Effect of misspecification of gene frequency on the two-point LOD score

被引:21
|
作者
Pal, DK
Durner, M
Greenberg, DA
机构
[1] Mt Sinai Med Ctr, Dept Psychiat, New York, NY 10029 USA
[2] Mt Sinai Med Ctr, Dept Biomath, New York, NY 10029 USA
关键词
linkage analysis; parameter misspecification; gene frequency;
D O I
10.1038/sj.ejhg.5200724
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
In this study, we used computer simulation of simple and complex models to ask: (1) What is the penalty in evidence for linkage when the assumed gene frequency is far from the true gene frequency? (2) If the assumed model for gene frequency and inheritance are misspecified in the analysis, can this lead to a higher maximum LOD score than that obtained under the true parameters? Linkage data simulated under simple dominant, recessive, dominant and recessive with reduced penetrance, and additive models, were analysed assuming a single locus with both the correct and incorrect dominance model and assuming a range of different gene frequencies. We found that misspecifying the analysis gene frequency led to little penalty in maximum LOD score in all models examined, especially if the assumed gene frequency was blower than the generating one. Analysing linkage data assuming a gene frequency of the order of 0.01 for a dominant gene, and 0.1 for a recessive gene, appears to be a reasonable tactic in the majority of realistic situations because underestimating the gene frequency, even when the true gene frequency is high, leads to little penalty in the LOD score.
引用
收藏
页码:855 / 859
页数:5
相关论文
共 50 条
  • [11] Two-Point Grasp Response
    Krishna, K. Rama
    Vipin, J. S.
    Sen, Dibakar
    MACHINES, MECHANISM AND ROBOTICS, 2019, : 795 - 805
  • [12] Two-point symmetrization and convexity
    Aubrun, G
    Fradelizi, M
    ARCHIV DER MATHEMATIK, 2004, 82 (03) : 282 - 288
  • [13] Introduction to two-point closures
    Cambon, C
    CLOSURE STRATEGIES FOR TURBULENT AND TRANSITIONAL FLOWS, 2002, : 299 - 327
  • [14] Wild two-point algebras
    Han, Y
    JOURNAL OF ALGEBRA, 2002, 247 (01) : 57 - 77
  • [15] Two-point Ostrowski inequality
    Matic, M
    Pecaric, J
    MATHEMATICAL INEQUALITIES & APPLICATIONS, 2001, 4 (02): : 215 - 221
  • [16] A degenerate two-point problem
    Barbu, V
    Favini, A
    EVOLUTION EQUATIONS, SEMIGROUPS AND FUNCTIONAL ANALYSIS: IN MEMORY OF BRUNELLO TERRENI, 2002, 50 : 27 - 37
  • [17] Symmetries of two-point sets
    Chad, Ben
    Suabedissen, Rolf
    TOPOLOGY AND ITS APPLICATIONS, 2008, 155 (11) : 1213 - 1220
  • [18] Two-point string amplitudes
    Erbin, Harold
    Maldacena, Juan
    Skliros, Dimitri
    JOURNAL OF HIGH ENERGY PHYSICS, 2019, 2019 (07)
  • [19] A horopter for two-point perspective
    Tyler, CW
    Human Vision and Electronic Imaging X, 2005, 5666 : 306 - 315
  • [20] Two-point string amplitudes
    Harold Erbin
    Juan Maldacena
    Dimitri Skliros
    Journal of High Energy Physics, 2019