IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0092553.html
   My bibliography  Save this article

Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues

Author

Listed:
  • Nur Zarina Ali Hassan
  • Norfilza Mohd Mokhtar
  • Teow Kok Sin
  • Isa Mohamed Rose
  • Ismail Sagap
  • Roslan Harun
  • Rahman Jamal

Abstract

Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.

Suggested Citation

  • Nur Zarina Ali Hassan & Norfilza Mohd Mokhtar & Teow Kok Sin & Isa Mohamed Rose & Ismail Sagap & Roslan Harun & Rahman Jamal, 2014. "Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-11, April.
    • Handle: RePEc:plo:pone00:0092553
    DOI: 10.1371/journal.pone.0092553
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0092553
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0092553&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0092553?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Peter Blume-Jensen & Tony Hunter, 2001. "Oncogenic kinase signalling," Nature, Nature, vol. 411(6835), pages 355-365, May.
    2. Richard Redon & Shumpei Ishikawa & Karen R. Fitch & Lars Feuk & George H. Perry & T. Daniel Andrews & Heike Fiegler & Michael H. Shapero & Andrew R. Carson & Wenwei Chen & Eun Kyung Cho & Stephanie Da, 2006. "Global variation in copy number in the human genome," Nature, Nature, vol. 444(7118), pages 444-454, November.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yichen Henry Liu & Can Luo & Staunton G. Golding & Jacob B. Ioffe & Xin Maizie Zhou, 2024. "Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    2. Albertas Dvirnas & Callum Stewart & Vilhelm Müller & Santosh Kumar Bikkarolla & Karolin Frykholm & Linus Sandegren & Erik Kristiansson & Fredrik Westerlund & Tobias Ambjörnsson, 2021. "Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach," PLOS ONE, Public Library of Science, vol. 16(11), pages 1-15, November.
    3. Patrick Breheny & Prabhakar Chalise & Anthony Batzler & Liewei Wang & Brooke L Fridley, 2012. "Genetic Association Studies of Copy-Number Variation: Should Assignment of Copy Number States Precede Testing?," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-9, April.
    4. Yu Chen & Amy Y. Wang & Courtney A. Barkley & Yixin Zhang & Xinyang Zhao & Min Gao & Mick D. Edmonds & Zechen Chong, 2023. "Deciphering the exact breakpoints of structural variations using long sequencing reads with DeBreak," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Jae Eun Lee & Jung Hye Sung & Daniel Sarpong & Jimmy T. Efird & Paul B. Tchounwou & Elizabeth Ofili & Keith Norris, 2018. "Knowledge Management for Fostering Biostatistical Collaboration within a Research Network: The RTRN Case Study," IJERPH, MDPI, vol. 15(11), pages 1-13, November.
    6. Qiwei Jiang & Xiaomei Zhang & Xiaoming Dai & Shiyao Han & Xueji Wu & Lei Wang & Wenyi Wei & Ning Zhang & Wei Xie & Jianping Guo, 2022. "S6K1-mediated phosphorylation of PDK1 impairs AKT kinase activity and oncogenic functions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    7. Yang Guo & Shuzhen Wang & A. K. Alvi Haque & Xiguo Yuan, 2022. "WAVECNV: A New Approach for Detecting Copy Number Variation by Wavelet Clustering," Mathematics, MDPI, vol. 10(12), pages 1-11, June.
    8. Sichun Yang & Benoît Roux, 2008. "Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms," PLOS Computational Biology, Public Library of Science, vol. 4(3), pages 1-14, March.
    9. Yu Wang & Wei Li & Yingying Xia & Chongzhi Wang & Y Tom Tang & Wenying Guo & Jinliang Li & Xia Zhao & Yepeng Sun & Juan Hu & Hefu Zhen & Xiandong Zhang & Chao Chen & Yujian Shi & Lin Li & Hongzhi Cao , 2015. "Identifying Human Genome-Wide CNV, LOH and UPD by Targeted Sequencing of Selected Regions," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-18, April.
    10. Zhongtao Zhao & Qiaojun Jin & Jin-Rong Xu & Huiquan Liu, 2014. "Identification of a Fungi-Specific Lineage of Protein Kinases Closely Related to Tyrosine Kinases," PLOS ONE, Public Library of Science, vol. 9(2), pages 1-8, February.
    11. Gianna Maria Nardi & Elisabetta Ferrara & Ilaria Converti & Francesca Cesarano & Salvatore Scacco & Roberta Grassi & Antonio Gnoni & Felice Roberto Grassi & Biagio Rapone, 2020. "Does Diabetes Induce the Vascular Endothelial Growth Factor (VEGF) Expression in Periodontal Tissues? A Systematic Review," IJERPH, MDPI, vol. 17(8), pages 1-16, April.
    12. Hipólito Nicolás Cuesta-Hernández & Julia Contreras & Pablo Soriano-Maldonado & Jana Sánchez-Wandelmer & Wayland Yeung & Ana Martín-Hurtado & Inés G. Muñoz & Natarajan Kannan & Marta Llimargas & Javie, 2023. "An allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    13. Andrew K MacLeod & Gail Davies & Antony Payton & Albert Tenesa & Sarah E Harris & David Liewald & Xiayi Ke & Michelle Luciano & Lorna M Lopez & Alan J Gow & Janie Corley & Paul Redmond & Geraldine McN, 2012. "Genetic Copy Number Variation and General Cognitive Ability," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-9, December.
    14. Hui-Rong Xu & Zhong-Fa Xu & Yan-Lai Sun & Jian-Jun Han & Zeng-Jun Li, 2013. "The −842G/C Polymorphisms of PIN1 Contributes to Cancer Risk: A Meta-Analysis of 10 Case-Control Studies," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-7, August.
    15. Martin Klammer & J Nikolaj Dybowski & Daniel Hoffmann & Christoph Schaab, 2015. "Pareto Optimization Identifies Diverse Set of Phosphorylation Signatures Predicting Response to Treatment with Dasatinib," PLOS ONE, Public Library of Science, vol. 10(6), pages 1-16, June.
    16. Soumya Raychaudhuri & Joshua M Korn & Steven A McCarroll & The International Schizophrenia Consortium & David Altshuler & Pamela Sklar & Shaun Purcell & Mark J Daly, 2010. "Accurately Assessing the Risk of Schizophrenia Conferred by Rare Copy-Number Variation Affecting Genes with Brain Function," PLOS Genetics, Public Library of Science, vol. 6(9), pages 1-12, September.
    17. Soohyun Lee & Simon Kasif & Zhiping Weng & Charles R Cantor, 2008. "Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation," PLOS ONE, Public Library of Science, vol. 3(12), pages 1-10, December.
    18. Kyungjoon Lee & John S Brownstein & Richard G Mills & Isaac S Kohane, 2010. "Does Collocation Inform the Impact of Collaboration?," PLOS ONE, Public Library of Science, vol. 5(12), pages 1-6, December.
    19. Michael I Falola & Howard W Wiener & Nathan E Wineinger & Gary R Cutter & Robert P Kimberly & Jeffrey C Edberg & Donna K Arnett & Richard A Kaslow & Jianming Tang & Sadeep Shrestha, 2013. "Genomic Copy Number Variants: Evidence for Association with Antibody Response to Anthrax Vaccine Adsorbed," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-9, May.
    20. Jeongah Yoon & Thomas S Deisboeck, 2009. "Investigating Differential Dynamics of the MAPK Signaling Cascade Using a Multi-Parametric Global Sensitivity Analysis," PLOS ONE, Public Library of Science, vol. 4(2), pages 1-14, February.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0092553. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.