3.8

CiteScore

2.4

Impact Factor
  • ISSN 1674-8301
  • CN 32-1810/R
Honggang Yi, Hongmei Wo, Yang Zhao, Ruyang Zhang, Junchen Dai, Guangfu Jin, Hongxia Ma, Tangchun Wu, Zhibin Hu, Dongxin Lin, Hongbing Shen, Feng Chen. Comparison of dimension reduction-based logistic regression models forcase-control genome-wide association study: principal components analysis vs. partial least squares[J]. The Journal of Biomedical Research, 2015, 29(4): 298-307. DOI: 10.7555/JBR.29.20140043
Citation: Honggang Yi, Hongmei Wo, Yang Zhao, Ruyang Zhang, Junchen Dai, Guangfu Jin, Hongxia Ma, Tangchun Wu, Zhibin Hu, Dongxin Lin, Hongbing Shen, Feng Chen. Comparison of dimension reduction-based logistic regression models forcase-control genome-wide association study: principal components analysis vs. partial least squares[J]. The Journal of Biomedical Research, 2015, 29(4): 298-307. DOI: 10.7555/JBR.29.20140043

Comparison of dimension reduction-based logistic regression models forcase-control genome-wide association study: principal components analysis vs. partial least squares

Funds: 

the National Natural Science Foundation of China (81202283, 81473070, 81373102 and 81202267), Key Grant of Natural Science Foundation of the Jiangsu Higher Education Institutions of China (10KJA330034 and 11KJA330001)

More Information
  • Received Date: March 10, 2015
  • With recent advances in biotechnology, genome-wide association study (GWAS) has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression (LR) based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logisticregression (PC-LR), partial least squares-based logistic regression (PLS-LR), have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor- mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism(SNP)setregion.WefoundthatPC-LRandPLScanreasonablycontroltypeIerrorundernullhypothesis. Oncontrast,LR,whichiscorrectedbyBonferronimethod,wasmoreconservedinallsimulationsettings.Inparticular,we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data.
  • Related Articles

    [1]Yinhe Feng, Yubin Wang, Xiaolong Li, Hui Mao. Anticoagulation therapy for pulmonary embolism involving a myxoma mimicking, giant type C thrombus: A case report[J]. The Journal of Biomedical Research, 2023, 37(2): 148-152. DOI: 10.7555/JBR.36.20220118
    [2]Tiwari-Heckler Shilpa, Jiang Z. Gordon, Popov Yury, J. Mukamal Kenneth. Daily high-dose aspirin does not lower APRI in the Aspirin-Myocardial Infarction Study[J]. The Journal of Biomedical Research, 2020, 34(2): 139-142. DOI: 10.7555/JBR.33.20190041
    [3]Tao Chun'ai, Gan Yongxin, Su Weidong, Li Zhutian, Tang Xiaolan. Effectiveness of hospital disinfection and experience learnt from 11 years of surveillance[J]. The Journal of Biomedical Research, 2019, 33(6): 408-413. DOI: 10.7555/JBR.33.20180118
    [4]Huan Liu, Shijiang Zhang, Yongfeng Shao, Xiaohu Lu, Weidong Gu, Buqing Ni, Qun Gu, Junjie Du. Biomechanical characterization of a novel ring connector for sutureless aortic anastomosis[J]. The Journal of Biomedical Research, 2018, 32(6): 454-460. DOI: 10.7555/JBR.31.20170011
    [5]Minbo Zang, Qiao Zhou, Yunfei Zhu, Mingxi Liu, Zuomin Zhou. Effects of chemotherapeutic agent bendamustine for nonhodgkin lymphoma on spermatogenesis in mice[J]. The Journal of Biomedical Research, 2018, 32(6): 442-453. DOI: 10.7555/JBR.31.20170023
    [6]Kaibo Lin, Shikun Zhang, Jieli Chen, Ding Yang, Mengyi Zhu, Eugene Yujun Xu. Generation and functional characterization of a conditional Pumilio2 null allele[J]. The Journal of Biomedical Research, 2018, 32(6): 434-441. DOI: 10.7555/JBR.32.20170117
    [7]Huanqiang Wang, Congying Yang, Siyuan Wang, Tian Wang, Jingling Han, Kai Wei, Fucun Liu, Jida Xu, Xianzhen Peng, Jianming Wang. Cell-free plasma hypermethylated CASZ1, CDH13 and ING2 are promising biomarkers of esophageal cancer[J]. The Journal of Biomedical Research, 2018, 32(6): 424-433. DOI: 10.7555/JBR.32.20170065
    [8]Fengzhen Wang, Mingwan Zhang, Dongsheng Zhang, Yuan Huang, Li Chen, Sunmin Jiang, Kun Shi, Rui Li. Preparation, optimization, and characterization of chitosancoated solid lipid nanoparticles for ocular drug delivery[J]. The Journal of Biomedical Research, 2018, 32(6): 411-423. DOI: 10.7555/JBR.32.20160170
    [9]Christopher J. Danford, Zemin Yao, Z. Gordon Jiang. Non-alcoholic fatty liver disease: a narrative review of genetics[J]. The Journal of Biomedical Research, 2018, 32(6): 389-400. DOI: 10.7555/JBR.32.20180045
    [10]Tongfu Yu, Mei Yuan, Qingbo Zhang, Haibing Shi, Dehang Wang. Evaluation of computed tomography obstruction index in guiding therapeutic decisions and monitoring percutanous catheter fragmentation in massive pulmonary embolism[J]. The Journal of Biomedical Research, 2011, 25(6): 431-437. DOI: 10.1016/S1674-8301(11)60057-2
  • Cited by

    Periodical cited type(3)

    1. Wang P, Ren D, Guo C, et al. A rare case of pulmonary artery embolism with choriocarcinoma: A case report and literature review. Oncol Lett, 2023, 26(5): 490. DOI:10.3892/ol.2023.14077
    2. Venturini M, Bergamini A, Colarieti A, et al. A rare case of a giant arterio-venous fistula (AVF) following metastatic choriocarcinoma conditioning pulmonary embolism: multimodal transcatheter embolization using a simultaneous transarterial and transvenous approach. CVIR Endovasc, 2018, 1(1): 30. DOI:10.1186/s42155-018-0039-8
    3. Kim GS, Heo JR, Kim SU, et al. Cancer-Specific Inhibitory Effects of Genetically Engineered Stem Cells Expressing Cytosine Deaminase and Interferon-β Against Choriocarcinoma in Xenografted Metastatic Mouse Models. Transl Oncol, 2018, 11(1): 74-85. DOI:10.1016/j.tranon.2017.11.003

    Other cited types(0)

Catalog

    Feng Chen

    1. On this Site
    2. On Google Scholar
    3. On PubMed

    Article Metrics

    Article views (3586) PDF downloads (828) Cited by(3)
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return