Accessing Genetic Variation by Microarray Technology
Microarray technology is a promising approach for the simultaneous analysis of multiple single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variation. In this thesis enzyme-assisted microarray-based methods were developed to improve the accuracy and genotype discrimin...
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Uppsala universitet, Institutionen för medicinska vetenskaper
2002
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ftuppsalauniv:oai:DiVA.org:uu-1792 2023-05-15T18:08:18+02:00 Accessing Genetic Variation by Microarray Technology Lindroos, Katarina 2002 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1792 eng eng Uppsala universitet, Institutionen för medicinska vetenskaper Uppsala : Acta Universitatis Upsaliensis Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, 0282-7476 1127 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1792 urn:isbn:91-554-5251-5 info:eu-repo/semantics/openAccess Medical sciences microarrays SNPs minisequencing four-colour detection allele frequency population study evolutionary biology MEDICIN OCH VÅRD MEDICINE MEDICIN Doctoral thesis, comprehensive summary info:eu-repo/semantics/doctoralThesis text 2002 ftuppsalauniv 2023-02-23T21:44:32Z Microarray technology is a promising approach for the simultaneous analysis of multiple single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variation. In this thesis enzyme-assisted microarray-based methods were developed to improve the accuracy and genotype discrimination power of the current methods for SNP genotyping. The improved technology was applied for analysing recessively inherited disease mutations, for Y-chromosomal SNPs in a population study, for an evolutionary analysis of SNPs in flycatchers and for multiplexed quantitative determination of SNP-allele frequencies in pooled DNA samples. A robust attachment chemistry for immobilising oligonucleotides on glass surface was established, based on an evaluation of eight covalent coupling methods. A four-colour fluorescence detection strategy, which enabled a multiplexed quantitative analysis for as little as 2% of a minority allele frequency in pooled samples was generated. Twenty-five Y-chromosomal SNPs were screened in a collection of 300 samples from five Finno-Ugric-speaking populations using minisequencing on microarrays. In these populations six distinct haplotypes were defined by the six SNPs that were polymorphic. Data from five microsatellite markers was combined with the SNP data, revealing shared Y-chromosomal haplotypes between the Finns and the Saami, indicating, in accordance with earlier data, at least two founding Y-chromosomal lineages in these populations. Database screening and subsequent validation of 125 potential SNPs in the highly repetitive type 1 interferon genes and genes coding for proteins in the interferon-related regulatory pathways revealed 25 informative SNPs in the Finnish and Swedish populations. These SNPs were included in a panel for microarray based genotyping that should find a variety of applications in genetic studies due to the important immunoregulatory functions of the IFN family. The significance of sex-chromosome evolution on speciation was investigated in two naturally ... Doctoral or Postdoctoral Thesis saami Uppsala University: Publications (DiVA) |
institution |
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collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Medical sciences microarrays SNPs minisequencing four-colour detection allele frequency population study evolutionary biology MEDICIN OCH VÅRD MEDICINE MEDICIN |
spellingShingle |
Medical sciences microarrays SNPs minisequencing four-colour detection allele frequency population study evolutionary biology MEDICIN OCH VÅRD MEDICINE MEDICIN Lindroos, Katarina Accessing Genetic Variation by Microarray Technology |
topic_facet |
Medical sciences microarrays SNPs minisequencing four-colour detection allele frequency population study evolutionary biology MEDICIN OCH VÅRD MEDICINE MEDICIN |
description |
Microarray technology is a promising approach for the simultaneous analysis of multiple single nucleotide polymorphisms (SNPs), which are the most abundant form of genetic variation. In this thesis enzyme-assisted microarray-based methods were developed to improve the accuracy and genotype discrimination power of the current methods for SNP genotyping. The improved technology was applied for analysing recessively inherited disease mutations, for Y-chromosomal SNPs in a population study, for an evolutionary analysis of SNPs in flycatchers and for multiplexed quantitative determination of SNP-allele frequencies in pooled DNA samples. A robust attachment chemistry for immobilising oligonucleotides on glass surface was established, based on an evaluation of eight covalent coupling methods. A four-colour fluorescence detection strategy, which enabled a multiplexed quantitative analysis for as little as 2% of a minority allele frequency in pooled samples was generated. Twenty-five Y-chromosomal SNPs were screened in a collection of 300 samples from five Finno-Ugric-speaking populations using minisequencing on microarrays. In these populations six distinct haplotypes were defined by the six SNPs that were polymorphic. Data from five microsatellite markers was combined with the SNP data, revealing shared Y-chromosomal haplotypes between the Finns and the Saami, indicating, in accordance with earlier data, at least two founding Y-chromosomal lineages in these populations. Database screening and subsequent validation of 125 potential SNPs in the highly repetitive type 1 interferon genes and genes coding for proteins in the interferon-related regulatory pathways revealed 25 informative SNPs in the Finnish and Swedish populations. These SNPs were included in a panel for microarray based genotyping that should find a variety of applications in genetic studies due to the important immunoregulatory functions of the IFN family. The significance of sex-chromosome evolution on speciation was investigated in two naturally ... |
format |
Doctoral or Postdoctoral Thesis |
author |
Lindroos, Katarina |
author_facet |
Lindroos, Katarina |
author_sort |
Lindroos, Katarina |
title |
Accessing Genetic Variation by Microarray Technology |
title_short |
Accessing Genetic Variation by Microarray Technology |
title_full |
Accessing Genetic Variation by Microarray Technology |
title_fullStr |
Accessing Genetic Variation by Microarray Technology |
title_full_unstemmed |
Accessing Genetic Variation by Microarray Technology |
title_sort |
accessing genetic variation by microarray technology |
publisher |
Uppsala universitet, Institutionen för medicinska vetenskaper |
publishDate |
2002 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1792 |
genre |
saami |
genre_facet |
saami |
op_relation |
Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, 0282-7476 1127 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-1792 urn:isbn:91-554-5251-5 |
op_rights |
info:eu-repo/semantics/openAccess |
_version_ |
1766180562142232576 |