>Magister Scientiae - MSc / The primary objective of this Masters project was to investigate the maternal ancient substructure of the Griqua population in South Africa. Genetic ancestry was determined by investigating ancestry informative single nucleotide polymorphisms. These are located in the control region of the mitochondrial genome. The auxiliary aim was to test the validity of the UWC 10plex system in relation to a sample group of Griqua males. This short tandem repeat multiplex targets specific mutations confined to paternal lineages. The Khoi Khoi or Hottentots were the first inhabitants in the Cape. Indigenous Khoi Khoi female slaves had offspring with the European settlers in the 1800s which resulted in the Griqua population group. The incorporated European paternal ancestry is what set the Griqua apart from the native population groups at that time. Colonisation events from the mid-17th to 19th Century and the apartheid regime resulted in land dispossession of the native population and an extensively mixed gene pool in South Africa. One hundred and seventy six (N=176) male and female Griqua people were collectively sampled in Kokstad (2012), Vredendal (2012 and 2013) and at the Griqua National Conference in Ratelgat (2013). All 176 samples were analysed using mtDNA control region Sanger sequencing. The sample group (N=176) was separated based on birthplace (Origin sample group and post-colonial sample group). The origin sample group consists of individuals whose ancestors were not part of the Griqua Trek to Northern regions of South Africa and were less likely to be exposed to colonial influences. Mutations within the hypervariable segments of the mtDNA control region were used to infer haplogroups with geographic-specific population data. In this way one can plot the extent of ancient Khoisan (L0d) and Bantu influences (L1-L5) as well as the influence of East (M, A, B, E) and West (N, R, J, H) Eurasian haplogroups in the maternal ancestry of the Griqua population group. The origin sample group showed 91% African ancestry (76.8% L0d) while the post-colonial group had 78% African ancestry (60% L0d). The origin sample group had 2% East Eurasian and 7% West Eurasian ancestry, while the post-colonial group contained 20% Eurasian ancestry. There is greater admixture in the post-colonial group which can be attributed to the integration of surrounding populations during settlement periods in parts of the Northern Cape and KwaZulu-Natal. The UWC 10plex STR kit was tested to see if it could discriminate between male individuals of this admixed sample group (N=91 males). The markers for this multiplex were selected according to their ability to differentiate between individuals of African descent. It proved to be a viable Y chromosome short tandem repeat testing tool, displaying a statistically significant discrimination capacity value of 0.966 and only having 3 shared haplotypes in the sample group of 91 Griqua males. / National Research Foundation (NRF)

No description available.

S'ha estudiat la variabilitat genètica de les poblacions del nord d'Àfrica a partir de l'anàlisi de diverses regions genòmiques per tal d'entendre les poblacions analitzades d'una banda, i comprendre la dinàmica del genoma per l'altra. Els resultats obtinguts ens han permès verificar diferents hipòtesis sobre la història de les poblacions d'aquesta regió com són l'efecte paral·lel i independent de l'onada de difusió del neolític des de l'Orient Mitjà al llarg d'ambdues ribes de la Mediterrànea; i l'efecte de l'arabització. S'ha pogut estimar també la contribució genètica masculina nord africana a la península ibèrica i detectat certa contribució genètica del pobles sub-saharians a les poblacions nordafricanes. Per altra banda, el tipatge de marcadors genètics que evolucionen a velocitats diferents al cromosoma Y ha permès mostrar que el background genètic predomina sobre el background poblacional en l'estructura de la variació genètica dels microsatèl·lits en la regió no recombinant del cromosoma Y humà. / The genetic variability of the North African populations has been studied through the analysis of different genomic regions in order to understand both the analysed populations and the dynamics of the genome. The obtained results allow us to verify different hypotheses about the population history of this region including the parallel and independent effect of the Neolithic wave of advance from the Middle East and along both Mediterranean coasts; and the effect of Arabization phenomena. We also tried to estimate the North African male genetic contribution to the Iberian peninsula and detected Sub-Saharian genetic influences to the North African peoples. Moreover, the typing of genetic markers with different evolutionary rates on the Y chromosome allowed us to demonstrate that variation in microsatellites is deeply structured by genetic background on the non-recombining region of the human Y chromosome.

Hematopoietic stem cell transplantation (HSCT) is used to treat patient with hematological diseases such as leukemia and genetic conditions such as sickle cell anemia. After HSCT the patients are supervised for signs of relapse of disease or rejection of transplanted cells. This is done by using chimerism analysis. At the department of clinical genetics at Akademiska sjukhuset fragment analysis of short tandem repeats is used for chimerism analysis, which is to be replaced by a Next generation sequencing (NGS) based method called Devyser chimerism, which includes an IVDR labelled kit. The aim of this project was to validate the new method for chimerism analysis. DNA samples from twelve HSCT patients and their donors were analyzed with Devyser chimerism and the results were compared to the results from the current method. The sensitivity of the new method was tested by analysis of artificial chimerism samples from blood donors. The results from the comparison showed a good correlation between methods (R2 = 0,9864) and the sensitivity of the method was confirmed to be 0,1% mixed chimerism. There was some difficulty in identifying enough informative markers for re-transplanted patients two had separate donors. This is a known problem for chimerism analysis in general and not a specific problem to the new method and will not be a hindrance for the implementation of Devyser chimerism at the clinical laboratory.

No description available.

<p>The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters.</p>

<p>The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters.</p>

The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa.In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases,missing persons work, and mass fatality disasters. After the successful implementation of the genotyping system in the laboratory, allele size range was determined for each of the loci and allelic ladders were constructed. The entire repeat regions of the six loci under investigation were successfully sequenced.Consequently, allele repeat number, structure and observed size were determined for each locus.An internal validation study of the six Non-CODIS miniSTR genotyping system was conducted following the SWGDAM guidelines. A comprehensive population study,covering five population groups from South Africa was also carried out.The genotyping system produced consistent, accurate and precise genetic profiles for low concentrations of template DNA. When analyzing mixed DNA samples, successful differentiation of minor and major DNA components was identifiable. Amplification products were observed in non-human DNA studies but in all instances complete genotype profiles were not obtained. Allele frequencies and forensic parameters were determined for the system in five South African population groups (i.e. Afrikaner, Asian-Indian, Mixed Ancestry, Xhosa and Cape Muslim). No deviation from Hardy-Weinberg equilibrium was observed in any of the populations. Furthermore, all populations displayed a high power of discrimination and a high power of exclusion.The six Non-CODIS miniSTR genotyping system has shown a good potential to aid in the analysis of degraded DNA samples. This system can be further improved by including additional loci. Even in its current form, it can certainly provide additional discrimination in complex paternity and/or missing person cases. / >Magister Scientiae - MSc

Magister Scientiae - MSc / The objective of this study was to develop and validate a six Non-CODIS miniSTR genotyping system and to determine its suitability for forensic casework in South Africa. In Non-CODIS miniSTR genotyping systems, smaller PCR products are amplified and the primers are positioned as close as possible to the repeat region. For this reason, these systems can be valuable in a variety of scenarios including complex paternity cases, missing persons work, and mass fatality disasters. / South Africa

No description available.