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1
Wang, Weixin, and 王煒欣. "A fast and accurate model to detect germline SNPs and somatic SNVs with high-throughput sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2014. http://hdl.handle.net/10722/197115.
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The rapid development of high-throughput sequencing technology provides a new chance to extend the scale and resolution of genomic research. How to efficiently and accurately call genetic variants in single base level (germline single nucleotide polymorphisms (SNPs) or somatic single nucleotide variants (SNVs)) is the fundamental challenge in sequencing data analysis, because these variants reported to influence transcriptional regulation, alternative splicing, non-coding RNA regulation and protein coding. Many applications have been developed to tackle this challenge. However, the shallow depth and cellular heterogeneity make those tools cannot attain satisfactory accuracy, and the huge volume of sequencing data itself cause this process inefficient.
In this dissertation, firstly the performance of prevalent reads aligners and SNP callers for second-generation sequencing (SGS) is evaluated. And due to the high GC-content, the significantly lower coverage and poorer SNP calling performance in the regulatory regions of human genome by SGS is investigated.
To enhance the capability to call SNPs, especially within the lower-depth regions, a fast and accurate SNP detection (FaSD) program that uses a binomial distribution based algorithm and a mutation probability is proposed. Based on the comparison with popular software and benchmarked by SNP arrays and high-depth sequencing data, it is demonstrated that FaSD has the best SNP calling accuracy in the aspects of genotype concordance rate and AUC. Furthermore, FaSD can finish SNP calling within four hours for 10X human genome SGS data on a standard desktop computer.
Lastly, combined with the joint genotype likelihoods, an updated version of FaSD is proposed to call the cancerous somatic SNVs between paired tumor and normal samples. With extensive assessments on various types of cancer, it is demonstrated that no matter benchmarked by the known somatic SNVs and germline SNPs from database, or somatic SNVs called from higher-depth data, FaSD-somatic has the best overall performance. Inherited and improved from FaSD, FaSD-somatic is also the fastest somatic SNV caller among current programs, and can finish calling somatic mutations within 14 hours for 50X paired tumor and normal samples on normal server.<br>published_or_final_version<br>Biochemistry<br>Doctoral<br>Doctor of Philosophy
2
O'Neill, Ann Marie Ewald Sandra J. "Polymorphism in chicken immune response genes and resistance to disease." Auburn, Ala., 2007. http://repo.lib.auburn.edu/2007%20Fall%20Dissertations/O'Neill_Ann_48.pdf.
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Liu, Shuk Ming. "Single nucleotide polymorphism in human microsomal glutathione s-transferase gene and colorectal cancer /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202003%20LIU.
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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003.<br>Includes bibliographical references (leaves 95-105). Also available in electronic version. Access restricted to campus users.
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Davison, Jerry. "Polymorphism and replication of heterochromatic repeats in the DNA of Arabidopsis /." Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/5134.
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Myka, Jennifer Leigh. "COMPARATIVE GENE MAPPING FOR EQUUS PRZEWALSKII AND E. HEMIONUS ONAGER WITH INVESTIGATION OF A HOMOLOGOUS CHROMOSOME POLYMORPHISM IN EQUIDAE." UKnowledge, 2003. http://uknowledge.uky.edu/gradschool_diss/476.
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The ten extant species in the genus Equus are separated by less than 3.7 million years of evolution. Three lines of investigation were pursued to further characterize equid genome organization. 1.) The Przewalski.s wild horse (E. przewalskii, EPR) has a diploid chromosome number of 2n=66, while the domestic horse (E. caballus, ECA) has 2n=64. A comparative gene map for E. przewalskii was constructed using 46 bacterial artificial chromosome (BAC) probes previously mapped to 38 of 44 E. caballus chromosome arms and ECAX. BAC clones were hybridized to metaphase spreads of E. przewalskii and localized by fluorescent in situ hybridization (FISH). No exceptions to homology between E. przewalskii and E. caballus were identified, except for ECA5, a metacentric chromosome with homology to two acrocentric chromosome pairs, EPR23 and EPR24. 2.) The onager (E. hemionus onager, EHO) has a modal diploid chromosome number 2n=56 and a documented chromosome number polymorphism within its population, resulting in individuals with 2n=55. Construction of a comparative gene map of a 2n=55 onager by FISH using 52 BAC probes previously mapped to 40 of 44 E. caballus chromosome arms and ECAX identified multiple chromosome rearrangements between E. caballus and E. h. onager. 3.) A centric fission (Robertsonian translocation) polymorphism has been documented in 5 of the ten extant equid species, namely, E. h. onager, E. h. kulan, E. kiang, E. africanus somaliensis, and E. quagga burchelli. BAC clones containing equine (E. caballus, ECA) genes SMARCA5 (ECA2q21 homologue to human (HSA) chromosome 4p) and UCHL1 (ECA3q22 homologue to HSA4q) were FISH mapped to metaphase spreads for individuals possessing the chromosome number polymorphism. These probes mapped to a single metacentric chromosome and two unpaired acrocentrics showing that the centric fission polymorphism involves the same homologous chromosome segments in each species and has homology to HSA4. These data suggest the polymorphism is either ancient and conserved within the genus or has occurred recently and independently within each species. Since these species are separated by 1-3 million years of evolution, the persistence of this polymorphism would be remarkable and worthy of further investigations.
6
Chung, Man-kin. "A study on the prevalence of AZFd Y-chromosome microdeletion in Hong Kong Chinese men with severe male factor infertility." Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B31971696.
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Ehrenreich, Liezle Suzette. "The evaluation of Y-STR loci for use in forensics." Thesis, University of the Western Cape, 2005. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_9766_1228396041.
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<p>The aim of this study was to investigate the forensic usefulness of various Y-chromosome short tandem repeat loci among South African sub-populations. Three different sets of Y-chromosome short tandem repeat loci were chosen for investigation.</p>
8
Chung, Man-kin, and 鍾文健. "A study on the prevalence of AZFd Y-chromosome microdeletion in Hong Kong Chinese men with severe male factor infertility." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B31971696.
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Varney, Robin Lynne. "Assessment of nuclear DNA variation and population structure in the eastern oyster, Crassostrea virginica, through discovery and analysis of single nucleotide polymorphisms (SNPs)." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 216 p, 2009. http://proquest.umi.com/pqdweb?did=1891582831&sid=1&Fmt=2&clientId=8331&RQT=309&VName=PQD.
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Boschiero, Clarissa [UNESP]. "Mapeamento fino de qtls e polimorfismos de genes candidatos associados ao crescimento no cromossomo 1 da galinha." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/104869.
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boschiero_c_dr_botfmvz.pdf: 635473 bytes, checksum: feca4297f6abf36be6a9c8cf72ce1eb6 (MD5)<br>Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)<br>Universidade Estadual Paulista (UNESP)<br>A partir de resultados de um estudo anterior, no qual foram mapeados QTLs para características de peso vivo, peso do coração e pulmões no GGA1, foi definida uma região no intervalo entre os marcadores ADL0234 e LEI0071, abrangendo 82,3 cM. Foram avaliadas três famílias de meios-irmãos paternos que compreendiam sete famílias de irmãos completos, num total de 652 F2 para as características: peso vivo aos 35 e 41 dias de idade, pesos do coração e pulmões e rendimentos de coração e pulmões. Os genótipos de seis marcadores microssatélites foram adicionados aos dez utilizados anteriormente. O mapa de ligação obtido da região compreendeu 110,8 cM com espaçamento médio entre os marcadores de 7,4 cM. Na análise de F2, em um único intervalo (LEI0146-LEI0174), compreendendo 28,8 cM, foram mapeados QTLs para todas as características estudadas, com exceção dos rendimentos de coração e pulmões. Neste intervalo estão localizados o gene IGF1 e o centrômero do cromossomo. A adição de seis marcadores confirmou os QTLs mapeados anteriormente, porém alguns em diferentes posições. A análise de meios-irmãos paternos indicou que os principais QTLs estavam segregando em apenas uma das famílias (7716), na qual cinco QTLs foram mapeados. Na análise de meios-irmãos maternos, duas famílias segregaram QTLs tanto na análise Individual como na Conjunta (7810 e 7971). As diferentes análises permitiram selecionar dois casais F1, que devem ser o alvo dos próximos estudos. Este estudo restringiu a busca por genes candidatos responsáveis pelas características de interesse a uma região de 28,8 cM (9,82 Mb) no GGA1.<br>Based on the results from a previous study, in which QTL for body weight, heart and lungs weights and heart and lungs percentages were mapped to GGA1, a region was defined between markers ADL0234 and LEI0071, spanning 82.3 cM. Three paternal half-sib families, comprising seven full-sib families, totaling 652 F2 were evaluated for body weight at 35 and 41 days of age, heart and lungs weights and heart and lungs yields. Genotypes of six microsatellite markers were added to those of ten previously used. The linkage map of this region spanned 110.8 cM, with average spacing of 7.4 cM between markers. In a single interval (LEI0146-LEI0174), comprising 28.8 cM, QTLs for all traits, except for heart and lungs yields were mapped in the F2 analysis. In this same interval the IGF1 gene, and the chromosome centromere, are located. The use of six additional markers confirmed the same QTLs mapped previously, but some of them, in different positions. The paternal half-sib analysis indicated that the main QTLs were segregating in one of the families only (7716), in which five QTLs were mapped. In the maternal half-sib analysis, two families segregated QTLs both, in the across and within families analyses (7810 and 7971). These analyses allowed the selection of two F1 couples to be the target for future studies. This study restricted the search for candidate genes responsible for the traits of interest to a region of 28.8 cM (9.82 Mb) in GGA1.
11
Jehangir, Maryam. "Genome assembly of the cichlid fish Astatotilapia latifasciata with focus in population genomics of B chromosome polymorphism." Botucatu, 2017. http://hdl.handle.net/11449/151740.
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Orientador: Cesar Martins<br>Resumo: B chromosomes (Bs) are additional to the standard regular chromosome set (As), and present in all groups of eukaryotes. A reference genome is key to understand genomics aspects of an organism. Here, we present the de novo genome assembly of the cichlid fish A. latifasciata: a well known model to study Bs. The assembly of A. latifasciata genome has not been performed so far. The main focus of this study is to analyze and assemble the A. latifasciata genome with no B (B-) and with B (B+) chromosomes. The assembled draft B- and B+ genomes comprised of 774 Mb and 781 Mb with 1.8 Mb and 2.5Mb of N50 value of scaffolds respectively, and spanning 23,391 number of genes. High coverage data with Illumina sequencing was obtained for males and females with 0B, 1B and 2B chromosomes to provide information regarding the population polymorphism of these genomes. We observed a high scale genomic diversity in all analyzed genomes showing a high rate/frequency of population polymorphism with no evident effect of B chromosome presence. However, the B specific single nucleotide polymorphisms were found in the sequences that were located on B chromosome. While, the whole-genome rearrangements (inter chromosomal translocations) were detected in B+ genome, and structural variations including insertions, deletions, inversions and duplications were predicted in a representative genomic region of B chromosome. These results bring an evidence that existence of Bs in a genome should favour the accumu... (Resumo completo, clicar acesso eletrônico abaixo)<br>Mestre
12
Yakova, D., M. Hristov, N. Stancheva, T. Rashev, and S. Tisheva. "Frequency of C > T polymorphism in fourth chromosome and levels of crp in patients with atrial." Thesis, Sumy State University, 2016. http://essuir.sumdu.edu.ua/handle/123456789/45055.
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Introduction. Atrial fibrillation is a heart rhythm disorder, characterized by rapid and uncoordinated atrial activation which is the most common arrhythmia in clinical practice. Atrial fibrillation is observed in 1.5 - 2% of the general population and its incidence increases with age reaching more than 8-15% by 80 years of age. Atrial fibrillation is traditionally considered as a non genetic disorder. The cause of atrial fibrillation in 10-20% of cases is unknown and it is diagnosed as idiopathic.
13
Fletcher, Jeremy Charles. "THE USE OF PYROSEQUENCING FOR THE ANALYSIS OF Y CHROMOSOME SINGLE NUCLEOTIDE POLYMORPHISMS." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4487.
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The potential value of the Y chromosome for forensic applications has been recognized for some time with the current work dedicated to Short Tandem Repeat analysis and Single Nucleotide Polymorphism (SNP) discovery. This study examined the ability of two different SNP analysis methods to determine if they could be utilized in forensic applications and ultimately be developed into an established system for Y chromosome SNP analysis. This study examined two principle SNP analysis systems: single base extension and Pyrosequencing. Pyrosequencing was determined to be superior to single base extension, due to the wealth of information provided with sequencing and the flexibility of designing primers for analysis. Using Pyrosequencing, 50 Y chromosome loci were examined and the minimum loci required for maximum diversity for the development of a Y chromosome SNP analysis system were chosen. Thirteen loci were selected based on their ability to discriminate 60 different individuals from three different racial groups into 15 different haplogroups. The Y chromosome SNP analysis system developed utilized nested PCR for the amplification of all 13 loci. Then they were sequenced as groups, ranging from one to three loci, in a single reaction. The Y chromosome SNP analysis system developed here has the potential for forensic application since it has shown to be successful in the analysis of blood, buccal swabs, semen, and saliva, works with as little as 5 pg of starting DNA material, and will amplify only male DNA in the presence of male/female mixtures in which the female portion of the sample overwhelmed the male portion 30,000 to 1.<br>M.S.<br>Department of Chemistry<br>Arts and Sciences<br>Chemistry
14
Rocha, Felipe Bastos 1981. "Pigmentação em Drosophila mediopunctata : plasticidade fenotipica e herdabilidade." [s.n.], 2007. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316971.
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Orientador: Louis Bernard Klaczko<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-08T11:40:37Z (GMT). No. of bitstreams: 1
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Previous issue date: 2007<br>Resumo: Drosophila mediopunctata é uma espécie pertencente ao grupo tripunctata, que tem como traço marcante um padrão de pigmentação abdominal, sob a forma de três pintas na região mediana dos últimos tergitos. Nesta espécie, este padrão é variável, havendo indivíduos com quatro fenótipos, que vão de zero a três pintas. Já se observou que esta variação tem determinação genética, com marcada influência do cromossomo II, e alta plasticidade fenotípica em resposta à temperatura de desenvolvimento. Neste trabalho, buscou-se caracterizar parte destas duas fontes de variação. Por um lado, foram estudadas as normas de reação da pigmentação a um gradiente térmico, investigando-se classes fenotípicas contrastantes. Devido ao desenho experimental, que buscou separar os efeitos desta variável de um possível papel das inversões do cromossomo II, foi possível evidenciar um forte efeito das classes fenotípicas utilizadas sobre a resposta das estirpes ao gradiente térmico, independente do cariótipo. Foram descritos, por polinômios, dois tipos de norma de reação relacionados ao fenótipo, ambos com forma de parábola, mas diferindo em relação ao coeficiente de curvatura. O grupo de estirpes de pigmentação clara apresentou uma curva côncava e o grupo escuro uma curva convexa. A norma de reação da taxa de desenvolvimento de ovo a adulto foi caracterizada a partir do mesmo procedimento. Entretanto, apesar dos efeitos significativos do cariótipo e da classe
fenotípica, a homogeneidade das normas de reação descritas por regressões lineares não possibilitou uma interpretação clara destes efeitos. A plasticidade do caráter também foi investigada quanto ao período de desenvolvimento termo-sensível. Assim, foi possível determinar a porção final da fase de pupa como o período no qual ocorre a influência da temperatura sobre o fenótipo de pintas do adulto. Por outro lado, em relação à determinação genética do caráter, foram obtidas estimativas de herdabilidade para o número de pintas abdominais, em condições quase naturais. Visando estabelecer um parâmetro de comparação com outros trabalhos, foi estimada a herdabilidade do tamanho do tórax a partir do mesmo material. Os resultados deste experimento, apresentaram grande contraste entre os dois traços: as estimativas foram baixas ou não significativas para o tamanho do tórax e, em geral, altas e significativas para o número de pintas<br>Abstract: Drosophila mediopunctata belongs to the tripunctata species group, which has a typical abdomen pigmentation pattern, consisting of three dark spots in the last tergites. In this species, this pattern is variable, with the phenotypes ranging from zero to three spots. It has been noted that this variation has genetical determination, with strong influence from the second chromosome, and high phenotypic plasticity in response to the developmental temperature. In this work, we attempted to describe part of these two variation sources. On one side, the pigmentation reaction norm to a thermal gradient was studied, by investigating the influence of contrasting phenotypical classes. Given the experimental design, which was planned to separate the effects of this variable from a possible influence of the second chromosome inversions, it was possible to detect a strong effect of the phenotypical classes on the lineages response to the thermal gradient, independent of the kariotype. Two types of reaction norms, related to the phenotype, were detected and described by polynomial adjustment. Both had a parabolic shape, but with different curvature coefficients. The light pigmentation lineage group showed a concave curve, and the dark group had a convex curve. The reaction norm of development rate from egg to adult was described according to the same procedure. However, despite the significant effects of the karyotype and phenotypical classes, the homogeneity of reaction norms, described by linear regression, hindered a clear interpretation of these effects. The character plasticity was also investigated in respect to the developmental thermosensitive period. Thus, it was possible to determine that the period in which the temperature influence on the adult phenotype occurs is the last portion of the pupal phase. On another side, relative to the character genetic determination, heritability estimates for the number of abdominal spots were obtained, in nearly natural conditions. Aiming to establish a comparison parameter with other studies, the heritability of thorax length was estimated based on the same material. The results of this experiment reveal a great contrast between these trait estimates: for the thorax they were low or non-significant, and, in general, for the abdominal spot number, they were high and significant<br>Mestrado<br>Genetica Animal e Evolução<br>Mestre em Genética e Biologia Molecular
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Michelle, Burrows Adria. "A comparative ancestry analysis of Y-chromosome DNA haplogroups using high resolution melting." University of the Western Cape, 2018. http://hdl.handle.net/11394/6489.
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Magister Scientiae - MSc (Biotechnology)<br>The objective of this study is to deduce paternal ancestry using ancestry
informative single nucleotide polymorphisms (SNPs) by means of High
Resolution Melting (HRM). This was completed by producing a multiplex system
that was designed in a hierarchical manner according to the YSNP tree. This
project mainly focused on African ancestry and was used to infer paternal
ancestral lineages on the Johannesburg Coloured population.
South Africa has a diverse population that has ancestral history from across the
globe. The South African Coloured population is the most admixed population as
it is derived from at least five different population groups: these being Khoisan,
Bantu, Europeans, Indians and Southeast Asians. There have been studies done on
the Western Cape/ Cape Town Coloured populations before but this study focused
on the Johannesburg Coloured population.
The first step was to design the multiplex system. This was done by using inhouse
SNPs. A total of seven multiplexes were designed and optimised, each
consisting of two, three or four different SNPs respectively.
A total of 143 saliva and buccal samples were collected from male Johannesburg
Coloureds. DNA was extracted from the saliva samples using an optimised
organic method. DNA was extracted from the buccal samples using an optimised
salting out method. DNA was successfully extracted from 77 of the male
samples.
A total of 69 samples were screened using Multiplex 1; of the 69 samples 56
samples were successfully screened to infer the paternal lineage of the samples.
The results show that the most frequent haplogroup of the Johannesburg male
samples was haplogroup CF (39%). The second most frequent haplogroup was
haplogroup DE (38%). Under further analysis of haplogroup DE it was seen that
37% of those samples were derived for the haplogroup E1b1b.
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Lappin, Fiona M. "REDEFINITION OF THE PSEUDOAUTOSOMAL BOUNDARY OF THE CARICA PAPAYA SEX CHROMOSOMES." Miami University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=miami1376205368.
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Wong, Chi-wai. "High resolution mapping of loss of heterozygosity and chromosomal aberrations using oligonucleotide single nucleotide polymorphism genotyping arrays in colorectal adenoma to carcinoma progression." Click to view the E-thesis via HKUTO, 2006. http://sunzi.lib.hku.hk/hkuto/record/B3871923X.
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Giedraitis, Vilmantas. "Candidate gene analyses and genome-wide screens in multiple sclerosis /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-408-9/.
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Miyagi, Mikiko. "Exploitation of bacterial artificial chromosome (BAC) libraries to enhance the efficiency of genome mapping." Thesis, Queensland University of Technology, 2002. https://eprints.qut.edu.au/37140/6/37140_Digitised%20Thesis.pdf.
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Boschiero, Clarissa 1979. "Mapeamento fino de qtls e polimorfismos de genes candidatos associados ao crescimento no cromossomo 1 da galinha /." Botucatu : [s.n.], 2009. http://hdl.handle.net/11449/104869.
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Orientador: Ana Silvia Alves Meira Tavares Moura<br>Banca: Luiz Lehmann Coutinho<br>Banca: Mônica Corrêa Ledur<br>Banca: Millor Fernandes do Rosário<br>Banca: José Roberto Sartori<br>Resumo: A partir de resultados de um estudo anterior, no qual foram mapeados QTLs para características de peso vivo, peso do coração e pulmões no GGA1, foi definida uma região no intervalo entre os marcadores ADL0234 e LEI0071, abrangendo 82,3 cM. Foram avaliadas três famílias de meios-irmãos paternos que compreendiam sete famílias de irmãos completos, num total de 652 F2 para as características: peso vivo aos 35 e 41 dias de idade, pesos do coração e pulmões e rendimentos de coração e pulmões. Os genótipos de seis marcadores microssatélites foram adicionados aos dez utilizados anteriormente. O mapa de ligação obtido da região compreendeu 110,8 cM com espaçamento médio entre os marcadores de 7,4 cM. Na análise de F2, em um único intervalo (LEI0146-LEI0174), compreendendo 28,8 cM, foram mapeados QTLs para todas as características estudadas, com exceção dos rendimentos de coração e pulmões. Neste intervalo estão localizados o gene IGF1 e o centrômero do cromossomo. A adição de seis marcadores confirmou os QTLs mapeados anteriormente, porém alguns em diferentes posições. A análise de meios-irmãos paternos indicou que os principais QTLs estavam segregando em apenas uma das famílias (7716), na qual cinco QTLs foram mapeados. Na análise de meios-irmãos maternos, duas famílias segregaram QTLs tanto na análise Individual como na Conjunta (7810 e 7971). As diferentes análises permitiram selecionar dois casais F1, que devem ser o alvo dos próximos estudos. Este estudo restringiu a busca por genes candidatos responsáveis pelas características de interesse a uma região de 28,8 cM (9,82 Mb) no GGA1.<br>Abstract: Based on the results from a previous study, in which QTL for body weight, heart and lungs weights and heart and lungs percentages were mapped to GGA1, a region was defined between markers ADL0234 and LEI0071, spanning 82.3 cM. Three paternal half-sib families, comprising seven full-sib families, totaling 652 F2 were evaluated for body weight at 35 and 41 days of age, heart and lungs weights and heart and lungs yields. Genotypes of six microsatellite markers were added to those of ten previously used. The linkage map of this region spanned 110.8 cM, with average spacing of 7.4 cM between markers. In a single interval (LEI0146-LEI0174), comprising 28.8 cM, QTLs for all traits, except for heart and lungs yields were mapped in the F2 analysis. In this same interval the IGF1 gene, and the chromosome centromere, are located. The use of six additional markers confirmed the same QTLs mapped previously, but some of them, in different positions. The paternal half-sib analysis indicated that the main QTLs were segregating in one of the families only (7716), in which five QTLs were mapped. In the maternal half-sib analysis, two families segregated QTLs both, in the across and within families analyses (7810 and 7971). These analyses allowed the selection of two F1 couples to be the target for future studies. This study restricted the search for candidate genes responsible for the traits of interest to a region of 28.8 cM (9.82 Mb) in GGA1.<br>Doutor
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Davids, Muneera. "Single nucleotide polymorphism association studies of ABCA13 and ABHD11 genes and the bioinformatics analysis of the autism candidate genes localized on chromosome 7." University of the Western Cape, 2016. http://hdl.handle.net/11394/4977.
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Magister Scientiae - MSc<br>Autism, Aspergers Syndrome and Pervasive Developmental Delay-Not Otherwise Specified (PDD-NOS), among others, fall under an umbrella of disorders known as Autism Spectrum Disorder. Twin studies show that autism is a highly heritable disorder. More than 100 genes have been implicated in the aetiology of autism, each of which is involved in numerous biological processes and a variety of molecular interactions. William-Beuren syndrome is a multisystem developmental disorder caused by the deletion of contiguous genes at the 7q11.23 position. The aims of this study were (i) to genotype three SNPs (rs10279013, rs2293484 and rs17060) in the ABHD11 and ABCA13 genes, respectively, using Taqman® SNP Genotyping assays to detect association with autism in three distinct South African (SA) ethnic groups (Black, Caucasian and Mixed), and (ii) to ascertain common pathways or regulating transcription factors for genes on chromosome 7 that may attribute to it being an “autism hotspot”. Chapter 3 objectives were to identify potential candidate genes using STRING analysis and the Gene Cards database. The Taqman® study indicated significant association for SNP rs2293484 in the South African Caucasian group, as well as for the G allele in the South African Mixed group, where p<0.001. STRING analysis yielded 2 new candidate genes, FZD1 and FZD9. It was also found that the Wnt pathway in mammals plays a significant role in both ASDs and cancer, and there is a definite link between genes regulating cancer, and genes implicated in autism. The study provides evidence for not only the association of the investigated SNP in a South African population, but also provides evidence for the co-morbidity of several neurological and psychological disorders such as depression and bipolar disorder with autism.
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King, Stephanie. "Capillary Electrophoresis Single-Strand Conformation Polymorphism Analysis for Monitoring Bacteria during the Remediation of TNT-Contaminated Soil." Ohio University / OhioLINK, 2004. http://www.ohiolink.edu/etd/view.cgi?ohiou1108061640.
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Trotter, Meridith V., and n/a. "Frequency-dependent selection and the maintenance of genetic variation." University of Otago. Department of Zoology, 2008. http://adt.otago.ac.nz./public/adt-NZDU20081114.120926.
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Frequency-dependent selection has long been a popular heuristic explanation for the maintenance of genetic diversity in natural populations. Indeed, a large body of theoretical and empirical work has already gone into elucidating the causes and consequences of frequency-dependent selection. Most theoretical work, to date, has focused either on the diallelic case, or dealt with only very specific forms of frequency-dependence. A general model of the maintenance of multiallelic genetic diversity has been lacking. Here we extend a flexible general model of frequency-dependent selection, the pairwise interaction model, to the case of multiple alleles.
First, we investigate the potential for genetic variation under the pairwise interaction model using a parameter-space approach. This approach involves taking a large random sample of all possible fitness sets and initial allele-frequency vectors of the model, iterating each to equilibrium from each set of random initial conditions, and measuring how often variation is maintained, and by which parameter combinations. We find that frequency- dependent selection maintains full polymorphism more often than classic constant-selection models and produces more skewed equilibrium allele frequencies. Fitness sets with some degree of rare advantage maintained full polymorphism most often, but a variety of non-obvious fitness patterns were also found to have positive potential for polymorphism.
Second, we further investigate some unusual dynamics uncovered by the parameter-space approach above. Long-period allele-frequency cycles and a small number of aperiodic trajectories were detected. We measured the number, length and domains of attraction of the various attractors produced by the model. The genetic cycles produced by the model did not have periods short enough to be observable on an ecological time scale. In a real world system, allele-frequency cycling is likely to be indistinguishable from stable equilibrium when observed over short time scales.
Third, we use a construction approach to model frequency-dependent selection with mutation under the pairwise interaction model. This approach involves the construction of an allelic polymorphism by bombarding an initial monomorphism with mutant alleles over many generations. We find that frequency-dependent selection is able to generate large numbers of alleles at a single locus. The construction process generates a wide range of allele- frequency distributions and genotypic fitness relationships. We find that constructed polymorphisms remain permanently invasible to new mutants. Analysis of constructed fitness sets may even reveal a signature of positive frequency dependence.
Finally, we examine the numbers and distributions of fitnesses and alleles produced by construction under the pairwise interaction model with mutation from existing alleles, using several different methods of generating mutant fitnesses. We find that, relative to more general construction models, generating mutants from existing alleles lowers the average number of alleles maintained by frequency-dependent selection. Nevertheless, while the overall numbers of alleles are lower, the polymorphisms produced are more stable, with more natural allele-frequency distributions.
Overall, frequency-dependent selection remains a powerful mechanism for the maintenance of genetic variation, although it does not always work in intuitively obvious ways.
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Qianren, Jin. "Search for susceptibility loci and candidate genes for breast cancer /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-030-3/.
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Capredon, Mélanie. "Histoire biologique d’une population du sud-est malgache : les Antemoro." Thesis, La Réunion, 2011. http://www.theses.fr/2011LARE0016/document.
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Entre le XIème et le XVIème siècle, la Mer des Indes fut le théâtre de nombreux mouvements populationnels aux fins essentiellement commerciales ou coloniales. Madagascar se trouve à la croisée des mondes asiatiques et africains. La côte sud-est malgache a vu l'arrivée de plusieurs migrations : la dernière, probablement vers la fin du XVème siècle, serait celle des Antemoro dont une partie d'entre eux se réclame d'une origine arabe et se rattache à La Mecque. L'éthnie des Antemoro a fait l'objet de nombreuses études anthropologiques et linguistiques. Néanmoins, le débat sur l'origine des migrants fait toujours l'objet d'hypothèses contradictoires. Leurs origines génétiques pourraient ainsi être l'Arabie, l'Afrique de l'Est, l'Inde ou encore l'Asie du Sud-Est à une époque où ces régions étaient déjà islamisées. Ce travail a consisté à étudier la diversité génétique d'une population Antemoro afin d'apporter des éléments de réponse à la question de leur origine biologique. Ce projet interdisciplinaire a pour objectif de mettre en relation l'anthropologie culturelle et sociale avec l'anthropologie biologique. Le polymorphisme du chromosome Y a été étudié afin de rechercher les origines des lignées paternelles par l'analyse de 17 marqueurs microsatellites ainsi que des mutations ponctuelles de l'ADN de la partie non recombinante du chromosome Y. De même, la variabilité génétique des lignées maternelles a été analysée par séquençage des régions hypervariables I et II de l'ADN mitochondrial, et par la définition de polymorphismes bialléliques dans sa région codante. Nous avons mis en évidence la présence de deux haplogroupes du chromosome Y chez certains groupes Antemoro, qui les différencient de la diversité habituellement rencontrée dans les populations malgaches. Bien que la majeure partie des Antemoro entre dans la diversité observée en Afrique sub-Saharienne et en Asie du Sud-Est, quelques haplotypes, des lignées paternelles, les lieraient au Moyen-Orient. Les lignées maternelles, quant à elles, ne les différencient pas de celles des autres populations malgaches. L'isolat génétique formé par certaines « pseudo-castes » Antemoro confirme bien l'isolat culturel. Ce travail apporte une nouvelle vision de la diversité génétique humaine à Madagascar<br>Between the 11th and 16th century, the Indian Ocean was the scene of many population movements notably for commercial and colonial purposes. Madagascar is located at the crossroads of the Asian and African continents. Several migrations have occurred in this region; the last one during the late 15th century involved the Antemoro population who claimed an Arabian origin in Mecca. Many anthropological and linguistic studies have been carried out on this ethnic group, but the origin of these migrants remains contentious. It is uncertain whether their origins were in Arabia, East Africa, India or Southeast Asia, when these regions were Islamized. In this study we assessed the genetic diversity of an Antemoro population from villages between Manakara and Vohipeno, to determine their biological origin. The aim of our interdisciplinary study was to link cultural and social anthropology with biological anthropology. Y-chromosome polymorphisms were studied by analyzing 17 microsatellites markers and some SNPs in the non-recombining region of the Y-chromosome to determine the biological origins of the paternal lineages. In addition, genetic variability of maternal lineages was analyzed by sequencing hypervariables regions I and II, and by defining bi-allelic polymorphisms in the coding region of mitochondrial DNA. We found two Y-chromosome haplogroups in some Antemoro groups that differentiated them from the typical genetic variability found in other Malagasy populations. Although most of the Antemoro showed a genetic diversity similar to that observed in sub-Saharan Africa and Southeast Asia, few haplotypes associated to paternal lineages linked them to the Middle East. Maternal lineages did not differ from those found in other Malagasy populations. The genetic isolate formed by some Antemoro groups confirmed their cultural isolation. This study provides a new view of the human genetic diversity in Madagascar
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Gerber, Jaclyn. "Cytochrome P450 polymorphisms : relevance in two South African disease populations." Thesis, Stellenbosch : Stellenbosch University, 2003. http://hdl.handle.net/10019.1/53345.
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Thesis (MSc)--Stellenbosch University, 2003.<br>ENGLISH ABSTRACT: With knowledge of the human genome increasing constantly we are continually faced
with new and potentially groundbreaking methods for managing, treating and/or
identifying diseases and predisposition to diseases and conditions at a genetic level.
The human cytochrome P450 (CYP) super-family of genes code for enzymes that can
participate in metabolism of drugs and foreign chemicals and in steroid synthesis and
metabolism. Mutations in these genes may contribute to clinically relevant diseases.
In this study, the effects of mutations within four CYP genes were evaluated in two
South African disease groups - variegate porphyria and breast cancer.
Variegate porphyria (VP) has an unusually high incidence in South Africa due to the
R59W founder mutation in the protoporphyrinogen oxidase (PPOX) gene that causes
a disruption in the haem biosynthetic pathway. VP presents with variable clinical
symptoms and has a relatively low penetrance. It is expected that environmental
factors and modifier genes play a role in the clinical expression of VP. CYP genes
are implicated as candidate modifier genes for the expression of VP due to the
function they have in metabolising many drugs contraindicated in porphyria patients,
and the necessity of haem binding to the apoprotein to produce a functional CYP
enzyme. This is the first study to investigate CYPs as possible modifier genes for VP
clinical expression. Six CYP polymorphisms (CYPIAlml, CYPIAlm2, CYPIA2 -
734 C>A, CYPIBI 8372 A>C, CYP2D6*3, CYP2D6*4), associated with four CYP
loci, were genotyped in a VP population and a suitable control population. The
results observed are suggestive of CYPIAlml and CYPIBI playing a role as
modifiers for the clinical expression of VP as they were significantly associated
(P<O.05) with the presence ofVP related symptoms.
Breast cancer is one of the leading causes of death in women due to cancer. It is
believed that breast cancer may be the result of co-participation between common
DNA alterations and environmental exposures. Polymorphisms in enzymes involved
with the metabolism of environmental exposures, such as the cytochrome P450
enzymes, are therefore expected to play an aetiological role in breast cancer. Two
groups of South African breast cancer patients (Caucasian and of mixed ancestry) and population-matched controls were genotyped for four CYP polymorphisms
(CYPIAlml, CYPIAlm2, CYPIA2 -734 C>A and CYPIBI 8372 A>C). This
represents the first investigation of the potential role of CYPs as breast cancer risk
modifiers in the two South African populations. Significant differences were
observed (P<O.003) in genotype and allele frequencies between the breast cancer
patients and controls for the CYPIBI 8372 A>C polymorphism in the population of
mixed ancestry. Vast differences in allele frequencies were also observed between
the two groups of breast cancer populations. These results emphasize the importance
of population-based risk assessment when genetic testing and counselling for complex
disease susceptibility is offered.
The results of this study provide the first evidence suggesting a role for CYPs in
modifying the clinical expression of VP and in acting as risk factors for developing
breast cancer in a South African population.<br>AFRIKAANSE OPSOMMING: Met die konstante toename van kennis oor die mensgenoom kom ons voortdurend te
staan voor nuwe metodes vir die beheer, behandeling en/of identifikasie van siektes
en vatbaarheid vir siektes op 'n genetiese vlak. Die mens sitochroom P450 geensuperfamilie
kodeer vir ensieme betrokke in die metabolisme van medisyne en ander
chemiese stowwe en steroïed-sintese en -metabolisme. Mutasies in hierdie gene kan
'n bydrae lewer tot kliniese relevante siektes. In hierdie studie is die effek van
mutasies in vier sitochroom gene bestudeer in twee Suid-Afrikaanse siekte groepe,
variegate porfirie en borskanker.
Variegate porfirie (VP) het 'n besonderse hoë frekwensie in Suid-Afrika as gevolg
van die R59W stigter-mutasie in die protoporfirinogeen oksidase (PPOX) geen.
Hierdie mutasie lei tot 'n versteuring in die heem biosintese padweg. VP presenteer
met variërende kliniese simptome en het 'n betreklike lae penetrasie. Daar word
vermoed dat omgewingsfaktore en kandidaat modifiserende gene 'n rol speel in die
kliniese beeld van VP. Sitochroom P450 gene is geïdentifiseer as kandidaat
modifiserende gene as gevolg van hulle rol in die metabolisme van verbode medikasie
vir porfirie pasiënte, asook die binding van heem aan die apoproteïen wat noodsaaklik
is vir die produksie van funksionele sitochroom P450 ensiem. Hierdie is die eerste
studie wat sitochroom P450 gene as moontlike modifiserende gene vir die kliniese
uitdrukking van VP ondersoek. Ses sitochroom P450 polimorfismes (CYPIAlml,
CYPIAlm2, CYPIA2 -734 C>A, CYPIBI 8372 A>C, CYP2D6*3, CYP2D6*4) is
ondersoek in beide 'n VP populasie en 'n geskikte kontrole populasie. Die resultate
suggereer 'n rol vir CYPIAlml en CYPIBI in die modifisering van die kliniese
uitdrukking van VP aangesien hulle betekenisvolle assosiasie (P<O.05) met die
voorkoms van VP-verwante simptome getoon het.
Borskanker IS een van die vernaamste oorsake van kankersterftes onder vroue.
Borskanker IS waarskynlik die resultaat van interaksie tussen algemene DNSveranderinge
en omgewings-blootstelling. Daar word dus verwag dat polimorfismes
in ensieme betrokke by die metabolisme van omgewingselemente, soos byvoorbeeld
die sitochroom P450 ensieme, 'n etiolgiese rol in borskanker sal speel. Die genotipes van twee groepe Suid-Afrikaanse borskanker lyers (Kaukasiërs en van gemengde
herkoms) en populasie-passende kontroles is bepaal vir vier sitochroom P450
polimorfismes (CYPIAlml, CYPIAlm2, CYPIA2 -734 C>A, CYPIBI 8372 A>C).
Hierdie studie verteenwordig die eerste ondersoek na die potensiële rol van
sitochroom P450s as risiko-modifiserende faktore vir borskanker in die twee
populasies. Betekenisvolle verskille (P<O.003) in genotipe en allele frekwensies is
waargeneem tussen die borskanker lyers en kontroles vir die CYPIBI 8372 A>C
polimorfisme in die gemengde herkoms populasie. Beduidende verskille in alleel
frekwensies is ook waargeneem tussen die twee borskanker populasies. Hierdie
resultate beklemtoon die belangrikheid van populasie gebaseerde risiko-beraming
wanneer genetiese toetse en voorligting vir komplekse siekte-vatbaarheid aangebied
word.
Die resultate van hierdie studie bied die eerste getuienis dat sitochroom P450s 'n rol
kan speel in die modifisering van die kliniese beeld van VP en ook kan optree as as
risiko faktore vir die ontwikkeling van borskanker in 'n Suid-Afrikaanse populasie.
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Barnett, Catherine Margaret Eleanor. "Association of Single Nucleotide Polymorphisms in Surfactant Protein A and D with Otitis Media." The University of Waikato, 2007. http://hdl.handle.net/10289/2338.
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Otitis Media is one of the most common childhood diseases. Recurrent acute otitis media RAOM is characterized by repeated episodes of inflammation of the middle ear in conjunction with middle ear fluid, and often with an inflamed or bulging eardrum. Defective clearance by the Eustachian tube results in mucus build-up and is characteristic of otitis media with effusion (OME). Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, respiratory syncytial virus, and rhinovirus are the most common contributors to otitis media pathogenesis. In New Zealand, OME has been implicated with conductive hearing loss in childhood and has been shown to significantly impact on speech and language development. New Zealand Māori and Polynesian children have displayed significantly higher hearing test failure rates than European-Caucasian children. The collectins, Surfactant Protein (SP)-A and -D are encoded by three genes (SP-A1, SP-A2, and SP-D) and are host defense proteins present in the middle ear and Eustachian tube. Single nucleotide polymorphisms (SNPs) in SP-A1 and SP-A2 have been associated with increased or decreased susceptibility to otitis media, meningococcal disease, and range of respiratory diseases. Using allele-specific primers and real-time PCR with SYBR Green I melting curve analysis, four groups of individuals were genotyped for eleven SP-A1, SP-A2, and SP-D SNPs: European-Caucasian individuals with RAOM/OME; New Zealand Māori/Polynesian individuals with RAOM/OME; individuals with meningococcal disease; and a control group. The computer program, Haploview, was employed to perform χ2 analyses and identify statistically significant associations of alleles/haplotypes with RAOM/OME or meningococcal disease. In the European-Caucasian population, two SP-A1 alleles, one SP-A2 allele, and four haplotypes (CGAGC, 1A3, 1A9, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). Conversely, haplotypes 6A2 and 1A2 were found to be protective against susceptibility to RAOM/OME (P lt; 0.05). In New Zealand Māori and Polynesian individuals, two SP-A1 alleles, three SP-A2 alleles, one SP-D allele, and four haplotypes (6A8, 6A10, 1A3, and 1A10) were found to be associated with increased risk of RAOM/OME (P lt; 0.05). An additional four haplotypes (6A2, 1A0, 1A2, and TA) were determined to be protective against susceptibility to RAOM/OME (P lt; 0.05). However, protective SPA1/SPA2/SPD haplotype 6A2-1A0-TA was significantly under-represented in the New Zealand Māori and Polynesian population (P lt; 0.05). A single allele and haplotype were associated with increased risk of meningococcal disease (P lt; 0.05). The findings of this study confirm that specific genetic variants of SP-A and SP-D are associated with either increased or decreased risk of developing RAOM and/or OME. Furthermore, it was demonstrated that New Zealand Māori and Polynesian individuals appear to exhibit more haplotypes susceptible to RAOM/OME. This may provide a partial explanation for the higher RAOM/OME-related failure rates of hearing tests in New Zealand Māori and Polynesian children. However, there are numerous socio-economic and environmental factors that also contribute to otitis media pathogenesis which were not considered in this study. The effects of the SP-A1, SP-A2, and SP-D alleles and haplotypes on the bacterial/viral binding efficiencies of SP-A and SP-D need to be investigated by further research, using a large population, to confirm the association with susceptibility or resistance with RAOM/OME.
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Lui, Weng-Onn. "Approaches for the localization and identification of human cancer genes /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-315-5/.
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Liu, Wanyang. "A rare Asian founder polymorphism of Raptor on chromosome 17q25.3 may explain the high prevalence of Moyamoya disease among East Asians and its low prevalence among Caucasians." Kyoto University, 2010. http://hdl.handle.net/2433/120583.
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Prades, Catherine. "Recherche de marqueurs polymorphes dans les régions centromériques des chromosomes humains." Montpellier 1, 1997. http://www.theses.fr/1997MON1T007.
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Batista, Marcos Roberto Dias. "Estudos citogeneticos em dipteros = inversões cromossomicas em Drosophila mediopunctata e fotomapa dos cromossomos politenicos de Cochliomyia hominivorax." [s.n.], 2010. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316982.
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Orientadores: Louis Bernard Klaczko, Galina Ananina<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia<br>Made available in DSpace on 2018-08-15T15:35:04Z (GMT). No. of bitstreams: 1
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Previous issue date: 2010<br>Resumo: Nesta tese, estudamos uma questão básica e uma aplicada: os determinantes da variação geográfica e temporal do polimorfismo de inversões do segundo cromossomo em populações naturais de Drosophila mediopunctata; ainda, adaptamos a técnica para análise de politênicos de Drosophila para estudos em Cochliomyia hominivorax e assim elaboramos um mapa dos cromossomos politênicos desta praga da pecuária. Duas décadas depois de estudos anteriores, realizamos cinco novas coletas no Itatiaia e observamos inesperadas mudanças nas frequências dos arranjos mais comuns e em sua variação microgeográfica em relação àquelas antes descritas. No segundo cromossomo, o arranjo DA continua sendo o mais frequente, porém não detectamos mais uma correlação significativa com a altitude. Para os arranjos DS e DP, além de não haver mais correlações significativas com a altitude, suas frequências se mostram ainda mais baixas, principalmente no inverno. Entretanto, o ciclo sazonal observado para estas inversões se mantém. O arranjo DI aumentou sua frequência significativamente e agora mostra uma correlação positiva e significativa com a altitude. Estes resultados sugerem que, depois de duas décadas, houve mudanças ambientais incluindo alterações climáticas e provavelmente fatores bióticos que devem ter afetado a arquitetura genética das populações. Observamos uma diferenciação entre o padrão das frequências de inversões do cromossomo II de populações vizinhas de D. mediopunctata. As matas estudadas estão situadas em duas diferentes unidades geomorfológicas, que apresentam diferenças marcantes em relação ao solo, relevo, paisagem, vegetação e fauna. Nossos resultados sugerem que a diferenciação geográfica observada nas frequências de inversões pode ser resultado de uma adaptação local às diferenças florísticas e climáticas. Entretanto, outros marcadores genéticos devem ser pesquisados para analisar os efeitos da fragmentação florestal sobre as populações. Cochliomyia hominivorax, conhecida no Brasil como a mosca-da-bicheira, é considerada uma das principais moscas causadoras de miíases primária na região Neotropical. Apesar de um fotomapa preliminar de seus cromossomos politênicos ter sido publicado anteriormente, com resultados encorajadores, não havia um mapa dos cromossomos politênicos com boa resolução para a espécie. Desta forma, elaboramos um novo fotomapa dos cinco autossomos com uma resolução total de 1450 bandas<br>Abstract: In this thesis, we studied a basic and an applied issue: the determinants of geographical and temporal variation of the second chromosome inversion polymorphism in natural populations of Drosophila mediopunctata; and, adapting the squashing technique used for Drosophila to Cochliomyia hominivorax, we made a map of the polytene autosomes of this livestock pest. Two decades after previous studies, we carried out five collections in Itatiaia, RJ. We observed unexpected changes in the frequencies of the most common inversions of the second chromosome. The DA gene arrangement is still the most common, but we no longer detect a significant correlation between its frequency and altitude. Furthermore, the frequencies of DS and DP inversions became even lower, especially in winter; and didn't show a significant correlation with altitude. However, the previously observed seasonal cycle for these inversions is still present. DI frequency increased significantly, and it is now significantly positively correlated with altitude. These results suggest that, after two decades, there were modifications in the climate, but other variables - such as biotic factors -have also probably changed and may be correlated with the changes in the genetic architecture of the Itatiaia population. Furthermore, we report a differentiation between frequencies of inversions of the second chromosome in neighboring populations of D. mediopunctata. The forests studied are located over two geomorphologic units that have marked differences regarding landscape, topography, soil, vegetation, and fauna. Our results suggest that the observed geographical variation in the inversion frequencies may be a result of local adaptation to climate and floral and faunal changes. However, further analysis with other genetic markers must be performed to assess the possible effects of forest fragmentation on different populations. Cochliomyia hominivorax, the New World screwworm fly is one of the main flies causing primary myiasis in the Neotropical region. Although a preliminary photomap of the polytene chromosomes of C. hominivorax was previously published, a good resolution map of the polytene chromosomes was not available for this species. Here, we present a new photomap of the five autosomes of this species with a total resolution of 1450 bands<br>Doutorado<br>Genetica Animal e Evolução<br>Doutor em Genetica e Biologia Molecular
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Vergnaud, Gilles. "Structure moleculaire du chromosome y humain : cartographie par deletion de la region specifique au sexe et minisatellites de la region pseudoautosomique." Paris 7, 1988. http://www.theses.fr/1988PA077216.
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Ordonnancement de 23 loci du chromosome y grace a l'etude de fragments d'adn et a la comparaison des chromosomes y d'individus porteurs d'anomalies de structure. La region specifique du sexe peut-etre separee en 7 blocs consecutifs definis par un evenement de cassure
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Aguiar, Hilton Jeferson Alves Cardoso de. "First report on spontaneous hybridization between Astyanax giton Baird & Girard 1854 and Oligosarcus argenteus Günther 1864 (Pisces : Characidae): ecological and phylogenetic inferences." Universidade Federal de Viçosa, 2011. http://locus.ufv.br/handle/123456789/4748.
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Previous issue date: 2011-02-14<br>Conselho Nacional de Desenvolvimento Científico e Tecnológico<br>A complexa família Characidae é parte da fauna ictiológica neotropical e conta com várias espécies e gêneros em condição de Incertae Sedis. Os gêneros Astyanax e Oligosarcus, considerados muito aparentados, estão incluídos nesta família e abrangem espécies de pequeno tamanho e expressiva abundância em muitos rios e córregos da América do sul. Na bacia do rio Doce, no sudeste brasileiro, uma análise morfológica preliminar permitiu a identificação de cinco peixes “semelhantes à Astyanax” que continham no seu osso maxilar de 8 a 13 dentes. Esses cinco peixes, chamados no presente trabalho de dentuços, foram coletados em simpatria com as espécies Astyanax bimaculatus (Linneaus, 1758), Astyanax giton (Eigenmann, 1908) e Oligosarcus argenteus Günther, 1864. De modo a determinar a natureza biológica dos dentuços, foi realizado um estudo multidisciplinar envolvendo dados morfológicos citogenéticos e moleculares. Os dentuços apresentaram configurações intermediárias entre as espécies A. giton e O. argenteus no que diz respeito ao número de escamas na linha lateral e ao número de dentes no osso maxilar. As análises citogenéticas, feitas através das técnicas de Giemsa, bandeamento NOR, bandeamento-C, fluorocromos, e FISH, indicaram que todas as espécies de caracídeos contaram com número diploide 2n=50 cromossomos diferindo, porém, em vários caracteres de sua morfologia cromossômica. Os dentuços caracterizaram-se por apresentar altos índices de variação cromossômica tanto intra- como inter-individual. Além do mais, eles contaram com vários cromossomos não pareáveis assim como cromossomos de tamanho diminuto que não são observados em nenhuma daquelas espécies simpátricas de Characidae. Três espécimes dos dentuços apresentaram seu fragmento de DNA do gene mitocondrial citocromo b (475 pb) idêntico aquele de O. argenteus e, contudo, todos os dentuços compartilhavam mais alelos ISSR com os espécimes de A. giton do que com os espécimes de O. argenteus. Por outro lado, uma espécie de dentuço conta com o gene cyt. b idêntico aquele das espécies de A. giton estudadas. A análise de fragmentos ITS-1 (1123 pb) mostrou que os dentuços têm sequencias mais relacionadas à Oligosarcus argenteus. Os dados, desse modo, sugeriram que os dentuços são híbridos entre as espécies A. giton e O. argenteus representando assim o primeiro caso de hibridismo espontâneo entre dois gêneros de peixes neotropicais. A relevância de tal descoberta para a biologia da conservação e para as investigações filogenéticas foram discutidas.<br>Within the Neotropical fish fauna, the taxonomically complex family Characidae has many species and genera in Incertae Sedis condition. Within this family, the closely related genera Astyanax and Oligosarcus are represented by small sized fishes that are an expressive proportion of the freshwater biodiversity in many rivers of South America. In the Doce River Basin, Southeastern Brazil, a preliminary morphologic analysis indicated the presence of 5 Astyanax-like fish with unusually high numbers (8-13) of maxillary teeth which are referred as “toothed morphs”. These fishes were collected in sympatry with Astyanax bimaculatus (Linneaus, 1758), Astyanax giton (Eigenmann, 1908), and Oligosarcus argenteus Günther, 1864. To determine the biological status of them a comparative multidisciplinary approach involving morphologic, cytogenetic and molecular data was conducted, with the toothed morphs and their sympatric species. The toothed morphs showed an intermediate position in lateral line scale numbers and maxillary teeth number between A. giton and O. argenteus. Cytogenetic analyses (Giemsa, NOR, C-banding, fluorochromes and FISH) indicated that all sympatric characids were 2n=50, although they differed from each other in many other karyotypic characters. The toothed morphs were characterized by high levels of intra and inter-individual chromosomal variation including several unpairable chromosomes and tiny chromosomes that were not observed in either of the other sympatric species. Three toothed morphs specimens had their cytochrome b DNA fragment (475 bp) identical to O. argenteus, with one exception which its cyt. b DNA sequence was identical to A. giton. Moreover, all toothed morphs ITS-1 DNA sequences were characterized by their similitude to those sequences of Oligosarcus argenteus. On the other hand, all toothed morphs shared more ISSR alleles with A. giton. The data suggested that the toothed morphs were hybrids between A. giton and O. argenteus, representing the first evidence for spontaneous hybridization between two Neotropical fish genera. The relevance of such findings in conservation biology and phylogeny assessment were discussed.
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Ge, Jianye. "Computational Algorithms and Evidence Interpretation in DNA Forensics based on Genomic Data." University of Cincinnati / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1234916402.
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Ramdayal, Kavisha. "Incidence and Regulatory Implications of Single Nucleotide Polymorphisms among Established Ovarian Cancer Genes." Thesis, Online access, 2009. http://etd.uwc.ac.za/usrfiles/modules/etd/docs/etd_gen8Srv25Nme4_5111_1277754725.pdf.
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Hanauer, André. "Le chromosome x humain : recherche de sequences exprimees et localisation genique de deux loci correspondanta des maladies." Université Louis Pasteur (Strasbourg) (1971-2008), 1989. http://www.theses.fr/1989STR13010.
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Caracterisation d'expressions geniques liees au chromosome x, de 6 sequences genomiques humaines liees au chromosome x; localisation du syndrome coffin-lowry par analyse de linkage et de la dysplasie ectodermique anhidrotique
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Cadenas, Alicia M. "Y-chromosome polymorphisms in southern Arabia." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/1962.
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In order to explore south Arabia's role in the migratory episodes leaving Africa to Eurasia and back, high-resolution Y-chromosome analyses of males from the United Arab Emirates (164), Qatar (72) and Yemen (62) were performed. The distribution of specific haplogroups (E3bl-M35 and J1-M267) and their microsatellite-based age estimates in southern Arabia offer additional insight on their dissemination. With the exception of Yemen, southern Arabia displays high diversity in its Y-haplogroup substructure and share similarities with populations along the eastern coast of the Gulf of Oman, possibly serving as a coastal corridor for migrations. Elevated rates of consanguinity may have had an impact in Yemen and Qatar, which experience deficiencies in their ratios of observed to expected heterozygosity at 15 hypervariable autosomal STR loci. Higher diversity along the Gulf of Oman may be due to trade emanating from the kingdom of Oman involving East Africa, southern Pakistan and western India.
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Gayden, Tenzin. "Y-chromosome polymorphisms in the Himalayas." FIU Digital Commons, 2006. http://digitalcommons.fiu.edu/etd/3587.
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In the present study, high resolution Y-chromosome SNP analyses were employed to investigate the genetic origins of three distinct groups from Nepal namely, the general population of Kathmandu, Newar, and Tamang, as well as a collection from Tibet. The results suggest that the Tibetans and Nepalese are descendants of Tibeto-Burman speaking groups originating in Northeast Asia. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to Indian Y haplogroup substructure. These results suggest recent gene flow from the Indian subcontinent, a conclusion that is also supported by the admixture analysis. In contrast, while YAP+ , a genetic signature of Central Asian origin, is completely absent in Nepal, it accounts for more than fifty percent of Tibetan Y-chromosome. Low frequencies of haplogroup R lineages in Tibet reflect limited gene flow from India most likely due to the Himalayan mountain range to the south.
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Borge, Thomas. "Genetics and the Origin of Two Flycatcher Species." Doctoral thesis, Uppsala University, Evolutionary Biology, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3919.
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<p>In this thesis, different genetic tools are used to investigate pre- and postzygotic barriers to gene exchange and their role in speciation in the pied flycatcher (<i>Ficedula hypoleuca</i>) and the collared flycatcher (<i>F. albicollis</i>). This species complex consists of four genetically distinct clades that apparently diverged in allopatry (I). Sequencing of introns from autosomal and Z-linked genes from the two species reveals signs of selection on the Z-chromosome. Sexual selection acting on Z-linked genes might explain this pattern (II). By using large-scale genotyping of single nucleotide polymorphisms (SNPs), introgression is observed at autosomal- but not Z-linked loci, mostly from the pied- to the collared flycatcher. Male plumage characters and genes involved in hybrid fitness are largely mapped to the Z-chromosome (III). By studying mate choice of female hybrids I show that there is a link between female preferences and the Z chromosome (IV). The rate of introgression in island versus clinal hybrid zones is consistent with regional differences in hybrid fertility. Asymmetric gene flow from allopatry on the islands may oppose reinforcement, leading to introgression and a partial breakdown of postzygotic isolation. Adaptive introgression may explain the high rate of introgression observed at one of the genetic markers (V). For late breeding female collared flycatchers it appears to be adaptive to use pied flycatchers as social fathers but conspecific males as genetic fathers. Additionally, females in mixed species pairs may reduce hybridization costs by producing an excess of male hybrid offspring that are more fertile than females (VI).</p><p>In conclusion, the Z-chromosome appears to play a major role in flycatcher speciation. Sexual selection and reinforcement are important mechanisms in the divergence of these birds. However, gene flow from allopatry, introgression of adaptive genes and adaptive hetrospecific pairing by late breeding collared flycatcher females may work in the opposite direction.</p>
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Mathias, Neal. "Y chromosome DNA polymorphisms and human evolution." Thesis, University of Oxford, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.333355.
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Polverari, Fernanda Silva. "Caracterização genética da população do Estado do Mato Grosso e do Distrito Federal (Brasília) pela análise de 32 polimorfismos de inserção/deleção (InDels) no cromossomo X /." Araraquara, 2018. http://hdl.handle.net/11449/154146.
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Orientadora: Regina Maria Barreto Cicarelli<br>Banca: Raquel Mantuaneli Scarel Caminaga<br>Banca: João Aristeu da Rosa<br>Banca: Leonor Gusmão<br>Banca: Rodrigo Rodenbusch<br>Resumo: A análise dos polimorfismos do DNA é a melhor ferramenta encontrada para resolução de casos de identificação humana, sendo os marcadores STRs (short tandem repeat) localizados em regiões autossômicas os principais e mais utilizados para esta finalidade. Apesar da indiscutível reprodutibilidade destes marcadores, quando são analisados em amostras degradadas podem não apresentar bons resultados, o que dificulta a resolução dos casos. Assim, há a necessidade de uma alternativa e, atualmente, a mais indicada é a utilização dos polimorfismos bialélicos. A análise do cromossomo sexual X também vem ganhando importância significativa no contexto forense, devido ao seu padrão de transmissão entre os genitores. Neste trabalho, caracterizamos as populações brasileiras do estado do Mato Grosso e do Distrito Federal pela análise de 32 polimorfismos de inserção/deleção no cromossomo X (X-InDels), tendo em vista que os dados destes polimorfismos nestas populações são ainda inéditos, e para que esses marcadores também possam no futuro auxiliar a resolução de casos forenses em nosso país. Para identificar a diversidade genética foram analisados os perfis genotípicos de 303 indivíduos não aparentados nascidos no estado do Mato Grosso e 179 indivíduos não aparentados e residentes em Brasília. Os resultados indicam que o painel dos 32 X-Indels é bastante eficiente para a sua finalidade, sendo que praticamente todos os marcadores se mostraram altamente informativos para as populações estudadas. O... (Resumo completo, clicar acesso eletrônico abaixo)<br>Abstract: The analysis of DNA polymorphisms is the best tool found for solving cases of human identification, and the Short Tandem Repeat (STR) markers used in the autosomal regions are the main and most marker used for this purpose. Despite the undeniable reproducibility of these markers, when analyzed in degraded samples they may not present good results, which makes it difficult to solve the cases. Because of this, there is a need for an alternative tool and currently the most indicated is the use of the biallelic polymorphisms. In this way, the analysis of the sex chromosome X has gained significant importance in the forensic context, due to its pattern of transmission between the parents. In this work, we characterize the Brazilian populations of the state of Mato Grosso and the Federal District by the analysis of 32 insertion/deletion polymorphisms on the X chromosome (X-InDels), considering that the data of this polymorphism in these populations are still unpublished, and for that these markers may also in the future help the resolution of forensic cases in our country. To identify the genetic diversity, the genotypic profiles of 303 unrelated individuals born in the state of Mato Grosso and 179 unrelated individuals living in Brasília were analyzed. The results shows that the 32 X-Indels panel is very efficient to its purpose, being almost all markers highly informative for the studied populations. The Hardy-Weinberg equilibrium test was performed on the female samples from bot... (Complete abstract click electronic access below)<br>Doutor
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Mwema, Hadija Saidi. "Forensic identification of six of Tanzanian populations using the extended haplotype markers." Thesis, University of the Western Cape, 2011. http://etd.uwc.ac.za/index.php?module=etd&action=viewtitle&id=gen8Srv25Nme4_2349_1325671867.
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The aim of the present study was to evaluate the power of discrimination and genetic (diversity) parameters in the Y chromosome extended haploytpe markers in populations of Tanzania for forensic and populations studies. Eleven Y chromosome extended haplotype markers were selected for this study, these includes Minimal haplotypes markers i.e. DYS19, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS389I/II and two additional markers DYS438 and DYS439. Six populations of Tanzania were investigated under this study. These populations were selected based on the language family categories<br>Niger Congo (Kuria and Sukuma), Nilo Saharan (Luo and Maasai) and Afro Asiatic (Iraqw and Alagwa).
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Vuturo, Brady Jennifer Ann 1966. "Y chromosome polymorphisms and the peopling of the Americas." Thesis, The University of Arizona, 1996. http://hdl.handle.net/10150/278563.
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Polymorphisms at four paternally-inherited loci (DYS287, SPY1, DYS199 and DXYS156) were surveyed in twenty-seven populations (n = 997) world-wide to trace the origins of Native Americans. One of the haplotypes (6) is found at relatively high frequencies in all seven Native American populations representing two of the major linguistic divisions in the New World. The same haplotype was found at low frequencies in Siberian Eskimos and was absent from eleven other Asian populations. A second haplotype (7) was present at high frequencies in all the Native American and several Siberian populations. It was present at moderate frequencies in European populations and at low frequencies in several Asian populations. These data best support the hypothesis of a single male-mediated migration wave for the early peopling of the Americas, although a multi-wave hypothesis is not rejected.
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Escouflaire, Clémentine. "Détection chez le bovin de polymorphismes génétiques au niveau du génome mitochondrial et des chromosomes sexuels et caractérisation de leurs effets sur les caractères de production, reproduction et santé." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASA015.
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Malgré leurs rôles dans l’expression de caractères de fertilité et dans le métabolisme énergétique, le génome mitochondrial et les chromosomes sexuels ne sont actuellement pas pris en compte dans les évaluations génomiques bovines françaises. Cette thèse a pour but d’étudier la variabilité génétique du génome mitochondrial et des chromosomes X et Y, de détecter des polymorphismes génétiques et de caractériser leurs effets sur les caractères de production, reproduction et santé. L’étude des schémas de transmission uniparentale, a mis en évidence une disparité entre une faible diversité des haplotypes du chromosome Y et un grand nombre de lignées mitochondriales dans de nombreuses races bovines. La présence à très faible fréquence de porteurs d’haplogroupes dont la divergence est antérieure à la domestication des bovins taurins a été identifié par génotypage. Deux études ont été réalisées pour estimer l’effet des différents variants identifiés sur le génome mitochondrial et le chromosome Y sur certains caractères d’intérêt zootechnique. Puis, une approche de génétique inverse a permis d’exploiter des données des séquences pour détecter sur le chromosome X des mutations candidates responsables d’anomalies et des mutations pouvant avoir un effet sur la fertilité mâle ou femelle ou entraînant un biais d’inactivation du chromosome X. En parallèle, le mécanisme génétique d’une anomalie liée au chromosome X responsable d’un cas de dysplasie ectodermique hypohidrotique a été décrit chez une génisse de race Holstein. Enfin, des pistes de réflexions sont proposées afin d’initier une meilleure prise en compte des chromosomes sexuels et du génome mitochondrial dans la sélection des bovins<br>In spite of the roles of the mitochondrial genome and sex chromosomes in the expression of fertility traits and energy metabolism, currently they are not considered in French bovine genomic evaluations. This work is aiming to study the genetic variability of the mitochondrial genome and the X and Y chromosomes, to detect genetic polymorphisms, and to characterize their effects on production, reproduction and health traits. Analysis of uniparental transmission patterns revealed a discrepancy between the low diversity of Y-chromosome haplotypes and the large number of mitochondrial lines in many cattle breeds. Identification of carriers of haplogroups whose divergence predates the domestication of taurine cattle has been made at a very low frequency by genotyping. Initial studies have been carried out to estimate the effect of the variants identified on the mitochondrial genome and the Y chromosome on certain traits of interest to the breeding sector. Then, a reverse genetics approach has been applied to use sequence data to detect candidate mutations responsible for defects and mutations that may have an effect on male or female fertility or lead to an X chromosome inactivation bias. In parallel, the genetic mechanism of an X-linked defect responsible for a case of hypohidrotic ectodermal dysplasia was investigated in a Holstein heifer. In conclusion, several lines for future research are proposed to initiate a better consideration of sex chromosomes and the mitochondrial genome in the selection of cattle
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Michaux, Sylvie. "Etude de l'organisation génomique dans le genre brucella : un exemple de bactérie possédant un génome complexe." Montpellier 1, 1995. http://www.theses.fr/1995MON1T026.
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Roewer, Lutz. "Die Haplotypisierung des Y-Chromosoms." Doctoral thesis, Humboldt-Universität zu Berlin, Medizinische Fakultät - Universitätsklinikum Charité, 2001. http://dx.doi.org/10.18452/13744.
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Haploid vererbte Polymorphismen des Y-Chromosoms sind wichtige diagnostische Werkzeuge der forensischen Genetik und verwandter Disziplinen, insbesondere der Anthropologie. Geschlechtsspezifität und uniparentaler Erbgang der Merkmale ermöglichen eine Reihe von Untersuchungen, die mit autosomalen Markern erfolglos bleiben müssen. Kurze tandem-repetitive STR-Sequenzen, die polymorphen Marker der Wahl im forensischen Labor, sind auch auf dem Y-Chromosom nachzuweisen. Aufgrund der rekombinationsfreien, paternalen Vererbung des größten Teils des Y-Chromosoms werden locus-spezifische Allele hier en bloc, als hochinformativer Haplotyp, vererbt. Die forensische Untersuchung profitiert insbesondere auf dem Gebiet der Untersuchung biologischer Spuren von der Y-chromosomalen Diagnostik: vor allem in Vergewaltigungsfällen kann die männliche DNA-Fraktion der Abstrichpräparate unabhängig von der weiblichen des Opfers untersucht und individualisiert werden. Bei der Abstammungsuntersuchung wird in solchen Fällen die Y-chromosomale Analyse empfohlen, in denen der Vater (eines männlichen Kindes) nicht zur Verfügung steht und paternale Verwandte an seiner statt untersucht werden müssen. Von den 14 evaluierten Y-chromosomalen STR-Systemen sind 9 für die forensische Praxis ausgewählt und empfohlen worden. Sie bilden den sogenannten "minimal haplotype", der heute international für die o. g. Analysen verwendet und von der zuständigen Fachgesellschaft (International Society of Forensic Genetics) in ihren Richtlinien empfohlen wird. Wegen der immensen Haplotyp-Variabilität und des uniparentalen Erbgangs ist die Frequenzbestimmung, und damit die Entscheidungsfindung für rechtsmedizinische Gutachter, nur über den Zugang zu großen Datenbanken möglich. Zu diesem Zweck wurde an der Charité die "European Y-STR Haplotype Reference Database" eingerichtet, die Frequenzabfragen auf Grundlage des aktuellen Datenmaterials online ermöglicht (http://ystr.charite.de). Aufgrund des uniparentalen Erbmodus und der im Vergleich zu Autosomen verringerten effektiven Zahl von Y-Chromosomen in der Population muß mit einem meßbaren Einfluß genetischer Drift auf die Y-STR-Haplotyp-Verteilung in der Population gerechnet werden. Mit Hilfe der AMOVA (Analysis of Molecular Variance) - Methode konnten genetische Distanzen für eine repräsentative Auswahl von über 50 weltweit verteilter Populationen berechnet werden. Der AMOVA-Test ist unentbehrlich für die Überprüfung der Eignung von Referenzdatenbanken als Grundlage der Frequenzbestimmung von Y-STR-Haplotypen.<br>There are a number of merits that qualify the Y chromosome as a special forensic genetic tool: the male specificity for most of its length, the absence of recombination which provides unambiguous male lineage's and the small effective population size that tends to create population specific allele distributions of the Y chromosomes. Particularly in cases of rape and other sexual assault as well as in kinship testing, Y-STR haplotyping can help to close informativity gaps. Since the main goal of forensic genetics is individualization of persons or lineages of descent an analytical strategy for the male chromosome must enable the expert to differentiate between the majority of unrelated haplotypes. For this to achieve the choice of the sequence type and its variability (i.e. its mutation rate) as well as the number of individual sequences to be used for profiling is crucial. We have introduced a STR profile for the Y-chromosome consisting of 11 microsatellite sequences which is both informative for individualization purposes as well as for a genetic distance analysis of populations. The technical simplicity of the approach led to a rapid introduction of the technique in many of the forensic labs world-wide. Intense international collaboration facilitates the generation of large haplotype reference databases, most of them are online available and searchable (Europe: http://ystr.charite.de and USA: http://www.ystr.org/usa/). By use of haplotype specific parameters such as the molecular distance (which equals the minimum number of mutational steps separating two haplotypes) and the largest available haplotype databases a Bayesian approach to evaluate Y-STR haplotype matches has been proposed. Directly inspired by our work are the recommendations of the International Society of Forensic Genetics (ISFG). These guidelines state some basic principles on forensic analysis using Y-STR polymorphisms: the use of sequenced allelic ladders, the application of a repeat-based nomenclature and the use of suitable haplotype reference databases for statistical evaluation of matches. Still a matter of research , but of the utmost interest is the potential of the Y-chromosome analysis to unravel the ethnological background of a given male profile. A dual approach - that using Y-STRs as well as Y-SNPs - probably renders the maximum amount of information about the descent of a male lineage typed in a forensic specimen.
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Moisan, Jean-Paul. "Etude et caracterisation de marqueurs genetiques specifiques du chromosome x humain (suivi de) etude des rearrangements du recepteur a l'antigene, sur des lymphocites t actives in vivo." Université Louis Pasteur (Strasbourg) (1971-2008), 1987. http://www.theses.fr/1987STR13231.
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Jutier, David. "Système Sex-Ratio chez Drosophila simulans : histoire et polymorphisme du chromosome Y." Paris 6, 2004. http://www.theses.fr/2004PA066172.
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Johnson, Andrew Danner. "Search for functional alleles in the human genome with focus on cardiovascular disease candidate genes." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1187018497.
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Varzari, Alexander. "Population History of the Dniester-Carpathians: evidence from Alu insertion and Y-chromosome polymorphisms." Diss., [S.l.] : [s.n.], 2006. http://edoc.ub.uni-muenchen.de/archive/00005868.
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