Statistical assessment of somatic mutations and genomic variability using DNA sequence data

The development of new DNA sequencing techniques have made it possible to generate high-resolution genomic data at an unprecedented pace. However, the high dimensionality in combination with the substantial levels of technical errors and biological variability make the analysis challenging. Tailored statistical methods need therefore to be developed and applied in order to facilitate correct biological interpretation. The first two papers in this thesis are focused on finding tumor-specific (somatic) mutations in cancer, while in the third paper a new method to assess genomic variability in microbial communities is developed. In paper I, the aim was to characterize somatic mutations in pheochromocytoma/paraganglioma, and to identify mutations that contribute to malignancy. Statistical analysis of exome sequencing data from nine replicated paired normal--tumor samples revealed 225 unique somatic mutations. A significantly higher rate of mutations was found in malignant compared to benign tumors. In addition, three genes with recurrent somatic mutations, exclusively located in malignant tumors, were identified. In paper II, exome sequencing data was used to detect somatic mutations in 17 patients with acute myeloid leukemia. The identified mutations were evaluated as markers in a more sensitive analysis of remaining cancer cell levels after treatment. All but one of the studied patients were found to have potential markers in their somatic mutation profiles. In paper III, a hierarchical Bayesian model for detecting genetic differences on nucleotide level between groups of microbial communities is proposed. The model is based on a Dirichlet-multinomial distribution and takes both within- and between-sample variability into account. The evaluation of the performance show that the model has a high sensitivity and maintains a low false positive rate even when the between-sample variability is high. The thesis demonstrates the importance of dedicated statistical analysis and understanding of the error structure in DNA sequence data, in order to assure accurate identification of mutations and differences in genomic variability

Statistical assessment of genomic variability in tumours and bacterial communities

Current high-throughput DNA sequencing technologies have the ability to generate large amounts of high-resolution genomic data. The high dimensionality in combination with the substantial levels of technical errors and biological variability typically present in the data make, however, the analysis challenging. Tailored statistical methods are therefore crucial for reaching valid biological conclusions. In this thesis, such methods were developed and applied to address research questions in biology and medicine.First, a method for identification of tumour-specific (somatic) mutations was developed, which included steps for noise-reduction, sensitive detection of\ua0 DNA alterations and removal of systematic errors. In Paper I, the method was applied to exome-sequenced paired normal–tumour samples from pheochromocytoma patients. A significantly higher mutation rate was found in malignant compared to benign tumours and three genes with recurrent somatic mutations, exclusively located in malignant tumours, were identified. In paper II and III, somatic mutations were identified in patients with acute myeloid leukemia and evaluated as biomarkers in personalised deep sequencing analysis of remaining cancer cells after treatment. In paper III, a statistical model correcting for position-specific errors in the data was developed and shown to provide superior sensitivity compared to standard techniques. In paper IV, clinically relevant molecular subgroups of metastatic small intestinal neuroendocrine tumours were identified based on miRNA gene expression profiles. Survival analysis and subsequent validation suggested miR-375 as a prognostic biomarker. In paper V, a hierarchical Bayesian model for detecting differences on nucleotide level between microbial communities is proposed. By including between-sample variability and utilizing a shrinkage approach, the model was able to perform well both in cases of few samples and high biological variability. Finally, the model was used to detect antibiotic resistance mutations in bacteria.This thesis demonstrates that dedicated statistical analysis and knowledge of the underlying error structure present in high-dimensional biological data is of importance for enabling accurate interpretation and sound conclusions

Creating Novel Product Form Based on Formal Aesthetics – A Method for Advanced Form Design Education

One of the most distinct aspects of creativity in design is an aesthetic sense, an indubitable determinant of product success in the market. It is therefore of great importance to nurture creativity in terms of formal aesthetics in design education. However, the focus of design education has shifted away from product form and instead towards user-centred design (UCD) practices. An intrinsic challenge in the tradition of user-centred design is that it initiates creating products from the definition of some user needs, educing design solutions that are, to some extent, already known by the user, as familiarity factors are favoured. In our research, we turn the established UCD process around and propose an approach for exploring and creating novel product form with a focus on formal aesthetics. This paper elaborates on the Formal Aesthetics Design Approach that has been explored during a three-year case study, performed within a Masters programme in Industrial Design Engineering. A deep exploration of aesthetic form opportunities, consciously without any respect to user demands, was carried out by a structured five-step method. There was no ‘given’ or predefined aim for the form design process, which lead to a creative and experimental yet structured generation of formal solutions beyond the functionality of use. Hence, a variety of novel and unexpected form ideas emerged, broadening the morphological form repertoire as a result of the suggested method of work. This research illustrates benefits offered by applying a formal aesthetic design approach as a creative form generation process in design education

Optical properties of carbon nanofiber photonic crystals

Carbon nanofibers (CNF) are used as components of planar photonic crystals. Square and rectangular lattices and random patterns of vertically aligned CNF were fabricated and their properties studied using ellipsometry. We show that detailed information such as symmetry directions and the band structure of these novel materials can be extracted from considerations of the polarization state in the specular beam. The refractive index of the individual nanofibers was found to be n_CNF = 4.1.Comment: 10 pages, 4 figure

SMAD4 haploinsufficiency in small intestinal neuroendocrine tumors

Background: Patients with small intestinal neuroendocrine tumors (SINETs) frequently present with lymph node and liver metastases at the time of diagnosis, but the molecular changes that lead to the progression of these tumors are largely unknown. Sequencing studies have only identified recurrent point mutations at low frequencies with CDKN1B being the most common harboring heterozygous mutations in less than 10% of all tumors. Although SINETs are genetically stable tumors with a low frequency of point mutations and indels, they often harbor recurrent hemizygous copy number alterations (CNAs) yet the functional implications of these CNA are unclear. Methods: Utilizing comparative genomic hybridization (CGH) arrays we analyzed the CNA profile of 131 SINETs from 117 patients. Two tumor suppressor genes and corresponding proteins i.e. SMAD4, and CDKN1B, were further characterized using a tissue microarray (TMA) with 846 SINETs. Immunohistochemistry (IHC) was used to quantify protein expression in TMA samples and this was correlated with chromosome number evaluated with fluorescent in-situ hybridization (FISH). Intestinal tissue from a Smad4+/− mouse model was used to detect entero-endocrine cell hyperplasia with IHC. Results: Analyzing the CGH arrays we found loss of chromosome 18q and SMAD4 in 71% of SINETs and that focal loss of chromosome 12 affecting the CDKN1B was present in 9.4% of SINETs. No homozygous loss of chromosome 18 was detected. Hemizygous loss of SMAD4, but not CDKN1B, significantly correlated with reduced protein levels but hemizygous loss of SMAD4 did not induce entero-endocrine cell hyperplasia in the Smad4+/− mouse model. In addition, patients with low SMAD4 protein expression in primary tumors more often presented with metastatic disease. Conclusions: Hemizygous loss of chromosome 18q and the SMAD4 gene is the most common genetic event in SINETs and our results suggests that this could influence SMAD4 protein expression and spread of metastases. Although SMAD4 haploinsufficiency alone did not induce tumor initiation, loss of chromosome 18 could represent an evolutionary advantage in SINETs explaining the high prevalence of this aberration. Functional consequences of reduced SMAD4 protein levels could hypothetically be a potential mechanism as to why loss of chromosome 18 appears to be clonally selected in SINETs

Electromechanically tunable carbon nanofiber photonic crystal

We demonstrate an electrically tunable 2D photonic crystal array constructed from vertically aligned carbon nanofibers. The nanofibers are actuated by applying a voltage between adjacent carbon nanofiber pairs grown directly on metal electrodes, thus dynamically changing the form factor of the photonic crystal lattice. The change in optical properties is characterized using optical diffraction and ellipsometry. The experimental results are shown to be in agreement with theoretical predictions and provide a proof-of-principle for rapidly switchable photonic crystals operating in the visible that can be fabricated using standard nanolithography techniques combined with plasma CVD growth of the nanofibers

Diffraction from carbon nanofiber arrays

We fabricate a square planar photonic crystal (PC) from carbon nanofibres (CNFs) using e-beam lithography and chemical vapour deposition and investigate the optical properties of this system. The system exhibit diffraction that is well described by diffraction theory. We measure the intensity of the (-1,0) and (-1,-1) diffraction spots as functions of angle of incidence. The radiation diagram obtained can be explained by interference between different diffraction beams. We observe a polarisation dependence of the intensity. In conclusion we suggest future applications of these structures

Säkert sittande - Ett produktutvecklingsprojekt mot Innovationsslussen i Västra Götaland

A thesis directed towards Innovationsslussen in Gothenburg about securing, improving and simplifying sitting on the toilet for patients with sitting difficulties. The primary target group for the project is patients who have had a stroke and as a consequence from that suffers from various kind of bodily paralysis. An overall goal was to design an aid that was comprehensive enough that the patient could manage sitting securely on the toilet without have a nurse giving physical support during defecation. Five conceptual proposals were developed and evaluated in consultation with Innovationsslussen and one was selected to be further developed. The result was an integrated support at the toilet that facilitates a good sitting posture which minimizes the risk of falling and provides comfortable support when leaning to the side. The product is divided in two with both a redesigned carryingsystem and a new type of support surface adapted for the purpose

Load Optimization in Reverberation Chambers

Optimal loading conditions of a reverberation chamber were investigated. The relevant figure of merit is discussed and defined. Multiple loading configurations were tested and results are reported. A simple model of how loading affects measurement uncertainty was developed and used to find a loading configuration that vastly improve results with regards to the defined figure of merit compared to other configurations

Tunable photonic crystals based on carbon nanofibers

Photonic crystals are materials with periodically varying refractive indices. In conventional photonic crystal design it is hard to achieve tunable structures in the visible range, i.e. structures with changeable optical properties.Carbon nanofibers have dimensions similar to multi-walled carbon nanotubes, but have the advantage that they can be fabricated vertically free-standing. In this thesis the possibility to use carbon nanofibers as the basic building block for tunable two-dimensional photonic crystals is investigated. By growing nanofibers in a lattice pattern and keeping neighbouring fibers at different electrostatic potentials, the nanofibers can be bent electrostatically. This changes the lattice, which in turn modifies the optical properties of the photonic crystal.A finite-difference time-domain method was used to model a photonic crystal with a changeable basis. It was shown that the optical transmission through a photonic crystal slab can, at a certain frequency, be switched from almost 100% to approximately 1% with only a few rows of nanofibers in the light propagation direction. It was shown that many features in the transmission can be attributed to changes in the bandstructure.Both static and tunable carbon nanofiber photonic crystals were fabricated using catalytic DC plasma enhanced chemical vapour deposition. An optical measurement set-up was developed and used for investigating diffraction from the samples. Samples were also investigated using ellipsometry.It was found that ellipsometry is a powerful tool for probing the band structure of 2D photonic crystal slabs. The intensity variations in diffracted beams, as functions of incidence angle, were measured and verified against theory. It was possible to detect carbon nanofiber actuation using both methods on the tunable samples and results are compared to theoretical expectations. The results from static and tunable structures are compared