Characterisation of eight non-codis Ministrs in four South African populations to aid the analysis of degraded DNA

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dc.contributor.advisorDavison, Sean
dc.contributor.advisord’Amato, Maria Eugenia
dc.contributor.authorIsmail, Aneesah
dc.contributor.otherDept. of Biotechnology
dc.contributor.otherFaculty of Science
dc.date.accessioned2014-02-03T06:59:27Z
dc.date.accessioned2024-05-09T07:45:03Z
dc.date.available2010/08/02 18:20
dc.date.available2010/08/02
dc.date.available2014-02-03T06:59:27Z
dc.date.available2024-05-09T07:45:03Z
dc.date.issued2009
dc.descriptionMagister Scientiae - MScen_US
dc.description.abstractIn many forensic cases, such as mass disasters reconstruction cases, the recovered DNA is highly degraded. In such incidences, typing of STR loci has become one of the most powerful tools for retrieving information from the degraded DNA. However, as DNA degradation proceeds, three phenomena occur consecutively: loci imbalance, allele dropout and no amplification. To solve the problem of degraded DNA, redesigned primer sets have been developed in which the primers were positioned as close as possible to the STR repeat region. These reduced primer sets were called Miniplexes. Unfortunately, a few of the CODIS STR loci cannot be made into smaller amplicons. For this reason non-CODIS miniSTRs have been developed. The present study was undertaken for the population genetic analysis of microsatellite variation in four South African populations; Afrikaner, Xhosa, Mixed Ancestry and Asian Indian using eight non-CODIS miniSTR loci. These miniSTRs loci were characterized within the populations by estimating the levels of diversity of the markers, estimating the population genetic parameters, and studying the inter-population relationships. All of the miniSTRs were amplified successfully and the genetic variability parameters across all loci in Afrikaner, Mixed Ancestry, Asian Indian and Xhosa were estimated to be in the range of 3 (D4S2364) to 12 (D9S2157) alleles, the total number of alleles over all loci ranged from 100 to 204, the allelic richness ranged from 3.612 to 10.307 and the heterozygosity ranged from 0.4360 to 0.8073. Genetic distance was least between Afrikaner and Asian Indian and highest between Xhosa and Mixed Ancestry. Deviations from Hardy-Weinberg equilibrium were not observed for most of the loci. The low mean FIS (-0.027) and FIT (-0.010) and FST (0.017) values across the populations indicated low level of inbreeding within (FIS) and among (FST) the populations. The Asian Indian population showed higher levels of the inbreeding coefficient, indicating less gene exchange between it and other populations. These 8 markers can be used for genetic investigations and assessing population structure. The study contributed to the knowledge and genetic characterization of four South African populations. In addition, these MiniSTRs prove to be useful in cases where more genetic information is needed.en_US
dc.description.countrySouth Africa
dc.identifier.urihttps://hdl.handle.net/10566/13276
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderUniversity of the Western Capeen_US
dc.subjectShort Tandem Repeat (STR)en_US
dc.subjectMicrosatellitesen_US
dc.subjectLocien_US
dc.subjectCombined DNA Index System (CODIS)en_US
dc.subjectDegraded DNAen_US
dc.subjectMitochondrial DNA (mtDNA)en_US
dc.subjectMiniSTRen_US
dc.subjectPolymerase Chain Reaction (PCR)en_US
dc.subjectElectrophoresisen_US
dc.subjectGenotypingen_US
dc.subjectPolymorphic Information Content (PIC)en_US
dc.subjectFixation indexesen_US
dc.titleCharacterisation of eight non-codis Ministrs in four South African populations to aid the analysis of degraded DNAen_US
dc.typeThesisen_US

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