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Karami F, Noori-Daloii MR, Omidfar K, Tabrizi M, Hantooshzadeh S, Aleyasin A, Daneshpour M, Modarressi MH. Modified methylated DNA immunoprecipitation protocol for noninvasive prenatal diagnosis of Down syndrome. J Obstet Gynaecol Res 2018; 44:608-613. [PMID: 29377389 DOI: 10.1111/jog.13577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Abstract
AIM Methylated DNA immunoprecipitation real-time quantitative polymerase chain reaction (MeDIP-real-time qPCR) has been introduced as noninvasive prenatal test that has shown absolute detection rate in the screening of Down syndrome. Herein, we aimed to propose a novel modification of MeDIP-qPCR and assess its potential to alleviate the overall cost of the test, being used in very early weeks of pregnancy, and develop it to a noninvasive prenatal diagnosis biosensor in future researches. METHODS Cell-free fetal DNA (cffDNA) isolated from 60 pregnant women, including 29 normal and 31 trisomy 21 pregnancies, were analyzed using proposed MeDIP protocol. Enriched methylated DNA sequences were amplified through real-time qPCR using eight fetal-specific primer pairs. The status of samples was determined through the calculation of D-value with the cutoff point of zero. RESULTS The sensitivity and specificity of the MeDIP protocols using nanoparticles were 100% and 100%, respectively. CONCLUSION Remarkable decrease in the price of MeDIP test per each patient would be a reasonable factor to confirm it on larger sample size. Moreover, the high detection rate of screening and the availability of the required instruments around the world make satisfactory reasons to be tested in earlier weeks of pregnancy, thanks to the high sensitivity of gold shell nanoparticles.
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Affiliation(s)
- Fatemeh Karami
- Department of Medical Genetics, Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohammad R Noori-Daloii
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolite Molecular Cellular Science Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Biosensor Research Center, Endocrinology and Metabolite Molecular Cellular Science Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mina Tabrizi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seddigheh Hantooshzadeh
- Faculty of Medicine, Vali-e-Asr Reproductive Health Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ashraf Aleyasin
- Department of Infertility, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Daneshpour
- Biosensor Research Center, Endocrinology and Metabolite Molecular Cellular Science Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad H Modarressi
- Department of Medical Genetics, Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Jaumot J, Navarro A, Faria M, Barata C, Tauler R, Piña B. qRT-PCR evaluation of the transcriptional response of zebra mussel to heavy metals. BMC Genomics 2015; 16:354. [PMID: 25943386 PMCID: PMC4422313 DOI: 10.1186/s12864-015-1567-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/23/2015] [Indexed: 02/06/2023] Open
Abstract
Background The transcriptional response of adult zebra mussels (Dreissena polymorpha) to heavy metals (mercury, copper, and cadmium) was analyzed by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) to study the coordinated regulation of different metal-, oxidative stress- and xenobiotic defence-related genes in gills and digestive gland. Regulatory network analyses allowed the comparison of this response between different species and taxa. Results Chemometric analyses allowed identifying the effects of these metals clearly separating control and treated samples of both tissues. Interactions between the different genes, either in the same or between both tissues, were analysed to identify correlations and to propose stress-related genes’ regulatory networks. These networks were finally compared with existing data from human, mouse, zebrafish, Drosophila and the roundworm to evaluate their mechanistically-known response to metals (and to stressors in general) with the correlations observed in the still poorly-known, invasive zebra mussel. Conclusions Our analyses found a general conservation of regulation genes and of their interactions among the different considered species, and may serve as a guide to extrapolate regulatory data from model species to lesser-known environmentally (or medically) relevant species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1567-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Anna Navarro
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Melissa Faria
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Carlos Barata
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
| | - Benjamín Piña
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.
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The Diagnosis Pattern of Mid-Trimester Fetal Chromosomal Aneuploidy in Xuzhou and the Clinical Applications. Cell Biochem Biophys 2015; 73:267-270. [DOI: 10.1007/s12013-015-0594-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Papageorgiou EA, Koumbaris G, Kypri E, Hadjidaniel M, Patsalis PC. The Epigenome View: An Effort towards Non-Invasive Prenatal Diagnosis. Genes (Basel) 2014; 5:310-29. [PMID: 24722507 PMCID: PMC4094935 DOI: 10.3390/genes5020310] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/05/2014] [Accepted: 03/27/2014] [Indexed: 02/06/2023] Open
Abstract
Epigenetic modifications have proven to play a significant role in cancer development, as well as fetal development. Taking advantage of the knowledge acquired during the last decade, great interest has been shown worldwide in deciphering the fetal epigenome towards the development of methylation-based non-invasive prenatal tests (NIPT). In this review, we highlight the different approaches implemented, such as sodium bisulfite conversion, restriction enzyme digestion and methylated DNA immunoprecipitation, for the identification of differentially methylated regions (DMRs) between free fetal DNA found in maternal blood and DNA from maternal blood cells. Furthermore, we evaluate the use of selected DMRs identified towards the development of NIPT for fetal chromosomal aneuploidies. In addition, we perform a comparison analysis, evaluate the performance of each assay and provide a comprehensive discussion on the potential use of different methylation-based technologies in retrieving the fetal methylome, with the aim of further expanding the development of NIPT assays.
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Affiliation(s)
| | - George Koumbaris
- NIPD Genetics Ltd., Neas Engomis 31, Engomi, Nicosia 2409, Cyprus.
| | - Elena Kypri
- NIPD Genetics Ltd., Neas Engomis 31, Engomi, Nicosia 2409, Cyprus.
| | - Michael Hadjidaniel
- The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Ayios Dometios, Nicosia 2370, Cyprus.
| | - Philippos C Patsalis
- The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, Ayios Dometios, Nicosia 2370, Cyprus.
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Petersen OB, Vogel I, Ekelund C, Hyett J, Tabor A. Potential diagnostic consequences of applying non-invasive prenatal testing: population-based study from a country with existing first-trimester screening. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:265-271. [PMID: 24375770 DOI: 10.1002/uog.13270] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/20/2013] [Accepted: 11/25/2013] [Indexed: 06/03/2023]
Abstract
OBJECTIVES Targeted non-invasive prenatal testing (NIPT) tests for trisomies 21, 18 and 13 and sex chromosome aneuploidies and could be an alternative to traditional karyotyping. The aim of this study was to determine the risk of missing other abnormal karyotypes of probable phenotypic significance by NIPT. METHODS This was a retrospective population-based analysis of all singleton pregnancies booked for combined first-trimester screening (cFTS) in Denmark over a 4-year period. Data concerning maternal demographics, cFTS and prenatal or postnatal karyotypes were collected from the Danish Fetal Medicine database. Karyotypes were classified according to whether the chromosomal anomaly would have been detected by NIPT and whether it was likely to affect phenotype. RESULTS cFTS was completed in 193638 pregnancies. 10205 (5.3%) had cytogenetic or molecular analysis performed. Of these, 1122 (11.0%) had an abnormal karyotype, of which 262 (23.4%) would have been missed by NIPT, but would probably have been clinically significant. The prevalence of such 'atypical abnormal karyotypes' was increased in women above 45 years of age, in pregnancies with increased nuchal translucency (NT) thickness (≥ 3.5 mm), with abnormal levels of free β-human chorionic gonadotropin (<0.2 or ≥ 5.0 multiples of the median (MoM)) or pregnancy-associated plasma protein-A<0.2 MoM. One or more of these factors was present in 3% of women, and the prevalence of atypical abnormal karyotypes in this high-risk cohort was 1.6%. CONCLUSIONS A significant proportion of karyotypic abnormalities will be missed by targeted NIPT. Women of advanced maternal age, or with increased fetal NT or abnormal biochemistry, have a higher risk of having a fetus affected by an atypical abnormal karyotype and need to be counseled accordingly when considering NIPT.
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Affiliation(s)
- O B Petersen
- Fetal Medicine Unit, Department of Obstetrics, Aarhus University Hospital, Aarhus, Denmark
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Hui L, Hyett J. Noninvasive prenatal testing for trisomy 21: Challenges for implementation in Australia. Aust N Z J Obstet Gynaecol 2013; 53:416-24. [DOI: 10.1111/ajo.12117] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 06/09/2013] [Indexed: 02/03/2023]
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The Future of Prenatal Cytogenetics: From Copy Number Variations to Non-invasive Prenatal Testing. CURRENT GENETIC MEDICINE REPORTS 2013. [DOI: 10.1007/s40142-013-0016-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Current World Literature. Curr Opin Obstet Gynecol 2013. [DOI: 10.1097/gco.0b013e32835f3eec] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Jensen TJ, Zwiefelhofer T, Tim RC, Džakula Ž, Kim SK, Mazloom AR, Zhu Z, Tynan J, Lu T, McLennan G, Palomaki GE, Canick JA, Oeth P, Deciu C, van den Boom D, Ehrich M. High-throughput massively parallel sequencing for fetal aneuploidy detection from maternal plasma. PLoS One 2013; 8:e57381. [PMID: 23483908 PMCID: PMC3590217 DOI: 10.1371/journal.pone.0057381] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/21/2013] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Circulating cell-free (ccf) fetal DNA comprises 3-20% of all the cell-free DNA present in maternal plasma. Numerous research and clinical studies have described the analysis of ccf DNA using next generation sequencing for the detection of fetal aneuploidies with high sensitivity and specificity. We sought to extend the utility of this approach by assessing semi-automated library preparation, higher sample multiplexing during sequencing, and improved bioinformatic tools to enable a higher throughput, more efficient assay while maintaining or improving clinical performance. METHODS Whole blood (10mL) was collected from pregnant female donors and plasma separated using centrifugation. Ccf DNA was extracted using column-based methods. Libraries were prepared using an optimized semi-automated library preparation method and sequenced on an Illumina HiSeq2000 sequencer in a 12-plex format. Z-scores were calculated for affected chromosomes using a robust method after normalization and genomic segment filtering. Classification was based upon a standard normal transformed cutoff value of z = 3 for chromosome 21 and z = 3.95 for chromosomes 18 and 13. RESULTS Two parallel assay development studies using a total of more than 1900 ccf DNA samples were performed to evaluate the technical feasibility of automating library preparation and increasing the sample multiplexing level. These processes were subsequently combined and a study of 1587 samples was completed to verify the stability of the process-optimized assay. Finally, an unblinded clinical evaluation of 1269 euploid and aneuploid samples utilizing this high-throughput assay coupled to improved bioinformatic procedures was performed. We were able to correctly detect all aneuploid cases with extremely low false positive rates of 0.09%, <0.01%, and 0.08% for trisomies 21, 18, and 13, respectively. CONCLUSIONS These data suggest that the developed laboratory methods in concert with improved bioinformatic approaches enable higher sample throughput while maintaining high classification accuracy.
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Affiliation(s)
- Taylor J. Jensen
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Tricia Zwiefelhofer
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Roger C. Tim
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Željko Džakula
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Sung K. Kim
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Amin R. Mazloom
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Zhanyang Zhu
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - John Tynan
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Tim Lu
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Graham McLennan
- Research and Development, Sequenom Inc., San Diego, California, United States of America
| | - Glenn E. Palomaki
- Women and Infants Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Jacob A. Canick
- Women and Infants Hospital, Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - Paul Oeth
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Cosmin Deciu
- Research and Development, Sequenom Center for Molecular Medicine, San Diego, California, United States of America
| | - Dirk van den Boom
- Research and Development, Sequenom Inc., San Diego, California, United States of America
| | - Mathias Ehrich
- Research and Development, Sequenom Inc., San Diego, California, United States of America
- * E-mail:
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Papageorgiou EA, Patsalis PC. Maternal plasma sequencing: a powerful tool towards fetal whole genome recovery. BMC Med 2013; 11:56. [PMID: 23445999 PMCID: PMC3621811 DOI: 10.1186/1741-7015-11-56] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 02/27/2013] [Indexed: 11/14/2022] Open
Abstract
Noninvasive prenatal diagnosis of chromosomal aneuploidies, although challenging, has been achieved through the implementation of novel methodologies such as methylated DNA immunoprecipitation and next generation sequencing technologies. Nevertheless, additional developments are required towards the interpretation of other fetal abnormalities of higher complexity, such as de novo mutations including microdeletion and microduplication syndromes as well as complex diseases. The application of next generation sequencing technologies towards fetal whole genome recovery has demonstrated great potential to achieve the above goal. In a research article published in Genome Medicine, Chen et al. presented a novel approach that allowed more robust and accurate characterization of parental alleles compared with previous studies. This was achieved through a revolutionary strategy based on the use of trios and unrelated individuals that simultaneously targets the interpretation of the fetal haplotype and phenotype in one step. It is hereby shown that the implementation of a more accurate experimental design in combination with proper analytical tools can provide robust noninvasive fetal whole genome recovery with the potential for further developments beyond the DNA level.
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