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Whole genome association mapping by incompatibilities and local perfect phylogenies

Thomas Mailund, Søren Besenbacher, Mikkel H Schierup
2006 BMC Bioinformatics  
This perfect phylogenetic tree is treated as a decision tree for determining disease status, and scored by its accuracy as a decision tree.  ...  Results: We present a fast method for accurate localisation of disease causing variants in high density case-control association mapping experiments with large numbers of cases and controls.  ...  Sainudiin and Y. Song for fruitful discussions and tests of the software, and E.B. Knudsen for improving the English of this manuscript. We are grateful to E.  ... 
doi:10.1186/1471-2105-7-454 pmid:17042942 pmcid:PMC1624851 fatcat:knyldrrgozhqxdupge7ujuskkm

Page 748 of Genetics Vol. 181, Issue 2 [page]

2009 Genetics  
Other haplotype-based methods for association map- ping in case/control studies have previously been adapted to mapping of quantitative traits, including the HapMiner method (LI ef al. 2006) and the QHPM  ...  METHODS Building local genealogies: At any given locus in the genome, the chromosomes of our sampled individuals are related by a tree genealogy.  ... 

Efficient whole-genome association mapping using local phylogenies for unphased genotype data

Z. Ding, T. Mailund, Y. S. Song
2008 Bioinformatics  
From unphased genotype data, our algorithm builds local phylogenies along the genome, and scores each tree according to the clustering of cases and controls.  ...  Results: In this paper, we devise an efficient method for scanning unphased whole-genome data for association.  ...  FUNDING AND ACKNOWLEDGMENT This research is supported in part by NSF grant IIS-0513910 (ZD); by the Danish Research Agency FNU grant 272-07-0380 (TM); and by NIH grants 1K99-GM080099 and 4R00-GM080099  ... 
doi:10.1093/bioinformatics/btn406 pmid:18667442 pmcid:PMC2553438 fatcat:v5j2vwflezcwhgaux7pue2xcmy

Local Phylogeny Mapping of Quantitative Traits: Higher Accuracy and Better Ranking Than Single-Marker Association in Genomewide Scans

S. Besenbacher, T. Mailund, M. H. Schierup
2008 Genetics  
The method builds local genealogies along the genome and looks for a significant clustering of quantitative trait values in these trees.  ...  We analyze its efficiency in terms of localization and ranking of true positives among a large number of negatives and compare the results with single-marker approaches.  ...  The method constructs a rough estimate of the local phylogenies along the genome and scores these with respect to the clustering of phenotypes on the tree.  ... 
doi:10.1534/genetics.108.092643 pmid:19064712 pmcid:PMC2644962 fatcat:uiyizvebsvhrzmco7vcpfxmtca

HTreeQA: Using Semi-Perfect Phylogeny Trees in Quantitative Trait Loci Study on Genotype Data

Zhaojun Zhang, Xiang Zhang, Wei Wang
2012 G3: Genes, Genomes, Genetics  
Local phylogeny-based methods have been demonstrated to be powerful tools for uncovering significant associations between phenotypes and single-nucleotide polymorphism markers.  ...  The semi-perfect phylogeny trees are used as high-level markers for association study. HTreeQA uses the genotype data as direct input without phasing.  ...  These methods examine possible groupings induced by each local phylogeny and report the ones showing strong statistical associations with the phenotype.  ... 
doi:10.1534/g3.111.001768 pmid:22384396 pmcid:PMC3284325 fatcat:gh2qmjt24rhjxicoe4nwcvgvle

HAPLOTYPE INFERENCE FROM SHORT SEQUENCE READS USING A POPULATION GENEALOGICAL HISTORY MODEL [chapter]

JIN ZHANG, YUFENG WU
2010 Biocomputing 2011  
Our method is finding the most likely haplotypes whose local genealogical history can be approximately modeled as a perfect phylogeny.  ...  In this paper, we study a population genomics problem motivated by the newly available short reads data from high-throughput sequencing.  ...  Funding and Acknowledgment The research is supported by grants from U.S. National Science Foundation (IIS-0803440, IIS-0916948 and IIS-0953563).  ... 
doi:10.1142/9789814335058_0030 fatcat:ipzrpwcu5fhrbkkh7qo4mjtn4e

Supergene evolution triggered by the introgression of a chromosomal inversion [article]

Paul Jay, Annabel Whibley, Lise Frezal, Angeles de Cara, Reuben W. Nowell, James Mallet, Kanchon K. Dasmahapatra, Mathieu Joron
2017 bioRxiv   pre-print
These "superalleles" have evolved from a chromosomal inversion captured by introgression and maintained in balanced polymorphism, triggering supergene inheritance.  ...  This mode of evolution is likely to be a common feature of complex structural polymorphisms associated with the coexistence of distinct adaptive syndromes, and shows that the reticulation of genealogies  ...  To search for such patterns, we computed a whole genome phylogeny and several phylogenies at different locations within and outside the inversion.The whole genome phylogeny was obtained with SNPhylo 43  ... 
doi:10.1101/234559 fatcat:faeek3m7tjas3eghridihwnmue

Modeling Mito-nuclear Compatibility and its Role in Species Identification

Débora Princepe, Marcus A M de Aguiar
2020 Systematic Biology  
We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally.  ...  Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes.  ...  First we analyzed the effect in the interacting genes -the whole mitochondrial genome and the first B M = 500 sites of the nuclear genome ( Fig. 6a) .  ... 
doi:10.1093/sysbio/syaa044 pmid:32497198 fatcat:gqxi4rg7fvarjjjclebsmfhyxm

Ten Years of the Collaborative Cross

David W. Threadgill, Gary A. Churchill
2012 G3: Genes, Genomes, Genetics  
by the CC project.  ...  The February 2012 issues of GENETICS and G3: Genes, Genomes, Genetics present a collection of articles reporting recent advances from the international Collaborative Cross (CC) project.  ...  multi-parental inbred lines (Broman 2005) , and QTL mapping simulations to predict the eventual power of the CC (Valdar et al. 2006) .  ... 
doi:10.1534/g3.111.001891 pmid:22384393 pmcid:PMC3284322 fatcat:pk53tkeihbhxvkdyfelvni6x3m

Reconstructing metastatic seeding patterns of human cancers

Johannes G. Reiter, Alvin P. Makohon-Moore, Jeffrey M. Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine A. Iacobuzio-Donahue, Bert Vogelstein, Martin A. Nowak
2017 Nature Communications  
and " are evolutionarily incompatible and no perfect and persistent phylogeny can explain these data ( Supplementary Fig. 2 ).  ...  No perfect and persistent phylogeny exists for the given data.  ...  If an identified evolutionarily incompatible mutation pattern has a reliability score higher than expected just by false-positives and false-negatives, we hypothesize that a metastasis might have been  ... 
doi:10.1038/ncomms14114 pmid:28139641 pmcid:PMC5290319 fatcat:25avxzcat5ddro6tysdkknom2u

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

James B. Pease, David C. Haak, Matthew W. Hahn, Leonie C. Moyle, David Penny
2016 PLoS Biology  
By analyzing patterns of genetic variation in thousands of PLOS Biology | expressed genes from multiple populations and species, we identify genome-wide signatures of rapid consecutive speciation events  ...  Lycopersicon), we infer the species phylogeny and patterns of genetic diversity in this group.  ...  Acknowledgments We thank Jamie Kostyun for assistance with tissue collection and RNA extraction, C. J.  ... 
doi:10.1371/journal.pbio.1002379 pmid:26871574 pmcid:PMC4752443 fatcat:tg7acededfb2jaeoiwlydncrzy

Evaluating Impacts of Syntenic Block Detection Strategies on Rearrangement Phylogeny Using Mycobacterium tuberculosis Isolates [article]

Afif Elghraoui, Siavash Mirarab, Krister M. Swenson, Faramarz Valafar
2022 bioRxiv   pre-print
Phylogenetic inference based on genomic structural variations, that manipulate the gene order and content of whole chromosomes, promises to inform a more comprehensive understanding of evolution.  ...  We test several methods for detecting homology and obtaining syntenic blocks, and two methods for inferring phylogenies, comparing them to the standard method that uses substitutions for inferring the  ...  SibeliaZ [Minkin and Medvedev, 2020 ] is a whole-genome alignment method for closely-related genomes based on de Bruijn graph analysis.  ... 
doi:10.1101/2022.02.18.481113 fatcat:7nkk3m6pjbcvjhvqltnojuvsye

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery

Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013 Journal of Computational Biology  
Our method then leverages the inferred phylogeny to improve the accuracy of SNV discovery.  ...  Next-generation sequencing technologies provide a powerful tool for studying genome evolution during progression of advanced diseases such as cancer.  ...  These assumptions are reasonable in the context of cancer genomics. Following the perfect phylogeny assumption, true variant calls are tree compatible.  ... 
doi:10.1089/cmb.2013.0106 pmid:24195709 pmcid:PMC3822366 fatcat:syr7jzsxnvgftblgpkhfrfutby

Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery [chapter]

Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E. Newburger, Robert B. West, Arend Sidow, Serafim Batzoglou
2013 Lecture Notes in Computer Science  
Our method then leverages the inferred phylogeny to improve the accuracy of SNV discovery.  ...  Next-generation sequencing technologies provide a powerful tool for studying genome evolution during progression of advanced diseases such as cancer.  ...  These assumptions are reasonable in the context of cancer genomics. Following the perfect phylogeny assumption, true variant calls are tree compatible.  ... 
doi:10.1007/978-3-642-37195-0_21 fatcat:2ajs67wvpjdhzah2gduodactqq

Dynamics of Rex3 in the genomes of endangered Iberian Leuciscinae (Teleostei, Cyprinidae) and their natural hybrids

Pereira Carla, Pazian Marlon, Rab Petr, Collares-Pereira Maria
2015 Frontiers in Marine Science  
With highly conservative karyotypes, Iberian Chondrostoma s.l. have recently demonstrated sub-chromosomal differentiation and rapid genome restructuring in natural hybrids, which was confirmed by ribosomal  ...  It helped outlining conceivable ancestral homologies and recognizing retrotransposon activation in hybrids, being possibly associated with genome diversification within the subfamily.  ...  Acknowledgements The study was supported by Centro  ... 
doi:10.3389/conf.fmars.2015.03.00024 fatcat:popua6ajs5b73buqscvqapgymq
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