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| 2. |
- Mostad, Petter, 1964, et al.
(author)
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The Quest for a Donor: Probability Based Methods Offer Help.
- 2005
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Journal article (other academic/artistic)abstract
- When a patient in need of a stem cell transplant has no compatible donor within his or herclosest family, and no matched unrelated donor can be found, a remaining option is to searchwithin the patient’s extended family. This situation often arises when the patient is of anethnic minority, originating from a country that lacks a well-developed stem cell donorprogram, and has HLA haplotypes that are rare in his or her country of residence. Searchingwithin the extended family may be time-consuming and expensive, and tools to calculate theprobability of a match within groups of untested relatives would facilitate the search.We present a general approach to calculating the probability of a match in a given relative, orgroup of relatives, based on the pedigree, and on knowledge of the genotypes of some of theindividuals. The method extends previous approaches by allowing the pedigrees to beconsanguineous and arbitrarily complex, with deviations from Hardy-Weinberg equilibrium.We show how this extension has a considerable effect on results, in particular for rarehaplotypes. The methods are exemplified using freeware programs to solve a case of practicalimportance.
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| 3. |
- Svennblad, Bodil, 1966-
(author)
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On Estimating Topology and Divergence Times in Phylogenetics
- 2008
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Doctoral thesis (other academic/artistic)abstract
- This PhD thesis consists of an introduction and five papers, dealing with statistical methods in phylogenetics.A phylogenetic tree describes the evolutionary relationships among species assuming that they share a common ancestor and that evolution takes place in a tree like manner. Our aim is to reconstruct the evolutionary relationships from aligned DNA sequences.In the first two papers we investigate two measures of confidence for likelihood based methods, bootstrap frequencies with Maximum Likelihood (ML) and Bayesian posterior probabilities. We show that an earlier claimed approximate equivalence between them holds under certain conditions, but not in the current implementations of the two methods.In the following two papers the divergence times of the internal nodes are considered. The ML estimate of the divergence time of the root is improved if longer sequences are analyzed or if more taxa are added. We show that the gain in precision is faster with longer sequences than with more taxa. We also show that the algorithm of the software package PATHd8 may give biased estimates if the global molecular clock is violated. A change of the algorithm to obtain unbiased estimates is therefore suggested.The last paper deals with non-informative priors when using the Bayesian approach in phylogenetics. The term is not uniquely defined in the literature. We adopt the idea of data translated likelihoods and derive the so called Jeffreys' prior for branch lengths using Jukes Cantor model of evolution.
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| 4. |
- Thelle, Dag, 1942, et al.
(author)
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Genetisk epidemiologi
- 2007
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In: Epidemiologiske og kliniske forskningsmetoder. - 8205335052 ; , s. 463-498
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Book chapter (other academic/artistic)
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| 5. |
- Tillmar, Andreas, et al.
(author)
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Analysis of linkage and linkage disequilibrium for eight X-STR markers.
- 2008
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In: Forensic science international. Genetics. - : Elsevier. - 1878-0326 .- 1872-4973. ; 3:1, s. 37-41
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Journal article (peer-reviewed)abstract
- X-chromosomal short tandem repeats (X-STR) have proven to be informative and useful in complex relationship testing. The main feature of X-STR markers, compared to autosomal forensic markers, is that all loci are located on the same chromosome. Thus, linkage and linkage disequilibrium may occur. The aim of this work was to study population genetic parameters of eight X-STR markers, located in four linkage groups. We present haplotype frequencies, based on 718 Swedish males, for the four linkage groups included in the Argus X-8 kit. Forensic efficiency parameters have been calculated as well as the allelic association between the tested markers for detection of linkage disequilibrium. To study the occurrences of recombination between the loci, both Swedish and Somali families were typed. A mathematical model for the estimation of recombination frequencies is presented and applied on the family samples. Our study showed that the tested markers all have highly informative forensic values and that there is a significant degree of linkage disequilibrium between the STR markers within the four linkage groups. Furthermore, based on the tested families, we also demonstrated that two of the linkage groups are partially linked. A consequence of these findings is that both linkage and linkage disequilibrium should be accounted for when producing likelihood ratios in relationship testing with X-STR markers.
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