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Process analysis and implementation of tools for forensic genetic genealogy
Černohousová, Zuzana ; Hoksza, David (advisor) ; Stenzl, Vlastimil (referee)
Forensic genetic genealogy is a new discipline that has seen a boom since the year 2018 when it was used to identify the Golden State Killer in the American State of California. Forensic genetic genealogy uses commercial genetic genealogy databases which today contain tens of millions of SNP profiles of people from all around the world, who use these services to connect with their unknown relatives. Each SNP profile consists of circa 650 000 loci which makes it possible not only to predict degrees of relationship between pairs of individuals but also to identify genomic segments that have been passed to the pair from their common ancestor. Since 2018, forensic genetic genealogy has routinely been used in the United States to identify unidentified remains or perpetrators of violent crimes and its introduction is also being considered in some European countries. The Czech Republic is one of those countries as the Institute of Criminalistics intends to create its own SNP profile database and implement its own genetic genealogy tools for forensic use. This thesis aims to map the issue of (forensic) genetic genealogy and describe it in such a way as to provide the reader with an understanding of the topic. Another part of this thesis is to create a basic framework for genetic genealogy data management...
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Y Chromosomal Characteristics of the Modern Rural Population in Klatovy Region
Doležalová, Veronika ; Ehler, Edvard (advisor) ; Stenzl, Vlastimil (referee)
Usage of genetic markers in non-recombining part of chromosome Y has been shown as a eligible tool for a study of history, diversity and migration of population. Applicable markers of chromosome Y are SNP and STR polymorphisms. There were collected 53 unique samples of DNA as a object of this work from unrelated origin males from 9 villages around Klatovy. Samples have been analyzed and its values have been determined by using the 17 STR markers by AmpFLSTR® Yfiler® Direct Kit. In total I have observed 7 different haplogroups. I have resulted samples from villages around Klatovy and they were analyzed by AMOVA. I have compared samples with the surrounding populations in neighborly Federal Republic of Germany, Austria, Central and South Bohemia. There were no significant differences founded in the genetic profile of this population to the surrounding populations.
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Forensic SNP identification of trichological material by High Resolution Melting analysis
Strobachová, Joanne ; Stenzl, Vlastimil (advisor) ; Korabečná, Marie (referee)
The analysis of mitochondrial DNA (mtDNA) from shed hairs has gained high importance in forensic casework since telogen hairs are one of the common type of evidence left at the crime scene. This type of evidence very often lack of nuclear DNA (nDNA), so the analysis of mtDNA is the only possibility. The analysis of trichological material lacking nDNA is not commonly done in the forensic practice because of the high price of the regularly used mtDNA analysis method, as well as the time demandingness. For these reasons we decided to analyze the mtDNA and identify the trichological material by analysis of chosen single based polymorphism's (SNP) followed by High Resolution Melting (HRM). In order to verify the robustness of the HRM analysis method on several types of biological material that belongs to one person, we tested trichological material in anagen and telogen. From total number of 5 selected SNP's, this paper was able to optimize analysis of 3 SNP's. Due to the analysis of SNP C14766T (applicable for the trichological material in anagen and telogen), SNPs C7028T and G3010A (applicable only for the trichological material in anagen). The mtDNA sequences of different biological materials did not show intra-individual differences. Protocol that could be used for the forensic practice with the use...
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Using of quantitative DNA method as a screening tool for effecient genotyping of samples in forensic DNA laboratory.
Koljenšič, Ivana ; Stenzl, Vlastimil (advisor) ; Daňková, Pavlína (referee)
Quantification of human DNA in forensic samples is an important step during STR profiling because the STR genotyping is sensitive to the quantity of DNA used in the PCR reaction. This study focuses on the importance of quantification in the entire process of genetic analysis. Two real time PCR platforms (Roche LightCycler480 System and ABI 7900 RT PCR) were used to compare two commercial kits in terms of DNA quantification. It was found out that accuracy of absolute quantification values in commercial quantification kits is strongly dependent on the construction of calibration curve. Especially low template DNA samples were used to assess whether QuantifilerTM or Plexor® HY System can determinate a minimum quantification value (cut off value) below which STR profiles would consistently fail to be detected. The usage of Plexor® HY System enabled to determine the cut off quantification value more exactly probably due to different molecular background and chemistry used in this kit. Reliability and other issues connected with cut off value are discussed. In order to better understand the relationship between the quantity of DNA and the number of detectable loci series the dilution experiment with standard DNA007 was done. Quantitative and qualitative consequences of input DNA amount in evaluation of...
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Y Chromosomal Characteristics of the Modern Rural Population in Klatovy Region
Doležalová, Veronika ; Ehler, Edvard (advisor) ; Stenzl, Vlastimil (referee)
Usage of genetic markers in non-recombining part of chromosome Y has been shown as a eligible tool for a study of history, diversity and migration of population. Applicable markers of chromosome Y are SNP and STR polymorphisms. There were collected 53 unique samples of DNA as a object of this work from unrelated origin males from 9 villages around Klatovy. Samples have been analyzed and its values have been determined by using the 17 STR markers by AmpFLSTR® Yfiler® Direct Kit. In total I have observed 7 different haplogroups. I have resulted samples from villages around Klatovy and they were analyzed by AMOVA. I have compared samples with the surrounding populations in neighborly Federal Republic of Germany, Austria, Central and South Bohemia. There were no significant differences founded in the genetic profile of this population to the surrounding populations.
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Forensic SNP identification of trichological material by High Resolution Melting analysis
Strobachová, Joanne ; Stenzl, Vlastimil (advisor) ; Korabečná, Marie (referee)
The analysis of mitochondrial DNA (mtDNA) from shed hairs has gained high importance in forensic casework since telogen hairs are one of the common type of evidence left at the crime scene. This type of evidence very often lack of nuclear DNA (nDNA), so the identification based on the STR analysis is not possible. The analysis of trichological material lacking nDNA is not a commonly used method of the forensic praxis because of the high price of the regularly used mtDNA analysis method, as well as the time demandingness. Based on this, the main goal of this work is to establish a relatively fast, easy and cheap method able to analyze trichological material lacking of nDNA. For these reasons we decided to analyze the mtDNA and identify the trichological material by analysis of chosen SNP's followed by High Resolution Melting. We have analyzed 12 series of different biological materials that belongs to one person (e.g. buccal cells, trichological material in anagen - head, axillary and pubic hair shafts) in order to confirm the identity of mtDNA isolated from different type of biological materials. We have analyzed several set's of buccal cells and head hair shafts in telogen from 17 specimens. From total number of 5 selected SNP's, this essay was able to optimize analysis of 3 SNP's. Due to the...
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Forensic SNP identification of trichological material by High Resolution Melting analysis
Strobachová, Joanne ; Stenzl, Vlastimil (advisor) ; Korabečná, Marie (referee)
The analysis of mitochondrial DNA (mtDNA) from shed hairs has gained high importance in forensic casework since telogen hairs are one of the common type of evidence left at the crime scene. This type of evidence very often lack of nuclear DNA (nDNA), so the analysis of mtDNA is the only possibility. The analysis of trichological material lacking nDNA is not commonly done in the forensic practice because of the high price of the regularly used mtDNA analysis method, as well as the time demandingness. For these reasons we decided to analyze the mtDNA and identify the trichological material by analysis of chosen single based polymorphism's (SNP) followed by High Resolution Melting (HRM). In order to verify the robustness of the HRM analysis method on several types of biological material that belongs to one person, we tested trichological material in anagen and telogen. From total number of 5 selected SNP's, this paper was able to optimize analysis of 3 SNP's. Due to the analysis of SNP C14766T (applicable for the trichological material in anagen and telogen), SNPs C7028T and G3010A (applicable only for the trichological material in anagen). The mtDNA sequences of different biological materials did not show intra-individual differences. Protocol that could be used for the forensic practice with the use...
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Using of quantitative DNA method as a screening tool for effecient genotyping of samples in forensic DNA laboratory.
Koljenšič, Ivana ; Stenzl, Vlastimil (advisor) ; Daňková, Pavlína (referee)
Quantification of human DNA in forensic samples is an important step during STR profiling because the STR genotyping is sensitive to the quantity of DNA used in the PCR reaction. This study focuses on the importance of quantification in the entire process of genetic analysis. Two real time PCR platforms (Roche LightCycler480 System and ABI 7900 RT PCR) were used to compare two commercial kits in terms of DNA quantification. It was found out that accuracy of absolute quantification values in commercial quantification kits is strongly dependent on the construction of calibration curve. Especially low template DNA samples were used to assess whether QuantifilerTM or Plexor® HY System can determinate a minimum quantification value (cut off value) below which STR profiles would consistently fail to be detected. The usage of Plexor® HY System enabled to determine the cut off quantification value more exactly probably due to different molecular background and chemistry used in this kit. Reliability and other issues connected with cut off value are discussed. In order to better understand the relationship between the quantity of DNA and the number of detectable loci series the dilution experiment with standard DNA007 was done. Quantitative and qualitative consequences of input DNA amount in evaluation of...
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