IDEAS home Printed from https://ideas.repec.org/a/hin/complx/5024867.html
   My bibliography  Save this article

FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis

Author

Listed:
  • Lin Yuan
  • Chang-An Yuan
  • De-Shuang Huang

Abstract

The epistasis is prevalent in the SNP interactions. Some of the existing methods are focused on constructing models for two SNPs. Other methods only find the SNPs in consideration of one-objective function. In this paper, we present a unified fast framework integrating adaptive ant colony optimization algorithm with multiobjective functions for detecting SNP epistasis in GWAS datasets. We compared our method with other existing methods using synthetic datasets and applied the proposed method to Late-Onset Alzheimer’s Disease dataset. Our experimental results show that the proposed method outperforms other methods in epistasis detection, and the result of real dataset contributes to the research of mechanism underlying the disease.

Suggested Citation

  • Lin Yuan & Chang-An Yuan & De-Shuang Huang, 2017. "FAACOSE: A Fast Adaptive Ant Colony Optimization Algorithm for Detecting SNP Epistasis," Complexity, Hindawi, vol. 2017, pages 1-10, September.
    • Handle: RePEc:hin:complx:5024867
    DOI: 10.1155/2017/5024867
    as

    Download full text from publisher

    File URL: http://downloads.hindawi.com/journals/8503/2017/5024867.pdf
    Download Restriction: no
    File URL: http://downloads.hindawi.com/journals/8503/2017/5024867.xml
    Download Restriction: no
    File URL: https://libkey.io/10.1155/2017/5024867?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. Lin Zhu & Zhu-Hong You & De-Shuang Huang & Bing Wang, 2013. "t-LSE: A Novel Robust Geometric Approach for Modeling Protein-Protein Interaction Networks," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-13, April.
    2. Wei Zhang & Jun Zhu & Eric E Schadt & Jun S Liu, 2010. "A Bayesian Partition Method for Detecting Pleiotropic and Epistatic eQTL Modules," PLOS Computational Biology, Public Library of Science, vol. 6(1), pages 1-10, January.
    3. Bryan N Howie & Peter Donnelly & Jonathan Marchini, 2009. "A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies," PLOS Genetics, Public Library of Science, vol. 5(6), pages 1-15, June.
    4. Teri A. Manolio & Francis S. Collins & Nancy J. Cox & David B. Goldstein & Lucia A. Hindorff & David J. Hunter & Mark I. McCarthy & Erin M. Ramos & Lon R. Cardon & Aravinda Chakravarti & Judy H. Cho &, 2009. "Finding the missing heritability of complex diseases," Nature, Nature, vol. 461(7265), pages 747-753, October.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Fang Liu & Hua Gong & Ligang Cai & Ke Xu, 2019. "Prediction of Ammunition Storage Reliability Based on Improved Ant Colony Algorithm and BP Neural Network," Complexity, Hindawi, vol. 2019, pages 1-13, March.

    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. Bo Jiang & Jun S. Liu, 2015. "Bayesian Partition Models for Identifying Expression Quantitative Trait Loci," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 110(512), pages 1350-1361, December.
    2. Daniel Svensson & Matilda Rentoft & Anna M Dahlin & Emma Lundholm & Pall I Olason & Andreas Sjödin & Carin Nylander & Beatrice S Melin & Johan Trygg & Erik Johansson, 2020. "A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences," PLOS ONE, Public Library of Science, vol. 15(9), pages 1-18, September.
    3. Chuan Gao & Nan Wang & Xiuqing Guo & Julie T Ziegler & Kent D Taylor & Anny H Xiang & Yang Hai & Steven J Kridel & Jerry L Nadler & Fouad Kandeel & Leslie J Raffel & Yii-Der I Chen & Jill M Norris & J, 2015. "A Comprehensive Analysis of Common and Rare Variants to Identify Adiposity Loci in Hispanic Americans: The IRAS Family Study (IRASFS)," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-17, November.
    4. Poojitha Balakrishnan & Miranda R. Jones & Dhananjay Vaidya & Maria Tellez-Plaza & Wendy S. Post & Joel D. Kaufman & Suzette J. Bielinski & Kent Taylor & Kevin Francesconi & Walter Goessler & Ana Nava, 2018. "Ethnic, Geographic, and Genetic Differences in Arsenic Metabolism at Low Arsenic Exposure: A Preliminary Analysis in the Multi-Ethnic Study of Atherosclerosis (MESA)," IJERPH, MDPI, vol. 15(6), pages 1-11, June.
    5. Wei-Yu Lin & Ian W Brock & Dan Connley & Helen Cramp & Rachel Tucker & Jon Slate & Malcolm W R Reed & Sabapathy P Balasubramanian & Lisa A Cannon-Albright & Nicola J Camp & Angela Cox, 2013. "Associations of ATR and CHEK1 Single Nucleotide Polymorphisms with Breast Cancer," PLOS ONE, Public Library of Science, vol. 8(7), pages 1-1, July.
    6. repec:plo:pgen00:1003258 is not listed on IDEAS
    7. Craig, Sarah J.C. & Kenney, Ana M. & Lin, Junli & Paul, Ian M. & Birch, Leann L. & Savage, Jennifer S. & Marini, Michele E. & Chiaromonte, Francesca & Reimherr, Matthew L. & Makova, Kateryna D., 2023. "Constructing a polygenic risk score for childhood obesity using functional data analysis," Econometrics and Statistics, Elsevier, vol. 25(C), pages 66-86.
    8. Ilias Georgakopoulos-Soares & Chengyu Deng & Vikram Agarwal & Candace S. Y. Chan & Jingjing Zhao & Fumitaka Inoue & Nadav Ahituv, 2023. "Transcription factor binding site orientation and order are major drivers of gene regulatory activity," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    9. Meida Wang & Shuanglin Zhang & Qiuying Sha, 2022. "A computationally efficient clustering linear combination approach to jointly analyze multiple phenotypes for GWAS," PLOS ONE, Public Library of Science, vol. 17(4), pages 1-13, April.
    10. Anshuman Sewda & A J Agopian & Elizabeth Goldmuntz & Hakon Hakonarson & Bernice E Morrow & Deanne Taylor & Laura E Mitchell & on behalf of the Pediatric Cardiac Genomics Consortium, 2019. "Gene-based genome-wide association studies and meta-analyses of conotruncal heart defects," PLOS ONE, Public Library of Science, vol. 14(7), pages 1-19, July.
    11. Harriëtte Riese & Loretto M Muñoz & Catharina A Hartman & Xiuhua Ding & Shaoyong Su & Albertine J Oldehinkel & Arie M van Roon & Peter J van der Most & Joop Lefrandt & Ron T Gansevoort & Pim van der H, 2014. "Identifying Genetic Variants for Heart Rate Variability in the Acetylcholine Pathway," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-9, November.
    12. Franz Förster & David Emmert & Katrin Horn & Janne Pott & Johannes Frasnelli & Mohammed Aslam Imtiaz & Konstantinos Melas & Valentina Talevi & Honglei Chen & Christoph Engel & Michele Filosi & Myriam , 2025. "Genome-wide association meta-analysis of human olfactory identification discovers sex-specific and sex-differential genetic variants," Nature Communications, Nature, vol. 16(1), pages 1-15, December.
    13. repec:plo:pone00:0037385 is not listed on IDEAS
    14. repec:plo:pgen00:1003520 is not listed on IDEAS
    15. repec:plo:pone00:0083057 is not listed on IDEAS
    16. Indra Adrianto & Chee Paul Lin & Jessica J Hale & Albert M Levin & Indrani Datta & Ryan Parker & Adam Adler & Jennifer A Kelly & Kenneth M Kaufman & Christopher J Lessard & Kathy L Moser & Robert P Ki, 2012. "Genome-Wide Association Study of African and European Americans Implicates Multiple Shared and Ethnic Specific Loci in Sarcoidosis Susceptibility," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-10, August.
    17. Bárbara Sousa da Mota & Simone Rubinacci & Diana Ivette Cruz Dávalos & Carlos Eduardo G. Amorim & Martin Sikora & Niels N. Johannsen & Marzena H. Szmyt & Piotr Włodarczak & Anita Szczepanek & Marcin M, 2023. "Imputation of ancient human genomes," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    18. Oren E Livne & Lide Han & Gorka Alkorta-Aranburu & William Wentworth-Sheilds & Mark Abney & Carole Ober & Dan L Nicolae, 2015. "PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population," PLOS Computational Biology, Public Library of Science, vol. 11(3), pages 1-14, March.
    19. repec:plo:pone00:0042530 is not listed on IDEAS
    20. Zhuoran Xu & Quan Li & Luigi Marchionni & Kai Wang, 2023. "PhenoSV: interpretable phenotype-aware model for the prioritization of genes affected by structural variants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    21. Oxley, Florence A.R. & Wilding, Kirsty & von Stumm, Sophie, 2024. "DNA and IQ: Big deal or much ado about nothing? – A meta-analysis," Intelligence, Elsevier, vol. 107(C).
    22. Paul S de Vries & Maria Sabater-Lleal & Daniel I Chasman & Stella Trompet & Tarunveer S Ahluwalia & Alexander Teumer & Marcus E Kleber & Ming-Huei Chen & Jie Jin Wang & John R Attia & Riccardo E Mario, 2017. "Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study," PLOS ONE, Public Library of Science, vol. 12(1), pages 1-22, January.
    23. Akinori Miyashita & Asako Koike & Gyungah Jun & Li-San Wang & Satoshi Takahashi & Etsuro Matsubara & Takeshi Kawarabayashi & Mikio Shoji & Naoki Tomita & Hiroyuki Arai & Takashi Asada & Yasuo Harigaya, 2013. "SORL1 Is Genetically Associated with Late-Onset Alzheimer’s Disease in Japanese, Koreans and Caucasians," PLOS ONE, Public Library of Science, vol. 8(4), pages 1-11, April.
    24. Guo, Fangqi & Harris, Kathleen Mullan & Boardman, Jason D. & Robinette, Jennifer W., 2022. "Does crime trigger genetic risk for type 2 diabetes in young adults? A G x E interaction study using national data," Social Science & Medicine, Elsevier, vol. 313(C).
    25. Reuben, Aaron & Arseneault, Louise & Belsky, Daniel W. & Caspi, Avshalom & Fisher, Helen L. & Houts, Renate M. & Moffitt, Terrie E. & Odgers, Candice, 2019. "Residential neighborhood greenery and children's cognitive development," Social Science & Medicine, Elsevier, vol. 230(C), pages 271-279.

    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:hin:complx:5024867. 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: Mohamed Abdelhakeem (email available below). General contact details of provider: https://www.hindawi.com .

    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.