Zhang Jun. / "August 2000." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2000. / Includes bibliographical references (p. 109-144). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Qin, Yun. / "April 2002." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2002. / Includes bibliographical references (p. 229-254). / 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.

Chiu Wai Kwun Rossa. / "July 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 144-176). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

The discovery of fetal-derived circulating nucleic acids in maternal plasma has opened up new opportunities for non-invasive prenatal diagnosis. This non-invasive means of obtaining fetal genetic materials is safer than invasive tissue-sampling procedures, which are associated with a small but finite chance of fetal loss. Over the past decade, the detection of fetal DNA in maternal plasma has evolved from dependency on discriminative genetic markers, such as Y-chromosome-specific loci or paternally-inherited polymorphisms, to detection of circulating RNA, fetal-specific methylation or by massively parallel sequencing. Fetal-specific methylation, or fetal epigenetic marker, does not require prior knowledge of the sex or polymorphic status of the fetus and thus can be applied in essentially all pergnancies. This thesis focuses on the development of this kind of marker for non-invasive monitoring and detection of pre-eclampsia and fetal aneuploidies. / The first part of this thesis describes the use of a reported fetal epigenetic marker, RASISF1A, to measure the fetal DNA concentrations in maternal plasma of pre-eclamptic subjects versus gestational-age-matched controls. The second part of this thesis describes a systematic search for potential epigenetic markers for pre-eclampsia and the second commonest fetal aneuploidy, trisomy 18. Numerous approaches for methylation profiling are described, such as methylation-specific polymerase chain reaction (MSP), bisulfite sequencing, a mass spectrometry-based platform (the Epityper assay), and methylated DNA immunoprecipitation coupled with tiling array analysis (MeDIP-chip). Using MeDIP-chip, I selected the most promising fetal epigenetic markers on chromosome 18, and further characterised their detection in maternal plasma. The final part of this thesis describes an approach called epigenetic-genetic (EGG) chromosome dosage for the detection of trisomy 18 based on those markers. I have demonstrated that it is feasible to detect fetal trisomy 18 by analysing maternal plasma in as early as the first trimester. / This thesis illustrates different strategies for methylation profiling and presented two examples of applying DNA methylation for the non-invasive prenatal assessment of pregnancy-associated disorders and fetal chromosomal aneuploidies. I envision that a similar strategy could be developed for other pregnancy-related diseases to broaden the application of epigenetic markers in non-invasive prenatal diagnosis. / Tsui, Wai Yi. / Adviser: Y.M. Dennis Lo. / Source: Dissertation Abstracts International, Volume: 73-02, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 198-221). / 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.

Prenatal diagnosis is an established obstetrics practice in many countries. Currently available methods to obtain fetal materials for a definitive diagnosis involve invasive procedures such as chorionic villus sampling and amniocentesis. Due to the invasive nature of the procedures, confirmatory testing is usually recommended only for pregnant women who are screened as being high risk of bearing a fetus with abnormalities. There has been an urge to develop safer alternatives in obtaining fetal genetic materials for prenatal assessment. Thus, the discovery of circulating fetal DNA in maternal plasma and serum has opened up new possibilities for noninvasive prenatal diagnosis. / The use of genetic markers such as Y chromosomal sequences from a male fetus or paternally-inherited polymorphic markers has been well-described in the literature. However, there is an obvious limitation on the use of these markers because they are gender- and/or polymorphism-dependent. This thesis focuses on the development of a universal fetal marker, namely SERPINB5 (encoding maspin), based on the intrinsic epigenetic differences between the placenta (the major contributor of fetal genetic materials in maternal plasma) and maternal blood cells (postulated to be the predominant source of cell-free DNA in the circulation). Analysis of the methylation profile of the SERPINB5 promoter in the placenta and maternal blood cells, and the development of methods and protocols to detect the differentially methylated SERPINB5 promoter molecules are described. The application of this epigenetic marker in prenatal assessment of the fetal chromosomal aneuploidy is illustrated by an epigenetic allelic ratio (EAR) approach. Basically, the ratio of a single-nucleotide polymorphism (SNP) on the placenta-derived SERPINB5 molecules is shown to be deviated in the maternal plasma from trisomic pregnancies when compared to the euploid ones. Results described in this thesis show the promising potential for the EAR approach for the noninvasive prenatal detection of fetal chromosomal aneuploidies. In addition, a novel approach for methylation analyses on the amplification and detection of restriction enzyme-digested DNA fragments will be discussed. This thesis has essentially described the evolution of a fetal epigenetic marker from basic science to potential clinical application. / Tong, Yu Kwan. / Adviser: Yuk-Ming Dennis Lo. / Source: Dissertation Abstracts International, Volume: 69-02, Section: B, page: 0953. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 149-172). / 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. / Abstract also in Chinese. / School code: 1307.

A insuficiência cardíaca é uma síndrome clínica de alta morbimortalidade e por este motivo é crescente o interesse em se estudar novos biomarcadores da doença visando buscar caminhos para novas estratégias terapêuticas. Neste contexto, a análise do ar exalado pode ser promissora. Baseado nestes dados e na observação de que pacientes com insuficiência cardíaca grave exalam odor peculiar, ainda em estudo piloto, nós identificamos acetona no ar exalado de pacientes com insuficiência cardíaca. Assim, nosso estudo teve por objetivo primário avaliar o papel da acetona exalada como biomarcador do diagnóstico de insuficiência cardíaca e de insuficiência cardíaca descompensada. Como objetivo secundário, avaliar sua relação com a classe funcional segundo a classificação da New York Heart Assocation (NYHA) e sua correlação com o peptídeo natriurético do tipo B (BNP). Entre maio de 2009 e setembro de 2010, pacientes consecutivos com disfunção sistólica (grupo IC) admitidos na emergência (insuficiência cardíaca descompensada grupo ICDESCOMP) e pacientes estáveis nos últimos três meses encaminhados para o teste cardiopulmonar (insuficiência cardíaca compensada grupo ICCOMP) foram submetidos à coleta de ar exalado (extração em água) para posterior análise qualitativa por cromatografia gasosa acoplado à espectrometria de massas e quantificação por espectrofotometria de absorção, através da reação com salicilaldeído. Entre os 235 pacientes avaliados, 89 foram incluídos (59 com insuficiência cardíaca descompensada e 30 com insuficiência cardíaca compensada), 61% do sexo masculino e com mediana de idade de 52 anos. Vinte indivíduos saudáveis (grupo controle) pareados por idade participaram do estudo. O valor mediano (intervalo interquartil) de acetona exalada foi maior no grupo IC em relação ao controle [3,70 g/L (1,69-10,45 g/L) versus 0,39 g/L (0,30-0,79 g/L), p < 0,001]. O valor mediano de acetona em pacientes com insuficiência cardíaca descompensada foi maior do que no grupo com insuficiência cardíaca compensada [7,80 g/L (3,60-15,20 g/L) versus 1,22 g/L (0,682,19 g/L), p < 0,001]. A acurácia do método tanto para o diagnóstico de insuficiência cardíaca (acetona > 1,16 g/L; área sob a curva = 0,94) quanto para o diagnóstico de insuficiência cardíaca descompensada (acetona > 2,50 g/L; área sob a curva = 0,93) foi aproximadamente 85 %, semelhante à acurácia do BNP (BNP > 42 pg/mL; área sob a curva = 0,97 e BNP > 424 pg/mL; área sob a curva = 0,94, respectivamente). Houve correlação positiva entre acetona exalada e BNP (r = 0,772, p < 0,001). Observamos aumento progressivo nas concentrações de acetona exalada de acordo com a piora da classe funcional segundo NYHA (p < 0,001). Assim, podemos concluir que nosso estudo revelou a acetona exalada como um novo biomarcador do diagnóstico de insuficiência cardíaca e de insuficiência cardíaca descompensada, que está associado à maior gravidade da doença e que apresenta correlação positiva com BNP. Sua dosagem é um novo método de diagnóstico não invasivo que pode ser realizado à beira leito, cuja acurácia é semelhante à do BNP / Heart failure (HF) is a condition associated with high mortality and frequent hospital admissions. In this context, multiple biomarkers of heart failure severity have emerged recently. However, the usefulness of most of these biomarkers has not been fully established. Exhaled breath has been considered a suitable tool (biomarker) to evaluate different diseases. Based on the clinical observation that patients with acute decompensated heart failure (ADHF) exhale a distinct odor, in a pilot study we have identified acetone in exhaled breath of heart failure patients and this study aimed to evaluate the role of acetone as a new biomarker of heart failure and ADHF disease. As secondary aims, we intended to analyze the relation to New York Heart Association (NYHA) class and the correlation with B-Type Natriuretic Peptide (BNP). Patients with systolic dysfunction (HF group) admitted consecutively at the emergency room (ADHF group) and stable patients referred to the cardiopulmonary test (chronic HF CHF group) between May 2009 and September 2010 were submitted to exhaled breath collection (extraction into water). Acetone identification was done by gas chromatography-mass spectrometry (GC-MS) and its determination by absorption spectrophotometry after reaction with salicylaldehyde. Twenty healthy subjects matched for age were enrolled (control group). Among 235 patients with HF, 89 were included in the study (59 ADHF and 30 CHF), 61% male, with median age of 52 years. Median exhaled breath acetone value (interquartile range) was higher in the HF group when compared to control group [3.7 g/L (1.69-10.45 g/L) versus 0.39 g/L (0.30-0.79 g/L), p < 0.001] and also higher in ADHF when compared to CHF group [7.80 g/L (3.60-15.20 g/L) versus 1.22 g/L (0.682.19 g/L), p < 0,001]. The accuracy of the method to diagnose CHF (Acetone > 1.16 g/L; AUC = 0.94) and ADHF (Acetone > 2.5 g/L; AUC = 0.93) was similar to the accuracy of BNP (BNP > 42 pg/mL; AUC = 0.97 and BNP > 424 pg/mL; AUC = 0.94, respectively). There was a positive correlation between exhaled breath acetone and plasmatic BNP (r = 0.772, p < 0.001). Levels of exhaled breath acetone were different among the four different NYHA classes (p<0.001). In summary, we can conclude that our study showed exhaled breath acetone as a new biomarker of heart failure and ADHF. It is associated with heart failure severity and has a good correlation with BNP. This is a promising non-invasive diagnostic method of heart failure, whose accuracy is equivalent to BNP

O desempenho de seis métodos de extração de DNA de oocistos de Cryptosporidium spp. em fezes foram avaliados pela nested PCR do gene SSU rRNA. Os métodos consistem na combinação com pequenas variações de duas técnicas para a liberação de esporozoítos (indução de excistamento/E ou choque térmico/C) e três técnicas de purificação de DNA (fenol-clorofórmio/F, GuSCN-sílica/S ou kit QIAmp DNA Stool Mini/K). Para a avaliação da sensibilidade analítica, os testes foram realizados a partir de diluições seriadas de oocistos purificados, na ausência e na presença de 100 &mu;l de fezes bovinas. A sensibilidade diagnóstica foi avaliada pela comparação com o método microscópico de centrífugo-flutuação em sacarose (padrão-ouro) em 15 amostras fecais de diferentes hospedeiros naturalmente infectados. Na ausência de fezes, foram avaliados apenas os métodos EF, ES, CF e CS, sendo que EF apresentou sensibilidade analítica superior, possibilitando a detecção de até 1 oocisto. Na presença de fezes, os métodos EF, EK e CK apresentaram desempenhos equivalentes, com sensibilidade de 104 oocistos. As maiores sensibilidades diagnósticas foram obtidas pelos métodos EK e CK, que possibilitaram a detecção de 13 (86,7%) das 15 amostras. Devido à alta sensibilidade analítica de EF em amostras purificadas, avaliou-se sua sensibilidade diagnóstica em amostras de oocistos purificados pelo método de centrífugo-flutuacão em sacarose, obtendo-se 100% de detecção. A presença de inibidores nas amostras fecais reduziu fortemente a sensibilidade das reações de PCR a partir de DNA extraído pelos métodos avaliados, sendo recomendável o emprego de técnicas de purificação de oocistos previamente à extração de DNA. Os resultados apontam para uma melhor eficiência dos métodos de indução de excistamento e kit QIAmp DNA Stool Mini. / The performance of six methods for DNA extraction from Cryptosporidium spp. oocysts in feces were evaluated by nested PCR of SSU rRNA gene. The methods are the combination with small variations of two techniques for the release of sporozoites (induction of excystation/E or thermal shock/C) and three techniques for DNA purification (phenol-chloroform/F, GuSCN-silica/S or QIAmp DNA Stool Mini kit/K). For the evaluation of analytical sensitivity, tests were made from serial dilutions of purified oocysts, in absence and in presence of 100 &mu;l of cattle feces. The diagnostic sensitivity was assessed by comparison with the microscopic method of centrifugalflotation in sucrose (gold standard) in 15 fecal samples from different naturally infected hosts. In the absence of feces, only methods EF, ES, FC, and CS were tested. EF had the highest analytical sensitivity, enabling the detection of up to 1 oocyst. In the presence of feces, methods EF, EK, and CK showed similar performance, with sensitivity of 104 oocysts. The highest sensitivities were obtained by methods EK and CK, which enabled the detection of 13 (86.7%) of 15 samples. Due to the high analytical sensitivity of EF in purified samples, its diagnostic sensitivity was evaluated in samples of purified oocysts by the method of centrifugal-flotation in sucrose, resulting in 100% detection. The presence of inhibitors in fecal samples greatly reduced the sensitivity of the PCR reactions from DNA extraction methods evaluated, and the use of techniques for purification of oocysts prior to DNA extraction is recommended. The results show a better performance of the methods of induction of excystation and QIAmp DNA Stool Mini kit.

In the first part of this thesis, two chromosome Y specific genes ( SRYand TSPY) were chosen as the molecular targets to investigate the characteristics of fetal-specific DNA fragments in maternal plasma. By employing the touch down ligation-mediated PCR coupled with cloning and sequencing, the end property and the fragment species of fetal DNA were studied. / Noninvasive prenatal detection of fetal chromosomal aneuploidies is a much sought-after goal in fetomaternal medicine. The discovery of fetal DNA in the plasma of pregnant women has offered new opportunities for this purpose. However, the fact that fetal DNA amounts to just a minor fraction of all DNA in maternal plasma makes it challenging for locus-specific DNA assays to detect the small increase in sequences derived from a trisomic chromosome. On the other hand, although the clinical applications of plasma DNA for prenatal diagnosis are expanding rapidly, the biological properties of circulating DNA in plasma remain unclear. Recently, next-generation sequencing technologies have transformed the landscape of biomedical research through the ultra-high-throughput sequence information generated in a single run. Massively parallel sequencing allows us to study plasma DNA at an unprecedented resolution and also precisely detect fetal chromosomal aneuploidies in a locus-independent way. / Our group has demonstrated the use of massively parallel sequencing to quantify maternal plasma DNA sequences for the noninvasive prenatal detection of fetal trisomy 21. In the second part of this thesis, the clinical utility of this new sequencing approach was extended to the prenatal detection of fetal trisomy 18 and 13. A region-selection method was developed to minimize the effects of GC content on the diagnostic sensitivity and precision for the prenatal diagnosis of trisomy 13. To facilitate the next-generation sequencing-based maternal plasma DNA analysis for clinical implementation, two measures, i.e., lowering the starting volume of maternal plasma and barcoding multiple maternal plasma samples, were investigated. / Taken together, the results presented in this thesis have demonstrated the clinical utility of massively parallel sequencing of maternal plasma DNA and have also provided us a better understanding of the biology of circulating DNA molecules. / The third part of this thesis focuses on the massively parallel paired-end sequencing of plasma DNA. By analyzing millions of sequenced DNA fragments, the biological properties of maternal plasma DNA were elucidated, such as the size distribution of fetal-derived and maternally-contributed DNA molecules and the potential effect of epigenetic modification on DNA fragmentation. Moreover, the plasma DNA from hematopoietic stem cell transplant patients was characterized by paired-end sequencing approach. These sequencing data not only confirmed the predominant hematopoietic origin of cell-free DNA but also revealed the size difference between hematologically-derived and other tissue-derived DNA molecules in plasma. / Zheng, Wenli. / Adviser: Lo Yu Ming Dennis. / Source: Dissertation Abstracts International, Volume: 73-03, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 261-275). / 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.

INTRODUÇÃO: A apnéia obstrutiva do sono é uma doença altamente prevalente na população adulta e associada à morbidade significante. A polissonografia noturna é o método padrão ouro para o diagnóstico de apnéia obstrutiva do sono. Entretanto seu custo é elevado e a disponibilidade de leitos para polissonografia é muito inferior a demanda. Por esta razão, estratégias para otimizar o diagnóstico de apnéia obstrutiva do sono são urgentes e necessárias. O objetivo deste estudo foi o de comparar um exame diurno de polissonografia, de curta duração e através de sono induzido por benzodiazepínico com a polissonografia noturna para o diagnóstico de apnéia obstrutiva do sono. MÉTODOS: Foram estudamos 40 pacientes divididos em dois grupos baseados no resultado da polissonografia noturna (Índice de Apnéia e Hipopnéia = 15 eventos/hora). Os dezoito Indivíduos portadores de apnéia obstrutiva do sono (id= 46 + 9 anos) e os vinte e dois controles (id= 38 + 10 anos) foram submetidos a uma polissonografia diurna, de curta duração, com indução de sono através de infusão intravenosa lenta de midazolam. RESULTADOS: O sono induzido foi obtido em todos indivíduos. O tempo total de sono foi de 41,5 + 18,9 minutos. A maioria dos eventos respiratórios durante o sono induzido forma obstrutivos e similares aos observados durante a polissonografia noturna. Não houve diferença estatisticamente significativa entre o índice de apnéia e hipopnéia bem como com a saturação mínima de oxigênio obtido pela polissonografia noturna e com sono induzido nos grupos estudados (p>0,05). Reunindo os dois grupos, o índice de apnéia e hipopnéia e a menor saturação de oxigênio obtidos pelos dois métodos tiveram correlação significativa (r=0,67 e r=0,77, respectivamente). A sensibilidade e especificidade para o diagnóstico de apnéia obstrutiva do sono através do sono induzido foi 0,83 e 0,72 respectivamente. Nenhuma complicação foi observada durante o sono induzido. CONCLUSÃO: A polissonografia com sono induzido é um método rápido e seguro que pode ser uma alternativa a polissonografia noturna para o diagnóstico de apnéia obstrutiva do sono. / Polysomnography is the gold standard method for diagnosing obstructive sleep apnea. However, the gap between demand and capacity in performig polysomnography is a major healthcare problem. We sought to compare a short day-time induced sleep with full overnight standard PSG (full PSG) monitoring for the diagnosis of obstructive sleep apnea. We studied 40 patients classified into subjects with obstructive sleep apnea (n=18, age= 46.8 + 9.1yr) and controls (n=22, age= 38.5 + 10,7yr) groups, based on the results of a full polysomnography (apnea-hypopnea index >= 15 events/hour). All subjects underwent a short day-time polysomnography. Sleep was induced by slow intravenous drip infusion of midazolam and achived in all subjects. Total time of induced sleep was 41.5 ± 18.9 min. The majority of the respiratory events during induced sleep were obstructive and similar to that observed during full polysomnography. There was no difference between apnea-hypopnea index obtained by full and short polysomnography in obstructive sleep apnea and control groups (p>0,05). The same occured to lowest O2 saturation. Taken all together, apnea-hypopnea index and lowest O2 saturation during short polysomnography correlated well with full polysomnography (r=0,67 and r=0,77, respectively). Sensitivity and specificity for the diagnosis of obstructive sleep apnea by induced sleep was 0,83 and 0,72, respectively. No complications were observed. Induced sleep PSG by midazolan is a short and safe study that may represent an alternative for full polysomnography in the diagnosis of obstructive sleep apnea.

1997年，胎兒DNA被首次證實存在於母體血漿中。這一發現促進了無創產前診斷技術的發展。由於孕婦血漿中含大量來自母體的背景DNA，這給針對胎兒特異性DNA序列以外的產前診斷變得有挑戰性。近期開發的大規模平行測序技術把DNA定量精度提升到了一個空前的水平。本團隊已證實這一技術可應用於對胎兒染色體非整倍體和對胎兒全基因組的檢測。由於目前平行測序的費用仍相當昂貴，目標性測序技術可提高目標區域的數據比例從而降低測序成本。 / 在論文第一部分，本人論述了目標性測序在母體血漿DNA應用的可行性。本實驗採用雜交型富集技術對X染色體的外顯子進行富集。我們用平行測序比較了經由和未經富集處理的樣本。對比發現，經富集處理的樣本在目標區域的平均測序深度是未經富集處理樣本的213倍。目標區域的母體和胎兒DNA分子的富集程度相當。經富集處理後，目標區域的胎兒特異性等位基因的檢測率從3.5%提升至95.9%。 / 在論文第二部分，本人論述了目標性測序對胎兒21三體無創產前診斷的應用價值。我們對7，13，18和21號染色體上的單核苷酸多態性位點進行目標性測序。目標性測序數據顯示，在父源性21三體的樣本中，21號染色體上的胎兒特異性等位基因與共有性等位基因的比值上升約2倍。而在母源性21三體的樣本中，這一比值則下降約11%。本人採用電腦模擬實驗探討胎兒DNA濃度，有效等位基因數量和測序深度對檢測準確率的影響。 / 在論文第三部分，本人論述了目標性測序對胎兒單基因疾病無創產前診斷的應用。針對兩個需進行β地中海貧血產前診斷的家庭，我們對其β球蛋白基因進行目標性測序。我們用數字PCR技術推導了父母親β球蛋白基因區域的單倍型。經過相對性單倍型劑量分析，兩個胎兒的β地中海貧血遺傳狀況均得到了正確的推斷。其中一對夫婦位於致病區域的單倍型結構相近。 / 鑒於目標性測序技術可降低測序成本和提高目標序列的通量，其在血漿DNA的應用將有助於平行測序技術在無創性產前診斷、癌症診斷和移植監控等分子診斷學領域的發展。 / The presence of fetal DNA in the cell-free plasma of pregnant women was first reported in 1997. This discovery has facilitated the development of noninvasive prenatal diagnosis. The coexistence in maternal plasma of a minor population of fetal DNA among a major background of maternal DNA has posed challenges for extending noninvasive prenatal diagnostic applications that require analytical information beyond the detection of fetus-specific DNA sequences. The recent availability of massively parallel sequencing has enhanced the precision of DNA quantification to an unprecedented level. Our group has demonstrated the application of massively parallel sequencing in noninvasive prenatal diagnosis of chromosomal aneuploidies, as well as genome-wide fetal whole genome sequencing and mutational profiling. While the current costs of massively parallel sequencing are relatively expensive, targeted massively parallel sequencing may enhance the cost-effectiveness compared with the non-targeted approach because it increases the proportion of informative data from the regions-of-interest. / In the first part of this thesis, I have demonstrated the feasibility of targeted massively parallel sequencing in maternal plasma DNA. In this proof-of-principle study, hybridization-based target enrichment was used to enrich exons on chromosome X. Plasma DNA libraries with and without target enrichment were analyzed by massively parallel sequencing. For the targeted regions, the mean sequencing depth of the enriched samples was 213-fold higher than that of the non-enriched samples. Maternal and fetal DNA molecules were enriched to similar extents within the targeted regions. With target enrichment, the detection rate of fetus-specific alleles within the targeted regions increased from 3.5% to 95.9%. / In the second part of this thesis, I have demonstrated the potential application of targeted massively parallel sequencing of plasma DNA for noninvasive prenatal diagnosis of trisomy 21 using an allelic ratio approach. Targeted sequencing was used to enrich single nucleotide polymorphism loci on chr7, chr13, chr18 and chr21. The targeted sequencing data showed that the ratio between fetus-specific and shared alleles increased by approximately 2-fold on chr21 in a paternally-derived trisomy 21 case, and decreased by approximately 11% on chr21 for maternally-derived trisomy 21 cases. I have also used computer simulation to determine the impact of fractional fetal DNA concentration, number of informative alleles and sequencing depth on the detection accuracy. / In the third part of this thesis, I have demonstrated the feasibility of targeted massively parallel sequencing of maternal plasma DNA for noninvasive prenatal diagnosis of monogenic diseases. Targeted sequencing was used to enrich the β-globin gene region in two families undergoing prenatal diagnosis for β-thalassemia. Parental haplotypes of the β-globin gene region were deduced via digital polymerase chain reaction. Relative haplotype dosage analysis was performed successfully to determine the β-thalassemic status for the fetuses, including one family in which the parents had similar haplotype structures in the disease-causing region. / Because of its potential to save costs and increase throughput, targeted sequencing may catalyse the translation of massively parallel sequencing based molecular diagnostics into many fields, including noninvasive prenatal diagnosis, cancer diagnostics and transplantation monitoring. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Liao, Jiawei. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 147-155). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese. / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.vi / PUBLICATIONS --- p.vii / CONTRIBUTORS --- p.viii / TABLE OF CONTENTS --- p.ix / LIST OF TABLES --- p.xiii / LIST OF FIGURES --- p.xiv / LIST OF ABBREVIATIONS --- p.xvi / Chapter SECTION I : --- BACKGROUND --- p.1 / Chapter CHAPTER 1: --- Cell-free fetal DNA and targeted massively parallel sequencing --- p.2 / Chapter 1.1 --- Cell-free fetal DNA in maternal plasma --- p.2 / Chapter 1.2 --- NIPD by qualitative analysis --- p.3 / Chapter 1.2.1. --- Fetal sex assessment --- p.4 / Chapter 1.2.2. --- RHD genotyping --- p.5 / Chapter 1.2.3. --- Other implementations --- p.5 / Chapter 1.3 --- NIPD by quantitative analysis --- p.6 / Chapter 1.3.1. --- NIPD of chromosomal aneuploidies --- p.6 / Chapter 1.3.2. --- NIPD of autosomal recessive monogenic diseases --- p.8 / Chapter 1.4 --- Massively parallel sequencing of maternal plasma --- p.9 / Chapter 1.4.1. --- Massively parallel sequencing --- p.9 / Chapter 1.4.2. --- MPS-based NIPD of chromosomal aneuploidies --- p.11 / Chapter 1.4.3. --- MPS-based prenatal fetal whole-genome scanning --- p.15 / Chapter 1.5 --- Targeted massively parallel sequencing of maternal plasma --- p.19 / Chapter 1.5.1. --- Microdroplet-based PCR --- p.19 / Chapter 1.5.2. --- Molecular inversion probe --- p.20 / Chapter 1.5.3. --- On-array capture --- p.21 / Chapter 1.5.4. --- In-solution capture --- p.21 / Chapter 1.5.5. --- Implementation on plasma DNA --- p.22 / Chapter 1.6 --- Aims of this thesis --- p.29 / Chapter SECTION II : --- Feasibility of targeted MPS in maternal plasma DNA --- p.30 / Chapter CHAPTER 2: --- Targeted MPS of maternal plasma DNA permits efficient and unbiased detection of fetal alleles --- p.31 / Chapter 2.1 --- Introduction --- p.31 / Chapter 2.2 --- Methods --- p.34 / Chapter 2.2.1 --- Study participants and sample collection --- p.34 / Chapter 2.2.2 --- Sample processing and DNA extraction --- p.34 / Chapter 2.2.3 --- DNA quantification --- p.36 / Chapter 2.2.4 --- Microarray genotyping --- p.39 / Chapter 2.2.5 --- Plasma DNA library preparation --- p.39 / Chapter 2.2.6 --- Plasma DNA library validation --- p.40 / Chapter 2.2.7 --- Target enrichment --- p.44 / Chapter 2.2.8 --- Massively parallel sequencing and alignment --- p.45 / Chapter 2.3 --- Results --- p.48 / Chapter 2.3.1 --- Efficiency of target enrichment --- p.48 / Chapter 2.3.2 --- Sequence coverage within the targeted region --- p.53 / Chapter 2.3.3 --- Fetus-specific allele detection --- p.59 / Chapter 2.3.4 --- Fractional fetal DNA concentrations before and after enrichment --- p.63 / Chapter 2.4 --- Discussion --- p.66 / Chapter SECTION III : --- NIPD of trisomy 21 by targeted MPS of maternal plasma DNA --- p.71 / Chapter CHAPTER 3: --- NIPD of fetal trisomy 21 by allelic ratio analysis using targeted MPS of maternal plasma DNA --- p.72 / Chapter 3.1 --- Introduction --- p.72 / Chapter 3.2 --- Methods --- p.74 / Chapter 3.2.1 --- Study participants and sample collection --- p.74 / Chapter 3.2.2 --- Sample processing and DNA extraction --- p.74 / Chapter 3.2.3 --- Targeted MPS of plasma DNA libraries --- p.74 / Chapter 3.2.4 --- F-S ratio calculation --- p.76 / Chapter 3.2.5 --- Microarray genotyping --- p.78 / Chapter 3.2.6 --- Computer simulation --- p.78 / Chapter 3.3 --- Results --- p.80 / Chapter 3.3.1 --- Efficiency of target enrichment --- p.80 / Chapter 3.3.2 --- Estimation of fractional fetal DNA concentrations --- p.83 / Chapter 3.3.3 --- F-S ratio calculation using non-targeted sequencing data --- p.83 / Chapter 3.3.4 --- F-S ratio calculation using targeted sequencing data --- p.85 / Chapter 3.3.5 --- Computer simulation --- p.85 / Chapter 3.4 --- Discussion --- p.90 / Chapter SECTION IV : --- NIPD of monogenic diseases by targeted MPS of maternal plasma DNA --- p.94 / Chapter CHAPTER 4: --- NIPD of monogenic diseases by targeted MPS of maternal plasma: application to Beta-thalassemia --- p.95 / Chapter 4.1 --- Introduction --- p.95 / Chapter 4.2 --- Methods --- p.98 / Chapter 4.2.1 --- Sample collection and DNA extraction --- p.98 / Chapter 4.2.2 --- Microarray-based genotyping --- p.100 / Chapter 4.2.3 --- Targeted MPS of plasma DNA libraries --- p.100 / Chapter 4.2.4 --- Genotyping by Sanger sequencing --- p.103 / Chapter 4.2.5 --- Haplotyping by digital PCR --- p.105 / Chapter 4.2.6 --- RHDO analysis --- p.105 / Chapter 4.3 --- Results --- p.110 / Chapter 4.3.1 --- Effectiveness of targeted sequencing --- p.110 / Chapter 4.3.2 --- Determination of fetal HBB genotype in the first family --- p.112 / Chapter 4.3.3 --- Determination of fetal HBB genotype in the second family --- p.113 / Chapter 4.4 --- Discussion --- p.115 / Chapter SECTION V : --- CONCLUDING REMARKS --- p.120 / Chapter CHAPTER 5: --- Conclusion and future perspectives --- p.121 / Chapter 5.1 --- Targeted MPS in plasma DNA --- p.121 / Chapter 5.2 --- Targeted MPS in NIPD of chromosomal aneuploidies --- p.124 / Chapter 5.3 --- Targeted MPS in NIPD of monogenic diseases --- p.126 / Chapter Appendix I: --- Primer names and sequences for genotyping and haplotyping of βeta-globin gene cluster region --- p.128 / Chapter Appendix II: --- Primers used in PCRs and sequencing for the parents in the first family --- p.132 / Chapter Appendix III: --- Primers used in PCRs and sequencing for the parents in the second family --- p.138 / Chapter Appendix IV: --- RHDO analysis on maternal plasma DNA in the first family --- p.140 / Chapter Appendix V: --- RHDO analysis on maternal plasma DNA in the second family --- p.145 / References --- p.147