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Objectives The objectives of this study were to compare the concentrations, size profiles and major tissue contributors of cell-free DNA (cfDNA) in plasma and in serum. Design and methods Thirteen pregnant women in the third trimester were recruited for this study. We collected EDTA-plasma and serum samples using various collection tubes. We determined their cfDNA concentrations and fetal cfDNA fractions using a zinc-finger X (ZFX)/zinc-finger Y (ZFY) droplet digital polymerase chain reaction (ZFX/ZFY ddPCR) assay. We used paired-end massively parallel sequencing (MPS) to measure plasma and serum cfDNA sizes at single-base resolution. We deconvoluted the genome-wide bisulfite sequencing data with reference to the methylation profiles of different tissues. Results The concentrations of cfDNA collected in Sarstedt Serum Z tubes were found to be significantly higher than those in Greiner Bio-One Vacuette® Z Serum Separator Clot Activator tubes or Vacuette® Z Serum Clot Activator tubes. The concentrations of fetal cfDNA were significantly reduced in samples collected in the Vacuette® serum collection tubes. Fetal cfDNA fractions were significantly reduced in all sera compared to plasma. MPS of serum cfDNA revealed a right shift of the size distributions compared to plasma. Methylation-based tissue mapping of serum cfDNA revealed an increase of cfDNA from neutrophils and B cells but not T cells. Conclusions The use of different serum collection tubes has a significant impact on serum cfDNA concentrations. This effect is likely mediated through the combined effect of genomic DNA release from white blood cells and DNA degradation or removal.

My group has a longstanding interest in the diagnostic applications of cell-free DNA in plasma. For example, we have pioneered noninvasive prenatal testing (NIPT) and the use of plasma DNA for cancer screening. We believe that understanding the fundamental biology of circulating DNA is essential to further advance the field. In this regard, we have been particularly interested in the fragmentation patterns of cell-free DNA in plasma. We have shown that cell-free fetal DNA molecules in the plasma of pregnant women are shorter than those of maternal origin. The differential size profiles between circulating fetal and maternal DNA have enabled the use of plasma DNA size as an independent metric for NIPT. In the area of cancer liquid biopsy, we have used circulating Epstein-Barr virus (EBV) DNA as an example of tumor-derived DNA in plasma. Hence, circulating EBV DNA molecules are also short fragments of DNA. In another example, we have used hepatocellular carcinoma as a model system and have found that circulating tumor-derived DNA molecules have a shorter size profile than those of nontumoral origin. We are exploring enzymes that might be involved in the fragmentation of plasma DNA. We have shown that mice in which both copies of the Dnase1l3 gene have been knocked out have a larger size profile of circulating DNA. We have also developed a plasma DNA end motif metric to measure the effect of disruption of this nuclease system. In addition to the fragmentation of linear DNA in plasma, my group is also interested in exploring the presence of nonlinear DNA in plasma. Hence, we have used mitochondrial DNA (mtDNA) as a model system as mtDNA exists as a circular molecule inside mitochondria. Interestingly, we have observed the existence of both linear and circular mtDNA in plasma. Using liver and bone marrow transplantation models, we have shown that the circular form is predominantly of hematopoietic origin while the linear form is predominantly from the liver. Plasma mtDNA topologics thus holds information on the origin of circulating DNA. These studies therefore demonstrate some of the exciting findings that can be revealed through the study of plasma DNA fragmentomics and topologics. We believe that such new biologic understandings will drive new diagnostic applications. Citation Format: Yuk Ming Dennis Lo. Plasma DNA-based molecular diagnostics: Fragments, circles and beyond [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA01.

Background We have previously reported an antigen-specific protocol to induce transplant tolerance and linked suppression to human embryonic stem cell (hESC)-derived tissues in immunocompetent mice through coreceptor and costimulation blockade. However, the exact mechanisms of acquired immune tolerance in this model have remained unclear. Methods We utilize the NOD.Foxp3 hCD2 reporter mouse line and an ablative anti-hCD2 antibody to ask if CD4+FOXP3+ regulatory T cells (Treg) are required for coreceptor and costimulation blockade-induced immune tolerance. We also perform genome-wide single-cell RNA-sequencing to interrogate Treg during immune rejection and tolerance and to indicate possible mechanisms involved in sustaining Treg function. Results We show that Treg are indispensable for tolerance induced by coreceptor and costimulation blockade as depletion of which with an anti-hCD2 antibody resulted in rejection of hESC-derived pancreatic islets in NOD.Foxp3 hCD2 mice. Single-cell transcriptomic profiling of 12,964 intragraft CD4+ T cells derived from rejecting and tolerated grafts reveals that Treg are heterogeneous and functionally distinct in the two outcomes of transplant rejection and tolerance. Treg appear to mainly promote chemotactic and ubiquitin-dependent protein catabolism during transplant rejection while seeming to harness proliferative and immunosuppressive function during tolerance. We also demonstrate that this form of acquired transplant tolerance is associated with increased proliferation and PD-1 expression by Treg. Blocking PD-1 signaling with a neutralizing anti-PD-1 antibody leads to reduced Treg proliferation and graft rejection. Conclusions Our results suggest that short-term coreceptor and costimulation blockade mediates immune tolerance to hESC-derived pancreatic islets by promoting Treg proliferation through engagement of PD-1. Our findings could give new insights into clinical development of hESC-derived pancreatic tissues, combined with immunotherapies that expand intragraft Treg, as a potentially sustainable alternative treatment for T1D.

The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type–specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions.

Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270× haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus’s maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195× coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.

BACKGROUND Tumor-derived DNA can be found in the plasma of cancer patients. In this study, we explored the use of shotgun massively parallel sequencing (MPS) of plasma DNA from cancer patients to scan a cancer genome noninvasively. METHODS Four hepatocellular carcinoma patients and a patient with synchronous breast and ovarian cancers were recruited. DNA was extracted from the tumor tissues, and the preoperative and postoperative plasma samples of these patients were analyzed with shotgun MPS. RESULTS We achieved the genomewide profiling of copy number aberrations and point mutations in the plasma of the cancer patients. By detecting and quantifying the genomewide aggregated allelic loss and point mutations, we determined the fractional concentrations of tumor-derived DNA in plasma and correlated these values with tumor size and surgical treatment. We also demonstrated the potential utility of this approach for the analysis of complex oncologic scenarios by studying the patient with 2 synchronous cancers. Through the use of multiregional sequencing of tumoral tissues and shotgun sequencing of plasma DNA, we have shown that plasma DNA sequencing is a valuable approach for studying tumoral heterogeneity. CONCLUSIONS Shotgun DNA sequencing of plasma is a potentially powerful tool for cancer detection, monitoring, and research.

Noninvasive prenatal testing using massively parallel sequencing of maternal plasma DNA has been rapidly adopted in clinical use worldwide. Fetal DNA fraction in a maternal plasma sample is an important parameter for accurate interpretations of these tests. However, there is a lack of methods involving low-sequencing depth and yet would allow a robust and accurate determination of fetal DNA fraction in maternal plasma for all pregnancies. In this study, we have developed a new method to accurately quantify the fetal DNA fraction by analysing the maternal genotypes and sequencing data of maternal plasma DNA. Fetal DNA fraction was calculated based on the proportion of non-maternal alleles at single-nucleotide polymorphisms where the mother is homozygous. This new approach achieves a median deviation of 0.6% between predicted fetal DNA fraction and the actual fetal DNA fraction using as low as 0.03-fold sequencing coverage of the human genome. We believe that this method will further enhance the clinical interpretations of noninvasive prenatal testing using genome-wide random sequencing.

The 15 years since the discovery of fetal DNA in maternal plasma have witnessed remarkable developments in noninvasive prenatal diagnosis. An understanding of biological parameters governing this phenomenon, such as the concentration and molecular size of circulating fetal DNA, has guided its diagnostic applications. Early efforts focused on the detection of paternally inherited sequences, which were absent in the maternal genome, in maternal plasma. Recent developments in precise measurement technologies such as digital polymerase chain reaction (PCR) have allowed the detection of minute allelic imbalances in plasma and have catalyzed analysis of single-gene disorders such as the hemoglobinopathies and hemophilia. The advent of massively parallel sequencing has enabled the robust detection of fetal trisomies in maternal plasma. Recent proof-of-concept studies have detected a chromosomal translocation and a microdeletion and have deduced a genome-wide genetic map of a fetus from maternal plasma. Understanding the ethical, legal, and social aspects in light of such rapid developments is thus a priority for future research.

Motivation: The fractional fetal DNA concentration is one of the critical parameters for non-invasive prenatal diagnosis based on the analysis of DNA in maternal plasma. Massively parallel sequencing (MPS) of DNA in maternal plasma has been demonstrated to be a powerful tool for the non-invasive prenatal diagnosis of fetal chromosomal aneuploidies. With the rapid advance of MPS technologies, the sequencing cost per base is dramatically reducing, especially when using targeted MPS. Even though several approaches have been developed for deducing the fractional fetal DNA concentration, none of them can be used to deduce the fractional fetal DNA concentration directly from the sequencing data without prior genotype information. Result: In this study, we implement a statistical mixture model, named FetalQuant, which utilizes the maximum likelihood to estimate the fractional fetal DNA concentration directly from targeted MPS of DNA in maternal plasma. This method allows the improved deduction of the fractional fetal DNA concentration, obviating the need of genotype information without loss of accuracy. Furthermore, by using Bayes’ rule, this method can distinguish the informative single-nucleotide polymorphism loci where the mother is homozygous and the fetus is heterozygous. We believe that FetalQuant can help expand the spectrum of diagnostic applications using MPS on DNA in maternal plasma. Availability: Software and simulation data are available at http://sourceforge.net/projects/fetalquant/ Contact: haosun@cuhk.edu.hk Supplementary Information: Supplementary data are available at Bioinformatics online.

The discovery of cell-free circulating fetal nucleic acids in maternal plasma has opened up new possibilities in non-invasive prenatal diagnosis. The rapid advancement of this field in the past decade is catalysed by the discovery of new classes of fetal nucleic acid markers and technological developments in nucleic acid detection and amplification. In this review, some of the more significant recent developments in this field will be discussed, including the detection of single molecule, chromosomal aneuploidies, single nucleotide variations and placental microRNAs in maternal plasma.

Tumour-associated changes have been observed in the circulating nucleic acids of cancer patients and have been proposed to be useful for the detection and monitoring of cancers. In this review, different approaches for detecting tumour-associated nucleic acids in the circulation and their potential applications as tumour markers are discussed.

Plasma consists of DNA released from multiple tissues within the body. Using genome-wide bisulfite sequencing of plasma DNA and deconvolution of the sequencing data with reference to methylation profiles of different tissues, we developed a general approach for studying the major tissue contributors to the circulating DNA pool. We tested this method in pregnant women, patients with hepatocellular carcinoma, and subjects following bone marrow and liver transplantation. In most subjects, white blood cells were the predominant contributors to the circulating DNA pool. The placental contributions in the plasma of pregnant women correlated with the proportional contributions as revealed by fetal-specific genetic markers. The graft-derived contributions to the plasma in the transplant recipients correlated with those determined using donor-specific genetic markers. Patients with hepatocellular carcinoma showed elevated plasma DNA contributions from the liver, which correlated with measurements made using tumor-associated copy number aberrations. In hepatocellular carcinoma patients and in pregnant women exhibiting copy number aberrations in plasma, comparison of methylation deconvolution results using genomic regions with different copy number status pinpointed the tissue type responsible for the aberrations. In a pregnant woman diagnosed as having follicular lymphoma during pregnancy, methylation deconvolution indicated a grossly elevated contribution from B cells into the plasma DNA pool and localized B cells as the origin of the copy number aberrations observed in plasma. This method may serve as a powerful tool for assessing a wide range of physiological and pathological conditions based on the identification of perturbed proportional contributions of different tissues into plasma.

Objective: To study the expression of nuclear β-catenin and Ki-67 in patients with normal gestation products (NGP), complete hydatidiform moles (CHM), and choriocarcinoma to elucidate their roles in carcinogenesis and their interrelations. Methods: Expression of nuclear β-catenin and Ki-67 was studied by immunohistochemistry using paraffin embedded blocks. Sixty NGP, 60 CHM, and 10 choriocarcinomas were analysed. In addition, approximately 400 trophoblasts each in 40 NGP, 40 CHM, and 10 choriocarcinomas from the same batch of samples were microdissected for quantitative reverse transcriptase polymerase chain reaction (Q-RT-PCR) to compare β-catenin mRNA concentration among them. Results: In the chorionic villi of NGP, β-catenin was consistently expressed in the nuclei of cytotrophoblasts but not syncytiotrophoblasts. Nuclear β-catenin expression was comparatively reduced in CHM trophoblasts and was absent in choriocarcinoma. By contrast, Ki-67 expression was increased from cytotrophoblasts but not in syncytiotrophoblasts in the chorionic villi of NGP to CHM trophoblasts and choriocarcinoma. Using Q-RT-PCR, β-catenin mRNA was detected in 10 NGP, 13 CHM, and three choriocarcinoma specimens, with median copy numbers of 43 230, 18 229, and 17 334 per 400 trophoblasts, respectively. A housekeeping gene glyceraldehyde-3-phosphate dehydrogenase ( GAPDH ) mRNA was detected as a control in the NGP, CHM, and choriocarcinoma specimens, with median copy numbers of 51 300, 54 270, and 97 150 per 400 trophoblasts, respectively. Thus median β-catenin mRNA values after normalisation were 0.85 in NGP (n = 10), 0.31 in CHM (n = 13), and 0.16 in choriocarcinoma (n = 3). Conclusions: Decreased nuclear β-catenin expression and increased Ki-67 expression may be involved in choriocarcinoma carcinogenesis. The findings also suggest that nuclear β-catenin may play a role in trophoblast differentiation during normal placental development.

Background: Molecular analysis of plasma DNA during human pregnancy has led to the discovery that maternal plasma contains both fetal and maternal DNA. This valuable source of fetal DNA opens up new possibilities for noninvasive prenatal diagnosis. Approach: Published data from the last 3 years demonstrating the feasibility and utility of analyzing fetal DNA in maternal plasma are reviewed. Content: The detection of fetal DNA in maternal plasma is much simpler and more robust than detecting fetal nucleated cells in maternal blood, and does not require prior enrichment. This approach has been shown to have application in the prenatal diagnosis of fetal rhesus D status, sex-linked disorders, and other paternally inherited genetic disorders. Abnormal fetal DNA concentrations in maternal plasma and serum have been found in common pregnancy-associated disorders, including preterm labor and preeclampsia, as well as in pregnancies complicated by fetal trisomy 21. After delivery, fetal DNA is cleared rapidly from maternal plasma, with a half-life in the order of minutes. These clearance kinetics exhibit an important difference from fetal cell clearance, where long-term persistence has been demonstrated. Summary: It has been only 3 years since fetal DNA was first detected in maternal plasma, and much remains to be learned about the biology of this phenomenon. In addition, additional diagnostic applications beyond those discussed here can be expected in the near future.

CD30 positive anaplastic large cell lymphoma (ALCL) is a type of non-Hodgkin's lymphoma associated with a specific chromosome translocation between chromosomes 2 and 5. Recent molecular characterization of the translocation breakpoint has identified a gene fusion between NPM (nucleophosmin) and ALK (anaplastic lymphoma kinase). Using a DNA hybridization technique, the NPM rearrangement was found among 5/5 ALCL samples. We have developed a PCT methodology which has enabled the detection of the NPM-ALK rearrangements amongst seven t(2;5)(p23;q35) ALCL cases based on a long-range PCR of genomic DNA. The rapidity and robustness of this method may have diagnostic applications for ALCL.

The analysis of circulating RNA in plasma opens up new possibilities for the noninvasive monitoring of a variety of physiological and pathological conditions (1). In this study, we demonstrate the usefulness of a bone marrow transplantation (BMT) model system for ascertaining the tissue origin of plasma RNA species. These data were generated as part of a project to develop plasma nucleic acid markers for brain injury. Because brain injury, such as stroke, involves cell death and disruption of the blood-brain barrier, we hypothesized that brain-derived nucleic acids may be released into the circulation. Hence, the measurement of brain-derived RNA markers in plasma may reflect the degree of brain tissue damage. Numerous reports indicate that S100 calcium binding protein B (S100B) is released after brain injury and its concentrations in serum are significantly correlated with injury severity and outcome (2). To investigate whether S100B mRNA might be detectable in the plasma and might serve as a marker for brain injury, we used a real-time reverse transcriptase PCR assay to measure plasma S100B mRNA concentrations in 67 stroke patients and 16 healthy age- and sex-matched …

Objectives Elevated albumin ( ALB ) mRNA concentration has been reported in the plasma of patients with liver diseases. The plasma ALB mRNA measurement was shown to be an effective indicator of liver pathologies with superior diagnostic sensitivity and specificity when compared with alanine transaminase (ALT). We hypothesized that serial plasma ALB mRNA analysis would be helpful in the early detection and monitoring of post-liver transplantation complications. Design and methods One hundred and five blood specimens were collected from 24 post-transplant recipients. Biochemical liver function test profiles and plasma ALB mRNA concentrations were assessed. Results Over the study period, the health status of 14 recipients (58%) remained stable (Stable group). Their plasma ALB mRNA concentrations remained within a low-concentration range. In contrast, 10 recipients (42%) developed 14 episodes of hepatic complications (Unstable group). The median plasma ALB mRNA concentration of the Unstable group was 6.5-times higher than that of the Stable group. Plasma ALB mRNA concentration was elevated on 13/14 (93%) episodes of the hepatic complications while ALT was elevated only on 8/14 (57%) episodes. Conclusions The elevation of plasma ALB mRNA may allow sensitive detection of hepatic complications and monitoring of the clinical course in a dynamic fashion. Serial plasma ALB mRNA measurement is potentially useful for post-liver transplantation management.

Fetal DNA is present in the plasma of pregnant women. Massively parallel sequencing of maternal plasma DNA has been used to detect fetal trisomies 21, 18, 13 and selected sex chromosomal aneuploidies noninvasively. Case reports describing the detection of fetal microdeletions from maternal plasma using massively parallel sequencing have been reported. However, these previous reports were either polymorphism-dependent or used statistical analyses which were confined to one or a small number of selected parts of the genome. In this report, we reported a procedure for performing noninvasive prenatal karyotyping at 3 Mb resolution across the whole genome through the massively parallel sequencing of maternal plasma DNA. This method has been used to analyze the plasma obtained from 6 cases. In three cases, fetal microdeletions have been detected successfully from maternal plasma. In two cases, fetal microduplications have been detected successfully from maternal plasma. In the remaining case, the plasma DNA sequencing result was consistent with the pregnant mother being a carrier of a microduplication. Simulation analyses were performed for determining the number of plasma DNA molecules that would need to be sequenced and aligned for enhancing the diagnostic resolution of noninvasive prenatal karyotyping to 2 Mb and 1 Mb. In conclusion, noninvasive prenatal molecular karyotyping from maternal plasma by massively parallel sequencing is feasible and would enhance the diagnostic spectrum of noninvasive prenatal testing.

The bilateral trafficking of nucleated cells between the fetus and the mother was studied using polymerase chain reaction (PCR)-based systems sensitive enough to detect 1 target cell in 100,000 background cells. Sixty-six mother-baby pairs were recruited; maternal and cord blood samples were collected at delivery for DNA extraction. Cell trafficking was studied in informative cases using PCR-genotyping of polymorphic regions in the beta-globin cluster, the glutathione S-transferase M1 locus and the angiotensin converting enzyme gene. In addition, Y-PCR was also used in conjunction with these systems for the detection of fetal cells in maternal circulation. Fetal cells were detected in maternal peripheral blood in 26 of 51 cases whereas maternal cells were detected in 16 of 38 fetal umbilical cord blood samples. The proportion of umbilical samples with detectable maternal sequences was much higher than previously reported. In the 28 cases informative for both mother and baby, there was no obvious correlation between the cell traffic from mother to baby as compared to that from baby to mother. These findings may have implications for the use of cord blood for bone marrow transplantation, the vertical transmission of infectious agents, and the physiology of the feto-maternal relationship.

AIM--To develop polymerase chain reaction based artificial restriction fragment length polymorphism (artificial RFLP PCR) assays for DR3 and DR4 alleles of the multiallelic DRB1 locus and to apply them to paraffin wax embedded archival material. METHODS--Sixty five samples from DRB1 typed cell lines were analysed using the artificial RFLP PCR method to determine the specificity and sensitivity of the system. RESULTS--The artificial RFLP PCR method for typing the DRB1 locus showed 100% accuracy in the 65 samples previously typed using allele specific PCR and serology. The samples included 18 combinations of alleles that included DR3, 18 that included DR4, four that were DR3/DR4 heterozygotes, and 10 samples that were neither DR3 nor DR4. Typing of 10 paraffin wax embedded samples using artificial RFLP PCR was in complete agreement with previous typing at the DRB1 locus. CONCLUSION--The application of artificial RFLP PCR for the analysis of multiallelic loci, such as those of the HLA system, in archival DNA samples has been achieved. Artificial RFLP PCR is a robust, easily implemented, non-isotopic system and may be useful for large retrospective studies.

The collection of fetal genetic materials is required for the prenatal diagnosis of fetal genetic diseases. The conventional methods for sampling fetal genetic materials, such as amniocentesis and chorionic villus sampling, are invasive in nature and are associated with a risk of fetal miscarriage. For decades, scientists had been pursuing studies with goals to develop non-invasive methods for prenatal diagnosis. In 1997, the existence of fetal derived cell-free DNA molecules in plasma of pregnant women was first demonstrated. This finding provided a new source of fetal genetic material that could be obtained safely through the collection of a maternal blood sample and provided a new avenue for the development of non-invasive prenatal diagnostic tests. Now 15 years later, the diagnostic potential of circulating fetal DNA analysis has been realized. Fruitful research efforts have resulted in the clinical implementation of a number of non-invasive prenatal tests based on maternal plasma DNA analysis and included tests for fetal sex assessment, fetal rhesus D blood group genotyping and fetal chromosomal aneuploidy detection. Most recently, research groups have succeeded in decoding the entire fetal genome from maternal plasma DNA analysis which paved the way for the achievement of non-invasive prenatal diagnosis of many single gene diseases. A paradigm shift in the practice of prenatal diagnosis has begun.

Purpose of review Noninvasive prenatal diagnosis can be achieved by analyzing cell-free fetal DNA in maternal plasma. The fact that circulating fetal DNA represents only a minor fraction of the DNA that is present in maternal plasma has presented analytical challenges for a number of applications. In this review, we discuss such challenges and how they have been resolved by recent developments in the field. Recent findings Digital molecular counting methods, such as digital PCR and massively parallel sequencing, have enabled high quantitative precision for maternal plasma DNA analysis. Noninvasive prenatal analysis of monogenic disease mutations has been achieved by identifying small quantitative differences between the mutant and wild-type alleles in maternal plasma. By measuring the small increment in the fractional concentrations of DNA derived from potentially aneuploid chromosomes in maternal plasma, fetal chromosomal aneuploidies have been detected with high diagnostic accuracies. Summary Recently, advances in molecular technologies have enhanced the diagnostic applications of maternal plasma DNA analysis for noninvasive prenatal diagnosis. We foresee that this technology could play an increasingly important role in prenatal investigations.

Objective To develop a novel prenatal assay based on selective analysis of cell-free DNA in maternal blood for evaluation of fetal Trisomy 21 (T21) and Trisomy 18 (T18). Methods Two hundred ninety-eight pregnancies, including 39 T21 and seven T18 confirmed fetal aneuploidies, were analyzed using a novel, highly multiplexed assay, termed digital analysis of selected regions (DANSR™). Cell-free DNA from maternal blood samples was analyzed using DANSR assays for loci on chromosomes 21 and 18. Products from 96 separate patients were pooled and sequenced together. A standard Z-test of chromosomal proportions was used to distinguish aneuploid samples from average-risk pregnancy samples. DANSR aneuploidy discrimination was evaluated at various sequence depths. Results At the lowest sequencing depth, corresponding to 204 000 sequencing counts per sample, average-risk cases where distinguished from T21 and T18 cases, with Z statistics for all cases exceeding 3.6. Increasing the sequencing depth to 410 000 counts per sample substantially improved separation of aneuploid and average-risk cases. A further increase to 620 000 counts per sample resulted in only marginal improvement. This depth of sequencing represents less than 5% of that required by massively parallel shotgun sequencing approaches. Conclusion Digital analysis of selected regions enables highly accurate, cost efficient, and scalable noninvasive fetal aneuploidy assessment. © 2012 John Wiley & Sons, Ltd.

The presence of foetal DNA in the plasma of pregnant women has opened up new possibilities for non-invasive prenatal diagnosis. The use of circulating foetal DNA for the non-invasive prenatal detection of foetal chromosomal aneuploidies is challenging as foetal DNA represents a minor fraction of maternal plasma DNA. In 2007, it was shown that single molecule counting methods would allow the detection of the presence of a trisomic foetus, as long as enough molecules were counted. With the advent of massively parallel sequencing, millions or billions of DNA molecules can be readily counted. Using massively parallel sequencing, foetal trisomies 21, 13 and 18 have been detected from maternal plasma. Recently, large-scale clinical studies have validated the robustness of this approach for the prenatal detection of foetal chromosomal aneuploidies. A proof-of-concept study has also shown that a genome-wide genetic and mutational map of a foetus can be constructed from the maternal plasma DNA sequencing data. These developments suggest that the analysis of foetal DNA in maternal plasma would play an increasingly important role in future obstetrics practice. It is thus a priority that the ethical, social and legal issues regarding this technology be systematically studied.

Fetal DNA is present at an approximate mean fractional concentration of 10% in the plasma of pregnant women. The detection of paternally-inherited DNA sequences that are absent in the maternal genome, e.g., Y chromosomal sequences for fetal sexing and the RHD gene for blood group genotyping, is well established. The recent emergence of single molecule counting technologies, such as digital polymerase chain reaction and massively parallel sequencing has allowed circulating fetal DNA to be used for the non-invasive prenatal diagnosis of fetal chromosomal aneuploidies and monogenic diseases. With large scale clinical validation and further reduction in costs, it is expected that the analysis of circulating fetal DNA will play an increasingly important role in the future practice of prenatal diagnosis.

Preeclampsia is a multisystem disorder specific to pregnant women. It remains one of the most important causes of maternal and fetal mortality and morbidity in developed countries (1). Although the pathogenesis of this condition is not fully understood, it is now widely accepted that vascular endothelial cell dysfunction is the final common pathway responsible for the maternal syndrome (2)(3). The underlying pathological changes that lead to the endothelial cell dysfunction remain incompletely understood, but poor placentation has been proposed as a major contributory factor (2)(4)(5). As a result of incomplete or failure of trophoblastic invasion of the spiral arteries, placental ischemia results, leading to the release of one or more factors that are responsible for the damage of the maternal vascular endothelium (5)(6). The normal process of trophoblastic invasion is complete by 20 weeks of gestation. Hence, the initiating placental pathology should exist prior to this stage of pregnancy, long before the onset of the clinical syndrome. Therefore, it might be possible to develop new plasma/serum biochemical markers for identifying subjects at increased risk of developing preeclampsia. We previously have shown that women with established preeclampsia have a fivefold increase in circulating fetal DNA concentrations in their plasma compared with control pregnant subjects (7). However, it is unknown whether this is a late phenomenon or whether it precedes the onset of clinical symptoms and signs. In this study, we aimed to test whether the abnormal increase in circulating fetal DNA concentrations can be detected in susceptible subjects before onset of the clinical disease. Pregnant women attending the Department of Obstetrics and Gynecology, Prince of Wales Hospital, Hong Kong were recruited with informed consent. The study was approved by the …

Bisulfite sequencing is used to detect the methylated status at single nucleotide resolution. Coupled with a recently developed next generation sequencing technology, it becomes a powerful tool for studying the epigenetic regulations in a variety of biological systems. However, due the large dataset generated from this kind of experiment, limited software packages are available for analyzing the resultant high-throughput bisulfite sequencing data with reasonable performance in terms of efficiency and accuracy. To solve this problem,, we developed an integrated data analysis pipeline Methy-Pipe for analyzing whole genome methylome data. The capability of it running in parallel on Linux cluster makes this pipeline superior to other exisetnent softwares.

The discovery of cell-free fetal DNA in maternal plasma has offered new possibilities for non-invasive prenatal diagnosis and monitoring. The co-existence of fetal DNA as a minor fraction with a major background of maternal DNA in maternal plasma has posed a challenge for non-invasive prenatal detection of fetal chromosomal aneuploidies. The early approaches focus on the detection of fetal-specific RNA or DNA molecules to develop strategies for chromosome dosage determination, such as the RNA-single nucleotide polymorphism (SNP), epigenetic allelic ratio, and the epigenetic-genetic chromosome dosage approaches. While the detection of polymorphism is involved in these methods, a polymorphism-independent method has been developed with the highly precise digital polymerase chain reaction (PCR) platform. The power of single molecule counting technology is further demonstrated by the massively parallel sequencing platform for the direct detection of fetal chromosomal aneuploidies from maternal plasma. The analytical power of the latter approach with an unprecedented sensitivity, specificity, accuracy and precision has made it the most promising strategy for the clinical implementation of non-invasive prenatal diagnosis.

We describe a codon 299 mutation in the glucokinase gene in a British pedigree with maturity-onset diabetes of the young (MODY) resulting in a substitution of glycine to arginine. One out of fifty patients diagnosed with classical late-onset type 2 diabetes mellitus was also found to have this mutation. All nine relatives of this patient who have inherited the mutation have type 2 diabetes, although six others without the mutation are also present with diabetes. The discovery that glucokinase mutations can cause MODY and was also found in ten affected members of a pedigree with type 2 diabetes in which MODY had not previously been considered indicates that diagnosis based on molecular pathology will be helpful in understanding the aetiology of type 2 diabetes.

AIM: Development of a specific polymerase chain reaction (PCR) assay for detection of the pre-core, stop codon, mutant of hepatitis B virus (HBV). METHODS: PCR primers, specific at the 3'-end for nucleotide 1896 of either the pre-core, stop codon, mutant or wild type HBV, were synthesised using published sequence data. Positive control templates for both types of virus were synthesised by the PCR, incorporating sequences specific for each virus type at the appropriate position. These templates were used to optimise the specificity of the procedure. Formalin fixed, paraffin wax embedded human tissue from acute or fulminant HBV hepatitis from Hong Kong or Oxford was then investigated for presence of mutant or wild type virus. The HBV DNA was amplified from this tissue using a two step procedure, with an initial amplification phase followed by a second diagnostic phase on optimally diluted target DNA. RESULTS: Specific detection of mutant or wild type HBV was achieved. An important factor in determining specificity was the temperature of annealing, 70 degrees C proving to be highly specific. To overcome the inherent variation of target copy number in clinical samples and to provide an intrinsic positive control, it was important to generate and standardise the amount of target HBV used for the specific PCR. Two cases of fulminant hepatitis and four cases of acute hepatitis from Hong Kong, and one case of fulminant hepatitis from Oxford, contained only wild type HBV, with no evidence of a mutant virus. CONCLUSION: This method can be applied to FFPE tissues. It is rapid, non-radioactive, and specific for the stop codon mutation at nucleotide 1896 of HBV. Preliminary investigation of a small number of cases of fulminant hepatitis from Oxford and Hong Kong showed only wild type virus. The result differs from results published from Japan and Israel.

The advent of the polymerase chain reaction has stimulated the development of a number of rapid methods for characterizing human genes. In addition, the unprecedented level of sensitivity offered by some of these methods may prove to be of great value in the detection of minority cell populations. Over the past year, technical developments have been made in this area.

We have developed a new method for analysis of complex genetic systems by a combination of the Amplification Refractory Mutation System (ARMS) and Single-Strand Conformation Polymorphism (SSCP) analysis: ARMS-SSCP. Thus, a complex allelic series is subdivided into a number of groups by ARMS followed by the identification of specific alleles using SSCP analysis. We have shown that the HLA alleles at the DRB3 and DQB1 loci were distinguishable from each other using ARMS-SSCP. In 36 individuals typed for the DRB3 and 48 individuals typed for the DQB1 loci, ARMS-SSCP results were in complete agreement with those obtained using the established method of sequence-specific oligonucleotide (SSO) hybridisation. With silver staining, ARMS-SSCP is a rapid, non-radioactive and reliable method which also offers the possibility for detecting new HLA alleles. We have demonstrated that ARMS-SSCP can be performed using fluorescent PCR primers, a feature which gives the method potential for automation.

Fetal nucleic acids in maternal plasma have opened up new possibilities for noninvasive prenatal diagnosis of chromosomal aneuploidies. One approach is based on the measurement of the allelic ratio of single nucleotide polymorphisms in the coding region of placental mRNA. Another approach is through the analysis of DNA fragments with different patterns of DNA methylation between fetal and maternal DNA. One other alternative is to enrich the fractional concentration of fetal DNA in maternal plasma using physical or chemical methods. Finally, the development of more precise digital polymerase chain reaction-based methods for fetal nucleic acid analysis might further catalyse the developments in this area. It is hoped that plasma-based molecular prenatal diagnosis might ultimately make prenatal testing safer for pregnant women and their fetuses.

An outbreak of severe acute respiratory syndrome (SARS) occurred in China and the first case emerged in mid November 2002. The etiologic agent of this disease was found to be a previously unknown coronavirus, SARS-CoV. The detailed pathology of SARS-CoV infection and the host response to the viral infection are still not known. The 3a gene encodes a non-structural viral protein which is predicted to be a transmembrane protein. In this study, we showed that the 3a protein was localized to the endoplasmic reticulum (ER) in 3a-transfected monkey kidney Vero E6 cells. In vitro experiments of chromatin condensation and DNA fragmentation suggest that the 3a protein may trigger apoptosis. Our data show that over-expression of a single SARS-CoV protein can induce apoptosis in vitro. Thus GFP-3a fusion protein could also be used as a biosensor for monitoring the cytopathic features of SARS infection, e.g. lymphopenia, in animal model systems, similar to nucleocapsid and 7a proteins.

Post-traumatic organ failure is common following severe injury and is an important cause of mortality (1). There is much recent interest in the use of circulating cellfree DNA in the plasma for clinical diagnosis (2). We hypothesize that DNA may be liberated from body tissues into the plasma following trauma and that plasma DNA may be a potentially useful monitoring tool for trauma patients.

Summary Severe acute respiratory syndrome (SARS) is a global health concern. In Hong Kong, two major outbreaks, one hospital based and the other in the Amoy Gardens apartments, were identified. The frequency of diarrhoea, admission to intensive care, and mortality differed significantly between the two outbreaks. We did genomic sequencing for viral isolates from five Amoy Gardens patients. The virus sequence was identical in four of these five patients. The sequence data from one hospital case and the four identical community cases had only three nucleotide differences. Alterations in the SARS coronavirus genome are unlikely to have caused the distinctive clinical features of the Amoy Gardens patients, and these results highlight the importance of non-viral genomic factors in this outbreak.

Technical concerns about immunoprecipitation of methylated fetal DNA for noninvasive trisomy 21 diagnosis

Recently published international guidelines recommend the clinical use of noninvasive prenatal test (NIPT) for aneuploidy screening only among pregnant women whose fetuses are deemed at high risk. The applicability of NIPT to aneuploidy screening among average risk pregnancies requires additional supportive evidence. A key determinant of the reliability of aneuploidy NIPT is the fetal DNA fraction in maternal plasma. In this report, we investigated if differences in fetal DNA fractions existed between different pregnancy risk groups. One hundred and ninety-five singleton pregnancies with male fetuses divided into 3 groups according to first trimester screening parameters were examined for fetal DNA percentage by counting Y chromosome DNA sequences using massively parallel sequencing. Fetal DNA fractions were compared between risk groups and assessed for correlations with first trimester screening parameters. There was no statistically significant difference in fetal DNA fractions across the high, intermediate and low risk groups. Fetal DNA fraction showed a strong negative correlation with maternal weight. Fetal DNA fraction also showed weak but significant correlations with gestational age, crown-rump length, multiple of medians of free β-subunit of human chorionic gonadotropin and pregnancy-associated plasma protein A. Similar fetal DNA fractions in maternal plasma between high, intermediate and low risk pregnant women is a precondition for uniform performance of the aneuploidy NIPTs for the general population. This study thus shows that the aneuploidy screening by NIPT is likely to offer similar analytical reliability without respect to the a priori fetal aneuploidy risk.

Background: The existence of high concentrations of circulating fetal DNA in maternal plasma may enable non-invasive prenatal diagnosis. There are many applications of fetal DNA in maternal plasma for clinical diagnosis. Conclusions: We expect fetal DNA in material plasma will be incorporated into past of the prenatal investigation of pregnant women in the near future.

Lack of support for an association between CLEC4M homozygosity and protection against SARS coronavirus infection

A high proportion of the female patients who are members of maturity onset diabetes of the young (MODY) pedigrees, and whose diabetes mellitus is due to a glucokinase mutation, originally presented with gestational diabetes. To establish whether glucokinase mutations could be a common cause of gestational diabetes, we studied 50 subjects who presented with gestational diabetes and on follow-up had hyperglycaemia (5.5–10.0 mmol/l). Screening for glucokinase mutations using single-stranded conformational polymorphism (SSCP) analysis detected a missense mutation at position 299 (Gly299→ Arg) in three subjects. As two pedigrees in the Oxford area had the same glucokinase mutation, we suspected the role of a founder-effect, and carried out pedigree extension, haplotype construction (using microsatellite markers GCK1 and GCK2) and mutation screening of at-risk subjects from the same geographical area. One of the gestational diabetic subjects was found to be related to one of the previous pedigrees via her paternal grandmother. Subjects with the mutation were found to have the Z + 4/2 (GCK1/GCK2) haplotype, suggesting that the observed high prevalence of the Gly299→ Arg glucokinase mutation in the Oxford region was due to a founder-effect. Since glucokinase mutations predominantly induce subclinical hyperglycaemia, it is likely that in the locality of other pedigrees there will be undiagnosed subjects with the same glucokinase mutation, which remains undetected unless pregnancy occurs. [Diabetologia (1996) 39: 1325–1328]

A highly sensitive Y-microsatellite amplification system was developed for the detection of post bone marrow transplantation (BMT) chimaerism. The system is able to detect the DNA equivalent of a single male cell in a background of 10(5) female cells. For clinical applications it has the distinct advantage that the polymorphic nature of the PCR product allows the checking of the genuineness of a positive PCR signal by reference to its allelic type. This extra degree of precision enhances the accuracy of Y-PCR for clinical diagnosis.

Background/Aims: Primary sclerosing cholangitis (PSC) is an inflammatory disease of the biliary tree associated with an increase in the HLA alleles DR3, DR52a, DR2, Dw2, and a decrease in DR4. However, it is not certain which of these alleles provides the primary associations. Our aim was to establish the primary HLA associations with PSC and to assess the ability of HLA alleles to mark for disease progression. Methods: By applying molecular techniques to archival tissue, we have genotyped 83 PSC patients from two populations and 131 controls for the alleles HLA DR2, DR3, DR4, DRw12, DR52a, and Dw2. Results: HLA DR3, DR52a, DR2, and Dw2 were all significantly increased in PSC, with the relative risk for DR52a and Dw2 being greater than for DR3 and DR2, respectively. HLA DR4 was significantly decreased, but this may be artifactual to the DR3, DR2 increase. HLA DR4 and not DR52a marks for rapid disease progression in both our PSC populations. Conclusions: HLA DR52a and Dw2 are the best candidate alleles for providing the known HLA association with PSC. HLA DR4 and not DR52a marks for rapid disease progression in our two PSC populations.

AIMS--To detect HLA susceptibility and protective alleles associated with insulin dependent diabetes mellitus (IDDM) using a multiplex amplification refractory mutation system (ARMS). These include DR3 and DR4 alleles at the DRB1 locus, presence or absence of aspartic acid at position 57 (Asp-57) of the DQB1 locus, and presence or absence of arginine at position 52 (Arg-52) of the DQA1 locus. METHODS--The ARMS approach was used to design allele specific primers for the detection of the major susceptibility and protective alleles for IDDM. These include DR3 and DR4 alleles at the DRB1 locus, Asp-57 and non-Asp-57 at the DQB1 locus, and Arg-52 and non-Arg-52 alleles at the DQA1 locus. The allele specificity of each set of primers was first tested separately using DNA samples from 15 individuals previously typed for the DRB1, DQB1, and DQA1 loci using the sequence specific oligonucleotide (SSO) technique. The possibility of using multiplex ARMS for typing multiple susceptibility/protective alleles for IDDM was further investigated by testing various combinations of allele specific primers, thereby reducing the number of separate polymerase chain reactions required to type all these alleles. RESULTS--A "three-tube" system worked well and gave accurate results. Tube 1 contained ARMS primers for the detection of IDDM susceptibility alleles DR3 and DR4; tube 2 contained ARMS primers for the detection of susceptibility alleles non-Asp-57 and Arg-52; and tube 3 contained ARMS primers for the detection of the protective alleles Asp-57 and non-Arg-52. DNA samples typed with this ARMS method were in complete agreement with those obtained using the SSO technique. CONCLUSION--This method is rapid and has no requirement for radioactivity. It is an efficient method for population screening.

We have developed a highly sensitive double amplification refractory mutation system (double ARMS) for the detection of extremely low levels of mixed chimaerism after bone marrow transplantation. The system we chose for double ARMS analysis is a highly polymorphic region 5' to the human delta-globin gene. Double ARMS analysis was found to correlate well with an established minisatellite system and was shown to demonstrate a very low level of mixed chimaerism in cases undetectable by the latter method.

AIMS--To develop a sensitive and specific polymerase chain reaction (PCR) based system for detecting genomic variation in JC virus. To apply this system to formalin fixed, paraffin wax embedded brain tissue from patients with and without progressive multifocal leucoencephalopathy (PML). METHODS--A pair of primers (JC1 and JC2) were designed to be complementary to the early and late regions of JC and BK polyomaviruses, respectively. A third primer (JC3), internal to JC1 and JC2, was designed to be specific for JC virus. The specificity of JC3 was investigated by amplifying plasmids with BK or JC virus genomes. Sensitivity was estimated by titration of a plasmid containing JC virus genome. Seven brains from patients with PML (PMLB) and 30 from patients without PML (non-PMLB) were amplified using JC1 and JC2, followed by JC1 and JC3. Amplification of the beta globin gene was used as an amplification control. RESULTS--Amplification with JC1 and JC2 was common for JC and BK viruses, but with JC1 and JC3 it was specific for JC virus. The sensitivity of the system was 25 copies of JC plasmid per 10 microliters of digested tissue. Five out of seven PMLB and 28 of the 30 non-PMLB amplified for beta globin, but only the PMLB gave a signal with polyoma primers. Hypervariation of the length of the regulatory region of the JC isolates in the PML tissues was consistent with the presence of multiple strains of JC. CONCLUSIONS--Variation in the regulatory region of JC virus can be specifically and sensitively detected from routinely processed, paraffin wax embedded brain tissue. Variation in the regulatory region is common in PML derived JC strains, but JC virus was not detectable in non-PMLB tissue.

The glycolytic enzyme glucokinase plays an important role in the regulation of insulin secretion and recent studies have shown that mutations in the human glucokinase gene are a common cause of an autosomal dominant form of non-insulin-dependent (type 2) diabetes mellitus (NIDDM) that has an onset often during childhood. The majority of the mutations that have been identified are missense mutations that result in the synthesis of a glucokinase molecule with an altered amino acid sequence. To characterize the effect of these mutations on the catalytic properties of human beta-cell glucokinase, we have expressed native and mutant forms of this protein in Escherichia coli. All of the missense mutations show changes in enzyme activity including a decrease in Vmax and/or increase in Km for glucose. Using a model for the three-dimensional structure of human glucokinase based on the crystal structure of the related enzyme yeast hexokinase B, the mutations map primarily to two regions of the protein. One group of mutations is located in the active site cleft separating the two domains of the enzyme as well as in surface loops leading into this cleft. These mutations usually result in large reductions in enzyme activity. The second group of mutations is located far from the active site in a region that is predicted to undergo a substrate-induced conformational change that results in closure of the active site cleft. These mutations show a small approximately 2-fold reduction in Vmax and a 5- to 10-fold increase in Km for glucose. The characterization of mutations in glucokinase that are associated with a distinct and readily recognizable form of NIDDM has led to the identification of key amino acids involved in glucokinase catalysis and localized functionally important regions of the glucokinase molecule.