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When processing a trace DNA sample at the Netherlands Forensic Institute, an STR electropherogram can be created. An analyst uses this electropherogram and analysis software to read out peaks signifying DNA. After analysis, the DNA profile is used in the interpretation process, which can include the comparison to a reference DNA profile of a person of interest. The software that is currently being used for profile analysis is threshold-based and the process includes the intervention of trained analysts. To further automate (allelic) peak identification in STR electropherograms, as well as to increase efficiency and uniformity, neural networks were studied and applied. Previous work by Duncan Taylor and David Powers provided a proof of concept using a simple fully connected neural net. After reviewing literature, the U-net was selected to be used in this thesis. Training U-net on electropherograms proved successful and achieved a 95% accuracy on the per-pixel labels. However, translating the per-pixel output to alleles was more difficult than expected, so an upper bound on the score was calculated. The upper bound got close to an analyst’s performance and demonstrated the potential of this method., Applied Mathematics | Optimization

When processing a trace DNA sample at the Netherlands Forensic Institute, an STR electropherogram can be created. An analyst uses this electropherogram and analysis software to read out peaks signifying DNA. After analysis, the DNA profile is used in the interpretation process, which can include the comparison to a reference DNA profile of a person of interest. The software that is currently being used for profile analysis is threshold-based and the process includes the intervention of trained analysts. To further automate (allelic) peak identification in STR electropherograms, as well as to increase efficiency and uniformity, neural networks were studied and applied. Previous work by Duncan Taylor and David Powers provided a proof of concept using a simple fully connected neural net. After reviewing literature, the U-net was selected to be used in this thesis. Training U-net on electropherograms proved successful and achieved a 95% accuracy on the per-pixel labels. However, translating the per-pixel output to alleles was more difficult than expected, so an upper bound on the score was calculated. The upper bound got close to an analyst’s performance and demonstrated the potential of this method., Applied Mathematics | Optimization

[Resumen]: Las mitocondrias son orgánulos intracelulares, y es el lugar donde tiene lugar la fosforilación oxidativa, a través de la cual se produce energía celular en forma de adenosina trifosfato (ATP). Estos orgánulos tienen su propio genoma constituido por genes que codifican para ARNs ribosomales (ARNr), ARNs de transferencia (ARNt), y proteínas de la cadena respiratoria y proteínas ribosomales. Drosophila melanogaster se ha utilizado como modelo animal para comprender la biología de distintas enfermedades mitocondriales relacionadas con el genoma mitocondrial, y, además, secuencias del ADN mitocondrial (ADNmt) se han usado para establecer relaciones filogenéticas entre especies próximas de Drosophila y de otros muchos géneros del reino animal. En el presente trabajo hemos amplificado mediante la reacción en cadena de la polimerasa (PCR) fragmentos del ADNmt de D. buzzatii B6 (salvaje) y D. buzzatii white (mutante), y se secuenciaron 6 fragmentos de ADNmt. Utilizando el software Ugene hemos realizado un alineamiento múltiple de secuencias con una secuencia de referencia consenso del genoma mitocondrial de Drosophila buzzatii. Los datos indican discrepancias entre las secuencias amplificadas y la secuencia de referencia, la mayor parte de los cambios son sustituciones, de las cuales, la mayoría son transiciones y también se observan transversiones y deficiencias. Hay estudios que muestran que alteraciones puntuales en el ADNmt de Drosophila tienen un efecto en el fenotipo de los individuos y en la biología mitocondrial. Sería necesario realizar más investigaciones para saber si los cambios que hemos detectado entre los fragmentos de ADNmt y la secuencia de referencia tienen algún efecto a nivel mitocondrial en Drosophila buzzatii., [Resumo]: As mitocondrias son orgánulos intracelulares e é o lugar onde ten lugar a fosforilación oxidativa, a través da cal prodúcese enerxía celular en forma de adenosin trifosfato (ATP). Estes orgánulos teñen un xenoma propio composto por xenes que codifican os ARN ribosómicos (ARNr), os ARN de transferencia (ARNt) e as proteínas da cadea respiratoria e as proteínas ribosómicas. Drosophila melanogaster usouse como modelo animal para comprender a bioloxía de diferentes enfermidades mitocondriales relacionadas co xenoma mitocondrial e, ademais, usáronse secuencias de ADNmt para establecer relacións filoxenéticas entre especies próximas de Drosophila e de outros moitos xéneros do reino animal. No presente traballo, amplificamos mediante a reacción en cadea da polimerasa (PCR) fragmentos de ADNmt de D. buzzatii B6 (salvaje) y D. buzzatii white (mutante), e se secuenciaron 6 fragmentos de ADNmt. Usando o software Ugene, realizamos unha aliñación de secuencias múltiples cunha secuencia de referencia do xenoma mitocondrial de Drosophila buzzatii. Os datos indican discrepancias entre as secuencias amplificadas e a secuencia de referencia, a maioría das modificacións son substitucións, e a maior parte delas son transicións, tamén se observan transversións e deficiencias. Outros estudos demostraron que os cambios puntuais no ADNmt de Drosophila teñen un efecto sobre o fenotipo de individuos e na bioloxía mitocondrial. Será necesario máis investigación para ver se os cambios detectados entre os fragmentos de ADNmt e a secuencia de referencia teñen algún efecto a nivel mitocondrial en Drosophila buzzatii., [Abstract]: Mitochondria are intracellular organelles, where oxidative phosphorylation takes place, through which cellular energy is produced in the form of adenosine triphosphate (ATP). These organelles have their own genome consisting of genes that code for ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and respiratory chain proteins and ribosomal proteins. Drosophila melanogaster has been used as an animal model to understand the biology of different mitochondrial diseases related to the mitochondrial genome. Additionally, mtDNA sequences have been used to establish phylogenetic relationships among closely related animal species. In the present work, we have amplified by PCR (polymerase chain reaction) several fragments of mtDNA of D. buzzatii B6 (wild type) and D. buzzatii white (mutant), and 6 fragments were sequenced. Using the Ugene software, we have performed a multiple sequence alignment with a reference sequence of the Drosophila buzzatii mitochondrial genome. The data indicates discrepancies between the amplified sequences and the reference sequence, most of the changes are substitutions, and most of them are transitions, and transversions, and deletions are also observed. Other studies have shown that point changes in Drosophila mtDNA have an effect on the phenotype of individuals and on mitochondrial biology. More research would be required to see if the changes we have detected between the mtDNA fragments and the reference sequence could have any effect at the mitochondrial level in Drosophila buzzatii.