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A DNA microarray system for forensic SNP analysis
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
2005 (English)In: Forensic Science International, ISSN 0379-0738, E-ISSN 1872-6283, Vol. 154, no 2-3, 111-121 p.Article in journal (Refereed) Published
Abstract [en]

Forensic DNA analysis is routinely performed using polymorphic short tandem repeat (STR) markers. However, for degraded or minute DNA samples, analysis of autosomal single nucleotide polymorphisms (SNPs) in short fragments might be more successful. Furthermore, sequencing of mitochondrial DNA (mtDNA) is often performed on highly degraded or scarce samples due to the high copy number of mtDNA in each cell. Due to the increasing number of complete mtDNA genome sequences available, the limited discrimination power of an mtDNA analysis, may be increased by analysis of coding region polymorphisms in addition to the non-coding variation. Since sequence analysis of the coding region would require more material than generally present in forensic samples, an alternative SNP analysis approach is required. We have developed a one-colour microarray-based SNP detection system for limited forensic materials. The method is based on minisequencing in solution prior to hybridisation to universal tag-arrays. In a first outline of a forensic chip, a combination of 12 nuclear and 21 mitochondrial SNP markers are analysed simultaneously. The mitochondrial markers on the chip are polymorphisms within the hypervariable region as well as in the coding region. Even though the number of markers in the current system is limited, it can easily be extended to yield a greater power of discrimination. When fully developed, microarray analysis provides a promising system for efficient sensitive SNP analysis of forensic samples in the future.

Place, publisher, year, edition, pages
2005. Vol. 154, no 2-3, 111-121 p.
Keyword [en]
Complementarity determining regions, DNA/*analysis, DNA fingerprinting/*methods, DNA primers, genetic markers, humans, oligonucleotide array sequence analysis, polymorphism, single nucleotide, research support, non-U.S. Gov't, sequence analysis, DNA
National Category
Forensic Science
Identifiers
URN: urn:nbn:se:uu:diva-92900DOI: 10.1016/j.forsciint.2004.09.134PubMedID: 16182957OAI: oai:DiVA.org:uu-92900DiVA: diva2:166215
Available from: 2005-04-13 Created: 2005-04-13 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Evaluation of New Technologies for Forensic DNA Analysis
Open this publication in new window or tab >>Evaluation of New Technologies for Forensic DNA Analysis
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

DNA samples from crime scenes or mass disasters are often limited and degraded which limits the possibility of successful traditional STR analysis. Moreover, there is a need to decrease the turnaround time in criminal investigations. These circumstances require a wider set of assays and technologies to be investigated for potential use in forensic DNA analysis, which has been explored in this thesis work. DNA analysis can also provide a useful tool in forensic pathology investigations.

In a search for mutations involved in The Sudden Infant death Syndrome (SIDS), the entire mitochondrial genome was sequenced in six SIDS infants and shorter mtDNA regions were analysed in paraffin-embedded tissues from an additional 14 SIDS cases. In this sample material no mutations associated with SIDS were found that could explain the death of these infants.

To reduce time, cost and effort related to sequencing of the mtDNA HVI/HVII regions in caseworks, a HVI/HVII mtDNA linear array assay was used as a pre-screening for exclusions of suspects or evidence samples. Using this assay, 56% of the samples involved in casework analysis could be excluded before sequencing was undertaken.

The possibility to use the new array technology was explored in a SNP assay targeting both mtDNA and nuclear SNPs. The system relies on minisequencing in solution prior to hybridisation to tag arrays. Using this system, we demonstrate a rapid, highly multiplexable and flexible array-format for SNP analysis.

The properties of the Pyrosequencing technology being a fast and user-friendly assay was utilised in a study to investigate the possibility to use this method for limited and degraded samples. Ten STR loci, overlapping with standardised kits, were genotyped in 114 Swedish individuals. We found additional variation and higher resolution of repeats at some of these loci that are not detected using standard fragment analysis.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2005. 59 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 27
Keyword
Genetics, STR, SNP, SIDS, mtDNA, HVI/HVII SSOP linear array, minisequencing, tag arrays, Pyrosequencing, Genetik
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-5744 (URN)91-554-6213-8 (ISBN)
Public defence
2005-05-04, Fåhraeussalen, Rudbecklaboratoriet C5, Rudbeck laboratoriet, Uppsala, 13:15
Opponent
Supervisors
Available from: 2005-04-13 Created: 2005-04-13Bibliographically approved

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