Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of “towards analysis” in chronic lymphocytic leukaemia

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• 作者：Ioannis Kavakiotis ; Aliki Xochelli ; Andreas Agathangelidis…
• 关键词：Data integration ; Feature extraction ; List aggregation ; Mutation patterns ; somatic hypermutation ; SHM ; Chronic lymphocytic leukaemia ; CLL
• 刊名：BMC Bioinformatics
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：5-supp
• 全文大小：1,845 KB
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• 作者单位：Ioannis Kavakiotis (1)
  Aliki Xochelli (2) (3)
  Andreas Agathangelidis (4)
  Grigorios Tsoumakas (1)
  Nicos Maglaveras (2) (5)
  Kostas Stamatopoulos (2) (3)
  Anastasia Hadzidimitriou (2) (3)
  Ioannis Vlahavas (1)
  Ioanna Chouvarda (2) (5)
  
  1. Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
  2. Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
  3. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
  4. Division of Molecular Oncology and Department of Onco-Hematology, San Raffaele Scientific Institute, Milan, Italy
  5. Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
  
• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105
• 卷排序：17

文摘

Background Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insight into the physiology and pathology of B cells, leading to strong prognostication markers for clinical outcome in chronic lymphocytic leukaemia (CLL), the most frequent adult B-cell malignancy. In this paper we present a methodology for integrating multiple immunogenetic and clinocobiological data sources in order to extract features and create high quality datasets for SHM analysis in IG receptors of CLL patients. This dataset is used as the basis for a higher level integration procedure, inspired form social choice theory. This is applied in the Towards Analysis, our attempt to investigate the potential ontogenetic transformation of genes belonging to specific stereotyped CLL subsets towards other genes or gene families, through SHM.