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Combinatorics of the Breakage-Fusion-Bridge Mechanism

Marcus Kinsella, Vineet Bafna
<span title="">2012</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/id6xbd2o6fhy7pts2djgwhtmvy" style="color: black;">Journal of Computational Biology</a> </i> &nbsp;
The breakage-fusion-bridge (BFB) mechanism was proposed over seven decades ago and is a source of genomic variability and gene amplification in cancer.  ...  Here we formally model and analyze the BFB mechanism, to our knowledge the first time this has been undertaken. We show that BFB can be modeled as successive inverted prefix duplications of a string.  ...  ACKNOWLEDGMENTS This research was supported in part by grants from the NIH (5RO1-HG004962) and the NSF (CCF-1115206).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2012.0020">doi:10.1089/cmb.2012.0020</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22506505">pmid:22506505</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3375649/">pmcid:PMC3375649</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qcg57xjlfveulf7esdb2kuk3he">fatcat:qcg57xjlfveulf7esdb2kuk3he</a> </span>
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Large Inverted Duplications in the Human Genome Form via a Fold-Back Mechanism

Karen E. Hermetz, Scott Newman, Karen N. Conneely, Christa L. Martin, Blake C. Ballif, Lisa G. Shaffer, Jannine D. Cody, M. Katharine Rudd, Beth A. Sullivan
<span title="2014-01-30">2014</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
There are several models for inverted duplication formation, most of which include a dicentric chromosome intermediate followed by breakage-fusion-bridge (BFB) cycles, but the mechanisms that give rise  ...  Inverted duplications are a common type of copy number variation (CNV) in germline and somatic genomes.  ...  Acknowledgments We thank Madhuri Hegde, Kirill Lobachev, and Francesca Storici for scientific discussions on duplication formation. Alev Cagla Ozdemir performed breakpoint junction experiments.  ... 
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The fabric of cancer cell biology—Weaving together the strands

Richard D. Klausner
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2hwv62sclrdpzax2yrwcjos34q" style="color: black;">Cancer Cell</a> </i> &nbsp;
Acknowledgments I would like to acknowledge Joe Harford for preparation of the figures.  ...  The fragmented chromosomes may again fuse and repeat the cycle of breakage-fusion-bridge formation first described by McClintock in 1941.  ...  breaks as a manifestation of repetitive breakage-fusion-bridge cycles initiated by telomeric shortening.  ... 
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An algorithmic approach for breakage-fusion-bridge detection in tumor genomes

S. Zakov, M. Kinsella, V. Bafna
<span title="2013-03-15">2013</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids.  ...  Making correct inferences from this data is not straightforward, particularly given the complexity of some cancer genomes and BFB's ability to generate a wide range of rearrangement patterns.  ...  Acknowledgements This research was supported by grants from the National Institute of Health (5RO1-HG004962, U54 HL108460) and the National Science Foundation (NSF-CCF-1115206).  ... 
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Stem Cell Plasticity [chapter]

Malcolm R. Alison
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> Encyclopedia of Cancer </i> &nbsp;
Schwab (ed.), Encyclopedia of Cancer,  ...  Is a low molecular weight protein normally present in cells derived from the neural crest (Schwann S1P Definition Sphingosine-1-phosphate, an anti-apoptotic, angiogenic sphingolipid.  ...  prostate cancer development and progression (▶ TMPRSS2/ERG Fusions).  ... 
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Snail Transcription Factors [chapter]

Amparo Cano, M. Angela Neto
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> Encyclopedia of Cancer </i> &nbsp;
Schwab (ed.), Encyclopedia of Cancer,  ...  Is a low molecular weight protein normally present in cells derived from the neural crest (Schwann S1P Definition Sphingosine-1-phosphate, an anti-apoptotic, angiogenic sphingolipid.  ...  prostate cancer development and progression (▶ TMPRSS2/ERG Fusions).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-16483-5_5389">doi:10.1007/978-3-642-16483-5_5389</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gmjzxqp2u5gljew5l3z7auflpq">fatcat:gmjzxqp2u5gljew5l3z7auflpq</a> </span>
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Stem Cell Markers [chapter]

Gail M. Seigel
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> Encyclopedia of Cancer </i> &nbsp;
Schwab (ed.), Encyclopedia of Cancer,  ...  Is a low molecular weight protein normally present in cells derived from the neural crest (Schwann S1P Definition Sphingosine-1-phosphate, an anti-apoptotic, angiogenic sphingolipid.  ...  prostate cancer development and progression (▶ TMPRSS2/ERG Fusions).  ... 
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The combinatorics of tandem duplication

L. Penso-Dolfin, T. Wu, C.D. Greenman
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lx7dev2le5anbg6oarljwh7lie" style="color: black;">Discrete Applied Mathematics</a> </i> &nbsp;
In any subword of the form min, i represents a connection between the right hand side of the DNA segment represented by m, and the left hand side of the DNA segment represented by n, formed during the  ...  Fourthly, we combine these two pieces of information and provide an explicit formula to answer Problem 1.1. Concluding remarks complete the paper.  ...  Acknowledgements This research was supported in part at KITP by the National Science Foundation under 264 Grant No. PHY11-25915.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.dam.2015.05.014">doi:10.1016/j.dam.2015.05.014</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zre22ktukfdxroqeabp2ny2uyu">fatcat:zre22ktukfdxroqeabp2ny2uyu</a> </span>
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Introduction to Epigenetics

Renato Paro, Ueli Grossniklaus, Raffaella Santoro, Anton Wutz, S.N.
<span title="2021-01-01">2021</span>
Acknowledgments We are grateful for the curiosity and interest of our students.  ...  Work by U.G. in this field was supported by the University of Zürich, and grants of the European Research Council (ERC AdG 250358 -MEDEA) and the Swiss National Science Foundation (31003A_179553, 310030B  ...  The best-known mechanism showing the contribution of HDACs in cancer is their interaction with oncogenic fusion proteins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5167/uzh-210441">doi:10.5167/uzh-210441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bfgzt6wq5rdrlfcoiav7uh27eq">fatcat:bfgzt6wq5rdrlfcoiav7uh27eq</a> </span>
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Exploiting Oxidative Stress as a Therapeutic Option in Rhabdomyosarcoma

Eva Brack
<span title="2018-05-01">2018</span>
Acknowledgements We thank Andres Kaech and Urs Ziegler at The Center for Microscopy and Image Analysis Zurich for their excellent service and support.  ...  We also thank Silvia Jenni, Gloria Pedot and Luca Pontiggia (University Children's Hospital Zurich) for assistance with the cell sorting.  ...  Another well recognized model is the cancer stem cell (SC) model, which states that normal SCs may suffer an initial oncogenic transformation followed by more and more mutations and eventually become cancer  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5167/uzh-162951">doi:10.5167/uzh-162951</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/evdwg3nnwbcudbafrrsuc6lvfu">fatcat:evdwg3nnwbcudbafrrsuc6lvfu</a> </span>
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Serine-Threonine Kinase Receptor-Associated Protein [chapter]

Nilesh D. Kashikar, Pran K. Datta
<i title="Springer Berlin Heidelberg"> Encyclopedia of Cancer </i> &nbsp;
Schwab (ed.), Encyclopedia of Cancer,  ...  Is a low molecular weight protein normally present in cells derived from the neural crest (Schwann S1P Definition Sphingosine-1-phosphate, an anti-apoptotic, angiogenic sphingolipid.  ...  prostate cancer development and progression (▶ TMPRSS2/ERG Fusions).  ... 
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