This thesis details the development of two computational tools, Telomerecat and Parabam, as well as their applications to whole genome sequencing (WGS) data. Telomerecat is a tool for estimating telomere length from WGS data. The strength of Telomerecat lies in its applicability. This applicability is due to a number of advantages over previous attempts to estimate telomere length from WGS. Chief amongst these advantages is that it makes no assumption about the underlying chromosome count or size of the genome within input samples. This means that Telomerecat lends itself well to analysing cancer samples where such assumptions are unfounded. This also means it is applicable to non-human samples, a first for tools of its kind. Furthermore, a novel method for filtering reads derived from interstitial telomere sequences means that it does not rely on previously applied analyses, a source of bias. The other tool described in this thesis is Parabam. Parabam is the first tool of its kind to allow users to apply a function to all of the reads in sequence alignment files, in parallel. Furthermore, Parabam includes a novel method for iterating over index sorted sequence files as if they were name sorted. We provide evidence that Parabam is a quicker way to create complex subsets and statistics from sequence alignment files. In the latter half of the thesis we detail two applications of Telomerecat to large scale WGS projects. The first application, to the Prostate ICGC UK cohort, unveils hitherto uncovered associations between telomere length and previously identified molecular subtypes as well as cancer stage. In the second application, to the NIHR BioResource - Rare Disease cohort, we discover a previously unidentified variant in DKC1 that we propose is directly linked to short telomeres and an immunodeficient phenotype.

Made available in DSpace on 2015-03-03T11:52:21Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-07-31Bitstream added on 2015-03-03T12:07:27Z : No. of bitstreams: 1 000808184.pdf: 1760486 bytes, checksum: d17168b15a06e6e493f69355772eb43c (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Foram sintetizados os compostos de fórmula geral LnL3nH2O, no estado sólido, onde Ln representa lantânio, lantanídeos e ítrio, L é o naproxeno e n+0 (Dy), 1 (La, Ce, Pr, Nd, Sm, Eu, Gd e Tb) e 2 (Ho, Er, Tm, Yb, Lu e Y). Os compostos foram caracterizados por termogravimetria/análise térmica diferencial (TG-DTA), calorimetria exploratória diferencial (DSC), difratometria de raios X pelo método do pó (XRD), espectroscopia de absorção na região do infravermelho (IR) e complexometria com EDTA. As curvas TG-DTA e DSC forneceram informações com relaçao ao comportamento térmico dos compostos e a decomposição dos compostos sintetizados. Os complexos de La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu e Y são termicamente estáveis até 227, 165, 221, 251, 248, 228, 249, 254, 240, 268, 260, 255, 263, 248, 255ºC, respectivamente. Os dados da espectroscopia de absorção na região do infravermelho sugerem uma coordenação bidentada entre o ligante e o íon metálico para os complexos de La, Ce, Pr, Nd, Sm, Eu, Gd, Tb e Dy, e uma coordenação bidentada e em ponte para os complexos de Ho, Er, Tm, Yb, Lu e Y. A utilização conjunta das técnicas IR, XRD e TG-DTA permitiu dividir os complexos em três grupos, de acordo com a quantidade de moléculas de águas presentes, com os complexos de cada grupo, isomórficos entre si. O DSC cíclico e o XRD com aquecimento mostrou que os complexos apresentam diversas transições cristalinas entre suas formas polimórficas / Solid-state compounds with general formula LnL3nH2O, in wich Ln represents lanthanum, lanthanides and yttrium, L is naproxen, and n + 0 (Dy), 1 (La, Ce, Pr, Nd, Sm, Eu, Gd e Tb) and 2 (Ho, Er, Tm, Yb, Lu e Y) were synthesized Simultaneous thermogravimetry-differential thermal analysis (TG-DTA), differential scanning calorimetry (DSC), X-ray powder diffractometry (XRD), infrared spectroscopy (IR) and EDTA complexometry were employed to characterize these compounds. The TG-DTA and DSC curves provided information concerning the thermal behaviour and thermal decomposition of synthesized compounds. La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu and Y complexes are thermally stable until 227, 221, 251, 248, 249, 254, 240, 268, 260, 255, 263, 248 and 255ºC, respectively. The infrared spectroscopic data suggested a bidented coordination between the ligand and the metal ion to the La, Ce, Pr, Nd, Sm, Eu, Gd, Tb and Dy complexes, and a bidented and bridge coordination to the Ho, Er, Tm, Yb, Lu and Y complexes. From IR, XRD and TG-DTA techniques allowed to divide the complexes in three groups, according to the number of water molecules, with the complexes of each group, isomorphics. Cyclic DSC and heated XRD show that complexes present various crystalline transitions between polymorphics forms

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