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Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements

Leila Taher, Ivan Ovcharenko
2009 Computer applications in the biosciences : CABIOS  
the ascertainment bias from the functional characterization of non-coding elements.  ...  We introduce a set of correction coefficients for the probabilities of the GO categories that accounts for the variability in the length of the non-coding DNA across different loci and effectively eliminates  ...  ACKNOWLEDGEMENTS We thank Adam Woolfe for his helpful comments on the article, as well as three anonymous reviewers.  ... 
doi:10.1093/bioinformatics/btp043 pmid:19168912 pmcid:PMC2647827 fatcat:wmdwto7agzh4djjmbvut4epome

Genome-Wide Analysis of Natural Selection on Human Cis-Elements

Praveen Sethupathy, Hoa Giang, Joshua B. Plotkin, Sridhar Hannenhalli, Matthew W. Hahn
2008 PLoS ONE  
It has been speculated that the polymorphisms in the non-coding portion of the human genome underlie much of the phenotypic variability among humans and between humans and other primates.  ...  However, the non-coding region is a heterogeneous mix of functional and non-functional regions.  ...  However, only recently has it become possible to infer natural selection on entire classes of non-coding elements due to the availability of genome-wide validated single nucleotide polymorphism (SNP) data  ... 
doi:10.1371/journal.pone.0003137 pmid:18781197 pmcid:PMC2522239 fatcat:bj244i4ppjdtxabhqcqfiudmvy

Abundant Raw Material for Cis-Regulatory Evolution in Humans

Matthew V. Rockman, Gregory A. Wray
2002 Molecular biology and evolution  
We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed.  ...  Ordinary smallscale mutations contribute to pervasive variation in transcription rates and consequently to patterns of human phenotypic variation.  ...  Acknowledgments We thank the National Science Foundation and NASA for support and E. Davidson  ... 
doi:10.1093/oxfordjournals.molbev.a004023 pmid:12411608 fatcat:p4mtgongtzfczodz6j35yenkli

Elevated Basal Slippage Mutation Rates among the Canidae

Jeffrey Laidlaw, Yevgeniy Gelfand, Kar-Wai Ng, Harold R. Garner, Rama Ranganathan, Gary Benson, John W. Fondon
2007 Journal of Heredity  
of polymorphism, but the fragmentary nature of the available dog genome sequence thwarted attempts to distinguish between locus-specific and genome-wide origins of this disparity.  ...  Building on the approach that gave rise to the initial observation in dogs, we sequenced 55 coding repeat regions in 42 species representing 10 major carnivore clades and found that a genome-wide elevated  ...  This will result in an ascertainment bias toward longer repeat length in primates, and no ascertainment bias among any members of a taxon with a common ancestor separating them from primates, as is the  ... 
doi:10.1093/jhered/esm017 pmid:17437958 fatcat:snqzubaijrbe5d6v2cjkx7ol7i

Comparative Genetics of Functional Trinucleotide Tandem Repeats in Humans and Apes

Aida M. Andrés, Marta Soldevila, Oscar Lao, Víctor Volpini, Naruya Saitou, Howard T Jacobs, Ikuo Hayasaka, Francesc Calafell, Jaume Bertranpetit
2004 Journal of Molecular Evolution  
The aims of our study are to infer the comparative pattern of variation and evolution of this set of loci in order to show species-specific features in this group of STRs and on their potential for expansion  ...  Humans present slightly larger alleles than the rest of species but a more relevant difference appears in variability levels: Humans are the species with the largest vari-ance, although only for the expanding  ...  disease) but do not try to generalize our observations to infer traits for the rest of STRs, which would produce a strong ascertainment bias.  ... 
doi:10.1007/s00239-004-2628-5 pmid:15553088 fatcat:hgwp5ffpbrdc7ku6chhctzv3xa

SNPs in ecology, evolution and conservation

Phillip A. Morin, Gordon Luikart, Robert K. Wayne, the SNP workshop group
2004 Trends in Ecology & Evolution  
Inferences drawn from mtDNA sequences are further limited by the fact that the mtDNA genome comprises a single maternally inherited locus.  ...  By contrast, mutations observed as SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) are abundant and widespread in many species' genomes (coding and non-coding regions), and they evolve in a manner well described  ...  We are grateful to Pascal Gagneux and three anonymous reviewers for helpful comments. Members of the SNP workshop group contributed extensively and nearly equally to the ideas presented here.  ... 
doi:10.1016/j.tree.2004.01.009 fatcat:obsmh4wenvhf3mkxpctjrnjs6y

Recent and ongoing selection in the human genome

Rasmus Nielsen, Ines Hellmann, Melissa Hubisz, Carlos Bustamante, Andrew G. Clark
2007 Nature reviews genetics  
| The recent availability of genome-scale genotyping data has led to the identification of regions of the human genome that seem to have been targeted by selection.  ...  These findings have increased our understanding of the evolutionary forces that affect the human genome, have augmented our knowledge of gene function and promise to increase our understanding of the genetic  ...  Acknowledgements We would like to thank D. Reich, M. Przeworski and two anonymous reviewers for their helpful comments on earlier versions of this manuscript.  ... 
doi:10.1038/nrg2187 pmid:17943193 pmcid:PMC2933187 fatcat:eqvyx7e6yvbordyjhp5lvx4nmm

Analysis of Microsatellite Variation in Drosophila melanogaster with Population-Scale Genome Sequencing

John W. Fondon, Andy Martin, Stephen Richards, Richard A. Gibbs, David Mittelman, Jeong-Sun Seo
2012 PLoS ONE  
Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between  ...  However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established.  ...  Acknowledgments The authors would like to thank Gareth Highnam, Phillip Whisenhunt, and the Human Genome Sequencing Center at BCM (particularly Dianhui Zhu) for helpful comments and suggestions.  ... 
doi:10.1371/journal.pone.0033036 pmid:22427938 pmcid:PMC3299726 fatcat:itir32odb5astimu44h3hrtagi

Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans

Matthew V Rockman, Matthew W Hahn, Nicole Soranzo, Fritz Zimprich, David B Goldstein, Gregory A Wray, Emmanouil T. Dermitzakis
2005 PLoS Biology  
The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution.  ...  Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking.  ...  Acknowledgments We thank Lisa Bukovnik, Manny Lopez, and Anjali Patel for assistance in the lab and Cliff Cunningham, Greg Gibson, Fred Nijhout, and Mark Rausher for helpful comments.  ... 
doi:10.1371/journal.pbio.0030387 pmid:16274263 pmcid:PMC1283535 fatcat:hkjw4mp5affxzijzstjkomwdsy

Mobile DNA elements in primate and human evolution

Jinchuan Xing, David J. Witherspoon, David A. Ray, Mark A. Batzer, Lynn B. Jorde
2007 American Journal of Physical Anthropology  
We demonstrate how they have been used to help resolve a number of questions in primate phylogeny, including the human-  ...  Roughly 50% of the primate genome consists of mobile, repetitive DNA sequences such as Alu and LINE1 elements.  ...  ACKNOWLEDGMENTS The authors thank the editor and the three anonymous reviewers for their constructive and valuable comments.  ... 
doi:10.1002/ajpa.20722 pmid:18046749 fatcat:g4h3sd5p6bgkbiprdydb5psgg4

The current excitement about copy-number variation: how it relates to gene duplications and protein families

Jan O Korbel, Philip M Kim, Xueying Chen, Alexander Eckehart Urban, Sherman Weissman, Michael Snyder, Mark B Gerstein
2008 Current Opinion in Structural Biology  
Acknowledgements Funding was provided by a Marie Curie Fellowship (J.O.K.) and the NIH (Yale Center of Excellence in Genomic Science grant).  ...  The authors thank Pedro Alves and Jeroen Raes for valuable comments on the manuscript.  ...  For instance, recent studies have revealed that protein-coding genes, and also other genomic elements including highly conserved non-coding regions, tend to be depleted among CNVs, indicating purifying  ... 
doi:10.1016/j.sbi.2008.02.005 pmid:18511261 pmcid:PMC2577873 fatcat:wuers2lucrdy3o34pm7lxucrha

PopHumanScan: the online catalog of human genome adaptation

Jesús Murga-Moreno, Marta Coronado-Zamora, Alejandra Bodelón, Antonio Barbadilla, Sònia Casillas
2018 Nucleic Acids Research  
Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at  ...  as a response to changes in the environment or lifestyle of human populations.  ...  ACKNOWLEDGEMENTS We thank Carla Giner for helpful comments on the PopHu-manScan data and implementation, and Esteve Sanz for help with the informatics infrastructure in which PopHu-manScan is implemented  ... 
doi:10.1093/nar/gky959 pmid:30335169 pmcid:PMC6323894 fatcat:fepixczm3vdtxm7cphrqe26gzi

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

Qiongshi Lu, Yiming Hu, Jiehuan Sun, Yuwei Cheng, Kei-Hoi Cheung, Hongyu Zhao
2015 Scientific Reports  
The GenoCanyon web server is available at http://genocanyon.med.yale.edu Annotating functional elements in the human genome is a major goal in human genetics.  ...  Identifying functional regions in the human genome is a major goal in human genetics.  ...  and Development, and the Yale World Scholars Program sponsored by the China Scholarship Council.  ... 
doi:10.1038/srep10576 pmid:26015273 pmcid:PMC4444969 fatcat:jeup7aoaf5flnltxvx7c4l6ogu

Alu repeats increase local recombination rates

David J Witherspoon, W Scott Watkins, Yuhua Zhang, Jinchuan Xing, Whitney L Tolpinrud, Dale J Hedges, Mark A Batzer, Lynn B Jorde
2009 BMC Genomics  
The loci and SNPs were chosen so as to minimize other factors (such as SNP ascertainment bias and SNP density) that could influence recombination rate estimates.  ...  If individual Alu insertions have even modest effects on local recombination rates, they could collectively have a significant impact on the pattern of linkage disequilibrium in the human genome and on  ...  Acknowledgements This work was supported by a grant to MAB and LBJ from the National Institutes of Health (GM-59290).  ... 
doi:10.1186/1471-2164-10-530 pmid:19917129 pmcid:PMC2785838 fatcat:j4qut5346vfsvdubgmsrv5xywq

Going down the rabbit hole: a review on methods characterizing selection and demography in natural populations [article]

Yann Bourgeois, Khaled Michel Hazzouri, Ben Warren
2016 bioRxiv   pre-print
The ongoing and constant improvement of next-generation sequencing (NGS) techniques has facilitated the production of an ever-increasing number of genetic markers across genomes of non-model species. 2  ...  The study of variation in these markers across natural populations has deepened the understanding of how population history and selection act on genomes.  ...  We want to thank two anonymous reviewers, Stephane Boissinot, Joris Bertrand and Anne Roulin for their insightful comments on previous versions of the manuscript.  ... 
doi:10.1101/052761 fatcat:hxnpz3gwkbfnrpx7pmxszaknb4
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