition target either absent recombination events or the efficient description of genomic variation. This thesis aims to define blocks of single nucleotide polymorphisms (SNP) as areas of elevated linkage disequilibrium (LD). To this end, a new entropy-based measure for LD between multiple markers/loci, the Normalized Entropy Difference, is developed and is characterized as a multilocus extension of the pairwise measure r2. A corresponding algorithm for the block definition is proposed. Its evaluation on a data set of human chromosome 12 from the International Haplotype Map project proves the usefulness of the derived blocks with respect to several features, including their chromosomal coverage and the number and portion of common block haplotypes. The critical role of the SNP density for detectable LD and block structure is demonstrated. The success of association studies in common diseases with block haplotypes serving as multi-allelic markers will depend on whether the Common Variants/Common Diseases (CV/CD) hypothesis holds true for those diseases.
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Azuero, Andres. "Comparisons of sequential testing approaches for detection of association between disease and haplotype blocks." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2009r/azuero.pdf.

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Borden, William Calvin. "Phylogeography of Smallmouth Bass (Micropterus Dolomieu) and Comparative Myology of the Black Bass (Micropterus, Centrarchidae)." Cleveland State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=csu1209066783.

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Andrade, Edilene Santos de. "Desequilíbrio de Ligação e Blocos de Haplótipos Determinados pela Análise de 250K SNPs em Três Remanescentes de Quilombos." Universidade de São Paulo, 2013. http://www.teses.usp.br/teses/disponiveis/17/17135/tde-24102013-105202/.

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A associação não aleatória entre alelos de diferentes lócus caracteriza o que é chamado de desequilíbrio de ligação (DL) entre eles. A extensão do DL nas populações humanas pode ser influenciada por muitos fatores, tais como taxa de recombinação, características demográficas (idade, tamanho e taxa de crescimento) e fatores evolutivos (deriva genética, efeito fundador, gargalos populacionais, mutação, seleção e fluxo gênico). Portanto, o conhecimento dos padrões do DL fornecem dados que auxiliam na descrição dos eventos demográficos e evolutivos sofridos pelas populações. O objetivo deste estudo foi descrever os padrões de DL de quatro populações brasileiras e correlacioná-los com suas respectivas histórias demográficas, uma vez que estas populações experimentaram alguns dos eventos evolutivos que geram ou retardam o decréscimo do DL, como fundação por poucos indivíduos, miscigenação no momento da fundação e posterior isolamento. Foram analisadas amostras de três populações remanescentes de quilombos do Estado do Piauí, Gaucinha (GAU, n = 14), Mimbó (MIB, n = 15) e Sítio Velho (STV, n = 15) e da população urbana de Teresina, Piauí (TES, n = 15), além de sete amostras populacionais do projeto HapMap (CEU, CHB, JPT, ASW, LWK, MKK, YRI, todas com n = 15). Foram genotipados mais de 250 mil SNPs (Single Nucleotide Polymorphisms) utilizando-se o GeneChip® Human Mapping 250K Nsp I Array - Affymetrix® nas amostras das quatro populações brasileiras. Os dados brutos das populações do HapMap para este array foram obtidos na página do projeto. Os genótipos para todas as amostras foram determinados pelo algoritmo CRLMM após comparação com o algoritmo BRLMM, e as análises de DL e determinação dos blocos de haplótipos foram realizadas com o uso do programa Haploview. Considerando-se o número de blocos de haplótipos detectados em cada população estudada, padrão semelhante foi observado em todos os autossomos. Em geral, a população europeia (CEU) e as duas populações asiáticas (CHB e JPT) do HapMap apresentaram os maiores números de blocos, enquanto que os menores números foram observados nos quilombos GAU e MIB e na população TES. As populações africanas LWK, MKK e YRI e a população afro-americana ASW apresentaram os valores intermediários e a população afro-brasileira STV, apresentou um número de blocos apenas inferior a CEU, CHB e JPT. A grande contribuição africana nos quilombos GAU e MIB pode explicar o menor DL observado nestas comunidades. Por outro lado, o menor DL em TES se deve, provavelmente, à sua fundação, que envolveu um maior número de indivíduos e foi seguida por um rápido crescimento. A possível explicação para o maior DL observado em STV, em relação aos demais quilombos, consiste em sua peculiar história demográfica: esta comunidade experimentou uma miscigenação no momento de sua fundação, que foi seguida por um crescimento lento e pouca diferenciação. Assim, foi demonstrado como os eventos demográficos de cada população influenciam seus respectivos padrões de DL.<br>The non-random association between alleles of different loci characterizes what is called linkage disequilibrium (LD) between them. The LD extent in human populations can be influenced by many factors, such as recombination rate, demographic features (age, size and growth rate) and evolutionary events (genetic drift, founder effects, population bottlenecks, mutation, selection and gene flow). Therefore, knowledge of the LD patterns provides data that assists in describing the evolutionary and demographic events experienced by populations. The aim of this study was to describe the LD patterns of four Brazilian populations and correlate these patterns with their respective demographic histories, since these populations have experienced some of the evolutionary events that produce or retard the LD decrease, such as foundation by few individuals, admixture at the founding moment and subsequent isolation. Samples from three quilombo remnants populations of the Piauí State, Gaucinha (GAU, n = 14), Mimbó (MIB, n = 15) and Sítio Velho (STV, n = 15) and the urban population of Teresina, Piauí (TES, n = 15), and seven population samples from the HapMap Project (CEU, CHB, JPT, ASW, LWK, MKK, YRI, all with n = 15) were analyzed. More than 250 thousand SNPs (Single Nucleotide Polymorphisms) were genotyped using the GeneChip ® Human Mapping 250K Nsp Array I - Affymetrix ® in the samples of the four Brazilian populations. Raw data of the HapMap population samples for this array were obtained from the HapMap homepage. Genotypes for all samples were determined by CRLMM algorithm after comparison with the BRLMM algorithm. LD analyzes and determination of haplotype blocks were performed using the Haploview software. Considering the number of haplotype blocks detected in each population, a consistent pattern was observed for all autosomes. The European population (CEU) and the two Asian populations (CHB and JPT) of the HapMap showed the highest numbers of blocks, while the lowest numbers were observed in the GAU and MIB quilombos and in the TES population. The African populations, LWK, MKK and YRI, and the African-American ASW exhibited intermediate values and the African-Brazilian population STV, presented a number of blocks smaller than that observed for CEU, CHB and JPT. The great African contribution in the GAU and MIB quilombos may explain the lower LD observed in these communities. On the other hand, the lower LD in TES is probably due to its foundation that involved a larger number of individuals and was followed by a fast growth. A possible explanation for the higher LD observed in STV, compared to other quilombos, consists in its particular demographic history: this community experienced admixture at the time of its foundation, which was followed by slow growth and low differentiation. Thus, it was shown how the demographic events of each population influence their respective LD patterns.
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Books on the topic "Haplotype block"

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

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Book chapters on the topic "Haplotype block"

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Zheng, Maoxia, and Mary Sara McPeek. "Assessment of Goodness of Fit of Models for Block Haplotype Structure." In Computational Methods for SNPs and Haplotype Inference. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_32.

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Sun, Fengzhu. "Dynamic Programming Algorithms for Haplotype Block Partition and Applications to Association Studies." In Computational Methods for SNPs and Haplotype Inference. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_28.

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Zheng, Maoxia, and Mary Sara McPeek. "Parametric Bootstrap for Assessment of Goodness of Fit of Models for Block Haplotype Structure." In Computational Methods for SNPs and Haplotype Inference. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_9.

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Zhang, Kui, Ting Chen, Michael S. Waterman, Zhaohui S. Qin, Jun S. Liu, and Fengzhu Sun. "Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data." In Computational Methods for SNPs and Haplotype Inference. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_8.

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Thompson, E. A., and N. H. Chapman. "Haplotype Blocks in Small Populations." In Computational Methods for SNPs and Haplotype Inference. Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-540-24719-7_6.

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Cunha, Luís, Yoan Diekmann, Luis Kowada, and Jens Stoye. "Identifying Maximal Perfect Haplotype Blocks." In Advances in Bioinformatics and Computational Biology. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-030-01722-4_3.

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Song, Yun S., and Jotun Hein. "Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks." In Lecture Notes in Computer Science. Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-540-39763-2_22.

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Bonizzoni, Paola, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, and Mattia Sgrò. "Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT." In Bioinformatics and Biomedical Engineering. Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-34953-9_5.

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Williams, Lucia, and Brendan Mumey. "Extending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics." In Algorithms for Computational Biology. Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-42266-0_4.

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Zhang, Xueyong, and Rudi Appels. "Genome Sequence-Based Features of Wheat Genetic Diversity." In Compendium of Plant Genomes. Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-38294-9_6.

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AbstractCommon wheat is a hexaploid species crop that is widely recognized as an important staple food crop. The establishment of a gold standard reference genome sequences of the well-studied CHINESE SPRING, and its progenitors (including Triticum turgidum ssp. dicoccoides accession Zavitan, Triticum durum accession Svevo, Triticum urartu, Aegilops tauschii), in the last 5 years has dramatically promoted our understanding of wheat genome diversity and evolution through the resequencing of collections of wheat and its progenitors. In this chapter, we review progress in the analysis and interpretation of genome‑based studies of wheat focusing on geographic genome differentiation, interspecies gene flow, haplotype blocks, and gene diversity in breeding. We also consider approaches for efficiently discovering and integrating the genes and genome variations, hidden in Genebank collections, into wheat breeding programs.
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Conference papers on the topic "Haplotype block"

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ZHU, X., S. ZHANG, D. KAN, and 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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KOIVISTO, M., M. PEROLA, T. VARILO, et al. "AN MDL METHOD FOR FINDING HAPLOTYPE BLOCKS AND FOR ESTIMATING THE STRENGTH OF HAPLOTYPE BLOCK BOUNDARIES." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776303_0047.

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Greenspan, Gideon, and Dan Geiger. "Model-based inference of haplotype block variation." In the seventh annual international conference. ACM Press, 2003. http://dx.doi.org/10.1145/640075.640092.

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Zhang, Kui, Fengzhu Sun, Michael S. Waterman, and Ting Chen. "Dynamic programming algorithms for haplotype block partitioning." In the seventh annual international conference. ACM Press, 2003. http://dx.doi.org/10.1145/640075.640119.

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CASTELLANA, NATALIE, KEDAR DHAMDHERE, SRINATH SRIDHAR, and RUSSELL SCHWARTZ. "RELAXING HAPLOTYPE BLOCK MODELS FOR ASSOCIATION TESTING." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2005. http://dx.doi.org/10.1142/9789812701626_0042.

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Yang, Yinghua, and Ioan Tabus. "Haplotype Block Partitioning using a Normalized Maximum Likelihood Model." In 2007 IEEE International Workshop on Genomic Signal Processing and Statistics. IEEE, 2007. http://dx.doi.org/10.1109/gensips.2007.4365840.

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Al-Khalifa, Azza M., Mohamed N. Saad, Muhammad A. Rushdi, and Ayman M. Eldeib. "Multithreaded Haplotype Block Partitioning of Rheumatoid Arthritis Genomic Data." In 2023 IEEE EMBS Special Topic Conference on Data Science and Engineering in Healthcare, Medicine and Biology. IEEE, 2023. http://dx.doi.org/10.1109/ieeeconf58974.2023.10404920.

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"Haplotype Block Analysis of FSHR Gene in Sragen and Jabres Cattle." In Technology Innovations and Collaborations in Livestock Production for Sustainable Food Systems. IAARD Press, 2021. http://dx.doi.org/10.14334/proc.intsem.lpvt-2021-p.16.

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Yun Xu, Ying Wang, Xiaohui Yao, and Yuzhong Zhao. "An EM method based on entropy LD block partition for haplotype inference." In 2010 IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA). IEEE, 2010. http://dx.doi.org/10.1109/bicta.2010.5645337.

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Ibrahim, Fatma S., Mohamed N. Saad, Ashraf M. Said, and Hesham F. A. Hamed. "Haplotype Block Partitioning for NARAC Dataset Using Interval Graph Modeling of Clusters Algorithm." In 2018 9th Cairo International Biomedical Engineering Conference (CIBEC). IEEE, 2018. http://dx.doi.org/10.1109/cibec.2018.8641758.

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