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Multiple displacement amplification for generating an unlimited source of DNA for genotyping in nonhuman primate species
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine.
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2006 (English)In: International journal of primatology, ISSN 0164-0291, E-ISSN 1573-8604, Vol. 27, no 4, 1145-1169 p.Article in journal (Refereed) Published
Abstract [en]

We evaluated a whole genome amplification method-multiple displacement amplification (MDA)-as a means to conserve valuable nonhuman primate samples. We tested 148 samples from a variety of species and sample sources, including blood, tissue, cell-lines, plucked hair and noninvasively collected semen. To evaluate genotyping success and accuracy of MDA, we used routine genotyping methods, including short tandem repeat (STR) analysis, denaturing gradient gel electrophoresis (DGGE), Alu repeat analysis, direct sequencing, and nucleotide detection by tag-array minisequencing. We compared genotyping results from MDA products to genotypes generated from the original (non-MD amplified) DNA samples. All genotyping methods showed good results with the MDA products as a DNA template, and for some samples MDA improved genotyping success. We show that the MDA procedure has the potential to provide a long-lasting source of DNA for genetic studies, which would be highly valuable for the primate research field, in which genetic resources are limited and for other species in which similar sampling constraints apply.

Place, publisher, year, edition, pages
2006. Vol. 27, no 4, 1145-1169 p.
Keyword [en]
Alu-SINE, minisequencing, multiple displacement amplification, short tandem repeat, single nucleotide polymorphism
National Category
Medical and Health Sciences Biological Sciences
URN: urn:nbn:se:uu:diva-95932DOI: 10.1007/s10764-006-9067-7ISI: 000241400100012OAI: oai:DiVA.org:uu-95932DiVA: diva2:170318
Available from: 2007-05-10 Created: 2007-05-10 Last updated: 2011-05-19Bibliographically approved
In thesis
1. Analysis of Nucleotide Variations in Non-human Primates
Open this publication in new window or tab >>Analysis of Nucleotide Variations in Non-human Primates
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Many of our closest relatives, the primates, are endangered and could be extinct in a near future. To increase the knowledge of non-human primate genomes, and at the same time acquire information on our own genomic evolution, studies using high-throughput technologies are applied, which raises the demand for large amounts of high quality DNA.

In study I and II, we evaluated the multiple displacement amplification (MDA) technique, a whole genome amplification method, on a wide range of DNA sources, such as blood, hair and semen, by comparing MDA products to genomic DNA as templates for several commonly used genotyping methods. In general, the genotyping success rate from the MDA products was in concordance with the genomic DNA. The quality of sequences of the mitochondrial control region obtained from MDA products from blood and non-invasively collected semen samples was maintained. However, the readable sequence length was shorter for MDA products.

Few studies have focused on the genetic variation in the nuclear genes of non-human primates. In study III, we discovered 23 new single nucleotide polymorphisms (SNPs) in the Y-chromosome of the chimpanzee. We designed a tag-microarray minisequencing assay for genotyping the SNPs together with 19 SNPs from the literature and 45 SNPs in the mitochondrial DNA. Using the microarray, we were able to analyze the population structure of wild-living chimpanzees.

In study IV, we established 111 diagnostic nucleotide positions for primate genera determination. We used sequence alignments of the nuclear epsilon globin gene and apolipoprotein B gene to identify positions for determination on the infraorder and Catarrhini subfamily level, respectively, and sequence alignments of the mitochondrial 12S rRNA (MT-RNR1) to identify positions to distinguish between genera. We designed a microarray assay for immobilized minisequencing primers for genotyping these positions to aid in the forensic determination of an unknown sample.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 41 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 263
Molecular genetics, SNP, genotyping, primate, chimpanzee, whole genome amplification, multiple displacement amplification, minisequencing, microarray, Y-chromosome, mitochondria, Genetik
urn:nbn:se:uu:diva-7904 (URN)978-91-554-6904-7 (ISBN)
Public defence
2007-06-01, Rudbecksalen, Rudbecklaboratoriet, Dag Hammarskjölds väg 20, Uppsala, 13:15
Available from: 2007-05-10 Created: 2007-05-10 Last updated: 2013-09-25Bibliographically approved

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Rönn, Ann-CharlotteSyvänen, Ann-Christine
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Molecular MedicineDepartment of Medical Sciences
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