"An ‘exponential growth of science’ throughout modern history has been frequently boasted by numerous narcissistic accounts of ‘modern humanity.’ Nonetheless, ‘modern science’ seems to have overwhelmingly compromised on its original promises by fitting into an ‘industrial scheme.’ With this concern, ‘molecular phylogeographics with conservational ambitions’ would look an intact ground for research efforts in a ‘school of biotechnology.’ The dog (Canis familiaris) as an earliest domestic animal has a history of conflicts over its origins and dispersal. Having those disputes addressed, valuable knowledge could be acquired on the nature and dynamics of domestication, and of human societies particularly of pre-agricultural ages. We employed two most widely-used genealogical markers, the mitochondrial DNA (mtDNA) and the non-recombining portion of the Y-chromosome (NRY), to address dog demography. Through 582 bps of mtDNA Control Region, complemented with whole mitochondrial genomes, it was established that almost all maternal lineages of the domestic dog worldwide coalesce to a population of at least 51 and perhaps many more female wolves in Asia South of Yangtze River (ASY) approximately 16,000 years before present (BP). This was based on the presence of a maximal diversity in this area, a descending gradient of diversity outward it, and a ubiquitous population structure everywhere in the world. A closer examination of this portrait in Southwest Asia (SwAsia) and the Fertile Crescent (FC), a region which has supplied persuasive evidence on early presence of the domestic dog, retrieved the same information, with implications for backbreeding with the local wolf population. Meanwhile, analyses of mtDNA dispersal showed that dogs took the long way via land to Madagascar Island, and not together with humans via sea. By the other approach, the NRY data in 14,437 bps length supplemented the mtDNA in reporting the height of diversity from ASY with a founding population of at least 13 male wolves, but expectably produced lower inter-regional differentiation by diversity. Screening of NRY by a SNP assay in the dingoes of Australia Island as a population of feral dogs revealed restricted and similar dispersal patterns for sires and dams. Prospects of ancient, multilocus and whole genome assays with the emerging high-throughput technologies has still more to promise on finer elaborations of these issues." / <p>QC 20120529</p>

This master thesis was performed at the personal genomics company DNA-Guide Europa AB. The goal was to create DNA tests for drug response and to update the already existing DNA test for autosomal ancestry. The DNA tests for drug response: The objective of this part of the master thesis was to create individual DNA test for response to each drug within different groups of medicines. The tests were meant to interest private customers. DNA-Guide uses a microarray technique for the DNA-analysis and this delimited the choice of SNPs. Inserts, deletions, repeats and copies of a whole gene can be difficult to implement on the microarray chip. The SNPs and studies used as a base for the tests had to fulfil several criteria. The studies must be large enough to prove that the association between the genotype and the response to the drug is valid among Europeans, since it’s the clientele of the company. The found association must also be strong enough to be of interest for a DNA test at DNA-Guide. If the SNPs could be implemented on the microarray chip a customer report was created about the possible results. The report had the same structure and design as those for the existing DNA tests at DNA-Guide. The work resulted in DNA tests and reports for medicines within the seven groups of medicines; anticoagulants, medicine against high cholesterol, blood pressure lowering medicine, asthma inhalers, antidepressants, birth-control pills and antiretroviral drugs. The DNA test for autosomal ancestry: The purpose of the update was to enhance to customers understanding of their results and the construction of the test. The update resulted in a description of how the used algorithm processes the results (from the DNA analysis) and a guide to interpret the results of the test. Conclusions: Both the DNA tests for drug response and the updated DNA test for autosomal ancestry can add value for the customers at DNA-Guide. The DNA tests for drug response can offer an explanation to why a medicine does not have an effect or reveal if the customer has higher risk of adverse effects. Even though recommendations for dosage or treatment could not be provided in almost all of the created DNA tests, being aware of the higher risk can be the first step to avoid adverse effects. The update of the DNA test report for autosomal ancestry resulted in a better description of the algorithm and limitations of the test, which can enhance the customers’ understanding of their results.

ABSTRACT Background: Palindromic rheumatism (PR) is the rare disease that generally occurs with multiple recurring attacks of painful inflammation affecting joints and adjacent tissues. The thesis attempts to characterize the association in 10 instances of the single nucleotide polymorphisms (SNPs) of tumor necrosis factor genes (TNF-£\, TNFRSF1A and TNFRSF1B), Interleukin-1£] genes and Palindromic rheumatism (PR). Methods: The genetic polymorphisms of TNF-£\, TNFR£L, TNFR£S and IL-1£] genes cluster were investigated among 56 PR patients identified from the Kaohsiung Veterans General Hospital (VGHKS, Kaohsiung, Taiwan) and compared with one hundred healthy subjects. The genotypes for ten SNPs in the TNF-£\, TNFRSF1A, TNFRSF1B and IL-1£] genes among these 156 individuals were examined. Results: Experiments indicate significant count of the TNFRSF1A+36 AG genotype in PR patients (OR=4.8, 95%CI=1.8-13.0, p=0.002) and TNFRSF1A+36G allele (OR=3.94, 95%CI=1.59-9.79, p=0.003).The results also have remarkable correlation with TNFRSF1B haplotype +676/+1663 T/A (OR=2.12, CI=1.2-3.8, p=0.010). However, on significant differences were found for all the TNF-£\and IL-1£]polymorphisms. Conclusions: Genetic polymorphisms in TNF-£\ receptors are associated with susceptibility and severity of the inflammatory response in the PR patients.

Osteosarcoma (OS) is a type of cancer that starts in the bone. It generally occurs in the cells called osteoblasts which form matrix of the bone. It is the most common malignant tumor of bone with an incidence rate of 19% among all cancer types. The vast majority of OS patients have pulmonary metastases at the time they are diagnosed, and about half develop lung disease later. Moreover, pulmonary metastatic tumors lead to poor prognosis and increased death rate. Although mutations in the genes coding for p53, Rb, fos and myc were detected in pulmonary metastatic tumors of OS, there is no unique genetic pathway identified for progression of pulmonary metastasis. In this research, a genome wide association study (GWAS) using FFPE samples from lung tissue of 9 patients with pulmonary metastatic OS was performed. Among 358 associated SNPs, rs6499861, rs10884554 and rs12154602 were found to be associated with metastatic OS most significantly. Moreover, second wave analysis of GWAS results provided the significant genes and pathways associated with metastatic OS. A methodology for copy number aberration and LOH analysis of SNP array data of a FFPE sample was generated using R-aroma package. Results were obtained by three different methods, namely, CalMaTe, TumorBoost and Virtual Normal algorithm. Among these, CalMaTe was found to produce less noisy data than VN Algorithm during total copy number segmentation. LOH analysis could only be performed for one sample with the second method due to poor data quality of the other samples. According to the results of copy number aberration and LOH analysis of one tumor sample T8, copy number gains in 1p31.1, 6p21.32, 7p14.3, 11q22.1, 12p12.1, and 18q12.1 chromosomal regions and copy number losses in 2p16.2, 8q24.13, 17q23.3 and 17q21.31 chromosomal regions have been found. Moreover, LOH events were observed in 2q14.3, 11q13.4, 18p11.21, 19q12, 20p13 and 23q21.1 chromosomal regions. Identification associated SNPs and significant copy number changes may be helpful in investigation of potential diagnostic and prognostic markers in metastatic osteosarcoma.

The evaluation of environmental and genotypic effects on fruit physical and chemical characteristics enables assessment of the feasibility of selecting diploid and/or triploid cultivars for either specific or more diverse locations. Isolation and characterization of genes encoding enzymes in the carotenoid biosynthetic pathway provides fundamental genetic information which can facilitate breeding of watermelon cultivars having desirable flesh colors and enhanced beneficial carotenoids. For the environmental studies, the effects of deficit irrigation on lycopene content, total soluble solids, firmness, and yield of diploid and triploid watermelon were evaluated in different locations and growing seasons. Irrigation regimes were 1.0 evapotranspiration (ET), 0.75 ET, and 0.5 ET. To investigate if there is a consistent response in cultivars across diverse locations, studies were conducted in three distinct Texas regions. Deficit irrigation reduced total marketable yield, and increased the yield of small fruits. Location and irrigation regimes had major influences on yield. Soluble solids content increased with deficit irrigation at 0.5 ET in triploids, but not in diploids. Flesh firmness also increased in triploids compared to diploids. Lycopene content increased with maturity at all irrigation regimes and cultivars. This work confirms that deficit irrigation directly reduces yield, but does not reduce lycopene and fruit quality of the triploids used in this study. From the genetic studies, a total of eight genes encoding enzymes in the carotenoid biosynthetic pathway were isolated and characterized. Two members of the phytoene synthase (PSY) gene family were identified; PSY-A was expressed in all type of tissues, but PSY-B transcript was detected only in ovary, leaf, and root tissues. Gene expression of carotenoid isomerase (CRTISO) was not detected in salmon yellow. A color inheritance study of watermelon flesh indicated that a single gene might determine color difference between canary yellow and red without an inhibitory effect. A cleaved amplified polymorphic sequence (CAPS) marker developed from the SNP marker tagging two different lycopene β-cyclase (LCYB) alleles cosegregated perfectly with color phenotypes. It was concluded that color determination may be due to a reduced activity of LCYB enzyme in red, whereby a phenylalanine is conserved among canary yellow and valine is conserved among red watermelon.

Abstract According to recent clinical treatment, doctors give patients medicines based on clinical experience and biochemical data. However, biochemical data simply provides an initial physiology reaction. Although the data is enough for doctors to diagnose diseases, it does not help much for doctors to indicate the most useful medicine. Therefore, doctors will use the first line, cheap or low dose medicine to cure patients by previous clinical experience. It will not only extend the time of treatment but also lower the medical quality. Not to mention the side effects and increases the cost. Consequently, using SNP¡]Single Nucleotide Polymorphism¡^will help doctors to find out different patients¡¦ genotype and forecast the result of medicine. It will control disease efficiently and decrease the medical costs. Methods: This study will be discussed with an accurate test of how to check the genotypes of diabetes mellitus and predict the result of treatment from pharmacogenetic. The method was using PCR (Polymerase Chain Reaction) and RFLP (Restriction Fragment Length Polymorphism) to analyze patients¡¦ different genotype. Besides, this study uses the One-Way ANOVA to interpret the relationship between ABCC8-E16 and type 2 diabetes. In conclusion, the antidiabetic drugs- Sulfonylurea derivatives are suitable for ABCC8-E16 genotype patients. This result can be a reference for doctors to remedy diabetics. It will not only save the cost but also shorten the time of treatment, and it will impact deeply for personalized medicine in the future. type 2 diabetes, Sulfonylurea, SNP, PCR, RFLP, pharmacogenetic, personalized medicine

Purpose¡G Many single nucleotide polymorphisms (SNPs) have been found to be associated with breast cancer but their SNP interactions are seldom addressed. In this study, we focused on the joint effect for SNP combinations of seven CXCL12-related genes involved in major cancer related pathways. Patients and Methods¡G SNP genotyping was determined by PCR-restriction fragment length polymorphism (RFLP) in this study (case = 220, control = 334). Different numbers of combinational SNPs with genotypes called the pseudo-haplotypes from different chromosomes were used to evaluate their joint effect on breast cancer risk. Results¡G Except for VEGF rs3025039-CT, none of these SNPs was found to individually contribute to breast cancer risk. However, for two combined SNPs, the proportion of subjects with breast cancer was significantly low in the pseudo-haplotype with CC-GG genotypes in rs2228014-1801157 (CXCR4-CXCL12) compared to those with non-CC-GG genotypes. Similarly, the pseudo-haplotype of rs12812942-rs2228014-rs3025039 (CD4-CXCR4-CXCL12) And rs12812942-rs3136685-rs2228014 -rs1801157(CD4-CCR7-CXCR4-CXCL12)with specific genotype pattern (AT-CC-CC and AT-AG-CC-GG) among three and four combinational SNPs were significantly low in breast cancer occurrence. More SNP combinations larger than five SNPs were also addressed and shown the similar effect. After controlling for age, comparing to their corresponding non-pseudo-haplotypes, the estimated odds ratios for breast cancer ranged between 0.20 and 0.71 for specific pseudo-haplotypes with two to seven SNPs. Conclusion¡G We have identified the potential combined CXCL12-related SNPs with genotypes that were protective against breast cancer and may have an impact on identification of a low risk population for the development of breast cancer.

<p>Imagine if you could combine the power and capabilities ofan entire laboratory in the palm of your hand. Advances inmicrofluidic chip technology promise to integrate andminiaturize multiple lab processes into a single palm-sizeddevice. The advantages of these lab-on-a-chip devices,sometimes also referred to as micro total analysis systems(µTAS), compared with conventional bench-scale systems arenumerous and wide ranging and include: less reagentconsumption, low manufacturing costs, increased performance,faster analysis, high sample throughput, integration andautomation possibilities, and disposability. However,microfluidic devices also present challenges such as theinterfacing to the macro world and detection limits.</p><p>In this thesis the focus has been to develop novel discretemicrofluidic components for biotechnology and organic chemicalapplications with the goal to integrate them to formlab-on-chips. A flow-through filter-chamber device has beendesigned, manufactured and evaluated for chemical analysis onbeads. Passive liquid handling has been integrated on the chipin the form of hydrophobic valves at the inlet channels. Anarray format has also been developed to allow parallel analysisof multiple samples. The filter-chamber functions well forsingle nucleotide analysis using pyrosequencing. Initialevaluations on catalyst screening in the filter-chamber devicehas been performed.</p><p>The suitability of valve-less micropumps for biochemicalapplications is presented. Fluids encountered in variousbiochemical methods, including living cells, that areproblematic for other micropumps have been pumped with goodperformance. This thesis also introduces expandablemicrospheres as a novel component in microfluidics includingapplications such as one-shot valves, micropositioning andsurface enlargement.</p><p>A novel technique for bead immobilization in microfluidicdevices based on surface chemistry is presented in this thesis.Beads for both biochemical assays and organic chemistry havebeen self-sorted and self-assembled in line patterns as narrowas 5 µm on both structured and unstructured substrates.This method will greatly facilitate the generation of screeningplatforms, for example.</p><p>To develop a microfluidic device for catalysis-on-chip,ligands for asymmetric catalysis have successfully beenimmobilized in silicon channels by consecutive microcontactprinting, which is a novel technique presented in thisthesis.</p><p><b>Keywords:</b>microfluidics, beads, microspheres, silicon,filter-chamber, flow-through, bead trapping, DRIE, passivevalves, fluorocarbon, microfluidic array, adhesive bonding,valve-less micropump, microcontact printing, PDMS,self-assembly, self-sorting, DNA, SNP, pyrosequencing,allele-specific extension, expandable microspheres, catalysis,chiral ligand, monolayer, miniaturization, lab-on-a-chip,µTAS.</p>

Genomic data facilitate opportunities to track complex population histories of divergence and gene flow. We used 47,506 single-nucleotide polymorphisms (SNPs) to investigate cattle population history. Cattle are descendants of two independently domesticated lineages, taurine and indicine, that diverged 200,000 or more years ago. We found that New World cattle breeds, as well as many related breeds of cattle in southern Europe, exhibit ancestry from both the taurine and indicine lineages. Although European cattle are largely descended from the taurine lineage, gene flow from African cattle (partially of indicine origin) contributed substantial genomic components to both southern European cattle breeds and their New World descendants. We extended these analyses to compare timing of admixture in several breeds of taurine-indicine hybrid origin. We developed a metric, scaled block size (SBS), that uses the unrecombined block size of introgressed regions of chromosomes to differentiate between recent and ancient admixture. By comparing test individuals to standards with known recent hybrid ancestry, we were able to differentiate individuals of recent hybrid origin from other admixed individuals using the SBS metric. We genotyped SNP loci using the bovine 50K SNP panel. The selection of sites to include in SNP analyses can influence inferences from the data, especially when particular populations are used to select the array of polymorphic sites. To test the impact of this bias on the inference of population genetic parameters, we used empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We compared the inference of population histories for simulated data sets across different ascertainment conditions using F[subscript ST] and principal components analysis (PCA). Ascertainment bias that results in an over-representation of within-group polymorphism decreases estimates of F[subscript ST] between groups. Geographically biased selection of polymorphic SNPs changes the weighting of principal component axes and can bias inferences about proportions of admixture and population histories using PCA. By combining empirical and simulated data, we were able to both test methods for inferring population histories from genomic SNP data and apply these methods to practical problems. / text

Cancer, the uncontrolled growth of morphologically and genetically abnormal cells in the body, is a major worldwide public health problem and there is a great need for novel insights into this disease. The majority of tumors arise from the acquisition of somatic alterations leading to changes in gene function and expression. The clinical success of targeted therapeutics in molecularly defined subsets of patients has highlighted the need for comprehensive characterization of the somatic alterations in individual cancer types. Copy number profiling using SNP arrays is a common approach for profiling the extent of copy number variation across the cancer genome. In addition, next-generation sequencing technologies now offer researchers the ability to also systematically catalog nucleotide substitutions and structural rearrangements in dramatically less time and expense. In this thesis, we describe the application of SNP arrays and whole-exome sequencing to characterize two separate cohorts of cancer samples, as well as describe the development of a software tool to aid in the annotation of mutational data. Specifically, we detailed focal amplifications of PDGFRA and KIT in a combined set of lung adenocarcinoma and squamous cell carcinomas. Furthermore, in a cohort of small bowel neuroendocrine tumors, we characterized the global genetic landscape to show that these tumors are molecularly distinct from other neuroendocrine tumors. Lastly, we report Oncotator, a novel web application and service for comprehensive annotation of point mutations and indels found in cancer. It is hoped that the knowledge gained from these studies will fuel improvements in cancer diagnosis, prognosis, and therapy.