A comparison of the association between large haplotype blocks under selection and the presence/absence of inversions
Sign Up to like & getrecommendations! Published in 2019 at "Ecology and Evolution"
DOI: 10.1002/ece3.5094
Abstract: Abstract Inversions may contribute to ecological adaptation and phenotypic diversity, and with the advent of “second” and “third” generation sequencing technologies, the ability to detect inversion polymorphisms has been enhanced dramatically. A key molecular consequence… read more here.
Keywords: large haplotype; inversion; presence; selection ... See more keywords
Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA
Sign Up to like & getrecommendations! Published in 2017 at "Nature genetics"
DOI: 10.1038/ng.3805
Abstract: Adjacent CpG sites in mammalian genomes can be co-methylated owing to the processivity of methyltransferases or demethylases, yet discordant methylation patterns have also been observed, which are related to stochastic or uncoordinated molecular processes. We… read more here.
Keywords: methylation; deconvolution heterogeneous; haplotype blocks; tissue ... See more keywords
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbaa227
Abstract: The triangular correlation heatmap aiming to visualize the linkage disequilibrium (LD) pattern and haplotype block structure of SNPs is ubiquitous component of population-based genetic studies. However, current tools suffered from the problem of time and… read more here.
Keywords: variant call; format files; haplotype blocks; haplotype ... See more keywords
On the origin and structure of haplotype blocks
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DOI: 10.1111/mec.16793
Abstract: The term “haplotype block” is commonly used in the developing field of haplotype‐based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains… read more here.
Keywords: ecology; structure; structure haplotype; haplotype blocks ... See more keywords
Prioritized candidate causal haplotype blocks in plant genome-wide association studies
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DOI: 10.1371/journal.pgen.1010437
Abstract: Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have… read more here.
Keywords: haplotype blocks; candidate causal; genome wide; gwas ... See more keywords
HaploBlocker: Creation of Subgroup-Specific Haplotype Blocks and Libraries.
Sign Up to like & getrecommendations! Published in 2019 at "Genetics"
DOI: 10.1534/genetics.119.302283
Abstract: The concept of haplotype blocks has been shown to be useful in genetics. Fields of application range from the detection of regions under positive selection to statistical methods that make use of dimension reduction... The… read more here.
Keywords: haploblocker creation; subgroup specific; genetics; creation subgroup ... See more keywords
Genomic prediction with haplotype blocks in wheat
Sign Up to like & getrecommendations! Published in 2023 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2023.1168547
Abstract: Haplotype blocks might carry additional information compared to single SNPs and have therefore been suggested for use as independent variables in genomic prediction. Studies in different species resulted in more accurate predictions than with single… read more here.
Keywords: genomic prediction; haplotype blocks; prediction; prediction accuracies ... See more keywords