Efficient computation of lod scores: Genotype elimination, genotype redefinition, and hybrid maximum likelihood algorithms. (English) Zbl 0663.92009
Calculation of multilocus lod scores presents challenging problems in numerical analysis, combinatorics, programming, and genetics. It is possible to accelerate these computations by exploiting the simple pedigree structure of a CEPH-type pedigree consisting of a nuclear family plus all four grandparents. G. M. Lathrop, J. M. Lalouel and R. L. White [Genet. Epidemiology 3, 39-52 (1986)] have done this by introducing likelihood factorization and transformation rules and E. S. Lander and P. Green [Proc. Natl. Acad. Sci. USA 84, 2363-2367 (1987)] by the method of ‘hidden Markov chains’. The present paper explores an alternative approach based on genotype redefinition in the grandparents and systematic phase elimination in all pedigree members. All three approaches accelerate the computation of a single likelihood. Equally relevant to multilocus mapping are search strategies for finding the maximum likelihood estimates of recombination fractions. Hybrid algorithms that start with the EM algorithm and switch midway to quasi- Newton algorithms show promise. These issues are investigated in the context of a simulated 10 locus example. The same example allows us to illustrate a simple strategy for determining locus order.
MSC:
| 92D10 | Genetics and epigenetics |
| 62P10 | Applications of statistics to biology and medical sciences; meta analysis |
| 65C99 | Probabilistic methods, stochastic differential equations |
Keywords:
Calculation of multilocus lod scores; CEPH-type pedigree; maximum likelihood estimates of recombination fractions; Hybrid algorithms; EM algorithm; quasi-Newton algorithmsReferences:
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