Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Approaches for analysis of mutations and genetic variations
KTH, Superseded Departments, Biotechnology.
2001 (English)Doctoral thesis, monograph (Other academic)
Abstract [en]

Detecting mutations and genomic variations is fundamental indiagnosis, isolating disease genes, association studies,functional genomics and pharmacogenomics. The objective hasbeen to use and further develop a variety of tools andtechnologies to analyze these genetic alterations andvariations.

The p53 tumor suppressor gene and short arm of chromosome 9have been used as genetic markers to investigate fundamentalquestions concerning early events preceding non-melanoma skincancers, clonal progression and timing of different mutationsand deletions. Conventional gel based DNA sequencing andfragment analysis of microsatellite markers were utilized forthis purpose. In addition, a sequence-specific PCR-mediatedartifact is discussed.

Pyrosequencing, a bioluminometric technique based onsequencing-by-synthesis, has been utilized to determinemutation ratios in the p53 gene. In addition, in the case ofmultiple mutations, pyrosequencing was adopted to determineallelic distribution of mutations without the use of cloningprocedures. Exons 5 to 8 of the p53 gene were also sequenced bythis method.

The possibility of typing single base variations bypyrosequencing has been evaluated. Two different nucleotidedispensation orders were investigated and data were comparedwith the predicted pattern for each alternative of the variableposition. Analysis of loss of heterozygosity was possible byutilizing single nucleotide polymorphisms.

A modified allele-specific extension strategy for genotypingof single nucleotide polymorphisms has been developed. Throughthe use of a real-time bioluminometric assay, it has beendemonstrated that reaction kinetics for a mismatchedprimer-template is slower than the matched configuration,butthe end-point signals are comparable. By introduction ofapyrase, the problems associated with mismatch extensions havebeen circumvented and accurate data has been obtained.

Keywords:fragment analysis, microsatellite, loss ofheterozygosity, DNA sequencing, pyrosequencing, cancer,mutation, variation, single nucleotide polymorphism,allele-specific extension, bioluminescence, apyrase.

Place, publisher, year, edition, pages
Stockholm: KTH , 2001. , 58 p.
Keyword [en]
LOH, microsatellite, fragment analysis, DNA sequencing, pyrosequencing, cancer, mutation, variation, SNP, allele-specific extension, apyrase
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:kth:diva-3113ISBN: 91-7283-062-X (print)OAI: oai:DiVA.org:kth-3113DiVA: diva2:8875
Public defence
2001-03-30, 00:00 (English)
Note
QC 20100415 NR 20140805Available from: 2001-03-21 Created: 2001-03-21 Last updated: 2010-04-28Bibliographically approved

Open Access in DiVA

fulltext(406 kB)1291 downloads
File information
File name FULLTEXT01.pdfFile size 406 kBChecksum MD5
3cf468d38dc36e4f9ff6bbe5b9a3b2f383f456cd4b825f483c1a28f337d426f1e58da02e
Type fulltextMimetype application/pdf

Search in DiVA

By author/editor
Ahmadian, Afshin
By organisation
Biotechnology
Engineering and Technology

Search outside of DiVA

GoogleGoogle Scholar
Total: 1291 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

isbn
urn-nbn

Altmetric score

isbn
urn-nbn
Total: 516 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf