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Haplotype block definition and its application

X Zhu, S Zhang, D Kan, R Cooper
2004 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
We present a simple two-stage procedure to define haplotype blocks and construct a statistic to test whether a polymorphism belongs to a block.  ...  Furthermore, across regions of the genome and among the four populations that were studied, we found that linkage disequilibrium between a given single nucleotide polymorphism (SNP) and the haplotype block  ...  In detail, we begin by generating a block definition in two steps: first, we define a basic block, then we extend it by sequential addition of the SNPs.  ... 
pmid:14992500 fatcat:jbocm4slo5h6jafyvveo6dskim

htSNPer1.0: software for haplotype block partition and htSNPs selection

Keyue Ding, Jing Zhang, Kaixin Zhou, Yan Shen, Xuegong Zhang
2005 BMC Bioinformatics  
We develop a software htSNPer1.0 to implement the algorithm, and integrate three htSNPs performance criteria and four haplotype block definitions for haplotype block partitioning.  ...  There is recently great interest in haplotype block structure and haplotype tagging SNPs (htSNPs) in the human genome for its implication on htSNPs-based association mapping strategy for complex disease  ...  and NSFC (Grants 39625007 and 39993420 to Y.S, 60275007 and 60234020 to X.Z).  ... 
doi:10.1186/1471-2105-6-38 pmid:15740612 pmcid:PMC1274247 fatcat:gsyuzp5b55bx5lvrwmgl3mbslm

HaploBlockFinder: haplotype block analyses

K. Zhang, L. Jin
2003 Bioinformatics  
Three definitions of haplotype block are supported, including minimal LD range, no historic recombination, and chromosome coverage.  ...  Two separate utilities were also provided to assist visual inspection of haplotype block structure and pattern of linkage disequilibrium.  ...  This program has several distinct features: • The structure of this program is independent of haplotype block definition, because definitions are usually † To whom correspondence should be addressed. application-dependent  ... 
doi:10.1093/bioinformatics/btg142 pmid:12835279 fatcat:bhkfht4cencsfpskrwmjyqs3qa

Will haplotype maps be useful for finding genes?

E J C G van den Oord, B M Neale
2003 Molecular Psychiatry  
We first take a closer look at the nature of haplotype blocks and then address the impact of block definitions and methodological factors, such as singlenucleotide polymorphism density and sample size,  ...  These queries involve the extent to which the haplotype blocks exist, the validity of fundamental concepts such as the recombination hotspot, and the application of this idea in the form of the HapMap  ...  Acknowledgements EvdO was supported in part by grants from the US National Institute of Mental Health (MH065320) and NARSAD.  ... 
doi:10.1038/sj.mp.4001449 pmid:14610524 fatcat:afj4rrzqknaffdsggimftthywu

HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations

S. Gu, A. J. Pakstis, K. K. Kidd
2005 Bioinformatics  
We present here a win32 system based Perl/Tk application for visual comparisons of these variations in different populations. Availability: The application package is available at  ...  Variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations can be used to infer the evolutionary pattern.  ...  Here, we present a win32 system based application, HAPLOT, for graphical comparisons of haplotype blocks, selected tagSNPs and SNP heterozygosity among populations.  ... 
doi:10.1093/bioinformatics/bti649 pmid:16131520 fatcat:2hm5ym5ajrd3ljf4po5lg6jahi

Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition

Eleftheria Zeggini, Anne Barton, Stephen Eyre, Daniel Ward, William Ollier, Jane Worthington, Sally John
2005 BMC Genetics  
The relative applicability of distinct block definitions to association studies, however, remains unclear.  ...  Blocks were found to be shorter and coverage of the region limited with methods based on LD measures, compared to the method based on haplotype diversity.  ...  This work was supported by funding from the MRC and arc, UK.  ... 
doi:10.1186/1471-2156-6-21 pmid:15850495 pmcid:PMC1090572 fatcat:rvhm4de72vgq3iodjsuvukojeq

Efficient haplotype block recognition of very long and dense genetic sequences

Daniel Taliun, Johann Gamper, Cristian Pattaro
2014 BMC Bioinformatics  
Conclusions: The MIG ++ enables to perform LD-based haplotype block recognition on genetic sequences of any length and density.  ...  Our most efficient solution, called MIG ++ , has only (n) memory complexity and, on a genome-wide scale, it omits >80% of the calculations, which makes it an order of magnitude faster than the original  ...  Weichenberger (European Academy of Bozen/Bolzano), and Cosetta Minelli (Imperial College London) for their valuable comments and helpful discussion.  ... 
doi:10.1186/1471-2105-15-10 pmid:24423111 pmcid:PMC3898000 fatcat:62a5vp5lw5edjcq72k542inqnq

iHAP--integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

Chun Meng Song, Boon Huat Yeo, Erwin Tantoso, Yuchen Yang, Yun Ping Lim, Kuo-Bin Li, Gunaretnam Rajagopal
2006 BMC Bioinformatics  
haplotype blocks and selecting tag SNPs that are representative of haplotype patterns.  ...  These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags.  ...  This work is supported by the Biomedical Research Council of the Agency for Science, Technology and Research (A*STAR) of Singapore.  ... 
doi:10.1186/1471-2105-7-525 pmid:17137522 pmcid:PMC1698582 fatcat:ffq3uzlio5cctoxvj6oji6ss2e

HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms

K. Zhang, Z. Qin, T. Chen, J. S. Liu, M. S. Waterman, F. Sun
2004 Bioinformatics  
Compared to other programs for haplotype block partitioning and tag SNP selection, our program has several notable features.  ...  Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program.  ...  R01ES09912 and NIH U54CA100949 (K.Z.).  ... 
doi:10.1093/bioinformatics/bth482 pmid:15333454 fatcat:ri2cna7rj5bzddb6edytgahd5a

Finding all maximal perfect haplotype blocks in linear time

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye
2020 Algorithms for Molecular Biology  
Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets.  ...  _3) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans.  ...  Henrichs for providing a script to convert VCF files to haplotype matrices and for assisting with the production of Figure 3 .  ... 
doi:10.1186/s13015-020-0163-6 pmid:32055252 pmcid:PMC7008532 fatcat:hksvts5candxxbpa7e53bbf724

Global haplotype partitioning for maximal associated SNP pairs

Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk, Elahe Elahi
2009 BMC Bioinformatics  
We set limits on the maximum acceptable proportion of independent pairs within all blocks and search for the partitioning with maximal proportion of associated SNP pairs.  ...  Compared to methods of haplotype block partitioning, we performed best on detection of recombination hotspots.  ...  Authors wish to thank Changiz Eslahchi (SBU, Tehran) and Mehrdad Pedram (TUMS, Tehran) repectively for comments on the method and editing the text.  ... 
doi:10.1186/1471-2105-10-269 pmid:19712447 pmcid:PMC2749056 fatcat:6cywpbdahrgyjgsva4sdhwzxh4

Software for tag single nucleotide polymorphism selection

Daniel O Stram
2005 Human Genomics  
A distinction between haplotype block-based and non-block-based approaches yields two classes of procedures.  ...  Block-based methods that exploit the linkage disequilibrium structure within haplotype blocks exploit this sort of redundancy, but run a risk of over-fitting if used without some care.  ...  Because the block-based approaches are, by definition, restricted to working within some sort of haplotype block definition (many have been considered in the literature), a problem arises; tag SNPs selected  ... 
doi:10.1186/1479-7364-2-2-144 pmid:16004730 pmcid:PMC3525260 fatcat:h2cfbtp75fcf3kvx4srykfuefu

The Haplotyping problem: An overview of computational models and solutions

Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li
2003 Journal of Computer Science and Technology  
This paper is a comprehensive study of some new combinatorial approaches proposed in this research area and it mainly focuses on the formulations and algorithmic solutions of some basic biological problems  ...  known as Haplotyping.  ...  The above facts make it interesting to build a SNP haplotype map that consists of the information of haplotype block structure, common haplotypes and their frequencies which, hopefully, could be used to  ... 
doi:10.1007/bf02945456 fatcat:liooyhtz55arjnwexxq7ooeare

D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples

K. Higasa, K. Miyatake, Y. Kukita, T. Tahira, K. Hayashi
2007 Nucleic Acids Research  
The database also presents maps of haplotype blocks and linkage disequilibrium bins together with tagSNPs that might prove useful for association studies of disease genes.  ...  The Definitive Haplotype Database (D-HaploDB) is a web-accessible resource of genome-wide definitive haplotypes determined from a collection of Japanese complete hydatidiform moles (CHMs), each of which  ...  Haplotype blocks and LD bins In D-HaploDB, haplotype blocks were partitioned using the methods of Zhang et al. (HapBlock v30) (11) .  ... 
doi:10.1093/nar/gkl848 pmid:17166862 pmcid:PMC1781173 fatcat:5innlmi5bndh3hgq7k7icgtkp4

Maximal Perfect Haplotype Blocks with Wildcards

Lucia Williams, Brendan Mumey
2020 iScience  
Missing values are treated as wildcards, and the definition of maximal perfect haplotype blocks is extended in a natural way.  ...  In this work, we consider the problem of finding maximal perfect haplotype blocks where some missing values may be present.  ...  Acknowledgements Support provided by US National Science Foundation grants DBI-1759522 and DBI-1661530.  ... 
doi:10.1016/j.isci.2020.101149 pmid:32446220 pmcid:PMC7243190 fatcat:vkmgkw4npzg5jhok24w7kffog4
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