Generating consistent genotypic configurations for multi-allelic loci and large complex pedigrees

被引:20
作者
Heath, SC [1 ]
机构
[1] Univ Washington, Dept Stat, Seattle, WA 98195 USA
关键词
genotype configurations; complex pedigrees; multi-allelic loci; peeling; genotype elimination; Gibbs sampling;
D O I
10.1159/000022775
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Markov chain Monte Carlo techniques have been applied to many different genetic analysis problems. Gibbs sampling in particular has been widely used because of its simplicity and because it can be extended to arbitrarily complex pedigrees and genetic models (albeit with modifications for multi-allelic loci). Gibbs sampling requires an initial genotypic configuration, consistent with observed data, the generation of which is not trivial with large complex pedigrees and multi-allelic loci. A method to generate feasible genotype configurations in these circumstances using a combination of peeling and genotype elimination is described. The method is illustrated using two complex multi-generation pedigrees, one real and one simulated, each partially typed for one highly polymorphic marker locus.
引用
收藏
页码:1 / 11
页数:11
相关论文
共 24 条
[1]   PROBABILITY FUNCTIONS ON COMPLEX PEDIGREES [J].
CANNINGS, C ;
THOMPSON, EA ;
SKOLNICK, MH .
ADVANCES IN APPLIED PROBABILITY, 1978, 10 (01) :26-61
[2]   GENERAL MODEL FOR GENETIC ANALYSIS OF PEDIGREE DATA [J].
ELSTON, RC ;
STEWART, J .
HUMAN HEREDITY, 1971, 21 (06) :523-&
[3]   COMBINED SEGREGATION AND LINKAGE ANALYSIS OF LATE-ONSET ALZHEIMERS-DISEASE IN DUKE FAMILIES USING GIBBS SAMPLING [J].
FAUCETT, C ;
GAUDERMAN, WJ ;
THOMAS, D ;
ZIOGAS, A ;
SOBEL, E .
GENETIC EPIDEMIOLOGY, 1993, 10 (06) :489-494
[4]   STOCHASTIC RELAXATION, GIBBS DISTRIBUTIONS, AND THE BAYESIAN RESTORATION OF IMAGES [J].
GEMAN, S ;
GEMAN, D .
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 1984, 6 (06) :721-741
[5]   ANNEALING MARKOV-CHAIN MONTE-CARLO WITH APPLICATIONS TO ANCESTRAL INFERENCE [J].
GEYER, CJ ;
THOMPSON, EA .
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1995, 90 (431) :909-920
[6]   Computing approximate monogenic model likelihoods in large pedigrees with loops [J].
Janss, LLG ;
VanArendonk, JAM ;
VanderWerf, JHJ .
GENETICS SELECTION EVOLUTION, 1995, 27 (06) :567-579
[7]   EFFICIENT COMPUTATION OF LOD SCORES - GENOTYPE ELIMINATION, GENOTYPE REDEFINITION, AND HYBRID MAXIMUM-LIKELIHOOD ALGORITHMS [J].
LANGE, K ;
WEEKS, DE .
ANNALS OF HUMAN GENETICS, 1989, 53 :67-83
[8]  
LANGE K, 1987, AM J HUM GENET, V40, P250
[9]  
LARSEN B, 1976, TISSUE ANTIGENS, V8, P207
[10]   A SCHEME FOR CONSTRUCTING AN IRREDUCIBLE MARKOV-CHAIN FOR PEDIGREE DATA [J].
LIN, SL .
BIOMETRICS, 1995, 51 (01) :318-322