Diss. (sammanfattning) Umeå : Umeå universitet, 2006. / Härtill 4 uppsatser.

Thesis--University of Oklahoma. / Includes bibliographical references.

Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2003. / Vita. Bibliography: 127-154.

Chen, Zhang. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (p. 109-114). / Abstracts in English and Chinese. / ABSTRACT --- p.I / 摘要 --- p.III / ACKNOWLEDGEMENTS --- p.IV / PUBLICATIONS --- p.VI / CONTRIBUTORS --- p.VII / TABLE OF CONTENTS --- p.VIII / LIST OF TABLES --- p.XIII / LIST OF FIGURES --- p.XIV / LIST OF ABBREVIATIONS --- p.XVI / Chapter SECTION I : --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- PRENATAL DIAGNOSIS OF FETAL TRISOMY BY NEXT GENERATION SEQUENCING TECHNOLOGY --- p.2 / Chapter 1.1 --- FETAL TRISOMY --- p.2 / Chapter 1.2 --- CONVENTIONAL PRENATAL DIAGNOSIS OF FETAL TRISOMIES --- p.3 / Chapter 1.3 --- CELL FREE FETAL D N A AND ITS APPLICATION IN PRENATAL DIAGNOSIS --- p.5 / Chapter 1.4 --- NEXT GENERATION SEQUENCING TECHNOLOGY --- p.5 / Chapter 1.5 --- SUBSTANTIAL BIAS IN THE NEXT GENERATION SEQUENCING PLATFORM --- p.9 / Chapter 1.6 --- PRENATAL DIAGNOSIS OF TRISOMY BY NEXT GENERATION SEQUENCING --- p.10 / Chapter 1.7 --- AIMS OF THIS THESIS --- p.11 / Chapter SECTION I I : --- MATERIALS AND METHODS --- p.13 / Chapter CHAPTER 2: --- METHODS FOR NONINVASIVE PRENATAL DIAGNOSIS OF FETAL TRISOMY MATERNAL PLASMA DNA SEQUENCING --- p.14 / Chapter 2.1 --- STUDY DESIGN AND PARTICIPANTS --- p.14 / Chapter 2.1.1 --- Ethics Statement --- p.14 / Chapter 2.1.2 --- "Study design, setting and participants" --- p.14 / Chapter 2.2 --- MATERNAL PLASMA D N A SEQUENCING --- p.17 / Chapter 2.3 --- SEQUENCING DATA ANALYSIS --- p.18 / Chapter SECTION I I I : --- TRISOMY 13 AND 18 DETECTION BY THE T21 BIOINFORMATICS ANALYSIS PIPELINE --- p.21 / Chapter CHAPTER 3: --- THE T21 BIOINFORMATICS ANALYSIS PIPELINE FOR TRISOMY 13 AND 18 DETECTION --- p.22 / Chapter 3.1 --- INTRODUCTION --- p.22 / Chapter 3.2 --- METHODS --- p.23 / Chapter 3.2.1 --- Bioinformatics analysis pipeline for trisomy 13 and 18 detection --- p.23 / Chapter 3.3 --- RESULTS --- p.23 / Chapter 3.3.1 --- Performance of the T21 bioinformatics analysis pipeline for trisomy 13 and 18 detection --- p.23 / Chapter 3.3.2 --- The precision of quantifying chrl 3 and chrl 8 --- p.27 / Chapter 3.4 --- DISCUSSION --- p.29 / Chapter SECTION IV : --- IMPROVING THE T21 BIOINFORMATICS ANALYSIS PIPELINE FOR TRISOMY 13 AND 18 DETECTION --- p.30 / Chapter CHAPTER 4: --- IMPROVING THE ALIGNMENT --- p.31 / Chapter 4.1 --- INTRODUCTION --- p.31 / Chapter 4.2 --- METHODS --- p.32 / Chapter 4.2.1 --- Allowing mismatches in the index sequences --- p.32 / Chapter 4.2.2 --- Calculating the mappability of the human reference genome --- p.33 / Chapter 4.2.3 --- Aligning reads to the non-repeat masked human reference genome --- p.34 / Chapter 4.2.4 --- Trisomy 13 and 18 detection --- p.34 / Chapter 4.3 --- RESULTS --- p.34 / Chapter 4.3.1 --- Increasing read numbers by allowing mismatches in the index sequences --- p.34 / Chapter 4.3.2 --- Increasing read numbers by using the non-masked reference genome for alignment . --- p.38 / Chapter 4.3.3 --- Allowing mismatches in the read alignment --- p.42 / Chapter 4.3.4 --- The performance of trisomy 13 and 18 detection after improving the alignment --- p.47 / Chapter 4.4 --- DISCUSSION --- p.50 / Chapter CHAPTER 5: --- REDUCING THE GC BIAS BY CORRECTION OF READ COUNTS --- p.53 / Chapter 5.1 --- INTRODUCTION --- p.53 / Chapter 5.2 --- METHODS --- p.54 / Chapter 5.2.1 --- Read alignment --- p.54 / Chapter 5.2.2 --- Calculating the correlation between GC content and read counts --- p.55 / Chapter 5.2.3 --- GC correction in read counts --- p.55 / Chapter 5.2.4 --- Trisomy 13 and 18 detection --- p.56 / Chapter 5.3 --- RESULTS --- p.56 / Chapter 5.3.1 --- GC bias in plasma DNA sequencing --- p.56 / Chapter 5.3.2 --- Correcting the GC bias in read counts by linear regression --- p.59 / Chapter 5.3.3 --- Correcting the GC bias in read counts by LOESS regression --- p.65 / Chapter 5.3.4 --- Bin size --- p.72 / Chapter 5.4 --- DISCUSSION --- p.75 / Chapter CHAPTER 6: --- REDUCING THE GC BIAS BY MODIFYING THE GENOMIC REPRESENTATION CALCULATION --- p.77 / Chapter 6.1 --- INTRODUCTION --- p.77 / Chapter 6.2 --- METHODS --- p.78 / Chapter 6.2.1 --- Modifying the genomic representation calculation --- p.78 / Chapter 6.2.2 --- Trisomy 13 and 18 detection --- p.78 / Chapter 6.2.3 --- Combining GC correction and modified genomic representation --- p.78 / Chapter 6.3 --- RESULTS --- p.79 / Chapter 6.3.1 --- Reducing the GC bias by modifying genomic representation calculation --- p.79 / Chapter 6.3.2 --- Combining GC correction and modified genomic representation --- p.86 / Chapter 6.4 --- DISCUSSION --- p.89 / Chapter CHAPTER 7: --- IMPROVING THE STATISTICS FOR TRISOMY 13 AND 18 DETECTION --- p.91 / Chapter 7.1 --- INTRODUCTION --- p.91 / Chapter 7.2 --- METHODS --- p.92 / Chapter 7.2.1 --- Comparing chrl 3 or chrl8 with other chromosomes within the sample --- p.92 / Chapter 7.2.2 --- Comparing chrl 3 or chrl 8 with the artificial chromosomes --- p.92 / Chapter 7.3 --- RESULTS --- p.93 / Chapter 7.3.1 --- Determining the trisomy 13 and 18 status by comparing chromosomes within the samples --- p.93 / Chapter 7.3.2 --- Determining the trisomy 13 and 18 status by comparing chrl3 or chrl 8 with artificial chromosomes --- p.97 / Chapter 7.4 --- DISCUSSION --- p.100 / Chapter SECTION V : --- CONCLUDING REMARKS --- p.102 / Chapter CHAPTER 8: --- CONCLUSION AND FUTURE PERSPECTIVES --- p.103 / Chapter 8.1 --- THE PERFORMANCE OF THE T21 BIOINFORMATICS ANALYSIS PIPELINE DEVELOPED FOR TRISOMY 21 DETECTION IS SUBOPTIMAL FOR TRISOMY 13 AND 18 DETECTION --- p.103 / Chapter 8.2 --- THE ALIGNMENT COULD BE IMPROVED BY ALLOWING ONE MISMATCH IN THE INDEX AND USING THE NON-REPEAT MASKED HUMAN REFERENCE GENOME AS THE ALIGNMENT REFERENCE --- p.104 / Chapter 8.3 --- THE PRECISION OF QUANTIFYING CHR13 AND CHR18 COULD BE IMPROVED BY THE G C CORRECTION OR THE MODIFIED GENOMIC REPRESENTATION --- p.104 / Chapter 8.4 --- THE STATISTICS FOR TRISOMY 13 AND 18 DETECTION COULD BE IMPROVED BY COMPARING CHR13 OR CHR18 WITH ARTIFICIAL CHROMOSOMES WITHIN THE SAMPLE --- p.105 / Chapter 8.5 --- PROSPECTS FOR FUTURE WORK --- p.106 / REFERENCE --- p.109

Objetivo: Investigar a presença de alterações (deleção e/ou duplicação) na região 22q11 em indivíduos até 02 anos de idade com fissura de palato, com o intuito de realizar diagnóstico precoce da síndrome da deleção 22q11 (SD22q11). Local: Laboratório de Genética e Citogenética Humana, HRAC/USP, Bauru-SP. Casuística e metodologia: Foram selecionados 55 indivíduos, de ambos os sexos, com idade até 2 anos e com fissura de palato, cadastrados e em tratamento no Hospital de Reabilitação de Anomalias Craniofaciais/USP. Todos os indivíduos foram analisados utilizando citogenética convencional por bandamento G e pela técnica de MLPA. Resultados e discussão: Foram analisados 55 indivíduos, dos quais 46 apresentaram fissura de palato isolada, 6 apresentaram fissura de palato e cardiopatia, 1 fissura de palato e atraso no desenvolvimento neuropsicomotor, 1 caso apresentou fissura de palato submucosa e 1 caso com fissura de palato submucosa e atraso no desenvolvimento neuropsicomotor. Não foram observadas anomalias cromossômicas numéricas ou estruturais por meio da análise citogenética. Embora não tenhamos encontrado nenhuma alteração, a análise citogenética inicial foi importante para detectar possíveis alterações em outras regiões cromossômicas que pudessem resultar em um fenótipo semelhante ao da SD22q11. Também não foram detectadas deleção ou duplicação na região 22q11 pela técnica de MLPA, a qual se mostrou um método rápido, sensível, eficaz e com um custo relativamente baixo em comparação a outras técnicas, para a investigação de alterações na região 22q11. Nossos resultados, associados aos da literatura, demonstram que a prevalência da deleção 22q11 nos casos de fissura de palato isolada é muito baixa. Mesmo sendo considerada como sugestiva da SD22q11, não detectamos nenhuma alteração na região 22q11 nos 6 indivíduos com cardiopatia. Somente foi possível identificar atraso no desenvolvimento em 2 indivíduos, ambos com dois anos de idade. Isso demonstra a dificuldade de realizar diagnóstico em idade precoce. Conclusão: O teste de rotina para investigação da deleção/duplicação da região 22q11 não se justifica em crianças com idade até dois anos que apresentam fissura de palato como principal achado clínico. Esses indivíduos devem ter um acompanhamento clínico criterioso, porque um comprometimento comportamental ou mental, bem como as características dismórficas da SD22q11 podem evoluir com o tempo. Devido ao tamanho relativamente pequeno desse estudo, e os dados inconsistentes da literatura atual, mais estudos são necessários para estabelecer critérios para indicação da rotina de investigação de deleção/duplicação 22q11 em indivíduos com anomalias palatinas. / Purpose: To investigate alterations (deletions/duplications) in the 22q11 region in individuals with cleft palate aged 0-2 years, in order to perform early diagnosis of 22q11 deletion syndrome (SD22q11). Local: Genetics and Human Cytogenetics Laboratory, HRAC/USP, Bauru-SP. Methods: We selected 55 individuals with cleft palate, both genders, registered and in treatment at Hospital de Reabilitação de Anomalias Craniofaciais/USP. All individuals were investigated by cytogenetics and MLPA techniques. Results and Discussion: 46 out of 55 individuals, presented isolated cleft palate, 6 cleft palate and heart malformations, 1 cleft palate and developmental delay, 1 submucous cleft, and 1 submucous cleft and developmental delay. G karyotype did not show any chromosomal abnormalities. Although we did not detect any alterations, the initial cytogenetics analysis was important to exclude alteration in other chromosomal region that could result in a similar phenotype. Deletion or duplication in 22q11 region by MLPA was not detected, which shown to be a rapid, sensitive, and low cost method in comparison with other methods to investigate 22q11 region. Results, associated with the literature, have shown that the prevalence of the 22q11 alteration is very low in cleft palate. The presence of heart malformation is suggestive of 22q11DS. Besides, there were no alterations in 22q11 region in 6 patients with cleft palate and heart malformations. We were able to identify developmental delay in only 2 individual, both aged 2 years which demonstrates the difficulty of making early diagnosis. Conclusion: There is no justification for routine screening for 22q11 region deletion/duplication in children aged 0-2 years with cleft palate as main feature. These individuals should be carefully followed because behavioral or mentalimpairments as well as dysmorphic features characteristic of 22q11DS may evolve with time.

Lam, Yuk Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 142-157). / Abstracts in English and Chinese. / ABSTRACT --- p.i / 摘要 --- p.iv / ACKNOWLEDGEMENTS --- p.vi / CONTRIBUTORS --- p.viii / PUBLICATIONS --- p.ix / LIST OF TABLES --- p.x / LIST OF FIGURES --- p.xi / LIST OF ABBREVIATIONS --- p.xiii / TABLE OF CONTENTS --- p.xiv / Chapter SECTION I: --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- PRENATAL DIAGNOSIS OF FETAL ANEUPLOIDIES --- p.2 / Chapter 1.1 --- The need for prenatal screening and diagnosis --- p.2 / Chapter 1.2 --- Patau Syndrome (Trisomy 13) --- p.2 / Chapter 1.3 --- Current methods for fetal aneuploidy detection --- p.4 / Chapter 1.3.1 --- Routine prenatal screening tests --- p.4 / Chapter 1.3.2 --- Definitive prenatal diagnosis by invasive procedures --- p.7 / Chapter 1.4 --- New approach for noninvasive prenatal diagnosis --- p.11 / Chapter 1.4.1 --- Circulating fetal cells --- p.11 / Chapter 1.4.2 --- Cell-free fetal nucleic acids in maternal circulation --- p.12 / Chapter 1.4.3 --- Diagnostic applications of cell-free fetal nucleic acids in maternal plasma --- p.12 / Chapter CHAPTER 2: --- DEVELOPMENT OF FETAL EPIGENETIC MARKERS IN MATERNAL PLASMA --- p.17 / Chapter 2.1 --- Limitations of fetal DNA markers --- p.17 / Chapter 2.2 --- DNA methylation is an actively-researched area under the field of epigenetics --- p.18 / Chapter 2.3 --- Genome-scale DNA methylation analysis brings new insight into epigenetics --- p.20 / Chapter 2.4 --- The first demonstration of using an epigenetic method for detecting maternally-inherited fetal DNA in maternal plasma --- p.22 / Chapter 2.5 --- The first universal marker for fetal DNA in maternal plasma --- p.24 / Chapter 2.6 --- Discovery of more fetal epigenetic markers --- p.25 / Chapter 2.6.1 --- Methylated fetal epigenetic markers are more desirable --- p.25 / Chapter 2.6.2 --- Discovery of hypermethylated fetal epigenetic markers by studying tumor suppressor genes --- p.26 / Chapter 2.6.3 --- Discovery of hypermethylated fetal epigenetic markers on chromosome 21 --- p.28 / Chapter 2.7 --- Noninvasive detection of fetal aneuploidies using fetal epigenetic markers --- p.29 / Chapter 2.7.1 --- Noninvasive detection of fetal trisomy 18 by the epigenetic allelic ratio (EAR) approach --- p.29 / Chapter 2.7.2 --- Noninvasive detection of fetal trisomy 21 by the epigenetic-genetic (EGG) approach --- p.30 / Chapter 2.8 --- Aim of thesis --- p.32 / Chapter SECTION II: --- MATERIALS AND METHODS --- p.34 / Chapter CHAPTER 3: --- METHODS FOR QUANTITATIVE ANALYSIS OF DNA METHYLATION --- p.35 / Chapter 3.1 --- Subject recruitment and sample collection --- p.35 / Chapter 3.2 --- Sample processing --- p.38 / Chapter 3.3 --- DNA extraction --- p.38 / Chapter 3.3.1 --- Placental tissues --- p.38 / Chapter 3.3.2 --- Maternal blood cells --- p.39 / Chapter 3.3.3 --- Maternal plasma --- p.40 / Chapter 3.4 --- Methylated DNA immunoprecipitation and tiling array analysis (MeDIP-chip) --- p.41 / Chapter 3.4.1 --- Principles --- p.41 / Chapter 3.4.2 --- DNA sample and array processing --- p.43 / Chapter 3.4.2.1 --- DNA preparation and target hybridization --- p.43 / Chapter 3.4.2.2 --- Data analysis --- p.44 / Chapter 3.5 --- DNA methylation analysis on randomly-chosen regions on chromosome / Chapter 3.6 --- Bisulfite conversion --- p.46 / Chapter 3.6.1 --- Principles of bisulfite conversion --- p.46 / Chapter 3.6.2 --- Procedures of bisulfite conversion --- p.46 / Chapter 3.7 --- Quantitative analysis of DNA methylation --- p.47 / Chapter 3.7.1 --- Bisulfite PCR and genomic sequencing --- p.47 / Chapter 3.7.1.1 --- Primer design for bisulfite polymerase chain reaction (PCR) --- p.47 / Chapter 3.7.1.2 --- Bisulfite PCR --- p.49 / Chapter 3.7.1.3 --- Cloning --- p.50 / Chapter 3.7.1.4 --- Bisulfite genomic sequencing --- p.52 / Chapter 3.7.1.5 --- Data acquisition and interpretation --- p.53 / Chapter 3.7.2 --- EpiTYPER，a mass-spectrometry-based method --- p.54 / Chapter 3.7.2.1 --- Principles of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) --- p.54 / Chapter 3.7.2.2 --- Primer design of the EpiTYPER assay --- p.55 / Chapter 3.7.2.3 --- The EpiTYPER assay and its principle --- p.56 / Chapter 3.8 --- Methylation-sensitive restriction enzyme (MSRE)-mediated real-time quantitative PCR (qPCR) --- p.61 / Chapter 3.9 --- Digital PCR --- p.66 / Chapter 3.9.1 --- Principles of digital PCR --- p.66 / Chapter 3.9.2 --- Poisson distribution --- p.68 / Chapter 3.10 --- Statistical analyses --- p.69 / Chapter SECTION III: --- SYSTEMATIC IDENTIFICATION OF A FETAL DNA METHYLATION MARKER ON CHROMOSOME 13 FOR DETECTION OF FETAL TRISOMY 13 --- p.70 / Chapter CHAPTER 4: --- SYSTEMATIC IDENTIFICATION OF POTENTIAL FETAL EPIGENETIC MARKERS BY MEDIP-CHIP ANALYSIS --- p.71 / Chapter 4.1 --- Systematic discovery of fetal epigenetic markers on chromosome 13 by MeDIP-chip analysis --- p.71 / Chapter 4.2 --- Experimental design --- p.73 / Chapter 4.3 --- Results --- p.76 / Chapter 4.3.1 --- Identification of differentially methylated DNA regions by MeDIP-chip or non-MeDIP-chip approaches followed by EpiTYPER analysis --- p.76 / Chapter 4.3.2 --- Confirmation of differential methylation patterns and exclusion of regions with high inter-individual variations by EpiTYPER analysis --- p.82 / Chapter 4.3.3 --- Confirmation of differential DNA methylation patterns with higher resolution by bisulfite sequencing --- p.85 / Chapter 4.4 --- Discussion --- p.95 / Chapter CHAPTER 5: --- THE APPLICATION OF FETAL EPIGENETIC MARKER ON CHROMSOME 13 FOR DETECTION OF FETAL TRISOMY 13 --- p.98 / Chapter 5.1 --- Identification of a fetal epigenetic marker on chromosome 13 for the detection of fetal trisomy 13 by the epigenetic-genetic (EGG) chromosome dosage approach --- p.98 / Chapter 5.2 --- Experimental design --- p.101 / Chapter 5.3 --- Results --- p.105 / Chapter 5.3.1 --- Optimization of the digestion protocol --- p.105 / Chapter 5.3.2 --- Detection of digestion-resistant EFNB2-3'UTR moleculesin maternal plasma --- p.109 / Chapter 5.3.3 --- Evaluation of the fetal specificity of digestion-resistant EFNB2´ؤ3 'UTR DNA molecules in maternal plasma --- p.111 / Chapter 5.3.4 --- Comparison of EFNB2-3'UTR methylation profiles between the euploid and trisomy 13 placental tissue samples --- p.115 / Chapter 5.3.5 --- Chromosome dosage analysis by the EGG analysis using placental tissue samples --- p.118 / Chapter 5.4 --- Discussion --- p.122 / Chapter SECTION IV: --- CONCLUDING REMARKS --- p.125 / Chapter CHAPTER 6: --- CONCLUSION AND FUTURE PERSPECTIVES --- p.126 / Chapter 6.1 --- Development of fetal epigenetic markers for noninvasive prenatal diagnosis --- p.126 / Chapter 6.2 --- Systematic identification of fetal epigenetic markers on chromosome13 --- p.127 / Chapter 6.3 --- Detection of fetal trisomy 13 by the epigenetic-genetic (EGG) relative chromosome dosage analysis --- p.129 / Chapter 6.4 --- Future perspectives --- p.132 / Appendix I --- p.134 / Appendix II --- p.136 / REFERENCES --- p.142

Diss. (sammanfattning) Stockholm : Karolinska institutet, 2007. / Härtill 4 uppsatser.

Diss. (sammanfattning) Linköping : Univ., 2004. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 5 uppsatser.