Recombination Fraction

Biased Estimation of the Recombination Fraction Using Half-Sib Families and Informative Offspring

Genetics ◽

10.1093/genetics/157.3.1357 ◽

2001 ◽

Vol 157 (3) ◽

pp. 1357-1367 ◽

Cited By ~ 1

Author(s):

L Gomez-Raya

Keyword(s):

Recombination Fraction ◽

Allele Frequencies ◽

Likelihood Method ◽

Simultaneous Estimation ◽

Sampling Variance ◽

Production Traits ◽

Lod Score ◽

Absolute Value ◽

Sib Families ◽

Map Distance

Abstract A maximum-likelihood method to estimate the recombination fraction and its sampling variance using informative and noninformative half-sib offspring is derived. Estimates of the recombination fraction are biased up to 20 cM when noninformative offspring are discarded. In certain scenarios, the sampling variance can be increased or reduced up to fivefold due to the bias in estimating the recombination fraction and the LOD score can be reduced up to 5 units when discarding noninformative offspring. Comparison of the estimates of recombination fraction, map distance, and LOD score when constructing a genetic map with 251 two-point linkage analyses and six families of Norwegian cattle was carried out to evaluate the implications of discarding noninformative offspring in practical situations. The average discrepancies in absolute value (average difference when using and neglecting noninformative offspring) were 0.0146, 1.64 cM, and 2.61 for the recombination fraction, map distance, and the LOD score, respectively. A method for simultaneous estimation of allele frequencies in the dam population and a transmission disequilibrium parameter is proposed. This method might account for the bias in estimating allele frequencies in the dam population when the half-sib offspring is selected for production traits.

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Sex differences in recombination fraction estimates and their effect on ordering of chromosome 11 markers

Genetic Epidemiology ◽

10.1002/gepi.1370030729 ◽

1986 ◽

Vol 3 (S1) ◽

pp. 185-190

Author(s):

F. Lennie Wong ◽

Kenneth Lange ◽

Gloria M. Petersen ◽

Jennie S. Jing ◽

Jerome I. Rotter

Keyword(s):

Sex Differences ◽

Recombination Fraction ◽

Chromosome 11

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On Genetic Map Functions

Genetics ◽

10.1093/genetics/142.4.1369 ◽

1996 ◽

Vol 142 (4) ◽

pp. 1369-1377

Author(s):

Hongyu Zhao ◽

Terence P Speed

Keyword(s):

Genetic Distance ◽

Genetic Map ◽

Probability Model ◽

Recombination Fraction ◽

Renewal Processes ◽

Gamma Distributions ◽

Multilocus Analysis ◽

Map Function ◽

Better Than

Abstract Various genetic map functions have been proposed to infer the unobservable genetic distance between two loci from the observable recombination fraction between them. Some map functions were found to fit data better than others. When there are more than three markers, multilocus recombination probabilities cannot be uniquely determined by the defining property of map functions, and different methods have been proposed to permit the use of map functions to analyze multilocus data. If for a given map function, there is a probability model for recombination that can give rise to it, then joint recombination probabilities can be deduced from this model. This provides another way to use map functions in multilocus analysis. In this paper we show that stationary renewal processes give rise to most of the map functions in the literature. Furthermore, we show that the interevent distributions of these renewal processes can all be approximated quite well by gamma distributions.

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Sperm typing allows accurate measurement of the recombination fraction between D3S2 and D3S3 on the short arm of human chromosome 3

Genomics ◽

10.1016/0888-7543(92)90294-3 ◽

1992 ◽

Vol 12 (4) ◽

pp. 683-687 ◽

Cited By ~ 14

Author(s):

Rene Hubert ◽

Vincent P. Stanton ◽

Hiroyuki Aburatani ◽

John Warren ◽

Honghua Li ◽

...

Keyword(s):

Human Chromosome ◽

Recombination Fraction ◽

Chromosome 3 ◽

Human Chromosome 3 ◽

Sperm Typing

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Linkage and gene localization of hereditary spherocytosis (HS)

Blood ◽

10.1182/blood.v52.5.859.859 ◽

1978 ◽

Vol 52 (5) ◽

pp. 859-867 ◽

Cited By ~ 24

Author(s):

WJ Kimberling ◽

RA Taylor ◽

RG Chapman ◽

HA Lubs

Keyword(s):

Linkage Analysis ◽

Hereditary Spherocytosis ◽

Recombination Fraction ◽

Gene Localization ◽

Lod Score ◽

Marker Loci

Abstract Fifteen kindreds with dominant hereditary spherocytosis (HS) were studied. Expansion of the data from a family with an 8/12 translocation provided further evidence that at least one locus for HS is located near the breakpoint of the translocation. Linkage analysis of all families showed a lack of linkage with all marker loci studied except for Gm (IgG). Linkage between Gm and HS was shown to be significant with a maximum lod score of 3.42 at a recombination fraction of 22%. No heterogeneity of the recombination fraction was observed either between sexes or between families. These results are compatible with the hypothesis that HS is not a heterogeneous disorder.

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Associative overdominance caused by linked detrimental mutations

Genetics Research ◽

10.1017/s0016672300012684 ◽

1971 ◽

Vol 18 (3) ◽

pp. 277-286 ◽

Cited By ~ 127

Author(s):

Tomoko Ohta

Keyword(s):

Blood Group ◽

Inbreeding Depression ◽

Recombination Fraction ◽

Abo Blood Group ◽

Deleterious Mutations ◽

Method Of Moment ◽

Moment Equations ◽

Neutral Locus ◽

Neutral Marker ◽

Image Position

SUMMARYAssociative overdominance due to linked detrimental mutations was investigated using the method of moment equations based on diffusion models. The expectation of the apparent selective value at the marker (neutral) locus has been evaluated. Assume two linked loci, at one of which the steady flux equilibrium is reached under constant mutational input of deleterious mutations (with rate v) having disadvantages hs in heterozygote and s in homozygotes. At another locus, the neutral alleles are segregating with frequencies near 0·5. Let Ne be the effective size of the population and c be the recombination fraction between the two loci. Then the coefficient of associative overdominance at the neutral locus can be obtained by taking the expectation with respect to chromosome frequencies at steady flux equilibrium. It becomes approximatelywhere (LI−L0) is the inbreeding depression caused by deleterious mutations under complete inbreeding, and Nehs ≫ l and hs ≫ v are assumed. More generally, if the inbreeding depression of a chromosome segment with a length of recombination fraction C is (LI−L0) then s′ at the neutral marker at the edge of the segment iswhere hs is the average heterozygote disadvantage of detrimentals.The significance of the associative overdominance is discussed in relation to actual observations. It is proposed that the most of the observed heterozygote superiority including inversion chromosomes of Drosophila, isozyme alleles in Avena and ABO blood group genes in man could be explained by the associated detrimentals.

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Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector

Bioinformatics ◽

10.1093/bioinformatics/btv669 ◽

2015 ◽

Vol 32 (6) ◽

pp. 801-807 ◽

Cited By ~ 2

Author(s):

Mookyung Cheon ◽

Choongrak Kim ◽

Iksoo Chang

Keyword(s):

Source Code ◽

Algebraic Property ◽

Laplacian Matrix ◽

Recombination Fraction ◽

Supplementary Information ◽

Supplementary Data ◽

Data Set ◽

Variable Threshold ◽

Fiedler Vector ◽

Complex Graph

AbstractMotivation: The loci-ordering, based on two-point recombination fractions for a pair of loci, is the most important step in constructing a reliable and fine genetic map.Results: Using the concept from complex graph theory, here we propose a Laplacian ordering approach which uncovers the loci-ordering of multiloci simultaneously. The algebraic property for a Fiedler vector of a Laplacian matrix, constructed from the recombination fraction of the loci-ordering for 26 loci of barley chromosome IV, 846 loci of Arabidopsisthaliana and 1903 loci of Malus domestica, together with the variable threshold uncovers their loci-orders. It offers an alternative yet robust approach for ordering multiloci.Availability and implementation : Source code program with data set is available as supplementary data and also in a software category of the website (http://biophysics.dgist.ac.kr)Contact: [email protected] or [email protected] information: Supplementary data are available at Bioinformatics online.

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DYNAMICS OF THE LINKAGE DISEQUILIBRIUM FUNCTION UNDER MODELS OF GENE-FREQUENCY HITCHHIKING

Genetics ◽

10.1093/genetics/99.2.337 ◽

1981 ◽

Vol 99 (2) ◽

pp. 337-356

Author(s):

Marjorie A Asmussen ◽

Michael T Clegg

Keyword(s):

Linkage Disequilibrium ◽

Gene Frequency ◽

Initial Conditions ◽

Recombination Fraction ◽

Qualitative Description ◽

Selection Intensity ◽

Gene Frequencies ◽

Dependent Behavior ◽

Wide Range ◽

Over Time

ABSTRACT The dynamic behavior of the linkage disequilibrium (D) between a neutral and a selected locus is analyzed for a variety of deterministic selection models. The time-dependent behavior of D is governed by the gene frequency at the selected locus (p) and by the selection (s) and recombination (r) parameters. Thomson (1977) showed numerically that D may increase under certain initial conditions. We give exact conditions for D to increase in time, which require that the selection intensity exceed the recombination fraction (s > r) and that p be near zero or one. We conclude from this result that gene frequency hitchhiking is most likely to be important when a new favorable mutant enters a population. We also show that, for what can be a wide range of gene frequencies, D will decay at a faster rate than the neutral rate. Consequently, the hitchhiking effect may quickly diminish as the selected gene becomes more common.—The method of analysis allows a complete qualitative description of the dynamics of D as a function of s and r. Two major findings concern the range of gene frequencies at the selected locus for which D either increases over time or decays at a faster rate than under neutrality. For all models considered, the region where D increases (i) first enlarges then shrinks as selection intensifies, and (ii) steadily shrinks as r increases. In contrast, the region of accelerated decay constantly enlarges as the selection intensity increases. This region will either shrink or enlarge as r increases, depending upon the form of selection in force.

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