Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process

详细信息    查看全文

• 作者：C. D. Greenman ; S. L. Cooke ; J. Marshall ; M. R. Stratton…
• 关键词：05A05 ; 60G99 ; 92B05 ; 92D15 ; 92D20
• 刊名：Journal of Mathematical Biology
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：72
• 期：1-2
• 页码：47-86
• 全文大小：1,624 KB
• 参考文献：Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C, Malig M, Mutlu O et al (2009) Personalized copy number and segmental duplication maps using next-generation sequencing. Nat Genet 41:1061–1067CrossRef
  Allouche J, Shallit J (2003) Automatic sequences. Theory, applications, generalizations, CUP
  Bentley JL (1975) Multidimensional binary search trees used for associative searching. Commun ACM 18:509–517CrossRef MATH
  Bignell GR, Santarius T, Pole JCM, Butler AP, Perry J, Pleasance E, Greenman CD, Menzies A, Taylor S, Edkins S, Campbell P, Quail M, Plumb B, Matthews L, McLay K, Edwards PAW, Rogers J, Wooster R, Futreal PA, Stratton MR (2007) Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution. Genome Res 17:1296–1303CrossRef
  Bignell GR, Greenman CD, Davies H, Butler AP, Edkins S, Andrews JM, Buck G, Chen L, Beare D, Latimer C, Widaa S, Hinton J, Fahey C, Fu B, Swamy S, Dalgliesh GL, Teh BT, Deloukas P, Yang F, Campbell PJ, Futreal PA, Stratton MR (2010) Signatures of mutation and selection in the cancer genome. Nature 463:893–898CrossRef
  Campbell PJ, Stephens PJ, Pleasance ED, O’Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA (2008) Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 40(6):722–9CrossRef
  Greenman CD, Pleasance ED, Newman S, Yang F, Fu B, Nik-Zainal S, Jones D, Lau KW, Carter N, Edwards PA, Futreal PA, Stratton MR, Campbell PJ (2011) Estimation of rearrangement phylogeny for cancer genomes. Genome Res 22(2):346–361CrossRef
  Greenman CD, Bignell G, Butler A, Edkins S, Hinton J, Beare D, Swamy S, Santarius T, Chen L, Widaa S, Futreal PA, Stratton MR (2010) PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 11(1):164–175CrossRef
  Kinsella M, Bafna V (2012) Modelling the breakage–fusion–bridge mechanism: combinatorics and cancer genomics, RECOMB 2012, LNBI 7262, pp 148–162
  Kinsella M, Bafna V (2012) Combinatorics of the breakage–fusion–bridge mechanism. J Comput Biol 19(6):662–678MathSciNet CrossRef
  Klambauer G, Schwarzbauer K, Mayr A, Clevert D, Mitterecker A, Bodenhofer U, Hochreiter S (2012) cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate. Nucleic Acids Res 40(9):e69CrossRef
  Lemaitre C, Zaghloul L, Sagot MF, Gautier C, Arneodo A, Tannier E, Audit B (2009) Analysis of fine-scale mammalian evolutionary breakpoints provides new insight into their relation to genome organization. BMC Genomics 10:335CrossRef
  McBride DJ, Etemadmoghadam D, Cooke SL, Alsop K, George J, Butler A, Cho J, Galappaththige D, Greenman CD, Howarth KD, Lau KW, Ng CK, Raine K, Teague J, Wedge DC, Australian Ovarian Cancer Study Group, Caubit X, Stratton MR, Brenton JD, Campbell PJ, Futreal PA, Bowtell DDL (2012) Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. J Pathol 227(4):446–455
  McClintock B (1941) The stability of broken ends of chromosomes in Zea mays. Genetics 26:234–282
  Neggers J, Kim HS (1998) Basic posets. World Scientfic, SingaporeCrossRef MATH
  Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA, Menzies A, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Lau KW, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jonsson G, Garber J, Silver D, Miron P, Fatima A, Boyault S, Langerød A, Tutt A, Martens J. WM, Aparicio SAJR, Borg A, Salomon AV, Thomas G, Børresen-Dale A, Richardson AL, Neuberger MS, Futreal PA, Campbell PJ, Stratton MR; The Breast Cancer Working Group of the International Cancer Genome Consortium (2012) Mutational processes moulding the genomes of 21 breast cancers. Cell 149(5):979–993
  Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, Raine K, Jones D, Marshall J, Hinton J, Menzies A, Stebbings LA, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jonsson G, Garber J, Silver D, Miron P, Fatima A, Boyault S, Langerød A, Tutt A, Martens JWM, Aparicio SAJR, Borg A, Salomon AV, Thomas G, Børresen-Dale A, Richardson AL, Neuberger MS, Futreal PA, Stratton MR, Campbell PJ; The Breast Cancer Working Group of the International Cancer Genome Consortium (2012) The life history of 21 breast cancers. Cell 149(5):994–1007
  Pleasance ED, Cheetham K, Stephens PJ, McBride D, Egocheaga I, Greenman CD, Lin M, Ordonez G, Bignell GR, Ye K et al (2010a) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463:191–196CrossRef
  Pleasance ED, Stephens PJ, O’Meara S, McBride D, Meynert A, Jones D, Lin M, Beare D, Lau KW, Greenman CD et al (2010b) A small cell lung cancer genome. Nature 463:184–190CrossRef
  Raphael BJ, Pevzner PA (2004) Reconstructing tumor amplisomes. Bioinformatics 20:i265–i273CrossRef
  Raphael BJ, Volik S, Collins C, Pevzner PA (2003) Reconstructing tumor genome architectures. Bioinformatics 19:ii162–ii171CrossRef
  Sankoff D (2009) The where and wherefore of evolutionary breakpoints. J Biol 8:66CrossRef
  Semple C, Steel M (2009) Phylogenetics, OUP
  The International Cancer Genome Consortium (2010) International network of cancer genome projects. Nature 464:993–998
  Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B et al (2010) Allele specific copy number analysis of tumors. Proc Natl Acad Sci 107:16910–16915CrossRef
  Xie C, Tammi MT (2009) CNV-Seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinform 10:80CrossRef
  Zakov S, Kinsella M, Bafna V (2013) An algorithmic approach for breakage–fusion–bridge detection in tumor genomes. Proc Natl Acad Sci 110(14):5546MathSciNet CrossRef
  Zakov S, Bafna V (2014) Reconstructing breakage fusion bridge architectures using noisy copy numbers. In: Research in computational molecular biology, proceedings RECOMB 2014. Springer, Berlin, pp 400–417
  
• 作者单位：C. D. Greenman (1) (2)
  S. L. Cooke (3)
  J. Marshall (3)
  M. R. Stratton (3)
  P. J. Campbell (3) (4)
  
  1. School of Computing Sciences, University of East Anglia, Norwich, UK
  2. The Genome Analysis Centre, Norwich Research Park, Norwich, UK
  3. Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
  4. Department of Haematology, University of Cambridge, Cambridge, UK
  
• 刊物类别：Mathematics and Statistics
• 刊物主题：Mathematics
  Mathematical Biology
  Applications of Mathematics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1432-1416

文摘

Breakage–fusion–bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then ‘unfolds’ into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. Here we study the evolution space of breakage–fusion–bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are \(2^{\frac{n(n-1)}{2}}\) qualitatively distinct evolutions involving \(n\) breakage–fusion–bridge cycles. Secondly we consider the stochastic nature of the process to show these evolutions are not equally likely, and also describe how amplicons become localized. Finally we highlight these methods by inferring the evolution of breakage–fusion–bridge cycles with data from primary tissue cancer samples. Mathematics Subject Classification 05A05 60G99 92B05 92D15 92D20