Topological Analysis of Amplicon Structure in Comparative Genomic Hybridization (CGH) Data: An Application to ERBB2/HER2/NEU Amplified Tumors

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• 关键词：Copy number aberrations ; Cancer ; Computational homology ; First homology group
• 刊名：Lecture Notes in Computer Science
• 出版年：2016
• 出版时间：2016
• 年：2016
• 卷：9667
• 期：1
• 页码：113-129
• 全文大小：754 KB
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• 作者单位：Sergio Ardanza-Trevijano (15)
  Georgina Gonzalez (16)
  Tyler Borrman (17)
  Juan Luis Garcia (18)
  Javier Arsuaga (16) (19)
  
  15. Department of Physics and Applied Mathematics, University of Navarra, 31080, Pamplona, Spain
  16. Department of Molecular and Cellular Biology, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
  17. Medical School, University of Massachusetts, 368 Plantation Street, Worcester, MA, 01605, USA
  18. Centro de Investigación del Cancer, Universidad de Salamanca, 37007, Salamanca, Spain
  19. Department of Mathematics, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA
  
• 丛书名：Computational Topology in Image Context
• ISBN：978-3-319-39441-1
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349
• 卷排序：9667

文摘

DNA copy number aberrations (CNAs) play an important role in cancer and can be experimentally detected using microarray comparative genomic hybridization (CGH) techniques. Amplicons, CNAs that extend over large sections of the genome, are difficult to study since they may contain multiple independent and dependent copy number changes. Here, we propose an algorithm to find the CNAs structure within a given amplicon. Our method relies on the observation that co-occurring CNAs can be encoded as 1-dimensional cycles. Applying this method to breast cancer patients known as ERBB2/HER2/NEU amplified we find three regions that can be co-occuring: the first region is in the cytoband 17q12, where the ERBB2 gene is located, the second region expands between 17q21.2 to 17q21.31 and includes the keratin genes, the third one is 17q21.33. We suggest that the first homology group helps uncovering the structure of amplicons.