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Yes / In many species, the offspring of related parents suffer reduced reproductive success, a phenomenon known as inbreeding depression. In humans, the importance of this effect has remained unclear, partly because reproduction between close relatives is both rare and frequently associated with confounding social factors. Here, using genomic inbreeding coefficients (FROH) for >1.4 million individuals, we show that FROH is significantly associated (p < 0.0005) with apparently deleterious changes in 32 out of 100 traits analysed. These changes are associated with runs of homozygosity (ROH), but not with common variant homozygosity, suggesting that genetic variants associated with inbreeding depression are predominantly rare. The effect on fertility is striking: FROH equivalent to the offspring of first cousins is associated with a 55% decrease [95% CI 44–66%] in the odds of having children. Finally, the effects of FROH are confirmed within full-sibling pairs, where the variation in FROH is independent of all environmental confounding.

Xiang Hai Liao. / "July 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 180-200). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

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

Thesis (M.Sc.). / Written for the Institute of Parasitology. Title from title page of PDF (viewed 2008/07/29). Includes bibliographical references.

Thesis (M.Sc.). / Written for the Institute of Parasitology. Title from title page of PDF (viewed 2008/07/29). Includes bibliographical references.

Another attempt was made to identify CpG-rich paralogues on chromosome 21 for dosage analysis. Methylation profiles of 14 paralogous CpG-rich clusters were screened by bisulfite genomic sequencing and/or combined bisulfite restriction analysis. One of the paralogue pairs showed similar differential methylation patterns, and three other CpG-rich clusters located on chromosome 21 were hypomethylated in the placentas and completely methylated in the maternal blood cells. Detection methods for these novel epigenetic markers were described and discussed, and potential applications were also suggested. / In the second part of this thesis, a technique called digital PCR was used for detecting and quantifying cell-free fetal DNA in maternal plasma. DNA templates are first diluted to a single molecule level and partitioned to separate compartments before subjecting to polymerase chain reaction amplification. Quantification is then made by counting the number of positive reactions directly. Such a technique has allowed the reliable detection of fetal DNA from a high background of maternal plasma DNA, and allows absolute quantification of fetal DNA without using a calibration curve. As a proof-of-principle project, a non-polymorphism-based approach called digital relative chromosome dosage (RCD) method was developed to detect chromosomal imbalance in trisomic cases. The implementation of digital PCR was further facilitated with the technology of integrated fluidics circuits (IFCs), by which nanolitre volumes of reaction mixtures could be manipulated in a high-throughput manner. Such a microfluidics digital PCR system was evaluated systematically and shown to be highly accurate, precise and sensitive compared to other existing detection platforms. The technology has been applied with the RCD approach for rapid detection of trisomy 21 from amniotic fluid samples and 100% accuracy was attained. With the development of new universal markers and robust detection platforms, it is envisioned that circulating fetal DNA in maternal plasma can be applied to an expanding range of clinical applications in the near future. / The first part of my thesis focused on the discovery of new epigenetic markers for fetal DNA detection. Methylation profiles of 7 selected CpG islands on chromosome 21 were revealed by bisulfite sequencing, in the hope of identifying regions with differential methylation patterns between placentas and maternal blood cells. Out of the 14 sub-regions of these CpG islands, five displayed significant difference between the two tissue type and were promising marker candidates. / The presence of circulating fetal DNA in maternal plasma provides a non-invasive source of fetal genetic materials for prenatal diagnosis. Reliance on Y-chromosomal sequences for detecting fetal-specific signals from the background of maternal plasma DNA, however, has restricted the applications to 50% of pregnancies. For a wider extent of diagnostic applications, sex- and polymorphism-independent fetal markers would be necessary. Recently, an epigenetic approach has been adopted to discriminate between the fetal and maternal DNA circulating in maternal plasma. Based on the differential DNA methylation status between the fetus and mother, universal fetal DNA markers have been developed and applied to detect fetal signals in maternal plasma. Identification of more of such markers is important for the development of the field. / Lun, Miu Fan. / Adviser: Yuk Ming Dennis Lo. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3292. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2008. / Includes bibliographical references (leaves 233-256). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

First, expression profiling of ZNFs with CpG islands at 10 clusters of Chr19 was examined in a panel of NPC and ESCC cell lines by semi-quantitative RT-PCR, with adult normal tissues - larynx and esophagus as controls. Several down-regulated genes were identified, and I further focused on 5 candidates: ZNF382, ZNF545, ZFP30, ZNFT1 and ZNFT2. These genes were frequently downregulated in NPC, ESCC, lung, gastric, colon and breast carcinomas. Their promoters were frequently methylated in multiple downregulated cell lines but less in non-tumor cell lines as revealed by methylation-specific PCR (MSP) and bisulfite genomic sequencing (BGS). Their expression could be restored by pharmacologic or genetic demethylation, suggesting that DNA methylation was directly involved in their silencing. The frequent methylation of these genes indicated they could act as potential biomarkers. / In conclusion, several novel candidate TSGs epigenetically silenced in tumor cells were identified in this study. Their downregulation by promoter methylation was tumor-specific, which could be use as epigenetic biomarkers for diagnosis. / More functional studies were done for ZNF382 and ZNF545, I found that ectopic expression of ZNF382 and ZNF545 in tumor cells lacking endogenous expression could inhibit tumor cell clonogenicity, proliferation and induce apoptosis. I found that ZNF382 suppressed tumorigenesis through mediating heterochromatin formation, as ZNF382 was revealed to be co-localized and interacts with heterochromatin protein. For ZNF545, I found that it is a transcriptional repressor. I further showed that ZNF545 was located in the nucleus and sequestered in the nucleolus. ZNF545 could inhibit tumorigenesis at least partially through downregulating the transcription of target genes or regulating nucleolus function such as ribosome biogenesis. / The development of a tumor from a normal cell is a complex and multi-step process. A large number of oncogenes, tumor suppressor genes (TSGs) and signal transduction pathways are involved in this process. Tumor-specific methylation of TSGs in multiple tumors indicated that it could be used as epigenetic biomarker for molecular diagnosis and therapeutics. / The functions of KRAB-containing proteins are critical to cell differentiation, proliferation, apoptosis and neoplastic transformation. A large number of ZNF genes are located in 10 clusters at chromosome 19. Some of the KRAB-ZNF may function as potential TSGs with epigenetic alterations. Thus, I try to identify silenced novel KRAB-ZNF candidate TSGs through screening chromosome 19. / Cheng, yingduan. / Adviser: Tao Qian. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 110-136). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.

BACKGROUND AND OBJECTIVES: Type 2 diabetes mellitus (T2DM) is a complex disease with genetic predisposition and histopathological characterization. Pancreatic islet amyloidosis, hyaline arteriolosclerosis, and diabetic glomerulopathy are histopathological hallmarks of T2DM at autopsy examination. The associations of genetic variants with diabetic amyloidosis, arteriosclerosis and glomerulopathy have not been fully elucidated. Several candidate genes including apolipoprotein E (ApoE), insulin degrading-enzyme (IDE) and glucose transporter-1 ( GLUT1) have been reported to increase risk of T2DM in human studies although results are not always consistent. Capitalizing on the pathological hallmarks of T2DM, I used autopsy specimens to investigate the risk associations of polymorphisms of ApoE (rs429358 and rs7412), IDE (rs6583813) and GLUT1 (rs710218) genes with clinical features and specific pathological changes in diabetic kidney and pancreas. I further explored the mechanisms of these associations by evaluating the histopathological changes and protein expression in pancreas and kidney. / CONCLUSIONS: These findings suggest that genetic factors have important effects in the development of tissue-specific changes and chronic complications in T2DM. Islet amyloidosis, arteriosclerosis and glomerulosclerosis in T2DM may share common pathogenetic processes as suggested by the coexistence of chaperone proteins, amyloid P and ApoE. Genetic--pathologic correlation studies are useful in advancing our understanding of the mechanisms of complex diseases such as T2DM. / METHODS AND MATERIALS: Genomic DNA was extracted from white blood cell-concentrated paraffin embedded formalin fixed spleen tissues. Genotyping for ApoE, IDE and GLUT1 polymorphisms was determined by polymerase chain reaction (PCR) and ligase detection reaction (LDR). The pathological changes were blindly assessed in pancreatic and kidney tissues of autopsy specimens. Protein expression of these genes was examined by immunostaining and quantified by using Metamorph image analysis system. / RESULTS: In a consecutive study population of 3693 autopsy specimens containing 328 T2DM and 209 control cases, the respective frequencies of genotypes were as follows: 1) TT of GLUT1 rs710218: 11.2% vs. 11.3%; 2) ApoE epsilon2: 19.4% vs. 10.9%; 3) ApoE epsilon4: 12.1% vs. 9.1% and 4) C carriers of IDE rs6583813: 51.2% vs. 47.9%. The key genotype-phenotype correlations were as follows. 1) In the T2DM cases, GLUT1 rs710218 IT genotype carriers (0% in TT genotype vs. 59.1% in AA genotype, P=0.0407) were less likely but ApoE epsilon 2 allele carriers (57.1% in epsilon2 allele carriers vs. 23.5% in epsilon3 allele carriers P=0.0382) were more likely to have diabetic glomerular hypertrophy than referential group. ApoE epsilon2 carriers showed increased glomerular ApoE protein expression with the immunoreactivity found mainly in the mesangial regions and nodular lesions. On the other hand, ApoE epsilon 3/epsilon4 cases had diffuse ApoE expression in glomerular capillaries. 2) ApoE epsilon4 carriers were more likely to have islet amyloidosis than non-carriers (62.5% in epsilon4 allele carriers vs. 23.6% in epsilon 3 allele carriers P=0.0232). There was immunolocalization of the chaperone proteins, amyloid P and ApoE in both islet amyloid deposits and arterial walls with hyaline arteriolosclerosis. 3) In T2DM cases, IDE rs6583813 C allele carriers had higher prevalence of vascular disorders [hypertension (67.4% vs. 43.6%, P=0.0332), death due to cardiovascular disease (58.1% vs. 25.6%, P=0.0479) and cerebral vascular accident (CVA) (20.9% vs. 2.4%, P=0.0412)1 than T allele carriers. / Guan, Jing. / Adviser: Chan Chung Ngor Juliana. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 175-192). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [201-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.