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Elahi AH, Morales CS, Xu XL, Eliades A, Patsalis PC, Abramson DH, Jhanwar SC. `Targeted pharmacologic inhibition of S-phase kinase-associated protein 2 (SKP2) mediated cell cycle regulation in lung and other RB-Related cancers: A brief review of current status and future prospects. Adv Biol Regul 2023; 88:100964. [PMID: 37004354 DOI: 10.1016/j.jbior.2023.100964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
Small cell lung cancer (SCLC) often exhibits Rb deficiency, TRβ and p130 deletion, and SKP2 amplification, suggesting TRβ inactivation and SKP2 activation. It is reported that SKP2 targeted therapy is effective in some cancers in vitro and in vivo, but it is not reported for the treatment of SCLC and retinoblastoma. SKP2 is the synthetic lethal gene in SCLC and retinoblastoma, so SKP2 can be used for targeted therapy in SCLC and retinoblastoma. RB1 knockout mice develop several kinds of tumors, but Rb1 and SKP2 double knockout mice are healthy, suggesting that SKP2 targeted therapy may have significant effects on Rb deficient cancers with less side effects, and if successful in SCLC and retinoblastoma in vitro and in animal model, such compounds may be promising for the clinical treatment of SCLC, retinoblastoma, and variety of Rb deficient cancers. Previously our studies showed that retinoblastomas exhibit retinal cone precursor properties and depend on cone-specific thyroid hormone receptor β2 (TRβ2) and SKP2 signaling. In this study, we sought to suppress SCLC and retinoblastoma cell growth by SKP2 inhibitors as a prelude to targeted therapy in vitro and in vivo. We knocked down TRβ2 and SKP2 or over-expressed p27 in SCLC and retinoblastoma cell lines to investigate SKP2 and p27 signaling alterations. The SCLC cell lines H209 as well as retinoblastoma cell lines Y79, WERI, and RB177 were treated with SKP2 inhibitor C1 at different concentrations, following which Western blotting, Immunostaining, and cell cycle kinetics studies were performed to study SKP2 and p27 expression ubiquitination, to determine impact on cell cycle regulation and growth inhibition. TRβ2 knockdown in Y79, RB177 and H209 caused SKP2 downregulation and degradation, p27 up-regulation, and S phase arrest, whereas, SKP2 knockdown or p27 over-expression caused p27 accumulation and G1-S phase arrest. In the cell lines Y79, WERI, RB177, and H209 treatment with C1 caused SKP2 ubiquitination and degradation, p27 de-ubiquitination and accumulation, and cell growth arrest. SKP2 inhibitor C1 significantly suppressed retinoblastoma as well as SCLC cell growth by SKP2 degradation and p27 accumulation. In vivo study also showed inhibition of tumor growth with C1 treatment. Potential limitations of the success of such a therapeutic approach and its translational application in human primary tumors, and alternative approaches to overcome such limitations are briefly discussed for the treatment of retinoblastoma, SCLC and other RB-related cancers.
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A Mini-Review Regarding the Clinical Outcomes of In Vitro Fertilization (IVF) Following Pre-Implantation Genetic Testing (PGT)-Next Generation Sequencing (NGS) Approach. Diagnostics (Basel) 2022; 12:diagnostics12081911. [PMID: 36010262 PMCID: PMC9406843 DOI: 10.3390/diagnostics12081911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/30/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Background: PGT-based NGS revolutionized the field of reproductive medicine, becoming an integrated component within current assisted reproductive technology (ART) protocols. Methods: We searched the literature published in the last half a decade in four databases (PubMed/Medline, ISI Web of Knowledge, ScienceDirect, and Scopus) between 2018 and 2022. Results: A total of 1388 articles were filtered, from which 60 met, initially, the eligibility criteria, but only 42 were included (≥100 patients/couples—62,465 patients and 6628 couples in total) in the present mini-review. In total, forty-two (70.0%) reported reproductive outcomes, while eighteen (30.0%) had distinct objectives. Furthermore, n = 1, 1.66% of the studies focused on PGT, n = 1, 1.66% on pre-implantation genetic testing for monogenic disorders (PGT-M), n = 3, 5.0% on pre-implantation genetic testing for structural rearrangements (PGT-SR) and n = 55, 91.66% on pre-implantation genetic testing for aneuploidies (PGT-A). Conclusions: PGT using NGS proved to be an excellent companion that folds within the current ascending tendency among couples that require specialty care. We strongly encourage future studies to provide a systematic overview expanded at a larger scale on the role of the PGT-NGS.
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Afzal M, Naeem MA, Ahmed S, Amin N, Rahim A, Munawar M, Ishaq M, Rathore A, Maria K. Noninvasive prenatal testing of beta-thalassemia for common Pakistani mutations: a comparative study using cell-free fetal DNA from maternal plasma and chorionic villus sampling. Hematology 2022; 27:353-359. [PMID: 35287566 DOI: 10.1080/16078454.2022.2045052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The discovery of circulating cell-free fetal DNA (cff-DNA) in maternal plasma has inspired the noninvasive prenatal testing (NIPT) approaches for various genetic fetal screening including rhesus D typing, sex determination, aneuploidies, and single-gene disorders. OBJECTIVE Noninvasive determination of paternally inherited beta-thalassemia mutations in maternal total cell-free DNA (cf-DNA) by using allele-specific amplification refractory mutation system (ARMS) real-time PCR (RT-PCR) in concordance with the conventional invasive method. METHODS An observational study was conducted at the Armed Forces Institute of Blood Transfusion in collaboration with the genetics resource center from March 2021 to August 2021. A total number of 26 couples were selected having a history of previously affected children with beta-thalassemia. A routine chorionic villus sampling (CVS) invasive procedure was carried out, and the mutation analysis was done using conventional PCR. To assess NIPT, a total cf-DNA was also extracted from maternal plasma and analyzed using allele-specific ARMS RT-PCR. RESULTS Based on conventional PCR testing, 13 of 26 couples were found having beta-thalassemia carriers with homozygous mutation, and 13 couples were carriers with heterozygous mutations. Further to assess NIPT, the cf-DNA of 13 pregnant females among the couples with different mutational patterns was analyzed by allele-specific ARMS RT-PCR to detect paternally inherited mutations. In comparison with conventional PCR, 11 cases (84.6%) were matched successfully, while two cases (15.4%) had no concordance with conventional invasive prenatal testing (IPT). CONCLUSION NIPT using maternal cf-DNA by allele-specific ARMS RT-PCR can be feasible to screen paternal inherited mutant alleles to rule out pregnant women from invasive procedures where the test would be negative for paternal inheritance. However, a low amount of fetal DNA in maternal plasma is a limiting factor and required further improvement to enrich fetal cf-DNA for complete concordance with conventional IPT.
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Affiliation(s)
- Muhammad Afzal
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | | | - Suhaib Ahmed
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Nayyar Amin
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Amena Rahim
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Manazza Munawar
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Mansoor Ishaq
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Ali Rathore
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - K Maria
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
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Mao X, Liu C, Tong H, Chen Y, Liu K. Principles of digital PCR and its applications in current obstetrical and gynecological diseases. Am J Transl Res 2019; 11:7209-7222. [PMID: 31934273 PMCID: PMC6943456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Digital PCR (dPCR) is a revolutionary technique to precisely quantify nucleic acids. For its high sensitivity and specificity, this technique has been widely replicated worldwide. To verify its applicability, we reviewed all the related articles in PubMed database published before May 10, 2019. Original articles and reviews on the topics were selected. Entered key words included "digital PCR/dPCR", "advantage", "combined use", "microfluidic chip", "gynecological cancer/tumor". We found that dPCR has shown great potential in clinical operations, like tumor liquid biopsy, non-invasive prenatal diagnosis, microorganism detection, and next-generation sequencing library quality-control.
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Affiliation(s)
- Xiaodong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Hua Tong
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Yajun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Kangsheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
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Zhang S, Han S, Zhang M, Wang Y. Non-invasive prenatal paternity testing using cell-free fetal DNA from maternal plasma: DNA isolation and genetic marker studies. Leg Med (Tokyo) 2018; 32:98-103. [PMID: 29626747 DOI: 10.1016/j.legalmed.2018.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 03/01/2018] [Accepted: 03/31/2018] [Indexed: 12/13/2022]
Abstract
Invasive prenatal paternity tests can result in miscarriage and congenital malformations; therefore, a non-invasive method of testing is preferable. However, little progress could be made in this field until the introduction of cell-free fetal DNA (cffDNA) in 2009. In this review, two aspects regarding the history and development of non-invasive prenatal paternity testing (NIPAT) are summarized: (1) extraction and enrichment of cffDNA and (2) genetic marker-based studies. Although column-based kits are used widely for NIPAT, some researchers have suggested that an automated method, such as magnetic extraction, generally has a higher cffDNA yield than that of manual column-based extraction; therefore, its popularity might increase in the near future. In addition, size- and methylation-based enrichment methods are expected to perform better than formaldehyde-based methods. On the other hand, single nucleotide polymorphism-based techniques have contributed to NIPAT, whereas the application of short tandem repeat testing has so far been restricted to pregnant women bearing male fetuses only. Additional methods and techniques are expected to be innovated to facilitate the forensic practice of NIPAT.
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Affiliation(s)
- Shanshan Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Shuyi Han
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
| | - Maoxiu Zhang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China
| | - Yunshan Wang
- Medical Research & Laboratory Diagnostic Center, Jinan Central Hospital Affiliated to Shandong University, No. 105 Jiefang Road, Jinan, Shandong 250013, PR China.
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Ye J, Chen C, Yuan Y, Han L, Wang Y, Qiu W, Zhang H, Asan, Gu X. Haplotype-based Noninvasive Prenatal Diagnosis of Hyperphenylalaninemia through Targeted Sequencing of Maternal Plasma. Sci Rep 2018; 8:161. [PMID: 29317692 PMCID: PMC5760544 DOI: 10.1038/s41598-017-18358-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/11/2017] [Indexed: 11/19/2022] Open
Abstract
Here we developed a haplotype-based noninvasive prenatal diagnosis method for hyperphenylalaninemia (HPA) and demonstrated its accuracy and feasibility during early pregnancy. Capture sequencing was performed on genomic DNA from parents and probands using customized hybridization probes targeting highly heterozygous single-nucleotide polymorphisms located within the 1 M region flanking phenylalanine hydroxylase (PAH) and 6-pyruvoyltetrahydropterin (PTS) and its coding region to determine the parental haplotypes and linkage to pathogenic mutations. Maternal plasma DNA obtained at 12–20 weeks of gestation was also subjected to targeted sequencing to deduce the fetal haplotypes based on the parental haplotypes. The fetal genotypes were further validated by invasive prenatal diagnosis. Haplotype-based noninvasive prenatal testing was successfully performed in 13 families. Five fetuses were identified to harbor bi-allelic pathogenic variants of PAH, four fetuses were carriers of one heterozygous PAH variant, three fetuses were normal, and the fetus of the 6-pyruvoyl tetrahydrobiopterin synthase family was identified as normal. The fetal genotypes at two gestational weeks from the same PAH family were identical. All results were consistent with the prenatal diagnosis based on amniotic fluid. Haplotype-based noninvasive prenatal testing for HPA through targeted sequencing is accurate and feasible during early gestation.
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Affiliation(s)
- Jun Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Chao Chen
- Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,BGI-Shenzhen, Shenzhen, China
| | - Yuan Yuan
- Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,BGI-Shenzhen, Shenzhen, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yaoshen Wang
- Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.,BGI-Shenzhen, Shenzhen, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Asan
- Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China. .,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China. .,BGI-Shenzhen, Shenzhen, China.
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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Badeau M, Lindsay C, Blais J, Nshimyumukiza L, Takwoingi Y, Langlois S, Légaré F, Giguère Y, Turgeon AF, Witteman W, Rousseau F. Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women. Cochrane Database Syst Rev 2017; 11:CD011767. [PMID: 29125628 PMCID: PMC6486016 DOI: 10.1002/14651858.cd011767.pub2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Common fetal aneuploidies include Down syndrome (trisomy 21 or T21), Edward syndrome (trisomy 18 or T18), Patau syndrome (trisomy 13 or T13), Turner syndrome (45,X), Klinefelter syndrome (47,XXY), Triple X syndrome (47,XXX) and 47,XYY syndrome (47,XYY). Prenatal screening for fetal aneuploidies is standard care in many countries, but current biochemical and ultrasound tests have high false negative and false positive rates. The discovery of fetal circulating cell-free DNA (ccfDNA) in maternal blood offers the potential for genomics-based non-invasive prenatal testing (gNIPT) as a more accurate screening method. Two approaches used for gNIPT are massively parallel shotgun sequencing (MPSS) and targeted massively parallel sequencing (TMPS). OBJECTIVES To evaluate and compare the diagnostic accuracy of MPSS and TMPS for gNIPT as a first-tier test in unselected populations of pregnant women undergoing aneuploidy screening or as a second-tier test in pregnant women considered to be high risk after first-tier screening for common fetal aneuploidies. The gNIPT results were confirmed by a reference standard such as fetal karyotype or neonatal clinical examination. SEARCH METHODS We searched 13 databases (including MEDLINE, Embase and Web of Science) from 1 January 2007 to 12 July 2016 without any language, search filter or publication type restrictions. We also screened reference lists of relevant full-text articles, websites of private prenatal diagnosis companies and conference abstracts. SELECTION CRITERIA Studies could include pregnant women of any age, ethnicity and gestational age with singleton or multifetal pregnancy. The women must have had a screening test for fetal aneuploidy by MPSS or TMPS and a reference standard such as fetal karyotype or medical records from birth. DATA COLLECTION AND ANALYSIS Two review authors independently carried out study selection, data extraction and quality assessment (using the QUADAS-2 tool). Where possible, hierarchical models or simpler alternatives were used for meta-analysis. MAIN RESULTS Sixty-five studies of 86,139 pregnant women (3141 aneuploids and 82,998 euploids) were included. No study was judged to be at low risk of bias across the four domains of the QUADAS-2 tool but applicability concerns were generally low. Of the 65 studies, 42 enrolled pregnant women at high risk, five recruited an unselected population and 18 recruited cohorts with a mix of prior risk of fetal aneuploidy. Among the 65 studies, 44 evaluated MPSS and 21 evaluated TMPS; of these, five studies also compared gNIPT with a traditional screening test (biochemical, ultrasound or both). Forty-six out of 65 studies (71%) reported gNIPT assay failure rate, which ranged between 0% and 25% for MPSS, and between 0.8% and 7.5% for TMPS.In the population of unselected pregnant women, MPSS was evaluated by only one study; the study assessed T21, T18 and T13. TMPS was assessed for T21 in four studies involving unselected cohorts; three of the studies also assessed T18 and 13. In pooled analyses (88 T21 cases, 22 T18 cases, eight T13 cases and 20,649 unaffected pregnancies (non T21, T18 and T13)), the clinical sensitivity (95% confidence interval (CI)) of TMPS was 99.2% (78.2% to 100%), 90.9% (70.0% to 97.7%) and 65.1% (9.16% to 97.2%) for T21, T18 and T13, respectively. The corresponding clinical specificity was above 99.9% for T21, T18 and T13.In high-risk populations, MPSS was assessed for T21, T18, T13 and 45,X in 30, 28, 20 and 12 studies, respectively. In pooled analyses (1048 T21 cases, 332 T18 cases, 128 T13 cases and 15,797 unaffected pregnancies), the clinical sensitivity (95% confidence interval (CI)) of MPSS was 99.7% (98.0% to 100%), 97.8% (92.5% to 99.4%), 95.8% (86.1% to 98.9%) and 91.7% (78.3% to 97.1%) for T21, T18, T13 and 45,X, respectively. The corresponding clinical specificities (95% CI) were 99.9% (99.8% to 100%), 99.9% (99.8% to 100%), 99.8% (99.8% to 99.9%) and 99.6% (98.9% to 99.8%). In this risk group, TMPS was assessed for T21, T18, T13 and 45,X in six, five, two and four studies. In pooled analyses (246 T21 cases, 112 T18 cases, 20 T13 cases and 4282 unaffected pregnancies), the clinical sensitivity (95% CI) of TMPS was 99.2% (96.8% to 99.8%), 98.2% (93.1% to 99.6%), 100% (83.9% to 100%) and 92.4% (84.1% to 96.5%) for T21, T18, T13 and 45,X respectively. The clinical specificities were above 100% for T21, T18 and T13 and 99.8% (98.3% to 100%) for 45,X. Indirect comparisons of MPSS and TMPS for T21, T18 and 45,X showed no statistical difference in clinical sensitivity, clinical specificity or both. Due to limited data, comparative meta-analysis of MPSS and TMPS was not possible for T13.We were unable to perform meta-analyses of gNIPT for 47,XXX, 47,XXY and 47,XYY because there were very few or no studies in one or more risk groups. AUTHORS' CONCLUSIONS These results show that MPSS and TMPS perform similarly in terms of clinical sensitivity and specificity for the detection of fetal T31, T18, T13 and sex chromosome aneuploidy (SCA). However, no study compared the two approaches head-to-head in the same cohort of patients. The accuracy of gNIPT as a prenatal screening test has been mainly evaluated as a second-tier screening test to identify pregnancies at very low risk of fetal aneuploidies (T21, T18 and T13), thus avoiding invasive procedures. Genomics-based non-invasive prenatal testing methods appear to be sensitive and highly specific for detection of fetal trisomies 21, 18 and 13 in high-risk populations. There is paucity of data on the accuracy of gNIPT as a first-tier aneuploidy screening test in a population of unselected pregnant women. With respect to the replacement of invasive tests, the performance of gNIPT observed in this review is not sufficient to replace current invasive diagnostic tests.We conclude that given the current data on the performance of gNIPT, invasive fetal karyotyping is still the required diagnostic approach to confirm the presence of a chromosomal abnormality prior to making irreversible decisions relative to the pregnancy outcome. However, most of the gNIPT studies were prone to bias, especially in terms of the selection of participants.
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Affiliation(s)
- Mylène Badeau
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Carmen Lindsay
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Jonatan Blais
- CHAU‐Hôtel‐Dieu de LévisDepartment of Medical Biology143 Rue WolfeLévisQCCanadaG6V 3Z1
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and PathologyQuebec CityQuebecCanada
| | - Leon Nshimyumukiza
- University of AlbertaSchool of Public Health8303 112 StreetEdmontonAlbertaCanadaT6G 2T4
| | - Yemisi Takwoingi
- University of BirminghamInstitute of Applied Health ResearchEdgbastonBirminghamUKB15 2TT
| | - Sylvie Langlois
- University of British ColumbiaDepartment of Medical Genetics, Faculty of MedicineC234, 4500 Oak StreetVancouverBCCanadaV6H 3N1
| | - France Légaré
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - Yves Giguère
- CHU de Québec ‐ Université LavalReproductive, Mother and Child Health Research Axis10, rue de l'Espinay, A2‐226Québec CityQCCanadaG1L 3L5
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
| | - Alexis F Turgeon
- CHU de Québec ‐ Université Laval, Université LavalDepartment of Anesthesiology and Critical Care Medicine, Division of Critical Care Medicine, and Population Health and Optimal Health Practices Research Unit, CHU de Québec ‐ Université Laval Research Center1401, 18eme rueQuebec CityQCCanadaG1J 1Z4
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
| | - William Witteman
- CHU de Québec ‐ Université LavalPopulation Health and Optimal Health Practices Research Axis45 Rue LeclercQuébec CityQCCanadaG1L 3L5
| | - François Rousseau
- Faculty of Medicine, Université LavalDepartment of Molecular Biology, Medical Biochemistry and Pathology10, rue de l'EspinayQuébec CityQcCanadaG1L 3L5
- CHU de Québec Research Center, Université LavalPopulation Health and Optimal Health Practices Research Axis1401, 18eme rueQuébec CityQuébecCanadaG1J 1Z4
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Wang Y, Bao J, Zhang L, Li Y, Zhang Y, Yin L. PLAC4 mRNA SNP in non-invasive prenatal testing of Down syndrome. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:7962-7967. [PMID: 31966647 PMCID: PMC6965248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/19/2017] [Indexed: 06/10/2023]
Abstract
The purpose of this study was to explore the mRNA expression level of PLAC4 in the maternal plasma and the clinical value of its single nucleotide polymorphism (SNP) rs8130833 in non-invasive prenatal testing (NIPT) of Down syndrome. 40 pregnant women were collected in Tianjin Medical University General Hospital from January 2014 to December 2015. Amniotic puncture karyotype analysis was adapted to determine whether the fetuses with Down syndrome (DS) or not. 20 fetuses were diagnosed with Down syndrome and recorded as the DS group, and 20 fetuses were normal and recorded as the control group. Quantitative reverse transcription-PCR (qRT-PCR) was used to detect the mRNA expression level of PLAC4 both in the whole blood and plasma of pregnant women. A/G polymorphism of rs8130833 was analyzed by pyrosequencing method using the cell-free fetal RNA (cff RNA) in maternal circulation. The mRNA expression level of PLAC4 in DS group was higher than the control group, but the difference was not statistically significant (P > 0.05). A/G polymorphism of rs8130833 was about 2:1 in DS group, and it was nearly 1:1 in control group. The PLAC4 mRNA SNP (rs8130833) has a certain value of research and application in NIPT of DS.
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Affiliation(s)
- Yujie Wang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Jianheng Bao
- Second Department of Hepatopancreatobiliary Surgery, Tianjin Nankai HospitalTianjin, People’s Republic of China
| | - Lijun Zhang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Yongmei Li
- Institute of Basic Medicine, Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Yu Zhang
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
| | - Lirong Yin
- Department of Obstetrics and Gynecology, The Second Hospital of Tianjin Medical UniversityTianjin, People’s Republic of China
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Olaya LF, Hyett JA, McLennan SV. Effects of sample processing and storage on the integrity of cell-free miRNAs in maternal plasma. Prenat Diagn 2017; 37:744-749. [PMID: 28556966 DOI: 10.1002/pd.5075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/13/2017] [Accepted: 05/17/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cell-free fetal miRNAs have been identified as potential biomarkers for fetal abnormalities and/or placental function. Factors affecting the stability of cell-free fetal miRNA samples (type of collection tube and time interval between sampling and analysis) have not previously been reported. METHODS Blood from pregnant women (n = 12, 18 ± 4 weeks' gestation) was collected into two types of tube (EDTA and RNA BCT) and was stored at different temperatures for up to 72 h. Expression of seven apparently placental specific miRNAs was then measured to compare the effects of sampling and storage. These miRNAs were also assessed in non-pregnant women (n = 9). RESULTS The quantity of miRNA extracted was not affected by time or tube. Three miRNAs (miR-518b, miR-525 and miR-526a*) were measureable only in pregnant women, but miR-518b was not always present. Detailed study of the two pregnancy specific miRNAs showed no effect of tube type at 4 h. However, variability in miRNA level was observed with increased time and was significant for one miRNA in the BCT tube at >48 h (p < 0.005). CONCLUSION Some cffmiRNAs are placental specific, and these samples are stable when analyzed within 48 h of collection in either tube type. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Luisa F Olaya
- Discipline of Obstetrics, Gynaecology and Neonatology and Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia.,Department of Endocrinology, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan A Hyett
- Discipline of Obstetrics, Gynaecology and Neonatology and Central Clinical School, Faculty of Medicine, University of Sydney, Sydney, Australia
| | - Susan V McLennan
- Department of Endocrinology, Central Clinical School, University of Sydney, Sydney, New South Wales, Australia.,NSW Health Pathology, Chemical Pathology, RPA Hospital Camperdown, New South Wales, Australia
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10
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Wang HD, Liu L, Zhao HR, Hou QF, Yan JB, Shi WL, Guo QN, Wang L, Liao SX, Zhu BF. Detection of fetal epigenetic biomarkers through genome-wide DNA methylation study for non-invasive prenatal diagnosis. Mol Med Rep 2017; 15:3989-3998. [PMID: 28440505 PMCID: PMC5436219 DOI: 10.3892/mmr.2017.6506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/13/2017] [Indexed: 12/20/2022] Open
Abstract
The discovery of cell-free DNA fetal (cff DNA) in maternal plasma during pregnancy provides a novel perspective for the development of non-invasive prenatal diagnosis (NIPD). Against the background of maternal DNA, the use of the relatively low concentration of cff DNA is limited in NIPD. Therefore, in order to overcome the complication of the background of maternal DNA and expand the scope of cff DNA application in clinical practice, it is necessary to identify novel universal fetal-specific DNA markers. The GeneChip Human Promoter 1.0R Array set was used in the present study to analyze the methylation status of 12 placental tissue and maternal peripheral blood whole-genome DNA samples. In total, 5 fetus differential hypermethylation regions and 6 fetus differential hypomethylation regions were identified. In order to verify the 11 selected methylation regions and detect the differential CpG sites in these regions, a bisulfate direct sequencing strategy was used. In total, 87 fetal differential methylation CpG sites were identified from 123 CpG sites. The detection of fetal differential methylation DNA regions and CpG sites may be instrumental in the development of efficient NIPD and in the expansion of its application in other disorders.
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Affiliation(s)
- Hong-Dan Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Lin Liu
- Department of Cardiovascular Ultrasound, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Hui-Ru Zhao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Qiao-Fang Hou
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Jing-Bin Yan
- Shanghai Children's Hospital, Shanghai Institute of Medical Genetics, Key Laboratory of Embryo Molecular Biology, Ministry of Health of China and Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, P.R. China
| | - Wei-Li Shi
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Qian-Nan Guo
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Li Wang
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Shi-Xiu Liao
- Medical Genetic Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Bo-Feng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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Non-invasive prenatal diagnosis of β-thalassemia by detection of the cell-free fetal DNA in maternal circulation: a systematic review and meta-analysis. Ann Hematol 2016; 95:1341-50. [DOI: 10.1007/s00277-016-2620-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/14/2016] [Indexed: 12/11/2022]
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12
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Zafari M, Gill P, Kowsaryan M, Alipour A, Banihashemi A. High-resolution melting analysis for noninvasive prenatal diagnosis of IVS-II-I (G-A) fetal DNA in minor beta-thalassemia mothers. J Matern Fetal Neonatal Med 2015; 29:3323-8. [PMID: 26600408 DOI: 10.3109/14767058.2015.1124263] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The high-resolution melting (HRM) technique is fast, effective and successful method for mutation detection. The aim of this study was to determine the sensitivity and specificity of the HRM method for detection of a paternally inherited mutation in a fetus as a noninvasive prenatal diagnosis of β-thalassemia. METHODS Genomic DNAs were prepared from 50 β-thalassemia minor couples whose pregnancy was at risk for homozygous β-thalassemia. Ten milliliters of the maternal blood from each pregnant woman were collected and after separating plasma stored at -80 °C until analysis. The extracted DNAs were analyzed by HRM real-time PCR for detection of IVS-II-I (G-A) as a paternally inherited mutation. The gold standard was the result of a chorionic villus sampling by a standard reverse dot blotting test. RESULTS The sensitivity and specificity of HRM real-time PCR were 92.6% and 82.6%, respectively. Also, the positive and negative predictive values were 86.2% and 90.47%, respectively. CONCLUSIONS HRM real-time PCR was a sensitive and specific method for determining the paternally inherited mutation in the fetus at risk with thalassemia major.
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Affiliation(s)
- Mandana Zafari
- a Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences , Sari , Iran
| | - Pooria Gill
- a Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences , Sari , Iran .,b Nanomedicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences , Sari , Iran , and
| | - Mehrnoush Kowsaryan
- a Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences , Sari , Iran
| | - Abbass Alipour
- a Thalassemia Research Center, Hemoglobinopathy Institute, Mazandaran University of Medical Sciences , Sari , Iran .,b Nanomedicine Group, Immunogenetics Research Center, Mazandaran University of Medical Sciences , Sari , Iran , and
| | - Ali Banihashemi
- c Amir Kola Genetic Laboratory, Babol University of Medical Sciences , Babol , Iran
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13
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A Non-Invasive Droplet Digital PCR (ddPCR) Assay to Detect Paternal CFTR Mutations in the Cell-Free Fetal DNA (cffDNA) of Three Pregnancies at Risk of Cystic Fibrosis via Compound Heterozygosity. PLoS One 2015; 10:e0142729. [PMID: 26561302 PMCID: PMC4641687 DOI: 10.1371/journal.pone.0142729] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/26/2015] [Indexed: 12/12/2022] Open
Abstract
Introduction Non-invasive prenatal diagnosis (NIPD) makes use of cell-free fetal DNA (cffDNA) in the mother’s bloodstream as an alternative to invasive sampling methods such as amniocentesis or CVS, which carry a 0.5–1% risk of fetal loss. We describe a droplet digital PCR (ddPCR) assay designed to inform the testing options for couples whose offspring are at risk of suffering from cystic fibrosis via compound heterozygosity. By detecting the presence or absence of the paternal mutation in the cffDNA, it is possible to predict whether the fetus will be an unaffected carrier (absence) or whether further invasive testing is indicated (presence). Methods We selected a family in which the parents were known to carry different mutated CFTR alleles as our test system. NIPD was performed for three of their pregnancies during the first trimester (at around 11–12 weeks of gestation). Taqman probes were designed against an amplicon in exon 11 of the CFTR gene, to quantify the proportion of mutant (ΔF508-MUT; FAM) and normal (ΔF508-NOR; VIC) alleles at position c.1521_1523 of the CFTR gene. Discussion The assay correctly and unambiguously recognized the ΔF508-MUT CFTR allele in the cffDNA of all three proband fetuses and none of the six unaffected control fetuses. In conclusion, the Bio-Rad QX100 was found to be a cost-effective and technically undemanding platform for designing bespoke NIPD assays.
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14
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Bisulfite Conversion of DNA: Performance Comparison of Different Kits and Methylation Quantitation of Epigenetic Biomarkers that Have the Potential to Be Used in Non-Invasive Prenatal Testing. PLoS One 2015; 10:e0135058. [PMID: 26247357 PMCID: PMC4527772 DOI: 10.1371/journal.pone.0135058] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 07/16/2015] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Epigenetic alterations, including DNA methylation, play an important role in the regulation of gene expression. Several methods exist for evaluating DNA methylation, but bisulfite sequencing remains the gold standard by which base-pair resolution of CpG methylation is achieved. The challenge of the method is that the desired outcome (conversion of unmethylated cytosines) positively correlates with the undesired side effects (DNA degradation and inappropriate conversion), thus several commercial kits try to adjust a balance between the two. The aim of this study was to compare the performance of four bisulfite conversion kits [Premium Bisulfite kit (Diagenode), EpiTect Bisulfite kit (Qiagen), MethylEdge Bisulfite Conversion System (Promega) and BisulFlash DNA Modification kit (Epigentek)] regarding conversion efficiency, DNA degradation and conversion specificity. METHODS Performance was tested by combining fully methylated and fully unmethylated λ-DNA controls in a series of spikes by means of Sanger sequencing (0%, 25%, 50% and 100% methylated spikes) and Next-Generation Sequencing (0%, 3%, 5%, 7%, 10%, 25%, 50% and 100% methylated spikes). We also studied the methylation status of two of our previously published differentially methylated regions (DMRs) at base resolution by using spikes of chorionic villus sample in whole blood. RESULTS The kits studied showed different but comparable results regarding DNA degradation, conversion efficiency and conversion specificity. However, the best performance was observed with the MethylEdge Bisulfite Conversion System (Promega) followed by the Premium Bisulfite kit (Diagenode). The DMRs, EP6 and EP10, were confirmed to be hypermethylated in the CVS and hypomethylated in whole blood. CONCLUSION Our findings indicate that the MethylEdge Bisulfite Conversion System (Promega) was shown to have the best performance among the kits. In addition, the methylation level of two of our DMRs, EP6 and EP10, was confirmed. Finally, we showed that bisulfite amplicon sequencing is a suitable approach for methylation analysis of targeted regions.
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15
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Cheng WL, Hsiao CH, Tseng HW, Lee TP. Noninvasive prenatal diagnosis. Taiwan J Obstet Gynecol 2015; 54:343-9. [DOI: 10.1016/j.tjog.2015.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2015] [Indexed: 01/14/2023] Open
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16
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Genomics-based non-invasive prenatal testing for detection of fetal chromosomal aneuploidy in pregnant women. THE COCHRANE DATABASE OF SYSTEMATIC REVIEWS 2015. [DOI: 10.1002/14651858.cd011767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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17
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Christopoulou G, Papageorgiou EA, Patsalis PC, Velissariou V. Comparison of next generation sequencing-based and methylated DNA immunoprecipitation-based approaches for fetal aneuploidy non-invasive prenatal testing. World J Med Genet 2015; 5:23-27. [DOI: 10.5496/wjmg.v5.i2.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 04/07/2015] [Accepted: 04/20/2015] [Indexed: 02/06/2023] Open
Abstract
Over the past few years, many researchers have attempted to develop non-invasive prenatal testing methods in order to investigate the genetic status of the fetus. The aim is to avoid invasive procedures such as chorionic villus and amniotic fluid sampling, which result in a significant risk for pregnancy loss. The discovery of cell free fetal DNA circulating in the maternal blood has great potential for the development of non-invasive prenatal testing (NIPT) methodologies. Such strategies have been successfully applied for the determination of the fetal rhesus status and inherited monogenic disease but the field of fetal aneuploidy investigation seems to be more challenging. The main reason for this is that the maternal cell free DNA in the mother’s plasma is far more abundant, and because it is identical to half of the corresponding fetal DNA. Approaches developed are mainly based on next generation sequencing (NGS) technologies and epigenetic genetic modifications, such as fetal-maternal DNA differential methylation. At present, genetic services for non-invasive fetal aneuploidy detection are offered using NGS-based approaches but, for reasons that are presented herein, they still serve as screening tests which are not readily accessed by the majority of couples. Here we discuss the limitations of both strategies for NIPT and the future potential of the methods developed.
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18
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Xu Y, Li X, Ge HJ, Xiao B, Zhang YY, Ying XM, Pan XY, Wang L, Xie WW, Ni L, Chen SP, Jiang WT, Liu P, Ye H, Cao Y, Zhang JM, Liu Y, Yang ZJ, Chen YW, Chen F, Jiang H, Ji X. Haplotype-based approach for noninvasive prenatal tests of Duchenne muscular dystrophy using cell-free fetal DNA in maternal plasma. Genet Med 2015; 17:889-96. [PMID: 25654318 DOI: 10.1038/gim.2014.207] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 12/22/2014] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study demonstrates noninvasive prenatal testing (NIPT) for Duchenne muscular dystrophy (DMD) using a newly developed haplotype-based approach. METHODS Eight families at risk for DMD were recruited for this study. Parental haplotypes were constructed using target-region sequencing data from the parents and the probands. Fetal haplotypes were constructed using a hidden Markov model through maternal plasma DNA sequencing. The presence of haplotypes linked to the maternal mutant alleles in males indicated affected fetuses. This method was further validated by comparing the inferred single-nucleotide polymorphism (SNP) genotypes to the direct sequencing results of fetal genomic DNA. Prenatal diagnosis was confirmed with amniocentesis, and those results were interpreted in a blinded fashion. RESULTS The results showed an average accuracy of 99.98% for the total inferred maternal SNPs. With a mean depth of 30× achieved in the 10-Mb target region of each sample, the noninvasive results were consistent with those of the invasive procedure. CONCLUSION This is the first report of NIPT for DMD and the first application of a haplotype-based approach in NIPT for X-linked diseases. With further improvements in accuracy, this haplotype-based strategy could be feasible for NIPT for DMD and even other X-linked single-gene disorders.
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Affiliation(s)
- Yan Xu
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | | | | | - Bing Xiao
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | | | - Xiao-Min Ying
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | | | - Lei Wang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Pediatric Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | | | - Lin Ni
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | | | - Wen-Ting Jiang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | | | - Hui Ye
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Ying Cao
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Jing-Min Zhang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Yu Liu
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Zu-Jing Yang
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Pediatric Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Ying-Wei Chen
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences of Copenhagen, Section of Molecular Disease Biology, Copenhagen, Denmark
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xing Ji
- Department of Prenatal Diagnosis Center, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,Department of Genetics, Shanghai Institute of Pediatric Research, Shanghai, China
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Günel T, Hosseini MK, Gümüşoğlu E, Zeybek G, Dölekçap İ, Kalelioğlu İ, Benian A, Ermiş H, Aydınlı K. Current approaches on non-invasive prenatal diagnosis: Prenatal genomics, transcriptomics, personalized fetal diagnosis. Turk J Obstet Gynecol 2014; 11:233-241. [PMID: 28913027 PMCID: PMC5558368 DOI: 10.4274/tjod.26817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 07/26/2014] [Indexed: 12/27/2022] Open
Abstract
Recent developments in molecular genetics improved our knowledge on fetal genome and physiology. Novel scientific innovations in prenatal diagnosis have accelerated in the last decade changing our vision immensely. Data obtained from fetal genomic studies brought new insights to fetal medicine and by the advances in fetal DNA and RNA sequencing technology novel treatment strategies has evolved. Non-invasive prenatal diagnosis found ground in genetics and the results are widely studied in scientific arena. When Lo and colleges proved fetal genetic material can be extracted from maternal plasma and fetal DNA can be isolated from maternal serum, the gate to many exciting discoveries was open. Microarray technology and advances in sequencing helped fetal diagnosis as well as other areas of medicine. Today it is a very crucial prerequisite for physicians practicing prenatal diagnosis to have a profound knowledge in genetics. Prevailing practical use and application of fetal genomic tests in maternal and fetal medicine mandates obstetricians to update their knowledge in genetics. The purpose of this review is to assist physicians to understand and update their knowledge in fetal genetic testing from maternal blood, individualized prenatal counseling and advancements on the subject by sharing our experiences as İstanbul University Fetal Nucleic Acid Research Group.
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Affiliation(s)
- Tuba Günel
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Mohammad Kazem Hosseini
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Ece Gümüşoğlu
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Görkem Zeybek
- Çanakkale Provincial State Hospital, Clinic of General Obstetrics and Gynecology, Çanakkale, Turkey
| | - İsmail Dölekçap
- İstanbul University, Faculty of Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - İbrahim Kalelioğlu
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Ali Benian
- İstanbul University Cerrahpaşa Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
| | - Hayri Ermiş
- İstanbul University İstanbul Faculty of Medicine, Department of Gynecology, İstanbul, Turkey
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20
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Gregg AR, Van den Veyver IB, Gross SJ, Madankumar R, Rink BD, Norton ME. Noninvasive prenatal screening by next-generation sequencing. Annu Rev Genomics Hum Genet 2014; 15:327-47. [PMID: 24849140 DOI: 10.1146/annurev-genom-090413-025341] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Noninvasive prenatal screening (NIPS) has emerged as a highly accurate method of screening for fetal Down syndrome, with a detection rate and specificity approaching 100%. Challenging the widespread use of this technology are cost and the paradigm shift in counseling that accompanies any emerging technology. The expense of the test is expected to decrease with increased utilization, and well beyond the current NIPS technology, its components (fetal genome measurements, sequencing technology, and bioinformatics) will be utilized alone or in combinations to interrogate the fetal genome. The end goal is simple: to offer patients information early in pregnancy about fetal genomes without incurring procedural risks. This will allow patients an opportunity to make informed reproductive and pregnancy management decisions based on precise fetal genomic information.
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Affiliation(s)
- Anthony R Gregg
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida 32610;
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21
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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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22
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Kantak C, Chang CP, Wong CC, Mahyuddin A, Choolani M, Rahman A. Lab-on-a-chip technology: impacting non-invasive prenatal diagnostics (NIPD) through miniaturisation. LAB ON A CHIP 2014; 14:841-854. [PMID: 24452749 DOI: 10.1039/c3lc50980j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper aims to provide a concise review of non-invasive prenatal diagnostics (NIPD) to the lab-on-a-chip and microfluidics community. Having a market of over one billion dollars to explore and a plethora of applications, NIPD requires greater attention from microfluidics researchers. In this review, a complete overview of conventional diagnostic procedures including invasive as well as non-invasive (fetal cells and cell-free fetal DNA) types are discussed. Special focus is given to reviewing the recent and past microfluidic approaches to NIPD, as well as various commercial entities in NIPD. This review concludes with future challenges and ethical considerations of the field.
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Affiliation(s)
- Chaitanya Kantak
- Institute of Microelectronics, Agency for Science Technology and Research, 11 Science Park Road, Singapore Science Park 2, Singapore 117685, Singapore.
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Sillence KA, Madgett TE, Roberts LA, Overton TG, Avent ND. Non-Invasive Screening Tools for Down's Syndrome: A Review. Diagnostics (Basel) 2013; 3:291-314. [PMID: 26835682 PMCID: PMC4665531 DOI: 10.3390/diagnostics3020291] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 01/16/2023] Open
Abstract
Down's syndrome (DS) is the most common genetic cause of developmental delay with an incidence of 1 in 800 live births, and is the predominant reason why women choose to undergo invasive prenatal diagnosis. However, as invasive tests are associated with around a 1% risk of miscarriage new non-invasive tests have been long sought after. Recently, the most promising approach for non-invasive prenatal diagnosis (NIPD) has been provided by the introduction of next generation sequencing (NGS) technologies. The clinical application of NIPD for DS detection is not yet applicable, as large scale validation studies in low-risk pregnancies need to be completed. Currently, prenatal screening is still the first line test for the detection of fetal aneuploidy. Screening cannot diagnose DS, but developing a more advanced screening program can help to improve detection rates, and therefore reduce the number of women offered invasive tests. This article describes how the prenatal screening program has developed since the introduction of maternal age as the original "screening" test, and subsequently discusses recent advances in detecting new screening markers with reference to both proteomic and bioinformatic techniques.
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Affiliation(s)
- Kelly A Sillence
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Tracey E Madgett
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Llinos A Roberts
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
| | - Timothy G Overton
- Department of Obstetrics, St Michael's Hospital, Southwell Street, Bristol, BS2 8EG, UK.
| | - Neil D Avent
- School of Biomedical and Biological Sciences, Plymouth University Peninsula School of Medicine and Dentistry, Plymouth University, Plymouth, PL4 8AA, UK.
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How Kit A, Nielsen HM, Tost J. DNA methylation based biomarkers: practical considerations and applications. Biochimie 2012; 94:2314-37. [PMID: 22847185 DOI: 10.1016/j.biochi.2012.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/16/2012] [Indexed: 02/06/2023]
Abstract
A biomarker is a molecular target analyzed in a qualitative or quantitative manner to detect and diagnose the presence of a disease, to predict the outcome and the response to a specific treatment allowing personalized tailoring of patient management. Biomarkers can belong to different types of biochemical molecules such as proteins, DNA, RNA or lipids, whereby protein biomarkers have been the most extensively studied and used, notably in blood-based protein quantification tests or immunohistochemistry. The rise of interest in epigenetic mechanisms has allowed the identification of a new type of biomarker, DNA methylation, which is of great potential for many applications. This stable and heritable covalent modification mostly affects cytosines in the context of a CpG dinucleotide in humans. It can be detected and quantified by a number of technologies including genome-wide screening methods as well as locus- or gene-specific high-resolution analysis in different types of samples such as frozen tissues and FFPE samples, but also in body fluids such as urine, plasma, and serum obtained through non-invasive procedures. In some cases, DNA methylation based biomarkers have proven to be more specific and sensitive than commonly used protein biomarkers, which could clearly justify their use in clinics. However, very few of them are at the moment used in clinics and even less commercial tests are currently available. The objective of this review is to discuss the advantages of DNA methylation as a biomarker, the practical considerations for their development, and their use in disease detection, prediction of outcome or treatment response, through multiple examples mainly focusing on cancer, but also to evoke their potential for complex diseases and prenatal diagnostics.
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Affiliation(s)
- Alexandre How Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, 75010 Paris, France
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