IDEAS home Printed from https://ideas.repec.org/a/eee/csdana/v53y2009i5p1794-1801.html
   My bibliography  Save this article

Fast implementation of a scan statistic for identifying chromosomal patterns of genome wide association studies

Author

Listed:
  • Sun, Yan V.
  • Jacobsen, Douglas M.
  • Turner, Stephen T.
  • Boerwinkle, Eric
  • Kardia, Sharon L.R.

Abstract

In order to take into account the complex genomic distribution of SNP variations when identifying chromosomal regions with significant SNP effects, a single nucleotide polymorphism (SNP) association scan statistic was developed. To address the computational needs of genome wide association (GWA) studies, a fast Java application, which combines single-locus SNP tests and a scan statistic for identifying chromosomal regions with significant clusters of significant SNP effects, was developed and implemented. To illustrate this application, SNP associations were analyzed in a pharmacogenomic study of the blood pressure lowering effect of thiazide-diuretics (N=195) using the Affymetrix Human Mapping 100 K Set. 55,335 tagSNPs (pair-wise linkage disequilibrium R2

Suggested Citation

  • Sun, Yan V. & Jacobsen, Douglas M. & Turner, Stephen T. & Boerwinkle, Eric & Kardia, Sharon L.R., 2009. "Fast implementation of a scan statistic for identifying chromosomal patterns of genome wide association studies," Computational Statistics & Data Analysis, Elsevier, vol. 53(5), pages 1794-1801, March.
    • Handle: RePEc:eee:csdana:v:53:y:2009:i:5:p:1794-1801
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0167-9473(08)00223-5
    Download Restriction: Full text for ScienceDirect subscribers only.
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Robert Sladek & Ghislain Rocheleau & Johan Rung & Christian Dina & Lishuang Shen & David Serre & Philippe Boutin & Daniel Vincent & Alexandre Belisle & Samy Hadjadj & Beverley Balkau & Barbara Heude &, 2007. "A genome-wide association study identifies novel risk loci for type 2 diabetes," Nature, Nature, vol. 445(7130), pages 881-885, February.
    2. Xiaoping Su & Sylvan Wallenstein & David Bishop, 2001. "Nonoverlapping Clusters: Approximate Distribution and Application to Molecular Biology," Biometrics, The International Biometric Society, vol. 57(2), pages 420-426, June.
    3. Andreas Wagner, 1997. "A Computational Genomics Approach to the Identification of Gene Networks," Working Papers 97-08-074, Santa Fe Institute.
    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. Fuzhong Xue & Shengxu Li & Jian'an Luan & Zhongshang Yuan & Robert N Luben & Kay-Tee Khaw & Nicholas J Wareham & Ruth J F Loos & Jing Hua Zhao, 2012. "A Latent Variable Partial Least Squares Path Modeling Approach to Regional Association and Polygenic Effect with Applications to a Human Obesity Study," PLOS ONE, Public Library of Science, vol. 7(2), pages 1-10, February.

    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. Ping Rao & Hao Wang & Honghong Fang & Qing Gao & Jie Zhang & Manshu Song & Yong Zhou & Youxin Wang & Wei Wang, 2016. "Association between IGF2BP2 Polymorphisms and Type 2 Diabetes Mellitus: A Case–Control Study and Meta-Analysis," IJERPH, MDPI, vol. 13(6), pages 1-13, June.
    2. Greve, Jane, 2008. "Obesity and labor market outcomes in Denmark," Economics & Human Biology, Elsevier, vol. 6(3), pages 350-362, December.
    3. John PA Ioannidis & Nikolaos A Patsopoulos & Evangelos Evangelou, 2007. "Heterogeneity in Meta-Analyses of Genome-Wide Association Investigations," PLOS ONE, Public Library of Science, vol. 2(9), pages 1-7, September.
    4. Paul F O’Reilly & Clive J Hoggart & Yotsawat Pomyen & Federico C F Calboli & Paul Elliott & Marjo-Riitta Jarvelin & Lachlan J M Coin, 2012. "MultiPhen: Joint Model of Multiple Phenotypes Can Increase Discovery in GWAS," PLOS ONE, Public Library of Science, vol. 7(5), pages 1-1, May.
    5. Sarah Meulebrouck & Judith Merrheim & Gurvan Queniat & Cyril Bourouh & Mehdi Derhourhi & Mathilde Boissel & Xiaoyan Yi & Alaa Badreddine & Raphaël Boutry & Audrey Leloire & Bénédicte Toussaint & Souhi, 2024. "Functional genetics reveals the contribution of delta opioid receptor to type 2 diabetes and beta-cell function," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    6. Sato Yasunori & Laird Nan & Suganami Hideki & Hamada Chikuma & Niki Naoto & Yoshimura Isao & Yoshida Teruhiko, 2009. "Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-23, November.
    7. Jiajin Li & Brandon Jew & Lingyu Zhan & Sungoo Hwang & Giovanni Coppola & Nelson B Freimer & Jae Hoon Sul, 2019. "ForestQC: Quality control on genetic variants from next-generation sequencing data using random forest," PLOS Computational Biology, Public Library of Science, vol. 15(12), pages 1-30, December.
    8. Guang Guo, 2008. "Introduction to the Special Issue on Society and Genetics," Sociological Methods & Research, , vol. 37(2), pages 159-163, November.
    9. Peristera Paschou & Petros Drineas & Jamey Lewis & Caroline M Nievergelt & Deborah A Nickerson & Joshua D Smith & Paul M Ridker & Daniel I Chasman & Ronald M Krauss & Elad Ziv, 2008. "Tracing Sub-Structure in the European American Population with PCA-Informative Markers," PLOS Genetics, Public Library of Science, vol. 4(7), pages 1-13, July.
    10. Hongyan Mao & Qin Li & Shujun Gao, 2012. "Meta-Analysis of the Relationship between Common Type 2 Diabetes Risk Gene Variants with Gestational Diabetes Mellitus," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-7, September.
    11. Ekaterina Alekseevna Sokolova & Irina Arkadievna Bondar & Olesya Yurievna Shabelnikova & Olga Vladimirovna Pyankova & Maxim Leonidovich Filipenko, 2015. "Replication of KCNJ11 (p.E23K) and ABCC8 (p.S1369A) Association in Russian Diabetes Mellitus 2 Type Cohort and Meta-Analysis," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-21, May.
    12. Xiaobo Li & Yuqiong Li & Bei Song & Shujie Guo & Shaoli Chu & Nan Jia & Wenquan Niu, 2012. "Hematopoietically-Expressed Homeobox Gene Three Widely-Evaluated Polymorphisms and Risk for Diabetes: A Meta-Analysis," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-10, November.
    13. Ren Matsuba & Kensuke Sakai & Minako Imamura & Yasushi Tanaka & Minoru Iwata & Hiroshi Hirose & Kohei Kaku & Hiroshi Maegawa & Hirotaka Watada & Kazuyuki Tobe & Atsunori Kashiwagi & Ryuzo Kawamori & S, 2015. "Replication Study in a Japanese Population to Evaluate the Association between 10 SNP Loci, Identified in European Genome-Wide Association Studies, and Type 2 Diabetes," PLOS ONE, Public Library of Science, vol. 10(5), pages 1-13, May.
    14. Shuang-Xia Zhao & Chun-Ming Pan & Huang-Ming Cao & Bing Han & Jing-Yi Shi & Jun Liang & Guan-Qi Gao & Yong-De Peng & Qing Su & Jia-Lun Chen & Jia-Jun Zhao & Huai-Dong Song, 2010. "Association of the CTLA4 Gene with Graves' Disease in the Chinese Han Population," PLOS ONE, Public Library of Science, vol. 5(3), pages 1-10, March.
    15. Ren Matsuba & Minako Imamura & Yasushi Tanaka & Minoru Iwata & Hiroshi Hirose & Kohei Kaku & Hiroshi Maegawa & Hirotaka Watada & Kazuyuki Tobe & Atsunori Kashiwagi & Ryuzo Kawamori & Shiro Maeda, 2016. "Replication Study in a Japanese Population of Six Susceptibility Loci for Type 2 Diabetes Originally Identified by a Transethnic Meta-Analysis of Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 11(4), pages 1-9, April.
    16. Ping Rao & Yong Zhou & Si-Qi Ge & An-Xin Wang & Xin-Wei Yu & Mohamed Ali Alzain & Andrea Katherine Veronica & Jing Qiu & Man-Shu Song & Jie Zhang & Hao Wang & Hong-Hong Fang & Qing Gao & You-Xin Wang , 2016. "Validation of Type 2 Diabetes Risk Variants Identified by Genome-Wide Association Studies in Northern Han Chinese," IJERPH, MDPI, vol. 13(9), pages 1-10, August.
    17. Nicholette D Palmer & Caitrin W McDonough & Pamela J Hicks & Bong H Roh & Maria R Wing & S Sandy An & Jessica M Hester & Jessica N Cooke & Meredith A Bostrom & Megan E Rudock & Matthew E Talbert & Jos, 2012. "A Genome-Wide Association Search for Type 2 Diabetes Genes in African Americans," PLOS ONE, Public Library of Science, vol. 7(1), pages 1-14, January.
    18. Minge Xie & Qiankun Sun & Joseph Naus, 2009. "A Latent Model to Detect Multiple Clusters of Varying Sizes," Biometrics, The International Biometric Society, vol. 65(4), pages 1011-1020, December.
    19. Qing Ma & Yini Xiao & Wenjun Xu & Menghan Wang & Sheng Li & Zhihao Yang & Minglu Xu & Tengjiao Zhang & Zhen-Ning Zhang & Rui Hu & Qiang Su & Fei Yuan & Tinghui Xiao & Xuan Wang & Qing He & Jiaxu Zhao , 2022. "ZnT8 loss-of-function accelerates functional maturation of hESC-derived β cells and resists metabolic stress in diabetes," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    20. Yuan Min & Tian Xin & Zheng Gang & Yang Yaning, 2009. "Adaptive Transmission Disequilibrium Test for Family Trio Design," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-22, June.

    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:eee:csdana:v:53:y:2009:i:5:p:1794-1801. 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: Catherine Liu (email available below). General contact details of provider: http://www.elsevier.com/locate/csda .

    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.