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SENSITIVITY ANALYSIS FOR REVERSAL DISTANCE AND BREAKPOINT REUSE IN GENOME REARRANGEMENTS

AMIT U SINHA, JAROSLAW MELLER
2007 Biocomputing 2008  
between genomes, namely the reversal distance and breakpoint reuse.  ...  Breakpoint reuse is also strongly correlated with evolutionary distances, increasing for pairs of more divergent genomes.  ...  Acknowledgements We would like to thank the reviewers for their insightful comments and suggestions. This work has been partially supported by NIH grant R01 AR050688.  ... 
doi:10.1142/9789812776136_0005 fatcat:buhvqef77fa2fm5djpf6suhae4

The rise and fall of breakpoint reuse depending on genome resolution

Oliver Attie, Aaron E Darling, Sophia Yancopoulos
2011 BMC Bioinformatics  
Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused.  ...  Some years ago, a controversy erupted in genome rearrangement studies over whether rearrangements recur, causing breakpoints to be reused.  ...  We thank Glenn Tesler for clarifying issues around internal vs external breakpoints as well as the differences in breakpoint reuse between the DCJ and HP formulations.  ... 
doi:10.1186/1471-2105-12-s9-s1 pmid:22151330 pmcid:PMC3283316 fatcat:2oa7yledbnh4xomejtih4w6wlu

SplitThreader: Exploration and analysis of rearrangements in cancer genomes [article]

Maria Nattestad, Marley C. Alford, Fritz J. Sedlazeck, Michael C. Schatz
2016 bioRxiv   pre-print
Here we present SplitThreader (http://splitthreader.com), an open- source interactive web application for analysis and visualization of genomic rearrangements and copy number variation in cancer genomes  ...  This is applied to detect gene fusions and other novel sequences, as well as to evaluate distances in the rearranged genome between any genomic regions of interest, especially the repositioning of regulatory  ...  If the end port is entered and the start port is exited, then this represents reading the sequence in the reverse complement All rights reserved. No reuse allowed without permission.  ... 
doi:10.1101/087981 fatcat:vwjdnrephbhaxpcrdshjxj45uu

Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement

David Sankoff, Phil Trinh
2005 Journal of Computational Biology  
In order to apply gene-order rearrangement algorithms to the comparison of genome sequences, Pevzner and Tesler bypass gene finding and ortholog identification and use the order of homologous blocks of  ...  Analytic and simulation methods show that reuse is very sensitive to the proportion of blocks excluded.  ...  D.S. holds the Canada Research Chair in Mathematical Genomics and is a Fellow in the Evolutionary Biology Program of the Canadian Institute for Advanced Research.  ... 
doi:10.1089/cmb.2005.12.812 pmid:16108718 fatcat:itu7y3uncvhkhb6ll5n76xnunu

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss

Pavel Avdeyev, Shuai Jiang, Sergey Aganezov, Fei Hu, Max A. Alekseyev
2016 Journal of Computational Biology  
One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution  ...  Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA.  ...  to cope with higher breakpoint reuse and process datasets inaccessible for MGRA.  ... 
doi:10.1089/cmb.2015.0160 pmid:26885568 fatcat:hip5sakfhzfudankl2iazhxesy

Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny

Amélie S Véron, Claire Lemaitre, Christian Gautier, Vincent Lacroix, Marie-France Sagot
2011 BMC Genomics  
Importantly, we show that this result holds for loci located on the same chromosome regardless of the genomic distance separating them, and the signal is stronger in gene-rich and open-chromatin regions  ...  Results: In this paper, we analysed the correlation between two datasets: (i) whole-genome chromatin contact data obtained in human cells using the Hi-C protocol; and (ii) a set of breakpoint regions resulting  ...  Acknowledgements The authors would like to thank Franck Picard for helpful discussions on the statistical analysis carried out in this article. This work was funded by the  ... 
doi:10.1186/1471-2164-12-303 pmid:21663614 pmcid:PMC3132170 fatcat:s2czlpbe5rghrhryygeg6tpdw4

Reconstruction of ancestral genomes in presence of gene gain and loss [article]

Pavel Avdeyev, Shuai Jiang, Sergey Aganezov, Fei Hu, Max A. Alekseyev
2016 bioRxiv   pre-print
One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution  ...  Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA.  ...  to cope with higher breakpoint reuse and process datasets inaccessible for MGRA.  ... 
doi:10.1101/040196 fatcat:7mgw55xeefexbc2dhlsfkx3vde

Genome-wide detection of structural variants and indels by local assembly [article]

Jeremiah Wala, Pratiti Bandopadhayay, Noah Greenwald, Ryan O'Rourke, Ted Sharpe, Chip Stewart, Steven E Schumacher, Yilong Li, Joachim Weischenfeldt, Xiaotong Yao, Chad Nusbaum, Peter Campbell (+4 others)
2017 bioRxiv   pre-print
SvABA demonstrates superior sensitivity and specificity across a large spectrum of SVs, and substantially improved detection performance for variants in the 20-300 bp range, compared with existing methods  ...  We applied SvABA to 344 cancer genomes from 11 cancer types, and found that templated-sequence insertions occur in ~4% of all somatic rearrangements.  ...  Acknowledgements The National Institutes of Health (T32 HG002295/HG/ NHGRI, U54CA143798, and Disclosure declaration The authors declare that there is no conflict of interest.  ... 
doi:10.1101/105080 fatcat:j5r4nxsbpzht5jjqgoeyywilmq

Microinversions in mammalian evolution

M. J. Chaisson, B. J. Raphael, P. A. Pevzner
2006 Proceedings of the National Academy of Sciences of the United States of America  
However, reverse-strand local alignments may also be caused by palindromes and inverted repeats (Fig. . ¶ We limited our analysis to genomes with no more than 200,000 unfinished base pairs.  ...  We estimate that there exist hundreds of thousands of microinversions in genomes of mammals from comparative sequencing projects, an untapped source of new phylogenetic characters. genome rearrangements  ...  We are grateful to Jian Ma and Jim Kent for the comparative analysis of humanchimpanzee microinversions found in this paper and many useful comments.  ... 
doi:10.1073/pnas.0603984103 pmid:17189424 pmcid:PMC1750909 fatcat:5ygns6oxuncmznhclf4gzb25by

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

L. Gordon, S. Yang, M. Tran-Gyamfi, D. Baggott, M. Christensen, A. Hamilton, R. Crooijmans, M. Groenen, S. Lucas, I. Ovcharenko, L. Stubbs
2007 Genome Research  
Twenty-two of the 31 breakpoint regions have been reused repeatedly as rearrangement breakpoints in vertebrate evolution.  ...  in GC content and CpG islands, highlighting a potential role for these features in genome instability.  ...  Acknowledgments We thank Elbert Branscomb, Joomyeong Kim, and Alice Yamada for critical reviews of the manuscript, Gawain Lavers for website development, and the following individuals for their contribu-tions  ... 
doi:10.1101/gr.6775107 pmid:17921355 pmcid:PMC2045143 fatcat:sbo7uhsezfhvhhrnchtccozvdy

Long-range regulation is a major driving force in maintaining genome integrity

Emmanuel Mongin, Ken Dewar, Mathieu Blanchette
2009 BMC Evolutionary Biology  
Large-scale genome rearrangement events modify the order of genes and non-coding conserved regions on chromosomes.  ...  In many regions, the fitness cost of altering the spatial association between long-range regulatory regions and their target genes may be so high that rearrangements are not allowed.  ...  We also wish to thank Francois Spitz from EMBL Heidelberg and Rob Sladek from McGill University for useful discussions. We also thank the reviewers for their helpful comments and suggestions.  ... 
doi:10.1186/1471-2148-9-203 pmid:19682388 pmcid:PMC2741452 fatcat:royggde6kjcullndfku46zoie4

Rearrangement Models and Single-Cut Operations [chapter]

Paul Medvedev, Jens Stoye
2009 Lecture Notes in Computer Science  
There have been many widely used genome rearrangement models, such as reversals, Hannenhalli-Pevzner, and double-cut and join.  ...  In this paper, we give a formal set-theoretic definition, which allows us to investigate and prove relationships between distances under various existing and new models.  ...  Most of the work was done while PM was a member of the International NRW Graduate School in Bioinformatics and Genome Research, and the AG Genominformatik group at Bielefeld, while being additionally funded  ... 
doi:10.1007/978-3-642-04744-2_8 fatcat:v2negq2yjjespmwaifthtifmxq

Diverse tumorigenic consequences of human papillomavirus integration in primary oropharyngeal cancers [article]

David E Symer, Keiko Akagi, Heather M Geiger, Yang Song, Gaiyun Li, Anne-Katrin Emde, Weihong Xiao, Bo Jiang, Jingfeng Li, Amit D Agrawal, Enzer Ozer, Adel K El-Naggar (+7 others)
2021 bioRxiv   pre-print
Analysis of 105 HPV-positive oropharyngeal cancers by whole genome sequencing detects viral integration in 77%, revealing five statistically significant integration hotspots near genes that regulate epithelial  ...  Human papillomavirus (HPV) causes 5% of all cancers and frequently integrates into host chromosomes, but the impacts of integration in tumorigenesis remain unclear.  ...  (D) Comparison of gene counts (y-axis) expressed at various levels (Z-scores, x-axis), grouped in 50 kb genomic distances from the nearest breakpoint, in tumors with (red) and without (blue) breakpoints  ... 
doi:10.1101/2021.06.20.449168 fatcat:yjcax3scdvf5hczwsta7xsi5r4

Fine-mapping complex inversion breakpoints and investigating somatic pairing in the Anopheles gambiae species complex using proximity-ligation sequencing [article]

Russell B. Corbett-Detig, Iskander Said, Maria Calzetta, Max Genetti, Jakob McBroome, Nicholas W. Maurer, Vincenzo Petrarca, Alessandra della Torre, Nora J. Besansky
2019 bioRxiv   pre-print
We found that inversion breakpoints occur in large repetitive regions, and strikingly among three inversions analyzed, two breakpoints appear to be reused in two separate inversions.  ...  Here, we develop an approach that uses Hi-C sequencing data to molecularly fine-map the breakpoints of inversions 2Rbc and 2Rd in A. coluzzii.  ...  Dotson, Principal Investigator for MR4 Vector Activity, for kindly supplying Mali-NIH, Pimperena, and Nkdokayo mosquitoes, and H. Ranson for sharing the Banfora M colony.  ... 
doi:10.1101/662114 fatcat:xdpes5j3pzgsxnnhukeqpim5wu

Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions

Ron Zeira, Ron Shamir, Oliver Stegle
2018 Bioinformatics  
Motivation: Problems of genome rearrangement are central in both evolution and cancer research.  ...  Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments.  ...  Funding Study supported in part by the Bella Walter Memorial Fund of the Israel Cancer Association and by Len Blavatnik and the Blavatnik Family foundation.  ... 
doi:10.1093/bioinformatics/bty381 pmid:29726899 fatcat:6m6bmifjpvcqpns7gedilpbteu
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