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Biomedical subjects

Y M Dennis Lo

Publications and source records attributed to Y M Dennis Lo.

At least 19 recordsLinked to original sources
PubMed2007

Plasma placental RNA allelic ratio permits noninvasive prenatal chromosomal aneuploidy detection.

Current methods for prenatal diagnosis of chromosomal aneuploidies involve the invasive sampling of fetal materials using procedures such as amniocentesis or chorionic villus sampling and constitute a finite risk to the fetus. Here, we outline a strategy for fetal chromosome dosage assessment that can be performed noninvasively through analysis of placental expressed mRNA in maternal plasma. We achieved noninvasive prenatal diagnosis of fetal trisomy 21 by determining the ratio between alleles of a single-nucleotide polymorphism (SNP) in PLAC4 mRNA, which is transcribed from chromosome 21 and expressed by the placenta, in maternal plasma. PLAC4 mRNA in maternal plasma was fetal derived and cleared after delivery. The allelic ratios in maternal plasma correlated with those in the placenta. Fetal trisomy 21 was detected noninvasively in 90% of cases and excluded in 96.5% of controls.

Asian People↗
PubMed2006

Prenatal diagnosis: progress through plasma nucleic acids.

Over the past 40 years, much effort has been spent on developing non-invasive prenatal diagnostic methods. Since 1997, the progress of this field has been accelerated by the unexpected finding of extracellular fetal nucleic acids in maternal plasma. These developments have been translated into many novel genetic, epigenetic and gene-expression markers, and are expected to have a fundamental impact on the future practice of prenatal diagnosis.

DNA↗
PubMed2006

Plasma Epstein-Barr viral deoxyribonucleic acid quantitation complements tumor-node-metastasis staging prognostication in nasopharyngeal carcinoma.

PURPOSE: To evaluate the effect of combining circulating Epstein-Barr viral (EBV) DNA load data with TNM staging data in pretherapy prognostication of nasopharyngeal carcinoma (NPC). PATIENTS AND METHODS: Three hundred seventy-six patients with all stages of NPC were studied. Pretreatment plasma/serum EBV DNA concentrations were quantified by a polymerase chain reaction assay. Determinants of overall survival were assessed by multivariate analysis. Survival probabilities of patient groups, segregated by clinical stage (I, II, III, or IV) alone and also according to EBV DNA load (low or high), were compared. RESULTS: Pretherapy circulating EBV DNA load is an independent prognostic factor for overall survival in NPC. Patients with early-stage disease were segregated by EBV DNA levels into a poor-risk subgroup with survival similar to that of stage III disease and a good-risk subgroup with survival similar to stage I disease. CONCLUSION: Pretherapy circulating EBV DNA load is an independent prognostic factor to International Union Against Cancer (UICC) staging in NPC. Combined interpretation of EBV DNA data with UICC staging data leads to alteration of risk definition of patient subsets, with improved risk discrimination in early-stage disease. Validation studies are awaited.

Biomarkers, Tumor↗
PubMed2006

Relationship between pretreatment level of plasma Epstein-Barr virus DNA, tumor burden, and metabolic activity in advanced nasopharyngeal carcinoma.

PURPOSE: Plasma Epstein-Barr virus DNA (pEBV DNA) is an important prognostic marker in nasopharyngeal carcinoma (NPC). This study tested the hypotheses that pEBV DNA reflects tumor burden and metabolic activity by evaluating its relationship with tumor volume and 18F-fluorodeoxyglucose (18F-FDG) uptake in NPC. METHODS AND MATERIALS: Pre-treatment pEBV DNA analysis, 18F-FDG positron emission tomography-computed tomography scan (PET-CT) and magnetic resonance imaging (MRI) of the head and neck were performed in 57 patients. Net volume (cm3) of the primary tumor (T(vol)) and regional nodes (N(vol)) were quantified on MRI. 18F-FDG uptake was expressed as the maximum standardized uptake value (SUV(max)) at the primary tumor (T(suv)) and regional nodes (N(suv)). Lesions with SUV(max) > or = 2.5 were considered malignant. Relationship between SUV(max), natural logarithm (log) of pEBV DNA, and square root (sq) of MRI volumes was analyzed using the Wilcoxon test. A linear regression model was constructed to test for any interaction between variables and disease stage. RESULTS: Log-pEBV DNA showed significant correlation with sq-T(vol) (r = 0.393), sq-N(vol) (r = 0.452), total tumor volume (sq-Total(vol) = T(vol) + N(vol), r = 0.554), T(suv) (r = 0.276), N(suv) (r = 0.434), and total SUV(max) (Total(suv) = T(suv) + N(suv), r = 0.457). Likewise, sq-T(vol) was correlated to T(suv) (r = 0.426), and sq-N(vol) with N(suv) (r = 0.651). Regression analysis showed that only log-pEBV DNA was significantly associated with sq-Total(vol) (p < 0.001; parameter estimate = 8.844; 95% confidence interval = 3.986-13.703), whereas Sq-T(vol) was significantly associated with T(suv) (p = 0.002; parameter estimate = 3.923; 95% confidence interval = 1.498-6.348). CONCLUSION: This study supports the hypothesis that cell-free plasma EBV DNA is a marker of tumor burden in EBV-related NPC.

Adult↗
PubMed2006

Hypermethylated RASSF1A in maternal plasma: A universal fetal DNA marker that improves the reliability of noninvasive prenatal diagnosis.

BACKGROUND: We recently demonstrated that the promoter of the RASSF1A gene is hypermethylated in the placenta and hypomethylated in maternal blood cells. This methylation pattern allows the use of methylation-sensitive restriction enzyme digestion for detecting the placental-derived hypermethylated RASSF1A sequences in maternal plasma. METHODS: We performed real-time PCR after methylation-sensitive restriction enzyme digestion to detect placental-derived RASSF1A sequences in the plasma of 28 1st-trimester and 43 3rd-trimester pregnant women. We used maternal plasma to perform prenatal fetal rhesus D (RhD) blood group typing for 54 early-gestation RhD-negative women, with hypermethylated RASSF1A as the positive control for fetal DNA detection. RESULTS: Hypermethylated RASSF1A sequences were detectable in the plasma of all 71 pregnant women. The genotype of plasma RASSF1A after enzyme digestion was identical to the fetal genotype in each case, thus confirming its fetal origin. Nineteen of the 54 pregnant women undergoing prenatal fetal RhD genotyping showed undetectable RHD sequences in their plasma DNA samples. The fetal DNA control, RASSF1A, was not detectable in 4 of the 19 women. Subsequent chorionic villus sample analysis revealed that 2 of these 4 women with negative RHD and RASSF1A signals were in fact carrying RhD-positive fetuses. CONCLUSIONS: Hypermethylated RASSF1A is a universal marker for fetal DNA and is readily detectable in maternal plasma. When applied to prenatal RhD genotyping, this marker allows the detection of false-negative results caused by low fetal DNA concentrations in maternal plasma. This new marker can also be applied to many other prenatal diagnostic and monitoring scenarios.

Actins↗
PubMed2006

Noninvasive prenatal detection of fetal trisomy 18 by epigenetic allelic ratio analysis in maternal plasma: Theoretical and empirical considerations.

BACKGROUND: The discovery of cell-free fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. However, the use of maternal plasma fetal DNA for the direct detection of fetal chromosomal aneuploidies has not been reported. We postulate that the aneuploidy status of a fetus could be revealed by an epigenetic allelic ratio approach, i.e., by analyzing the allelic ratio of a single-base variation present within DNA molecules exhibiting a placental-specific epigenetic signature in maternal plasma. METHODS: Placental-derived fetal-specific unmethylated maspin (SERPINB5) promoter sequences on human chromosome 18 were detectable in placental-maternal DNA mixtures and in maternal plasma by bisulfite modification followed by methylation-specific PCR (MSP) and primer extension. The ratios between the extension products of the 2 alleles were calculated for heterozygous placentas, placental-maternal blood cell DNA mixtures, and maternal plasma samples. The allelic ratios were compared between pregnancies carrying trisomy 18 and euploid fetuses. RESULTS: The epigenetic allelic ratios of all tested trisomy 18 samples deviated from the reference range obtained from euploid samples (placental DNA, 1.135 to 2.052; placental-maternal DNA mixtures, 1.170 to 1.985; maternal plasma, 0.330 to 3.044; without skew correction on the raw mass spectrometric data). A theoretical model was established and validated that predicted that a minimum of 200 copies of genomic DNA after bisulfite conversion were required for distinguishing euploid and aneuploid fetuses with confidence. CONCLUSION: Epigenetic allelic ratio analysis of maternal plasma DNA represents a promising approach for noninvasive prenatal diagnosis of fetal chromosomal aneuploidies.

Chromosomes, Human, Pair 18↗
PubMed2006

Comparison of plasma beta-globin DNA and S-100 protein concentrations in acute stroke.

BACKGROUND: This study aimed to compare changes in plasma beta-globin DNA and serum S100 protein to diagnose stroke and for predicting mortality and morbidity. METHODS: Patients with stroke-like symptoms presenting to the emergency department of a Hong Kong hospital were recruited. Plasma DNA was analyzed for the beta-globin gene with fluorescent-based PCR. S100 concentrations were determined using ELISA. Primary outcomes were diagnosis of stroke, mortality, and modified Rankin Score (mRS) after 6 months. RESULTS: One hundred ninety-seven consecutive patients recruited, 118 (60%) ischemic stroke, 35 (18%) hemorrhage and 44 (22%) with no acute neuroimaging changes. Serum S100 and plasma DNA were increased in 126 (p<0.0010) and 36 (p=0.21) stroke patients respectively vs. controls. Median plasma DNA was higher in hemorrhagic stroke than those without (1725 vs. 1050 kilogenome-equivalents/l, p=0.0104). Median plasma DNA was higher in mRS>2 vs. mRS 2 patients vs. mRS<or=2 (0.152 vs. 0.131 microg/l, p=0.0003). The odds ratio (OR) of discriminating hemorrhagic from non-hemorrhagic stroke with DNA was 4.24 (95% CI 1.88-9.56); S100 and DNA together give an OR of 16.55. CONCLUSION: For stroke diagnosis, S100 performs better than DNA; DNA is a better marker for hemorrhage. For diagnosis of hemorrhagic stroke, combined S100 and DNA performs better than either alone. Plasma DNA and serum S100 predict morbidity and mortality in stroke.

Adult↗
PubMed2006

Reduced plasma RNA integrity in nasopharyngeal carcinoma patients.

PURPOSE: Recent research has shown the feasibility of detecting cell-free RNA markers in human subjects. As elevated RNase activity has previously been described in the circulation of cancer patients, we hypothesized that cancer patients may have reduced plasma RNA integrity. In this study, we used nasopharyngeal carcinoma (NPC) as a model system to test this hypothesis. EXPERIMENTAL DESIGN: Plasma RNA integrity was determined using the ratio of the concentrations of transcript sequences corresponding to the 3' to those from the 5' end of a housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Transcript concentrations were measured using real-time quantitative reverse transcription-PCR assays targeting the 5' and 3' regions. We analyzed the plasma RNA integrity in 49 untreated NPC patients and 53 healthy controls. We also assessed the plasma samples from 19 NPC patients before and after radiotherapy to further show the clinical potential of this marker. RESULTS: The 3' to 5' GAPDH ratio was significantly lower in the plasma of untreated NPC patients when compared with healthy controls (0.0252 versus 0.0485, P = 0.024). Statistical analysis showed that plasma GAPDH ratio was correlated with tumor stage but not with sex and age. Moreover, 14 of 19 NPC patients (74%) showed significant increase in the plasma GAPDH ratio following radiotherapy (P = 0.003). All of these patients were in clinical remission after treatment. CONCLUSIONS: Our findings suggest that NPC is associated with disturbances in the integrity of cell-free circulating RNA, raising the possibility that measurement of plasma RNA integrity may serve as a useful marker for the diagnosis and monitoring of malignant diseases.

Adult↗
PubMed2006

Plasma beta-globin DNA as a prognostic marker in chest pain patients.

BACKGROUND: Acute coronary syndrome may involve cell death and the release of nucleic acids into the circulation. We thus investigated whether plasma DNA concentrations are increased and determined its prognostic significance in patients with ACS. METHODS: Real-time polymerase chain reaction was used to quantitatively measure the beta-globin gene from blood samples taken from patients presenting to an emergency department with chest pain of probable cardiac cause. RESULTS: Samples from 58 patients with chest pain, and from 21 age- and sex-matched healthy control subjects were analysed. Compared with the control group, median plasma DNA concentrations were increased 1.5-fold in patients with minor cardiac injury, were increased further in patients with STEA and STEMI, and were the highest in those patients who died within 2 years (P=0.0005; post-hoc Dunn's, P<0.05). Median plasma DNA concentrations were higher in patients who later developed heart failure (1060 vs. 500 kGE/l; P=0.0095); higher in patients who later reinfarcted (1000 vs. 530 kGE/l; P=0.0298); higher in patients who had a cardiac arrest in that admission (1350 vs. 525 kGE/l; P=0.04); and were higher in patients who were readmitted within 6 months of discharge (725 vs. 475 kGE/l; P=0.04). CONCLUSION: Plasma DNA is a potential marker for post-ACS complications.

Adult↗
PubMed2006

Automated extraction protocol for quantification of SARS-coronavirus RNA in serum: an evaluation study.

BACKGROUND: We have previously developed a test for the diagnosis and prognostic assessment of the severe acute respiratory syndrome (SARS) based on the detection of the SARS-coronavirus RNA in serum by real-time quantitative reverse transcriptase polymerase chain reaction (RT-PCR). In this study, we evaluated the feasibility of automating the serum RNA extraction procedure in order to increase the throughput of the assay. METHODS: An automated nucleic acid extraction platform using the MagNA Pure LC instrument (Roche Diagnostics) was evaluated. We developed a modified protocol in compliance with the recommended biosafety guidelines from the World Health Organization based on the use of the MagNA Pure total nucleic acid large volume isolation kit for the extraction of SARS-coronavirus RNA. The modified protocol was compared with a column-based extraction kit (QIAamp viral RNA mini kit, Qiagen) for quantitative performance, analytical sensitivity and precision. RESULTS: The newly developed automated protocol was shown to be free from carry-over contamination and have comparable performance with other standard protocols and kits designed for the MagNA Pure LC instrument. However, the automated method was found to be less sensitive, less precise and led to consistently lower serum SARS-coronavirus concentrations when compared with the column-based extraction method. CONCLUSION: As the diagnostic efficiency and prognostic value of the serum SARS-CoV RNA RT-PCR test is critically associated with the analytical sensitivity and quantitative performance contributed both by the RNA extraction and RT-PCR components of the test, we recommend the use of the column-based manual RNA extraction method.

Humans↗
PubMed2006

Serum proteomic fingerprints of adult patients with severe acute respiratory syndrome.

BACKGROUND: Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a new coronavirus strain, SARS-CoV. Specific proteomic patterns might be present in serum in response to the infection and could be useful for early detection of the disease. METHODS: Using surface-enhanced laser desorption/ionization (SELDI) ProteinChip technology, we profiled and compared serum proteins of 39 patients with early-stage SARS infection and 39 non-SARS patients who were suspected cases during the SARS outbreak period. Proteomic patterns associated with SARS were identified by bioinformatic and biostatistical analyses. Features of interest were then purified and identified by tandem mass spectrometry. RESULTS: Twenty proteomic features were significantly different between the 2 groups. Fifteen were increased in the SARS group, and 5 were decreased. Their concentrations were correlated with 2 or more clinical and/or biochemical variables. Two were correlated with the SARS-CoV viral load. Hierarchical clustering analysis showed that a majority of the SARS patients (95%) had similar serum proteomic profiles and identified 2 subgroups with poor prognosis. ROC curve analysis identified individual features as potential biomarkers for SARS diagnosis (areas under ROC curves, 0.733-0.995). ROC curve areas were largest for an N-terminal fragment of complement C3c alpha chain (m/z 28 119) and an internal fragment of fibrinogen alpha-E chain (m/z 5908). Immunoglobulin kappa light chain (m/z 24 505) positively correlated with viral load. CONCLUSIONS: Specific proteomic fingerprints in the sera of adult SARS patients could be used to identify SARS cases early during onset with high specificity and sensitivity.

Adult↗
PubMed2006

Fetal DNA in maternal plasma: progress through epigenetics.

The discovery of cell-free fetal DNA in maternal plasma has opened up new possibilities for noninvasive prenatal diagnosis. Most of the work in this field has focused on the detection of fetal genetic markers that are distinguishable from the background maternal DNA. The feasibility of detecting fetal epigenetic markers in maternal plasma using an imprinted locus was demonstrated in 2002. This work has recently led to the development of the first universal fetal epigenetic marker, hypomethylated maspin, which can be used for fetal DNA detection in maternal plasma, irrespective of fetal gender and genetic polymorphisms. It is expected that many more fetal epigenetic markers that can be used in this manner will be developed over the next few years. These markers may catalyze the eventual clinical use of circulating fetal DNA for noninvasive prenatal diagnosis, such as for the detection of fetal chromosomal aneuploidies.

DNA↗
PubMed2006

Placental RNA in maternal plasma: toward noninvasive fetal gene expression profiling.

The recent demonstration of the presence of placenta-derived fetal RNA in maternal plasma has opened up new opportunities for noninvasive prenatal investigation. Circulating fetal RNA analysis could in principle be applied to all pregnancies without the limitations by fetal gender or polymorphisms between the mother and fetus. The use of fetus- or disease-specific circulating RNA markers would greatly increase the number of markers that can be used for prenatal monitoring. With the recent advances in microarray technology, new placenta-derived plasma RNA markers could be rapidly identified. These newly identified placental transcripts were robustly detectable in maternal plasma and were pregnancy-specific. Remarkably, the relative concentrations of the placental mRNA in maternal plasma directly reflect the gene expression patterns in the placenta, an observation which suggests that placental gene expression level plays a predominant role in determining the placental mRNA concentrations in maternal plasma. Thus, fetal mRNA measurement in maternal plasma may be a useful tool for noninvasive prenatal placental gene expressing profiling.

Female↗
PubMed2006

Plasma RNA integrity analysis: methodology and validation.

The detection of cell-free RNA in plasma and serum of human subjects has found increasing applications in the field of medical diagnostics. However, many questions regarding the biology of circulating RNA remain to be addressed. One issue concerns the molecular nature of these circulating RNA species. We have recently developed a simple and quantitative method to investigate the integrity of plasma RNA. Our results have suggested that cell-free RNA in plasma is generally present as fragmented molecules instead of intact transcripts, with a predominance of 5' fragments. In this article, we summarize the basic principles in the experimental design for plasma RNA integrity analysis and highlight some of the important technical considerations for this type of investigation.

Humans↗
PubMed2006

Time profile of appearance and disappearance of circulating placenta-derived mRNA in maternal plasma.

BACKGROUND: Fetal RNA of placental origin has been detected in the plasma of pregnant women, but the timing of the first appearance and the detailed kinetics of postdelivery clearance of such circulating RNA have not been studied. METHODS: To address the timing of the first appearance of circulating placental RNA, we collected serial maternal blood samples from 47 women who had conceived by assisted reproductive procedures. To address the postdelivery clearance kinetics, we collected serial postdelivery blood samples from 6 pregnant women who had delivered by cesarean section. Placenta-derived transcripts were sought by real-time quantitative reverse transcription-PCR. RESULTS: The earliest gestational age at which human placental lactogen and human chorionic gonadotropin beta-subunit mRNAs were detectable in a proportion of the pregnant women was the 4th week of gestation. The postdelivery study indicated that the median apparent half-life for the clearance of human placental lactogen mRNA was 14 min. CONCLUSIONS: Placenta-derived mRNA can be found in maternal plasma from very early on in gestation, suggesting a possible role for early noninvasive prenatal diagnosis or monitoring. The rapid kinetics of circulating placental mRNA suggest that its plasma concentrations may be used to monitor recent physiologic or pathologic events.

Female↗
PubMed2006

Introduction to the polymerase chain reaction.

The polymerase chain reaction (PCR) is an in vitro method for the amplification of DNA. Since the introduction of the PCR in 1985, it has become an indispensable technique for many applications in scientific research and clinical and forensic investigations. In this chapter, the principle and setup of PCR, as well as the methods for analyzing PCR products, will be discussed.

DNA↗