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Sun K, Lun FMF, Leung TY, Chiu RWK, Lo YMD, Sun H. Noninvasive reconstruction of placental methylome from maternal plasma DNA: Potential for prenatal testing and monitoring. Prenat Diagn 2018; 38:196-203. [PMID: 29334402 DOI: 10.1002/pd.5214] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE During human pregnancy, the DNA methylation of placental tissue is highly relevant to the normal growth and development of the fetus; therefore, methylomic analysis of the placental tissue possesses high research and clinical value in prenatal testing and monitoring. Thus, our aim is to develop an approach for reconstruction of the placental methylome, which should be completely noninvasive and achieve high accuracy and resolution. RESULTS We propose a novel size-based algorithm, FEtal MEthylome Reconstructor (FEMER), to noninvasively reconstruct the placental methylome by genomewide bisulfite sequencing and size-based analysis of maternal plasma DNA. By applying FEMER on a real clinical dataset, we demonstrate that FEMER achieves both high accuracy and resolution, thus provides a high-quality view of the placental methylome from maternal plasma DNA. FEtal MEthylome Reconstructor could also predict the DNA methylation profile of CpG islands with high accuracy, thus shows potential in monitoring of key genes involved in placental/fetal development. Source code and testing datasets for FEMER are available at http://sunlab.cpy.cuhk.edu.hk/FEMER/. CONCLUSION FEtal MEthylome Reconstructor could enhance the noninvasive fetal/placental methylomic analysis and facilitate its application in prenatal testing and monitoring.
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Cheng THT, Lui KO, Peng XL, Cheng SH, Jiang P, Chan KCA, Chiu RWK, Lo YMD. DNase1 Does Not Appear to Play a Major Role in the Fragmentation of Plasma DNA in a Knockout Mouse Model. Clin Chem 2017; 64:406-408. [PMID: 29097509 DOI: 10.1373/clinchem.2017.280446] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Chan KCA, Woo JKS, King A, Zee BCY, Lam WKJ, Chan SL, Chu SWI, Mak C, Tse IOL, Leung SYM, Chan G, Hui EP, Ma BBY, Chiu RWK, Leung SF, van Hasselt AC, Chan ATC, Lo YMD. Analysis of Plasma Epstein-Barr Virus DNA to Screen for Nasopharyngeal Cancer. N Engl J Med 2017; 377:513-522. [PMID: 28792880 DOI: 10.1056/nejmoa1701717] [Citation(s) in RCA: 432] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Circulating cell-free Epstein-Barr virus (EBV) DNA is a biomarker for nasopharyngeal carcinoma. We conducted a prospective study to investigate whether EBV DNA in plasma samples would be useful to screen for early nasopharyngeal carcinoma in asymptomatic persons. METHODS We analyzed EBV DNA in plasma specimens to screen participants who did not have symptoms of nasopharyngeal carcinoma. Participants with initially positive results were retested approximately 4 weeks later, and those with persistently positive EBV DNA in plasma underwent nasal endoscopic examination and magnetic resonance imaging (MRI). RESULTS A total of 20,174 participants underwent screening. EBV DNA was detectable in plasma samples obtained from 1112 participants (5.5%), and 309 (1.5% of all participants and 27.8% of those who initially tested positive) had persistently positive results on the repeated sample. Among these 309 participants, 300 underwent endoscopic examination, and 275 underwent both endoscopic examination and MRI; of these participants, 34 had nasopharyngeal carcinoma. A significantly higher proportion of participants with nasopharyngeal carcinoma that was identified by screening had stage I or II disease than in a historical cohort (71% vs. 20%, P<0.001 by the chi-square test) and had superior 3-year progression-free survival (97% vs. 70%; hazard ratio, 0.10; 95% confidence interval, 0.05 to 0.18). Nine participants declined to undergo further testing, and 1 of them presented with advanced nasopharyngeal carcinoma 32 months after enrollment. Nasopharyngeal carcinoma developed in only 1 participant with negative EBV DNA in plasma samples within 1 year after testing. The sensitivity and specificity of EBV DNA in plasma samples in screening for nasopharyngeal carcinoma were 97.1% and 98.6%, respectively. CONCLUSIONS Analysis of EBV DNA in plasma samples was useful in screening for early asymptomatic nasopharyngeal carcinoma. Nasopharyngeal carcinoma was detected significantly earlier and outcomes were better in participants who were identified by screening than in those in a historical cohort. (Funded by the Kadoorie Charitable Foundation and the Research Grants Council of the Hong Kong government; ClinicalTrials.gov number, NCT02063399 .).
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Lam WKJ, Gai W, Sun K, Wong RSM, Chan RWY, Jiang P, Chan NPH, Hui WWI, Chan AWH, Szeto CC, Ng SC, Law MF, Chan KCA, Chiu RWK, Lo YMD. DNA of Erythroid Origin Is Present in Human Plasma and Informs the Types of Anemia. Clin Chem 2017; 63:1614-1623. [PMID: 28784691 DOI: 10.1373/clinchem.2017.272401] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/20/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND There is much interest in the tissue of origin of circulating DNA in plasma. Data generated using DNA methylation markers have suggested that hematopoietic cells of white cell lineages are important contributors to the circulating DNA pool. However, it is not known whether cells of the erythroid lineage would also release DNA into the plasma. METHODS Using high-resolution methylation profiles of erythroblasts and other tissue types, 3 genomic loci were found to be hypomethylated in erythroblasts but hypermethylated in other cell types. We developed digital PCR assays for measuring erythroid DNA using the differentially methylated region for each locus. RESULTS Based on the methylation marker in the ferrochelatase gene, erythroid DNA represented a median of 30.1% of the plasma DNA of healthy subjects. In subjects with anemia of different etiologies, quantitative analysis of circulating erythroid DNA could reflect the erythropoietic activity in the bone marrow. For patients with reduced erythropoietic activity, as exemplified by aplastic anemia, the percentage of circulating erythroid DNA was decreased. For patients with increased but ineffective erythropoiesis, as exemplified by β-thalassemia major, the percentage was increased. In addition, the plasma concentration of erythroid DNA was found to correlate with treatment response in aplastic anemia and iron deficiency anemia. Plasma DNA analysis using digital PCR assays targeting the other 2 differentially methylated regions showed similar findings. CONCLUSIONS Erythroid DNA is a hitherto unrecognized major component of the circulating DNA pool and is a noninvasive biomarker for differential diagnosis and monitoring of anemia.
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Hudecova I, Jiang P, Davies J, Lo YMD, Kadir RA, Chiu RWK. Noninvasive detection of F8 int22h-related inversions and sequence variants in maternal plasma of hemophilia carriers. Blood 2017; 130:340-347. [PMID: 28490568 PMCID: PMC5532756 DOI: 10.1182/blood-2016-12-755017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/19/2017] [Indexed: 12/15/2022] Open
Abstract
Direct detection of F8 and F9 sequence variants in maternal plasma of hemophilia carriers has been demonstrated by microfluidics digital PCR. Noninvasive prenatal assessment of the most clinically relevant group of sequence variants among patients with hemophilia, namely, those involving int22h-related inversions disrupting the F8 gene, poses additional challenges because of its molecular complexity. We investigated the use of droplet digital PCR (ddPCR) and targeted massively parallel sequencing (MPS) for maternal plasma DNA analysis to noninvasively determine fetal mutational status in pregnancies at risk for hemophilia. We designed family-specific ddPCR assays to detect causative sequence variants scattered across the F8 and F9 genes. A haplotype-based approach coupled with targeted MPS was applied to deduce fetal genotype by capturing a 7.6-Mb region spanning the F8 gene in carriers with int22h-related inversions. The ddPCR analysis correctly determined fetal hemophilia status in 15 at-risk pregnancies in samples obtained from 8 to 42 weeks of gestation. There were 3 unclassified samples, but no misclassification. Detailed fetal haplotype maps of the F8 gene region involving int22h-related inversions obtained through targeted MPS enabled correct diagnoses of fetal mutational status in 3 hemophilia families. Our data suggest it is feasible to apply targeted MPS to interrogate maternally inherited F8 int22h-related inversions, whereas ddPCR represents an affordable approach for the identification of F8 and F9 sequence variants in maternal plasma. These advancements may bring benefits for the pregnancy management for carriers of hemophilia sequence variants; in particular, the common F8 int22h-related inversions, associated with the most severe clinical phenotype.
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Vong JSL, Tsang JCH, Jiang P, Lee WS, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Single-Stranded DNA Library Preparation Preferentially Enriches Short Maternal DNA in Maternal Plasma. Clin Chem 2017; 63:1031-1037. [DOI: 10.1373/clinchem.2016.268656] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/11/2017] [Indexed: 01/04/2023]
Abstract
Abstract
BACKGROUND
Recent studies have suggested that single-stranded DNA (ssDNA) library preparation can enrich short DNA species from the plasma of healthy individuals, cancer patients, and transplant recipients. Based on previous observations that fetal DNA molecules in the maternal plasma are shorter than maternal DNA molecules, ssDNA library preparation may potentially enrich fetal DNA and provide substantial improvement in noninvasive prenatal testing.
METHODS
We tested this hypothesis by comparing the maternal plasma DNA sequencing results using 2 types of ssDNA library preparation methods and a standard double-stranded DNA (dsDNA) library method using samples from first- and third-trimester pregnancies. We also evaluated the performance of ssDNA and dsDNA library methods in the noninvasive prenatal detection of trisomy 21 from maternal plasma.
RESULTS
Short DNA species were significantly enriched in ssDNA libraries. However, contrary to previous speculation, no significant enrichment was observed in the overall fetal fraction in maternal plasma collected in the first trimester. Our use of an ssDNA library did not reduce the variation in chromosomal representation when compared with a standard dsDNA library in the first-trimester plasma samples. ssDNA libraries also showed inferior performance in the noninvasive prenatal detection of trisomy 21 from maternal plasma. Detailed fetal fraction analysis using size-fractionated Y chromosome sequences and fetal-specific single-nucleotide polymorphisms (SNPs) revealed an unexpected finding that short maternal DNA was preferentially enriched over short fetal DNA in an ssDNA library irrespective of GC content.
CONCLUSIONS
Our findings have shown that ssDNA library preparation preferentially enriches short maternally derived DNA in maternal plasma.
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Sun K, Chan KCA, Hudecova I, Chiu RWK, Lo YMD, Jiang P. Cover Image, Volume 37, Issue 4. Prenat Diagn 2017. [DOI: 10.1002/pd.4891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sun K, Chan KCA, Hudecova I, Chiu RWK, Lo YMD, Jiang P. COFFEE: control-free noninvasive fetal chromosomal examination using maternal plasma DNA. Prenat Diagn 2017; 37:336-340. [PMID: 28165140 DOI: 10.1002/pd.5016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 11/07/2022]
Abstract
OBJECTIVE The aim of this study is to develop an approach for analyzing plasma DNA sequencing data for noninvasive fetal chromosomal aneuploidy testing that does not require the comparison with control samples or a series of selected genomic regions. RESULTS We developed the control-free noninvasive fetal chromosomal examination (COFFEE) algorithm by utilizing the size differences between the fetally derived and maternally derived DNA molecules in maternal plasma. We applied COFFEE on three datasets generated in different experimental settings. COFFEE showed 100% accuracy in trisomy 21 testing on these datasets. In contrast, samples analyzed using an existing control-based z-score method would introduce a false-positive result because of batch-to-batch variation, when the tested samples were analyzed using control samples from other batches. We believe that COFFEE is useful for enhancing the cost-effectiveness of noninvasive fetal chromosomal aneuploidy testing particularly in laboratories with small caseloads. Source code and testing datasets for COFFEE are available for download at http://www.cuhk.edu.hk/med/cpy/Research/COFFEE/. CONCLUSION Control-free noninvasive fetal chromosomal examination is demonstrated to be a versatile data analysis approach and could enhance the application of noninvasive fetal chromosomal aneuploidy detection. © 2017 John Wiley & Sons, Ltd.
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Hui WWI, Jiang P, Tong YK, Lee WS, Cheng YKY, New MI, Kadir RA, Chan KCA, Leung TY, Lo YMD, Chiu RWK. Universal Haplotype-Based Noninvasive Prenatal Testing for Single Gene Diseases. Clin Chem 2017; 63:513-524. [DOI: 10.1373/clinchem.2016.268375] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/17/2016] [Indexed: 01/02/2023]
Abstract
Abstract
BACKGROUND
Researchers have developed approaches for the noninvasive prenatal testing of single gene diseases. One approach that allows for the noninvasive assessment of both maternally and paternally inherited mutations involves the analysis of single nucleotide polymorphisms (SNPs) in maternal plasma DNA with reference to parental haplotype information. In the past, parental haplotypes were resolved by complex experimental methods or inferential approaches, such as through the analysis of DNA from other affected family members. Recently, microfluidics-based linked-read sequencing technology has become available and allows the direct haplotype phasing of the whole genome rapidly. We explored the feasibility of applying this direct haplotyping technology in noninvasive prenatal testing.
METHODS
We first resolved the haplotypes of parental genomes with the use of linked-read sequencing technology. Then, we identified SNPs within and flanking the genes of interest in maternal plasma DNA by targeted sequencing. Finally, we applied relative haplotype dosage analysis to deduce the mutation inheritance status of the fetus.
RESULTS
Haplotype phasing and relative haplotype dosage analysis of 12 out of 13 families were successfully achieved. The mutational status of these 12 fetuses was correctly classified.
CONCLUSIONS
High-throughput linked-read sequencing followed by maternal plasma-based relative haplotype dosage analysis represents a streamlined approach for noninvasive prenatal testing of inherited single gene diseases. The approach bypasses the need for mutation-specific assays and is not dependent on the availability of DNA from other affected family members. Thus, the approach is universally applicable to pregnancies at risk for the inheritance of a single gene disease.
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Yu SCY, Jiang P, Chan KCA, Faas BHW, Choy KW, Leung WC, Leung TY, Lo YMD, Chiu RWK. Combined Count- and Size-Based Analysis of Maternal Plasma DNA for Noninvasive Prenatal Detection of Fetal Subchromosomal Aberrations Facilitates Elucidation of the Fetal and/or Maternal Origin of the Aberrations. Clin Chem 2016; 63:495-502. [PMID: 27974386 DOI: 10.1373/clinchem.2016.254813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 10/10/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Noninvasive prenatal detection of fetal subchromosomal copy number aberrations (CNAs) can be achieved through massively parallel sequencing of maternal plasma DNA. However, when a mother herself is a carrier of a CNA, one cannot discern if her fetus has inherited the CNA. In addition, false-positive results would become more prevalent when more subchromosomal regions are analyzed. METHODS We used a strategy that combined count- and size-based analyses of maternal plasma DNA for the detection of fetal subchromosomal CNAs in 7 target regions for 10 test cases. RESULTS For the 5 cases in which CNAs were present only in the fetus, the size-based approach confirmed the aberrations detected by the count-based approach. For the 5 cases in which the mother herself carried an aberration, we successfully deduced that 3 of the fetuses had inherited the aberrations and that the other 2 fetuses had not inherited the aberrations. No false positives were observed in this cohort. CONCLUSIONS Combined count- and size-based analysis of maternal plasma DNA permits the noninvasive elucidation of whether a fetus has inherited a CNA from its mother who herself is a carrier of the CNA. This strategy has the potential to improve the diagnostic specificity of noninvasive prenatal testing.
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Christensen RH, Master SR, Lo YMD, Baird GS, Wilding P, Jones PM. Theranos Session at the 2016 AACC Annual Scientific Meeting & Clinical Lab Expo: Expectations, Impressions, and Takeaways. J Appl Lab Med 2016; 1:329-338. [PMID: 33626851 DOI: 10.1373/jalm.2016.021709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 11/06/2022]
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Lo YMD. Noninvasive prenatal testing complicated by maternal malignancy: new tools for a complex problem. NPJ Genom Med 2016; 1:15002. [PMID: 29263801 PMCID: PMC5685289 DOI: 10.1038/npjgenmed.2015.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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Khattab A, Yuen T, Sun L, Yau M, Barhan A, Zaidi M, Lo YMD, New MI. Noninvasive Prenatal Diagnosis of Congenital Adrenal Hyperplasia. ENDOCRINE DEVELOPMENT 2016; 30:37-41. [PMID: 26683339 DOI: 10.1159/000439326] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A major hallmark of classical congenital adrenal hyperplasia (CAH) is genital ambiguity noted at birth in affected females, which leads to psychological and psychosexual issues in adult life. Attempts to correct genital ambiguity through surgical intervention have been partially successful. Fetal hyperandrogenemia and genital ambiguity have been shown to be preventable by prenatal administration of low-dose dexamethasone initiated before the 9th week of gestation. In 7 of 8 at-risk pregnancies, the unaffected fetus is unnecessarily exposed to dexamethasone for weeks until the diagnosis of classical CAH is ruled out by invasive procedures. This therapeutic dilemma calls for early prenatal diagnosis so that dexamethasone treatment can be directed to affected female fetuses only. We describe the utilization of cell-free fetal DNA in mothers carrying at-risk fetuses as early as 6 gestational weeks by targeted massively parallel sequencing of the genomic region including and flanking the CYP21A2 gene. Our highly personalized and innovative approach should permit the diagnosis of CAH before genital development begins, therefore restricting the purposeful administration of dexamethasone to mothers carrying affected females.
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Cheng SH, Jiang P, Sun K, Cheng YKY, Chan KCA, Leung TY, Chiu RWK, Lo YMD. Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment. Clin Chem 2015; 61:1305-6. [DOI: 10.1373/clinchem.2015.245076] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Rifai N, Topol E, Chan E, Lo YMD, Wittwer CT. Disruptive Innovation in Laboratory Medicine. Clin Chem 2015; 61:1129-32. [DOI: 10.1373/clinchem.2015.243667] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 06/04/2015] [Indexed: 11/06/2022]
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Chitty LS, Lo YMD. Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA. Cold Spring Harb Perspect Med 2015; 5:a023085. [PMID: 26187875 PMCID: PMC4561399 DOI: 10.1101/cshperspect.a023085] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders.
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Tsui NBY, Jiang P, Wong YF, Leung TY, Chan KCA, Chiu RWK, Sun H, Lo YMD. Maternal Plasma RNA Sequencing for Genome-Wide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts. Clin Chem 2014; 60:954-62. [DOI: 10.1373/clinchem.2014.221648] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Analysis of circulating RNA in the plasma of pregnant women has the potential to serve as a powerful tool for noninvasive prenatal testing and research. However, detection of circulating RNA in the plasma in an unbiased and high-throughput manner has been technically challenging. Therefore, only a limited number of circulating RNA species in maternal plasma have been validated as pregnancy- and placenta-specific biomarkers.
METHODS
We explored the use of massively parallel sequencing for plasma transcriptome profiling in first-, second-, and third-trimester pregnant women. Genotyping was performed for amniotic fluid, placental tissues, and maternal blood cells, with exome-enriched sequencing.
RESULTS
In the early pregnancy group comprising 1 first- and 1 second-trimester pregnancy cases, the fetal contribution to the RNA pool in maternal plasma was 3.70%. The relative proportion of fetal contribution was increased to 11.28% in the late pregnancy group comprising 2 third-trimester pregnancy cases. The placental biallelic expression pattern of PAPPA (pregnancy-associated plasma protein A, pappalysin 1), a known pregnancy-specific gene, and the monoallelic expression pattern of H19 [H19, imprinted maternally expressed transcript (non-protein coding)], an imprinted maternally expressed gene, were also detected in the maternal plasma. Furthermore, by direct examination of the maternal plasma transcriptomic profiles before and after delivery, we identified a panel of pregnancy-associated genes.
CONCLUSIONS
Plasma RNA sequencing provides a holistic view of the maternal plasma transcriptomic repertoire. This technology is potentially valuable for using circulating plasma nucleic acids for prenatal testing and research.
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Jiang P, Sun K, Lun FMF, Guo AM, Wang H, Chan KCA, Chiu RWK, Lo YMD, Sun H. Methy-Pipe: an integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS One 2014; 9:e100360. [PMID: 24945300 PMCID: PMC4063866 DOI: 10.1371/journal.pone.0100360] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Accepted: 05/23/2014] [Indexed: 12/13/2022] Open
Abstract
DNA methylation, one of the most important epigenetic modifications, plays a crucial role in various biological processes. The level of DNA methylation can be measured using whole-genome bisulfite sequencing at single base resolution. However, until now, there is a paucity of publicly available software for carrying out integrated methylation data analysis. In this study, we implemented Methy-Pipe, which not only fulfills the core data analysis requirements (e.g. sequence alignment, differential methylation analysis, etc.) but also provides useful tools for methylation data annotation and visualization. Specifically, it uses Burrow-Wheeler Transform (BWT) algorithm to directly align bisulfite sequencing reads to a reference genome and implements a novel sliding window based approach with statistical methods for the identification of differentially methylated regions (DMRs). The capability of processing data parallelly allows it to outperform a number of other bisulfite alignment software packages. To demonstrate its utility and performance, we applied it to both real and simulated bisulfite sequencing datasets. The results indicate that Methy-Pipe can accurately estimate methylation densities, identify DMRs and provide a variety of utility programs for downstream methylation data analysis. In summary, Methy-Pipe is a useful pipeline that can process whole genome bisulfite sequencing data in an efficient, accurate, and user-friendly manner. Software and test dataset are available at http://sunlab.lihs.cuhk.edu.hk/methy-pipe/.
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New MI, Tong YK, Yuen T, Jiang P, Pina C, Chan KCA, Khattab A, Liao GJW, Yau M, Kim SM, Chiu RWK, Sun L, Zaidi M, Lo YMD. Noninvasive prenatal diagnosis of congenital adrenal hyperplasia using cell-free fetal DNA in maternal plasma. J Clin Endocrinol Metab 2014; 99:E1022-30. [PMID: 24606108 PMCID: PMC4037720 DOI: 10.1210/jc.2014-1118] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Congenital adrenal hyperplasia (CAH) is an autosomal recessive condition that arises from mutations in CYP21A2 gene, which encodes for the steroidogenic enzyme 21-hydroxylase. To prevent genital ambiguity in affected female fetuses, prenatal treatment with dexamethasone must begin on or before gestational week 9. Currently used chorionic villus sampling and amniocentesis provide genetic results at approximately 14 weeks of gestation at the earliest. This means that mothers who want to undergo prenatal dexamethasone treatment will be unnecessarily treating seven of eight fetuses (males and three of four unaffected females), emphasizing the desirability of earlier genetic diagnosis in utero. OBJECTIVE The objective of the study was to develop a noninvasive method for early prenatal diagnosis of fetuses at risk for CAH. PATIENTS Fourteen families, each with a proband affected by phenotypically classical CAH, were recruited. DESIGN Cell-free fetal DNA was obtained from 3.6 mL of maternal plasma. Using hybridization probes designed to capture a 6-Mb region flanking CYP21A2, targeted massively parallel sequencing (MPS) was performed to analyze genomic DNA samples from parents and proband to determine parental haplotypes. Plasma DNA from pregnant mothers also underwent targeted MPS to deduce fetal inheritance of parental haplotypes. RESULTS In all 14 families, the fetal CAH status was correctly deduced by targeted MPS of DNA in maternal plasma, as early as 5 weeks 6 days of gestation. CONCLUSIONS MPS on 3.6 mL plasma from pregnant mothers could potentially provide the diagnosis of CAH, noninvasively, before the ninth week of gestation. Only affected female fetuses will thus be treated. Our strategy represents a generic approach for noninvasive prenatal testing for an array of autosomal recessive disorders.
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Leung SF, Chan KCA, Ma BB, Hui EP, Mo F, Chow KCK, Leung L, Chu KW, Zee B, Lo YMD, Chan ATC. Plasma Epstein-Barr viral DNA load at midpoint of radiotherapy course predicts outcome in advanced-stage nasopharyngeal carcinoma. Ann Oncol 2014; 25:1204-8. [PMID: 24638904 DOI: 10.1093/annonc/mdu117] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To test the hypothesis that prognostication of treatment outcome is feasible by biomarker response at midcourse of chemoradiotherapy (CRT)/radiotherapy (RT), with respect to the plasma load of Epstein-Barr viral (EBV) DNA in nasopharyngeal carcinoma (NPC). PATIENTS AND METHODS One hundred seven patients with stage IIB-IV NPC were prospectively studied. Plasma EBV DNA load was measured by quantitative PCR before therapy (pre-DNA), at completion of 4 weeks of CRT/RT (mid-DNA), and within 3 months of completion of therapy (post-DNA). The end points are post-DNA load, a recognized surrogate of survival, and clinical outcome. RESULTS Ninety-three percent of patients had detectable EBV DNA before therapy (median load = 972 copies/ml). EBV DNA became undetectable in 55 (51%) patients at the end of week 4 of therapy. Detectable mid-DNA was associated with worse clinical outcome (median follow-up time, 6.2 years), for distant failure [hazard ratio (HR) 12.02, 95% confidence interval (CI) 2.78-51.93; P < 0.0001], progression-free survival (PFS; HR 4.05, 95% CI 1.89-8.67, P < 0.0001), and overall survival (OS; HR 3.29, 95% CI 1.37-7.90, P = 0.0077). Seventy-four percent of all failures were associated with detectable mid-DNA, whereas 34% of all failures were associated with detectable post-DNA. Stratification by tumor stage (IIB, III, IV) has no significant prognostic effect. CONCLUSIONS Unfavorable EBV DNA response at midcourse of RT/CRT is an adverse prognosticator for treatment outcome, is linked to majority of all failures, and discriminates outcome better than tumor stage. The data could provide a basis for trial design that addresses alteration of therapy intensity during the latter phase of CRT, and adjuvant therapy. Validation studies are awaited.
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Abstract
The recent interest in plasma nucleic acids has opened up many new promising possibilities for the noninvasive detection and monitoring of a variety of diseases. The discovery of tumor-derived DNA in the plasma of cancer patients has provided an alternative method for cancer detection, monitoring and prognostication, whereas the presence of fetal DNA in maternal plasma has revealed significant clinical potential for the prenatal diagnosis of fetal genetic diseases and pregnancy-associated complications. Further applications have been reported in transplantation, traumatology and acute medicine. Extending beyond plasma DNA, a new field of investigation has also been developed in the analysis of plasma RNA, which holds promise for noninvasive gene expression profiling. Biologically, future work will focus on the elucidation of the origin and clearance of circulating DNA, as well as the unexpected stability of circulating RNA.
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Tsui NBY, Hyland CA, Gardener GJ, Danon D, Fisk NM, Millard G, Flower RL, Lo YMD. Noninvasive fetal RHD genotyping by microfluidics digital PCR using maternal plasma from two alloimmunized women with the variant RHD(IVS3+1G>A) allele. Prenat Diagn 2013; 33:1214-6. [PMID: 23999893 DOI: 10.1002/pd.4230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/20/2013] [Accepted: 08/29/2013] [Indexed: 01/17/2023]
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Lo YMD. Non-invasive prenatal testing using massively parallel sequencing of maternal plasma DNA: from molecular karyotyping to fetal whole-genome sequencing. Reprod Biomed Online 2013; 27:593-8. [PMID: 24140310 DOI: 10.1016/j.rbmo.2013.08.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Revised: 07/23/2013] [Accepted: 08/13/2013] [Indexed: 12/16/2022]
Abstract
The discovery of cell-free fetal DNA in maternal plasma in 1997 has stimulated a rapid development of non-invasive prenatal testing. The recent advent of massively parallel sequencing has allowed the analysis of circulating cell-free fetal DNA to be performed with unprecedented sensitivity and precision. Fetal trisomies 21, 18 and 13 are now robustly detectable in maternal plasma and such analyses have been available clinically since 2011. Fetal genome-wide molecular karyotyping and whole-genome sequencing have now been demonstrated in a number of proof-of-concept studies. Genome-wide and targeted sequencing of maternal plasma has been shown to allow the non-invasive prenatal testing of β-thalassaemia and can potentially be generalized to other monogenic diseases. It is thus expected that plasma DNA-based non-invasive prenatal testing will play an increasingly important role in future obstetric care. It is thus timely and important that the ethical, social and legal issues of non-invasive prenatal testing be discussed actively by all parties involved in prenatal care.
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