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Using X-chromosomal markers in relationship testing: How to calculate likelihood ratios taking linkage and linkage disequilibrium into account
Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Forensic Genetics.
University of Oslo, Institute of Forensic Medicine, Oslo, Norway.
Linköping University, Department of Clinical and Experimental Medicine, Forensic Genetics. Linköping University, Faculty of Health Sciences.
Linköping University, Faculty of Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Forensic Genetics.
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2011 (English)In: Forensic Science International: Genetics, ISSN 1872-4973, E-ISSN 1878-0326, Vol. 5, no 5, 506-511 p.Article in journal (Refereed) Published
Abstract [en]

X-chromosomal markers in forensic genetics have become more widely used during the recent years, particularly for relationship testing. Linkage and linkage disequilibrium (LD) must typically be accounted for when using close X-chromosomal markers. Thus, when producing the weight-of-evidence, given by a DNA-analysis with markers that are linked, the normally used product rule is invalid. Here we present an efficient model for calculating likelihood ratio (LR) with markers on the X-chromosome which are linked and in LD. Furthermore, the model was applied on several cases based on data from the eight X-chromosomal loci included in the Mentype® Argus X-8 (Biotype). Using a simulation approach we showed that the use of X-chromosome data can offer valuable information for choosing between the alternatives in each of the cases we studied, and that the LR can be high in several cases. We demonstrated that when linkage and LD were disregarded, as opposed to taken into account, the difference in calculated LR could be considerable. When these differences were large, the estimated haplotype frequencies often had a strong impact and we present a method to estimate haplotype frequencies. Our conclusion is that linkage and LD should be accounted for when using the tested set of markers, and the presented model is an efficient way of doing so.

Place, publisher, year, edition, pages
Elsevier , 2011. Vol. 5, no 5, 506-511 p.
Keyword [en]
X-chromosome, Linkage, Linkage disequilibrium, Simulation, Haplotype frequency
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:liu:diva-54741DOI: 10.1016/j.fsigen.2010.11.004ISI: 000294297700023OAI: oai:DiVA.org:liu-54741DiVA: diva2:309701
Available from: 2010-04-08 Created: 2010-04-08 Last updated: 2017-12-12
In thesis
1. Populations and Statistics in Forensic Genetics
Open this publication in new window or tab >>Populations and Statistics in Forensic Genetics
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA has become a powerful forensic tool for solving cases such as linking a suspect to a crime scene, resolving biological relationship issues and identifying disaster victims. Traditionally, DNA investigations mainly involve two steps; the establishment of DNA profiles from biological samples and the interpreta-tion of the evidential weight given by theses DNA profiles. This thesis deals with the latter, with focus on models for assessing the weight of evidence and the study of parameters affecting these probability figures.

In order to calculate the correct representative weight of DNA evidence, prior knowledge about the DNA markers for a relevant population sample is required. Important properties that should be studied are, for example, how frequently certain DNA-variants (i.e. alleles) occur in the population, the differences in such frequencies between subpopulations, expected inheritance patterns of the DNA markers within a family and the forensic efficiency of the DNA markers in casework.

In this thesis we aimed to study important population genetic parameters that influence the weight of evidence given by a DNA-analysis, as well as models for proper consideration of such parameters when calculating the weight of evi-dence in relationship testing.

We have established a Swedish frequency database for mitochondrial DNA haplotypes and a haplotype frequency database for markers located on the X-chromosome. Furthermore, mtDNA haplotype frequencies were used to study the genetic variation within Sweden, and between Swedish and other European populations. No genetic substructure was found in Sweden, but strong similari-ties with other western European populations were observed.

Genetic properties such as linkage and linkage disequilibrium could be im-portant when using X-chromosomal markers in relationship testing. This was true for the set of markers that we studied. In order to account for this, we pro-posed a model for how to take linkage and linkage disequilibrium into account when calculating the weight of evidence provided by X-chromosomal analysis.

Finally, we investigated the risk of erroneous decisions when using DNA in-vestigations for family reunification. We showed that the risk is increased due to uncertainties regarding population allele frequencies, consanguinity and compet-ing close relationship between the tested individuals. Additional information and the use of a refined model for the alternative hypotheses reduced the risk of making erroneous decisions.

In summary, as a result of the work on this thesis, we can use mitochondrial DNA and X-chromosome markers in order to resolve complex relationship in-vestigations. Moreover, the reliability of likelihood estimates has been increased by the development of models and the study of relevant parameters affecting probability calculations.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2010. 55 p.
Series
Linköping University Medical Dissertations, ISSN 0345-0082 ; 1175
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-54742 (URN)978-91-7393-420-6 (ISBN)
Public defence
2010-05-07, Elsa Brändström-salen, Campus US, Linköpings universitet, Linköping, 09:00 (English)
Opponent
Supervisors
Available from: 2010-04-08 Created: 2010-04-08 Last updated: 2010-04-08Bibliographically approved

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Lindblom, BertilHolmlund, Gunilla

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