DNA microarray as a tool in establishing genetic relatedness—Current status and future prospects

Kling, Daniel; Welander, Jenny; Tillmar, Andreas; Skare, Øivind; Egeland, Thore; Holmlund, Gunilla

doi:10.1016/j.fsigen.2011.07.007

« Previous Next »Forensic Science International: Genetics
Volume 6, Issue 3 , Pages 322-329, May 2012

DNA microarray as a tool in establishing genetic relatedness—Current status and future prospects

Daniel Kling
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Artillerigatan 12, SE-587 58, Linköping, Sweden
- Department for Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
- Norwegian Institute of Public Health, P.O. Box 4040, Nydalen, NO-0403 Oslo, Norway
- Corresponding author at: Norwegian Institute of Public Health, Familiegenetikk, Gaustadalléen 30, NO-0027 Oslo, Norway. Tel.: +47 210 77663.
Jenny Welander
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-581 85, Linköping, Sweden
Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Artillerigatan 12, SE-587 58, Linköping, Sweden
Øivind Skare
- Norwegian Institute of Public Health, P.O. Box 4040, Nydalen, NO-0403 Oslo, Norway
- Department of Public Health and Primary Health Care, University of Bergen, P.O. Box 7804, NO-5020 Bergen, Norway
Thore Egeland
- Department for Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Norway
Gunilla Holmlund
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Artillerigatan 12, SE-587 58, Linköping, Sweden
- Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, SE-581 85, Linköping, Sweden

Received 21 March 2011; received in revised form 12 June 2011; accepted 5 July 2011. published online 03 August 2011.

Abstract

In the past decades, microarray technology has definitely put an edge to the field of genetic research. Our aim was to determine whether single nucleotide polymorphism (SNP) microarrays could be used as a tool in establishing genetic relationships where current molecular genetic methods are not sufficient. We used the Genechip, Affymetrix GenomeWide SNP Array 6.0, which detects more than 900,000 SNP markers dispersed throughout the human genome. The intention was to find a good selection of SNP markers that could be used for statistical evaluation of relatedness in a forensic setting. We conducted pairwise comparisons in the R-package FEST as well as pedigree comparisons in Merlin. Our methods were applied on two separate families, where relationships as distant as 3rd cousins were known. In addition, a question about a possible common ancestry between the two families was tested. Relationships as distant as 2nd cousins could be readily distinguished both from unrelated and other, genetically, closer relationships. This was achieved with a selection of 5774 markers, where each pair of markers was separated by a genetic distance of at least 0.5cM (centiMorgan). When considering 3rd cousins, and more distant relationships, the number of markers needs to be extended, consequently decreasing the genetic distance between the markers. However, inclusion of a too large number of markers presents new challenges and our results imply that the use of too dense sets of markers always yields the highest probability for the genetically closest relationship hypothesis. Simulations confirm that this is most probably caused by the fact that the computational model assumes linkage equilibrium between markers, a problem that will be further evaluated. Our results do however suggest that SNP-data derived from microarrays are well suited for kinship determination provided linkage disequilibrium is properly accounted for.