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Giambona A, Vinciguerra M, Leto F, Cassarà F, Marchese G, Cigna V, Orlandi E, Mugavero ME, Cucinella G, Maggio A, Termini L, Makrydimas G, D’Alcamo E, Picciotto F. Prenatal Diagnosis of Cystic Fibrosis by Celocentesis. Genes (Basel) 2024; 15:662. [PMID: 38927598 PMCID: PMC11203072 DOI: 10.3390/genes15060662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Celocentesis is a new sampling tool for prenatal diagnosis available from 7 weeks in case of couples at risk for genetic diseases. In this study, we reported the feasibility of earlier prenatal diagnosis by celocentesis in four cases of cystic fibrosis and one case of cystic fibrosis and β-thalassemia co-inherited in the same fetus. Celomic fluids were aspired from the celomic cavity between 8+2 and 9+3 weeks of gestation and fetal cells were picked up by micromanipulator. Maternal DNA contamination was tested and target regions of fetal DNA containing parental pathogenetic variants of CFTR and HBB genes were amplified and sequenced. Four of the five fetuses resulted as being affected by cystic fibrosis and, in all cases, the women decided to interrupt the pregnancy. In the other case, the fetus presented a healthy carrier of cystic fibrosis. The results were confirmed in three cases on placental tissue. In one case, no abortive tissue was obtained. In the last case, the woman refused the prenatal diagnosis to confirm the celocentesis data; the pregnancy is ongoing without complications. This procedure provides prenatal diagnosis of monogenic diseases at least four weeks earlier than traditional procedures, reducing the anxiety of patients and providing the option for medical termination of the affected fetus at 8-10 weeks of gestation, which is less traumatic and safer than surgical termination in the second trimester.
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Affiliation(s)
- Antonino Giambona
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Margherita Vinciguerra
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Filippo Leto
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Filippo Cassarà
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Giuseppe Marchese
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Valentina Cigna
- Unit of Fetal Medicine and Prenatal Diagnosis, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (V.C.); (E.O.); (M.E.M.); (G.C.); (F.P.)
| | - Emanuela Orlandi
- Unit of Fetal Medicine and Prenatal Diagnosis, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (V.C.); (E.O.); (M.E.M.); (G.C.); (F.P.)
| | - Maria Elena Mugavero
- Unit of Fetal Medicine and Prenatal Diagnosis, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (V.C.); (E.O.); (M.E.M.); (G.C.); (F.P.)
| | - Gaspare Cucinella
- Unit of Fetal Medicine and Prenatal Diagnosis, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (V.C.); (E.O.); (M.E.M.); (G.C.); (F.P.)
| | - Aurelio Maggio
- Unit of Hematology for Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy;
| | - Lisa Termini
- Ospedale dei Bambini G. Di Cristina, ARNAS Civico, 90134 Palermo, Italy;
| | - George Makrydimas
- Department of Obstetrics & Gynecology, University of Ioannina, 45110 Ioannina, Greece;
| | - Elena D’Alcamo
- Unit of Molecular Diagnosis of Rare Hematological Diseases, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (M.V.); (F.L.); (F.C.); (G.M.); (E.D.)
| | - Francesco Picciotto
- Unit of Fetal Medicine and Prenatal Diagnosis, Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, 90146 Palermo, Italy; (V.C.); (E.O.); (M.E.M.); (G.C.); (F.P.)
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Abedalthagafi M, Bawazeer S, Fawaz RI, Heritage AM, Alajaji NM, Faqeih E. Non-invasive prenatal testing: a revolutionary journey in prenatal testing. Front Med (Lausanne) 2023; 10:1265090. [PMID: 38020177 PMCID: PMC10666054 DOI: 10.3389/fmed.2023.1265090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) is a pioneering technique that has consistently advanced the field of prenatal testing to detect genetic abnormalities and conditions with the aim of decreasing the incidence and prevalence of inherited conditions. NIPT remains a method of choice for common autosomal aneuploidies, mostly trisomy 21, and several monogenic disorders. The advancements in gene sequencing techniques have expanded the panel of conditions where NIPT could be offered. However, basic research on the impact of several genetic conditions lags behind the methods of detection of these sequence aberrations, and the impact of the expansion of NIPT should be carefully considered based on its utility. With interest from commercial diagnostics and a lack of regulatory oversight, there remains a need for careful validation of the predictive values of different tests offered. NIPT comes with many challenges, including ethical and economic issues. The scientific evidence, technical feasibility, and clinical benefit of NIPT need to be carefully investigated before new tests and developments are translated into clinical practice. Moreover, the implementation of panel expansion of NIPT should accompany expert genetic counseling pre- and post-testing.
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Affiliation(s)
- Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory School of Medicine, Atlanta, GA, United States
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Shahad Bawazeer
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | | | | | - Nouf M. Alajaji
- Department of Maternal Fetal Medicine, Women's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Eissa Faqeih
- Department of Medical Genetics, Children's Specialized Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
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Kenderdine T, Fabris D. The multifaceted roles of mass spectrometric analysis in nucleic acids drug discovery and development. MASS SPECTROMETRY REVIEWS 2023; 42:1332-1357. [PMID: 34939674 PMCID: PMC9218015 DOI: 10.1002/mas.21766] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/23/2021] [Accepted: 11/22/2021] [Indexed: 06/07/2023]
Abstract
The deceptively simple concepts of mass determination and fragment analysis are the basis for the application of mass spectrometry (MS) to a boundless range of analytes, including fundamental components and polymeric forms of nucleic acids (NAs). This platform affords the intrinsic ability to observe first-hand the effects of NA-active drugs on the chemical structure, composition, and conformation of their targets, which might affect their ability to interact with cognate NAs, proteins, and other biomolecules present in a natural environment. The possibility of interfacing with high-performance separation techniques represents a multiplying factor that extends these capabilities to cover complex sample mixtures obtained from organisms that were exposed to NA-active drugs. This report provides a brief overview of these capabilities in the context of the analysis of the products of NA-drug activity and NA therapeutics. The selected examples offer proof-of-principle of the applicability of this platform to all phases of the journey undertaken by any successful NA drug from laboratory to bedside, and provide the rationale for its rapid expansion outside traditional laboratory settings in support to ever growing manufacturing operations.
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Affiliation(s)
| | - Dan Fabris
- Department of Chemistry, University of Connecticut
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Zaninović L, Bašković M, Ježek D, Katušić Bojanac A. Accuracy of Non-Invasive Prenatal Testing for Duchenne Muscular Dystrophy in Families at Risk: A Systematic Review. Diagnostics (Basel) 2023; 13:diagnostics13020183. [PMID: 36672993 PMCID: PMC9858348 DOI: 10.3390/diagnostics13020183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Methodological advancements, such as relative haplotype and relative mutation dosage analyses, have enabled non-invasive prenatal diagnosis of autosomal recessive and X-linked diseases. Duchenne muscular dystrophy (DMD) is an X-linked recessive disease characterized by progressive proximal muscular dystrophy and a high mortality rate before the age of twenty. We aimed to systematically present obtainable data regarding a non-invasive prenatal diagnosis of DMD and provide a comprehensive resume on the topic. The emphasis was given to the comparison of different available protocols and molecular methods used for fetal inheritance deduction, as well as their correlation with prognostic accuracy. METHODS We searched the Scopus and PubMed databases on 11 November 2022 and included articles reporting a non-invasive prenatal diagnosis of DMD in families at risk using relative dosage analysis methods. RESULTS Of the 342 articles identified, 7 met the criteria. The reported accuracy of NIPT for DMD was 100% in all of the studies except one, which demonstrated an accuracy of 86.67%. The combined accuracy for studies applying indirect RHDO, direct RHDO, and RMD approaches were 94.74%, 100%, and 100%, respectively. Confirmatory results by invasive testing were available in all the cases. Regardless of the technological complexity and low prevalence of the disease that reduces the opportunity for systematic research, the presented work demonstrates substantial accuracy of NIPT for DMD. CONCLUSIONS Attempts for its implementation into everyday clinical practice raise many ethical and social concerns. It is essential to provide detailed guidelines and arrange genetic counseling in order to ensure the proper indications for testing and obtain informed parental consent.
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Affiliation(s)
- Luca Zaninović
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- Department of Obstetrics and Gynecology, University Hospital Centre Zagreb, Petrova 13, 10000 Zagreb, Croatia
| | - Marko Bašković
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-3636-379
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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Identifying the minimum concentrations of cell-free fetal DNA in maternal blood required for bovine fetal sexing using PCR. Theriogenology 2022; 191:192-199. [PMID: 35998402 DOI: 10.1016/j.theriogenology.2022.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/27/2022] [Accepted: 08/07/2022] [Indexed: 11/21/2022]
Abstract
We evaluated the feasibility of cffDNA extraction from the maternal blood samples regarding the threshold concentrations required for fetal sexing in pregnant cattle by PCR. In four trials, we 1) compared the extraction efficiency of seven methods using freshly harvested plasma/blood of cows carrying male fetii (150-240 d gestation) bovine amelogenin (bAML) and Y-specific gene sequences, 2) identified the minimum amounts of spiked cffDNA needed for a PCR for fetal sexing, 3) determined the most optimal protocol among three commercial kits for cffDNA extraction from neat and spiked plasma samples (181-240 d gestation) for PCR detection of Y-specific sequence and 4) tested Y-specific sequence PCR on pregnant cows at different stages of gestation (60-150 versus 151-240 d pregnant). In these experiments, blood samples from unbred dairy heifers (Canadian Holstein, n = 10), pregnant dairy cows (Canadian Holstein, 60-240 d gestation, n = 25 with male fetii), and aborting beef cows (Angus cross, n = 5, 100-150 d pregnant) were used for DNA extraction, spiking, and PCR. Extracted DNA from the blood samples of unbred heifers (n = 5) and bull calves (n = 5) served as controls in all trials. In the first trial, DNeasy Blood and Tissue, Qiagen DSP Virus, and NucleoMag cfDNA isolation kits were relatively successful among seven methods to isolate cffDNA from freshly harvested maternal plasma/blood of pregnant cows. In trial 2, using serial dilutions of cffDNA from male fetii spiked in cow plasma samples, a positive and unambiguous detection by PCR targeting Y-specific sequence and bAML gene was observed when spiked cffDNA concentration in plasma was >31.3 pg/ml and >2 ng/ml, respectively. In the third trial, the DNeasy Blood and Tissue kit was most successful in extracting cffDNA spiked at the minimum concentrations in maternal plasma and subsequent PCR for Y-specific sequence. In our fourth trial, more cows in the second half (9/10) of gestation showed a positive Y-specific PCR outcome than those in the first half (3/9, Fischer's exact test; P < 0.05, 90%; CI: 55.5-99.75 vs 33%; CI: 7.5-70.1). In conclusion, we observed variability between different DNA extraction methodologies and stages of gestation results in the PCR for prenatal sexing. Thus, the current PCR methodologies are unreliable for detecting cffDNA in pregnant cows. Additionally, ≥10 (≥31.3 pg/ml of cffDNA) and ≥648 (≥2 ng/ml of cffDNA) copies of the whole fetal genome in bovine maternal plasma are needed for Y-specific PCR and bAML PCR, respectively.
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Wu W, Zhou X, Jiang Z, Zhang D, Yu F, Zhang L, Wang X, Chen S, Xu C. Noninvasive fetal genotyping of single nucleotide variants and linkage analysis for prenatal diagnosis of monogenic disorders. Hum Genomics 2022; 16:28. [PMID: 35897115 PMCID: PMC9327225 DOI: 10.1186/s40246-022-00400-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background High-cost, time-consuming and complex processes of several current approaches limit the use of noninvasive prenatal diagnosis (NIPD) for monogenic disorders in clinical application. Thus, a more cost-effective and easily implementable approach is required. Methods We established a low-cost and convenient test to noninvasively deduce fetal genotypes of the mutation and single nucleotide polymorphisms (SNPs) loci by means of targeted amplification combined with deep sequencing of maternal genomic and plasma DNA. The sequential probability ratio test was performed to detect the allelic imbalance in maternal plasma. This method can be employed to directly examine familial pathogenic mutations in the fetal genome, as well as infer the inheritance of parental haplotypes through a group of selected SNPs linked to the pathogenic mutation. Results The fetal mutations in 17 families with different types of monogenic disorders including hemophilia A, von Willebrand disease type 3, Duchenne muscular dystrophy, hyper-IgM type 1, glutaric acidemia type I, Nagashima-type palmoplantar keratosis, and familial exudative vitreoretinopathy were identified in the study. The mutations included various forms: point mutations, gene inversion, deletions/insertions and duplication. The results of 12 families were verified by sequencing of amniotic fluid samples, the accuracy of the approach in fetal genotyping at the mutation and SNPs loci was 98.85% (172/174 loci), and the no-call rate was 28.98% (71/245 loci). The overall accuracy was 12/12 (100%). Moreover, the approach was successfully applied in plasma samples with a fetal fraction as low as 2.3%. Conclusions We have shown in this study that the approach is a cost-effective, less time consuming and accurate method for NIPD of monogenic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00400-4.
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Affiliation(s)
- Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China
| | - Zhengwen Jiang
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Dazhi Zhang
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Feng Yu
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China. .,Shanghai Academy of Experimental Medicine, Shanghai, People's Republic of China.
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China.
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Bayefsky MJ, Berkman BE. Implementing Expanded Prenatal Genetic Testing: Should Parents Have Access to Any and All Fetal Genetic Information? THE AMERICAN JOURNAL OF BIOETHICS : AJOB 2022; 22:4-22. [PMID: 33459580 PMCID: PMC10066540 DOI: 10.1080/15265161.2020.1867933] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Prenatal genetic testing is becoming available for an increasingly broad set of diseases, and it is only a matter of time before parents can choose to test for hundreds, if not thousands, of genetic conditions in their fetuses. Should access to certain kinds of fetal genetic information be limited, and if so, on what basis? We evaluate a range of considerations including reproductive autonomy, parental rights, disability rights, and the rights and interests of the fetus as a potential future child. We conclude that parents should be able to access information that could be useful during pregnancy, but that testing for non-medical information should be limited. Next, we argue that the government lacks a compelling state interest in regulating prenatal genetic testing and propose that regulation should occur through medical professional organizations. Finally, we present a framework for determining what testing physicians should recommend, offer neutrally, or not offer at all.
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Affiliation(s)
- Michelle J. Bayefsky
- New York University Langone Health, Department of Obstetrics and Gynecology, New York, NY, USA
| | - Benjamin E. Berkman
- National Institutes of Health, Department of Bioethics, Bethesda, MD, USA
- National Human Genome Research Institute, Bethesda, MD, USA
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Chen C, Chen M, Zhu Y, Jiang L, Li J, Wang Y, Lu Z, Guo F, Wang H, Peng Z, Yang Y, Sun J. Noninvasive prenatal diagnosis of monogenic disorders based on direct haplotype phasing through targeted linked-read sequencing. BMC Med Genomics 2021; 14:244. [PMID: 34627256 PMCID: PMC8502361 DOI: 10.1186/s12920-021-01091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 09/22/2021] [Indexed: 11/30/2022] Open
Abstract
Background Though massively parallel sequencing has been widely applied to noninvasive prenatal screen for common trisomy, the clinical use of massively parallel sequencing to noninvasive prenatal diagnose monogenic disorders is limited. This study was to develop a method for directly determining paternal haplotypes for noninvasive prenatal diagnosis of monogenic disorders without requiring proband’s samples. Methods The study recruited 40 families at high risk for autosomal recessive diseases. The targeted linked-read sequencing was performed on high molecular weight (HMW) DNA of parents using customized probes designed to capture targeted genes and single-nucleotide polymorphisms (SNPs) distributed within 1Mb flanking region of targeted genes. Plasma DNA from pregnant mothers also underwent targeted sequencing using the same probes to determine fetal haplotypes according to parental haplotypes. The results were further confirmed by invasive prenatal diagnosis. Results Seventy-eight parental haplotypes of targeted gene were successfully determined by targeted linked-read sequencing. The predicted fetal inheritance of variant was correctly deduced in 38 families in which the variants had been confirmed by invasive prenatal diagnosis. Two families were determined to be no-call. Conclusions Targeted linked-read sequencing method demonstrated to be an effective means to phase personal haplotype for noninvasive prenatal diagnosis of monogenic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01091-x.
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Affiliation(s)
- Chao Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yaping Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Lu Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Jia Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaoshen Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Zhe Lu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Fengyu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Hairong Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yun Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, 430074, China. .,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Jun Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China. .,Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China.
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Zhytnik L, Peters M, Tilk K, Simm K, Tõnisson N, Reimand T, Maasalu K, Acharya G, Krjutškov K, Salumets A. From late fatherhood to prenatal screening of monogenic disorders: evidence and ethical concerns. Hum Reprod Update 2021; 27:1056-1085. [PMID: 34329448 DOI: 10.1093/humupd/dmab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/27/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the help of ART, an advanced parental age is not considered to be a serious obstacle for reproduction anymore. However, significant health risks for future offspring hide behind the success of reproductive medicine for the treatment of reduced fertility associated with late parenthood. Although an advanced maternal age is a well-known risk factor for poor reproductive outcomes, understanding the impact of an advanced paternal age on offspring is yet to be elucidated. De novo monogenic disorders (MDs) are highly associated with late fatherhood. MDs are one of the major sources of paediatric morbidity and mortality, causing significant socioeconomic and psychological burdens to society. Although individually rare, the combined prevalence of these disorders is as high as that of chromosomal aneuploidies, indicating the increasing need for prenatal screening. With the help of advanced reproductive technologies, families with late paternity have the option of non-invasive prenatal testing (NIPT) for multiple MDs (MD-NIPT), which has a sensitivity and specificity of almost 100%. OBJECTIVE AND RATIONALE The main aims of the current review were to examine the effect of late paternity on the origin and nature of MDs, to highlight the role of NIPT for the detection of a variety of paternal age-associated MDs, to describe clinical experiences and to reflect on the ethical concerns surrounding the topic of late paternity and MD-NIPT. SEARCH METHODS An extensive search of peer-reviewed publications (1980-2021) in English from the PubMed and Google Scholar databases was based on key words in different combinations: late paternity, paternal age, spermatogenesis, selfish spermatogonial selection, paternal age effect, de novo mutations (DNMs), MDs, NIPT, ethics of late fatherhood, prenatal testing and paternal rights. OUTCOMES An advanced paternal age provokes the accumulation of DNMs, which arise in continuously dividing germline cells. A subset of DNMs, owing to their effect on the rat sarcoma virus protein-mitogen-activated protein kinase signalling pathway, becomes beneficial for spermatogonia, causing selfish spermatogonial selection and outgrowth, and in some rare cases may lead to spermatocytic seminoma later in life. In the offspring, these selfish DNMs cause paternal age effect (PAE) disorders with a severe and even life-threatening phenotype. The increasing tendency for late paternity and the subsequent high risk of PAE disorders indicate an increased need for a safe and reliable detection procedure, such as MD-NIPT. The MD-NIPT approach has the capacity to provide safe screening for pregnancies at risk of PAE disorders and MDs, which constitute up to 20% of all pregnancies. The primary risks include pregnancies with a paternal age over 40 years, a previous history of an affected pregnancy/child, and/or congenital anomalies detected by routine ultrasonography. The implementation of NIPT-based screening would support the early diagnosis and management needed in cases of affected pregnancy. However, the benefits of MD-NIPT need to be balanced with the ethical challenges associated with the introduction of such an approach into routine clinical practice, namely concerns regarding reproductive autonomy, informed consent, potential disability discrimination, paternal rights and PAE-associated issues, equity and justice in accessing services, and counselling. WIDER IMPLICATIONS Considering the increasing parental age and risks of MDs, combined NIPT for chromosomal aneuploidies and microdeletion syndromes as well as tests for MDs might become a part of routine pregnancy management in the near future. Moreover, the ethical challenges associated with the introduction of MD-NIPT into routine clinical practice need to be carefully evaluated. Furthermore, more focus and attention should be directed towards the ethics of late paternity, paternal rights and paternal genetic guilt associated with pregnancies affected with PAE MDs.
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Affiliation(s)
- Lidiia Zhytnik
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kadi Tilk
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Kadri Simm
- Institute of Philosophy and Semiotics, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia.,Centre of Ethics, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Reproductive Medicine, West Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia.,Department of Traumatology and Orthopaedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ganesh Acharya
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Genomics, University of Tartu, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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11
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Deguchi M, Tsuji S, Katsura D, Kasahara K, Kimura F, Murakami T. Current Overview of Osteogenesis Imperfecta. ACTA ACUST UNITED AC 2021; 57:medicina57050464. [PMID: 34068551 PMCID: PMC8151368 DOI: 10.3390/medicina57050464] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022]
Abstract
Osteogenesis imperfecta (OI), or brittle bone disease, is a heterogeneous disorder characterised by bone fragility, multiple fractures, bone deformity, and short stature. OI is a heterogeneous disorder primarily caused by mutations in the genes involved in the production of type 1 collagen. Severe OI is perinatally lethal, while mild OI can sometimes not be recognised until adulthood. Severe or lethal OI can usually be diagnosed using antenatal ultrasound and confirmed by various imaging modalities and genetic testing. The combination of imaging parameters obtained by ultrasound, computed tomography (CT), and magnetic resource imaging (MRI) can not only detect OI accurately but also predict lethality before birth. Moreover, genetic testing, either noninvasive or invasive, can further confirm the diagnosis prenatally. Early and precise diagnoses provide parents with more time to decide on reproductive options. The currently available postnatal treatments for OI are not curative, and individuals with severe OI suffer multiple fractures and bone deformities throughout their lives. In utero mesenchymal stem cell transplantation has been drawing attention as a promising therapy for severe OI, and a clinical trial to assess the safety and efficacy of cell therapy is currently ongoing. In the future, early diagnosis followed by in utero stem cell transplantation should be adopted as a new therapeutic option for severe OI.
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12
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Caswell RC, Snowsill T, Houghton JAL, Chakera AJ, Shepherd MH, Laver TW, Knight BA, Wright D, Hattersley AT, Ellard S. Noninvasive Fetal Genotyping by Droplet Digital PCR to Identify Maternally Inherited Monogenic Diabetes Variants. Clin Chem 2021; 66:958-965. [PMID: 32533152 PMCID: PMC7611030 DOI: 10.1093/clinchem/hvaa104] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023]
Abstract
BACKGROUND Babies of women with heterozygous pathogenic glucokinase (GCK) variants causing mild fasting hyperglycemia are at risk of macrosomia if they do not inherit the variant. Conversely, babies who inherit a pathogenic hepatocyte nuclear factor 4α (HNF4A) diabetes variant are at increased risk of high birth weight. Noninvasive fetal genotyping for maternal pathogenic variants would inform pregnancy management. METHODS Droplet digital PCR was used to quantify reference and variant alleles in cell-free DNA extracted from blood from 38 pregnant women heterozygous for a GCK or HNF4A variant and to determine fetal fraction by measurement of informative maternal and paternal variants. Droplet numbers positive for the reference/alternate allele together with the fetal fraction were used in a Bayesian analysis to derive probability for the fetal genotype. The babies' genotypes were ascertained postnatally by Sanger sequencing. RESULTS Droplet digital PCR assays for GCK or HNF4A variants were validated for testing in all 38 pregnancies. Fetal fraction of ≥2% was demonstrated in at least 1 cell-free DNA sample from 33 pregnancies. A threshold of ≥0.95 for calling homozygous reference genotypes and ≤0.05 for heterozygous fetal genotypes allowed correct genotype calls for all 33 pregnancies with no false-positive results. In 30 of 33 pregnancies, a result was obtained from a single blood sample. CONCLUSIONS This assay can be used to identify pregnancies at risk of macrosomia due to maternal monogenic diabetes variants.
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Affiliation(s)
- Richard C Caswell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Tristan Snowsill
- Institute of Health Research, University of Exeter Medical School, Exeter, UK
| | - Jayne A L Houghton
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Ali J Chakera
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Royal Sussex County Hospital, Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Maggie H Shepherd
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Thomas W Laver
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Bridget A Knight
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter NIHR Clinical Research Facility, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - David Wright
- Institute of Health Research, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.,Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
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13
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Mirzaei Gisomi N, Javadi G, Zare Karizi S, Miryounesi M, Keshavarz P. Evaluation of beta-thalassemia in the fetus through cffDNA with multiple polymorphisms as a haplotype in the beta-globin gene. Transfus Clin Biol 2020; 27:243-252. [PMID: 32798758 DOI: 10.1016/j.tracli.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Invasive biopsy during the pregnancy is associated with an abortion risk of approximately 1% for the fetus. Free fetal DNA in maternal plasma is an excellent source of genetic material for prenatal molecular diagnoses. This study was conducted to investigate beta-thalassemia mutation in the fetus through maternal blood with multiple polymorphisms as haplotypes in the beta-globin gene. METHODS In this study, a total of 33 beta-thalassemia carrier (minor) couples were genotyped by ARMS-PCR for IVSII-IG>A mutation. During pregnancy, 10mL of blood was collected from pregnant women, and DNA was extracted by the magnetic bead-based extraction, and fetal DNA was enriched with AMPure XP kit. Five polymorphisms in 4 haplotype groups were evaluated by the Sanger Sequencing method. Finally, results were compared with those of the invasion method. RESULTS Participants in study were 33 couples, mean age of the men was 26±5 years, and mean age of women was 23±4 years, and mean MCV, MCH, HbA2 blood parameters were 62.4±5.3, 19.6±3.1, 4.2±2.1 respectively. A total of 33 fetuses were genotyped for IVSII-IG>A mutation. Nine fetuses were affected, 10 fetuses were normal and 14 fetuses were carrier of beta-thalassemia. Sensitivity and specificity of Sanger Sequencing were equal to 88.8% and 91.6% respectively. Positive and negative predictive values were obtained as 80% and 95.6%, respectively. CONCLUSION Mutational status of the fetus can be assessed by determining inheritance of paternally-derived alleles based on detection of haplotype-associated SNP in maternal plasma. Magnetic-based DNA extraction and fetal DNA enrichment are very simple and easy to perform and have satisfactory accuracy.
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Affiliation(s)
- Nadia Mirzaei Gisomi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Gholamreza Javadi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Shohre Zare Karizi
- Department of biology, faculty of biological sciences, Islamic Azad university, Varamin-Pishva Branch, Varamin, Iran
| | - Mohammad Miryounesi
- Department of medical genetics, Shahid Beheshti university of medical sciences, Tehran, Iran
| | - Parvaneh Keshavarz
- Cellular and molecular research center, faculty of medicine, Guilan university of medical sciences, Rasht, Iran; Medical genetics laboratory, Rasht, Iran.
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14
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How will new genetic technologies, such as gene editing, change reproductive decision-making? Views of high-risk couples. Eur J Hum Genet 2020; 29:39-50. [PMID: 32773775 PMCID: PMC7852899 DOI: 10.1038/s41431-020-00706-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/03/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
Couples at increased risk of having offspring with a specific genetic disorder who want to avoid having an affected child have several reproductive options including prenatal diagnosis (PND) and preimplantation genetic testing (PGT). In the future, non-invasive prenatal diagnosis (NIPD), germline gene editing (GGE) and somatic gene editing (SGE) might become available. This study explores if, and how, availability of new genetic technologies, including NIPD, GGE, SGE, would change reproductive decision-making of high-risk couples. In 2018, semi-structured interviews were conducted with 25 genetically at-risk couples. Couples previously had received genetic counselling for PND and PGT, and in most cases opted for (one of) these techniques, at one Dutch Clinical Genetics Center between 2013 and 2017. Considerations participants mentioned regarding the hypothetical use of NIPD, GGE and SGE, seem similar to considerations regarding PND and PGT and are reflected in underlying concepts. These include safety and burden for mother and child, and moral considerations. Couples generally favoured NIPD over PND as this would be safe and enables earlier diagnosis. Increased opportunities of having a 'healthy' embryo and less embryo disposal were considerations in favour of GGE. Some regarded GGE as unsafe and feared slippery slope scenarios. Couples were least favourable towards SGE compared to choosing for a genetic reproductive technology, because of the perceived burden for the affected offspring. With the possibly growing number of technological options, understanding high risk couples' perspectives can assist in navigating the reproductive decision-making process. Counsellors should be prepared to counsel on more and complex reproductive options.
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15
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Chen M, Chen C, Huang X, Sun J, Jiang L, Li Y, Zhu Y, Tian C, Li Y, Lu Z, Wang Y, Zeng F, Yang Y, Song X, Peng Z, Yin C, Chen D. Noninvasive prenatal diagnosis for Duchenne muscular dystrophy based on the direct haplotype phasing. Prenat Diagn 2020; 40:918-924. [PMID: 31916613 DOI: 10.1002/pd.5641] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 01/31/2023]
Abstract
OBJECTIVE We aimed to investigate the validity of noninvasive prenatal diagnosis (NIPD) based on direct haplotype phasing without the proband or other family members and its feasibility for clinical application in the case of Duchenne muscular dystrophy (DMD). METHODS Thirteen singleton-pregnancy families affected by DMD were recruited. The pathogenic variants in the pregnant females have been identified by multiplex ligation-dependent probe amplification (MLPA). We resolved maternal haplotypes for each family by performing targeted linked-read sequencing of their high molecular weight DNA, respectively. Then, we integrated the maternal haplotypes and the targeted sequencing results of maternal plasma DNA to infer the fetal haplotype and the DMD gene variant status. The fetal genotypes were further validated by using chorionic villus sampling. RESULTS The method of directly resolving maternal haplotype through targeted linked-read sequencing was smoothly performed in 12 participated families, but one failed (F11). The predicted variant status of 12 fetuses was correct, which had been confirmed by invasive prenatal diagnosis. CONCLUSION Direct haplotyping of NIPD based on linked-read sequencing for DMD is accurate.
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Affiliation(s)
- Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics and Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | | | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Lu Jiang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yingting Li
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yaping Zhu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | | | - Yufan Li
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics and Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China
| | - Zhe Lu
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | | | - Yun Yang
- Wuhan BGI Clinical Laboratory Co., Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Xiwei Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Chenghong Yin
- Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Dunjin Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics and Gynecology Institute of Guangzhou, Guangzhou, China.,The Medical Centre for Critical Pregnant Women in Guangzhou, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Guangzhou, China.,Key Laboratory for Reproduction and Genetics of Guangdong Higher Education Institutes, Guangzhou, China
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16
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Eintracht J, Corton M, FitzPatrick D, Moosajee M. CUGC for syndromic microphthalmia including next-generation sequencing-based approaches. Eur J Hum Genet 2020; 28:679-690. [PMID: 31896778 PMCID: PMC7171178 DOI: 10.1038/s41431-019-0565-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 01/29/2023] Open
Affiliation(s)
| | - Marta Corton
- Department of Genetics, IIS-University Hospital Fundación Jiménez Díaz-CIBERER, Madrid, Spain
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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17
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Clausen FB, Barrett AN, Advani HV, Choolani M, Dziegiel MH. Impact of long-term storage of plasma and cell-free DNA on measured DNA quantity and fetal fraction. Vox Sang 2020; 115:586-594. [PMID: 32342989 DOI: 10.1111/vox.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal sample storage conditions are essential for non-invasive prenatal testing of cell-free fetal and total DNA. We investigated the effect of long-term storage of plasma samples and extracted cfDNA using qPCR. MATERIALS AND METHODS Fetal and total cfDNA yield and fetal fraction were calculated before and after storage of plasma for 0-6 years at -25°C. Dilution experiments were performed to investigate PCR inhibition. Extraction with or without proteinase K was used to examine protein dissociation. Storage of extracted cfDNA was investigated by testing aliquots immediately, and after 18 months and 3 years of storage at -25°C. RESULTS We observed a marked increase in the levels of amplifiable fetal and total DNA in plasma stored for 2-3 years, and fetal fraction was slightly decreased after 3 years of storage. cfDNA detection was independent of proteinase K during DNA extraction in plasma samples stored >2 years, indicating a loss of proteins from DNA over time, which was likely to account for the observed increase in DNA yields. Measured fetal and total DNA quantities, as well as fetal fraction, increased in stored, extracted cfDNA. CONCLUSION Fetal and total cell-free DNA is readily detectable in plasma after long-term storage at -25°C. However, substantial variation in measured DNA quantities and fetal fraction means caution may be required when using stored plasma and extracted cfDNA for test development or validation purposes.
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Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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18
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Harding P, Brooks BP, FitzPatrick D, Moosajee M. Anophthalmia including next-generation sequencing-based approaches. Eur J Hum Genet 2020; 28:388-398. [PMID: 31358957 PMCID: PMC7029013 DOI: 10.1038/s41431-019-0479-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/06/2019] [Accepted: 07/16/2019] [Indexed: 11/09/2022] Open
Abstract
Name of the disease (synonyms) See Table 1, Column 1-"Name of disease" and Column 2-"Alternative names". OMIM# of the disease See Table 1, Column 3-"OMIM# of the disease". Name of the analysed genes or DNA/chromosome segments and OMIM# of the gene(s) Core genes (irrespective of being tested by Sanger sequencing or next-generation sequencing): See Table 1, Column 4-"Cytogenetic location", Column 5-"Associated gene(s)" and Column 6-"OMIM# of associated gene(s)". Additional genes (if tested by next-generation sequencing, including Whole exome/genome sequencing and panel sequencing): See Table 2, Column 1-"Gene", Column 2-"Alternative names", Column 3-"OMIM# of gene" and Column 4-"Cytogenetic location". Review of the analytical and clinical validity as well as of the clinical utility of DNA-based testing for mutations in the gene(s) in diagnostic, predictive and prenatal settings, and for risk assessment in relatives.
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Affiliation(s)
| | - Brian P Brooks
- Ophthalmic Genetics & Visual Function Branch, National Eye Institute, Bethesda, MD, USA
| | | | - Mariya Moosajee
- UCL Institute of Ophthalmology, London, UK. .,Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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19
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Jiang F, Yang X, He X, Yang M. Circulating DNA, a Potentially Sensitive and Specific Diagnostic Tool for Future Medicine. Dose Response 2019; 17:1559325819891010. [PMID: 31827416 PMCID: PMC6886285 DOI: 10.1177/1559325819891010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 11/28/2022] Open
Abstract
Liquid biopsy has the great potential of detecting early diseases before deterioration and is valued for screening abnormalities at early stage. In oncology, circulating DNA derived from shed cancer cells reflects the tissue of origin, so it could be used to locate tissue sites during early screening. However, the heterogenous parameters of different types limit the clinical application, making it inaccessible to encompass all the cancer types. Instead, for reproducible scenario as pregnancy, fetal cell-free DNA has been well utilized for screening aneuploidies. Noninvasive and convenient as is, it would be of great value in the next decades far more than early diagnosis. This review recapitulates the discovery and development of tumor and fetal cell-free DNA. The common factors are also present that could be taken into consideration when collecting, transporting, and preserving samples. Meanwhile, several protocols used for purifying cell-free DNA, either classic ones or through commercial kits, are compared carefully. In addition, the development of technologies for analyzing cell-free DNA have been summarized and discussed in detail, especially some up-to-date approaches. At the end, the potential prospect of circulating DNA is bravely depicted. In summary, although there would be a lot of efforts before it’s prevalent, cell-free DNA remains a promising tool in point-of-care diagnostic medicine.
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Affiliation(s)
- Fan Jiang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiaoxiao Yang
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Xiping He
- Department of Rehabilitation Medicine, The First People's Hospital of Wenling, Wenzhou Medical University, Wenling, Zhejiang, China
| | - Mingming Yang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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20
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Novel Epigenetic Biomarkers in Pregnancy-Related Disorders and Cancers. Cells 2019; 8:cells8111459. [PMID: 31752198 PMCID: PMC6912400 DOI: 10.3390/cells8111459] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 12/11/2022] Open
Abstract
As the majority of cancers and gestational diseases are prognostically stage- and grade-dependent, the ultimate goal of ongoing studies in precision medicine is to provide early and timely diagnosis of such disorders. These studies have enabled the development of various new diagnostic biomarkers, such as free circulating nucleic acids, and detection of their epigenetic changes. Recently, extracellular vesicles including exosomes, microvesicles, oncosomes, and apoptotic bodies have been recognized as powerful diagnostic tools. Extracellular vesicles carry specific proteins, lipids, DNAs, mRNAs, and miRNAs of the cells that produced them, thus reflecting the function of these cells. It is believed that exosomes, in particular, may be the optimal biomarkers of pathological pregnancies and cancers, especially those that are frequently diagnosed at an advanced stage, such as ovarian cancer. In the present review, we survey and critically appraise novel epigenetic biomarkers related to free circulating nucleic acids and extracellular vesicles, focusing especially on their status in trophoblasts (pregnancy) and neoplastic cells (cancers).
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21
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Abou Tayoun A, Mason-Suares H. Considerations for whole exome sequencing unique to prenatal care. Hum Genet 2019; 139:1149-1159. [PMID: 31701237 DOI: 10.1007/s00439-019-02085-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022]
Abstract
Whole exome sequencing (WES) is increasingly being used in the prenatal setting. The emerging data support the clinical utility of prenatal WES based on its diagnostic yield, which can be as high as 80% for certain ultrasound findings. However, detailed practice and laboratory guidelines, addressing the indications for prenatal WES and the surrounding technical, interpretation, ethical, and counseling issues, are still lacking. Herein, we review the literature and summarize the most recent findings and applications of prenatal WES. This review offers specialists and clinical genetic laboratorians a body of evidence and expert opinions that can serve as a resource to assist in their practice. Finally, we highlight the emerging technologies that promise a future of prenatal WES without the risks associated with invasive testing.
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Affiliation(s)
| | - Heather Mason-Suares
- Departments of Pathology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA. .,Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, 65 Landsdowne Street, Cambridge, MA, 02115, USA.
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22
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Abstract
BACKGROUND The number of citations a published article receives can be used to demonstrate its impact on a field of study. The objective of this study was to identify and characterize the 100 most-cited research articles (T100) published on prenatal diagnosis. METHODS The Web of Science (WOS) database was searched for papers on prenatal diagnosis published between 1900 and 2018. The 100 most-cited original articles and reviews were recorded. Each eligible paper was reviewed for authors, journal name, year of publication, country, institution, total citations, citation density, H-index, research field, article type, and keywords. RESULTS The T100 were published between 1972 and 2015 with a mean of 332.7 citations per paper (range: 196-1254). Most of the T100 were published between 1990 and 2005, in 35 journals led by New England Journal of Medicine (n = 14) followed by Lancet (n = 10), and Proceedings of The National Academy of Sciences of the United States of America (n = 8). Studies on method application, which promotes field development, were the majority article type. The team of Lo YM featured prominently in the field, and the United States of America, United Kingdom, and Hong Kong, China were the leading countries/regions. Frequency of cooperation was also highest among these 3 regions. Hierarchical cluster analysis produced 4 groups of keywords. CONCLUSION Our analysis provides a historical perspective on scientific progress in prenatal diagnosis and may assist clinicians and researchers in assessing the quality of research over the past 50 years. It also provides concise information to guide future research.
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Affiliation(s)
- Meilian Zhang
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
| | - Yu Zhou
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fujian Medical University
| | - Yanfang Lu
- Clinical Laboratory, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Suhui He
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
| | - Min Liu
- Department of Ultrasound, Fujian Provincial Maternity and Children's Hospital Affiliated Hospital of Fujian Medical University
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23
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Barati Z, Farsimadan M, Sharafshah A, Peymani M, Bijanzadeh M. Association study of rs10768683 and rs968857 polymorphisms with transfusion-dependent thalassemia (TDT) in a southern Iranian population. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:88-99. [PMID: 30849277 DOI: 10.1080/15257770.2018.1498514] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Previous studies reported that detection of polymorphisms inherited through paternal model could be potential markers for the Non-Invasive Prenatal Diagnosis (NIPD) of β-thalassemia. The aim of the current study was to find out the associations of rs10768683 and rs968857 with transfusion-dependent thalassemia (TDT) in a southern Iranian population. A total of 175 subjects were investigated, divided into patients with TDT as case group (n = 75) and healthy people as control group (n = 100). Genomic DNAs were extracted from peripheral blood using salting out procedure. Genotyping rs10768683 and rs968857 was carried out by ARMS-PCR, then statistical analyses were assessed using SPSS, and Medcalc ver. 18 software. Data showed that rs10768683 was statistically significant in co-dominant model of inheritance (P = 0.025, OR = 2.11 [1.08-4.15]) and genotype frequencies of CG among controls and cases were 0.68 and 0.80, respectively. However, according to genotype frequencies, there was no association between rs968857 and TDT among cases and healthy controls in any models of inheritance. In conclusion, the present study showed the association of rs10768683 with major β-thalassemia through ARMS-PCR technique.
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Affiliation(s)
- Zahed Barati
- a Department of Biology, Faculty of Basic Sciences , Shahrekord Branch, Islamic Azad University , Shahrekord , Iran
| | - Marziye Farsimadan
- b Department of Biology Faculty of Sciences , Guilan University , Rasht , Iran
| | - Alireza Sharafshah
- c Cellular and Molecular Research Center, Faculty of Medicine , Guilan University of Medical Sciences , Rasht , Iran
| | - Maryam Peymani
- a Department of Biology, Faculty of Basic Sciences , Shahrekord Branch, Islamic Azad University , Shahrekord , Iran
| | - Mahdi Bijanzadeh
- d Department of Medical Genetics School of Medicine , Ahvaz Jundishapur University of Medical Sciences , Ahvaz , Iran
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24
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Stevens BK, Noblin SJ, Chen HY, Czerwinski J, Friel LA, Wagner C. Introduction of cell-free DNA screening is associated with changes in prenatal genetic counseling indications. J Genet Couns 2019; 28:692-699. [PMID: 30791172 DOI: 10.1002/jgc4.1095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 11/10/2022]
Abstract
The introduction of cell-free DNA screening, or non-invasive prenatal testing (NIPT), for chromosome abnormalities has greatly impacted prenatal care since its introduction in late 2011. We aimed to evaluate the association between the introduction of cell-free DNA screening and indication and referral patterns for genetic counseling at a large US academic medical center by comparing the percentage of each counseling indication between the time period prior to the introduction of cell-free DNA screening (2006-2011) and following its introduction (2012-2016) using multivariable Poisson regression models. Genetic counseling indications for positive carrier screens, average risk patients, abnormal ultrasound findings, and family history indications were significantly higher following the introduction of NIPT while advanced maternal age and abnormal maternal serum screening indications dropped significantly. We also showed that the uptake of amniocentesis dropped significantly after the introduction of cell-free DNA screening, while chorionic villus sampling uptake increased. These results provide evidence that the introduction of new genetic screening technologies is associated with a shift in genetic counseling referral indications and an increased uptake in genetic screening. Additional research is needed to explore the impact of expanded testing options on the need for genetic counseling services.
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Affiliation(s)
- Blair K Stevens
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
| | - Sarah J Noblin
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
| | - Han-Yang Chen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
| | - Jennifer Czerwinski
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
| | - Lara A Friel
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
| | - Chelsea Wagner
- Department of Obstetrics, Gynecology, and Reproductive Sciences, McGovern Medical School, UTHealth, Houston, Texas
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25
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Zhang J, Li J, Saucier JB, Feng Y, Jiang Y, Sinson J, McCombs AK, Schmitt ES, Peacock S, Chen S, Dai H, Ge X, Wang G, Shaw CA, Mei H, Breman A, Xia F, Yang Y, Purgason A, Pourpak A, Chen Z, Wang X, Wang Y, Kulkarni S, Choy KW, Wapner RJ, Van den Veyver IB, Beaudet A, Parmar S, Wong LJ, Eng CM. Non-invasive prenatal sequencing for multiple Mendelian monogenic disorders using circulating cell-free fetal DNA. Nat Med 2019; 25:439-447. [PMID: 30692697 DOI: 10.1038/s41591-018-0334-x] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 12/17/2018] [Indexed: 02/02/2023]
Abstract
Current non-invasive prenatal screening is targeted toward the detection of chromosomal abnormalities in the fetus1,2. However, screening for many dominant monogenic disorders associated with de novo mutations is not available, despite their relatively high incidence3. Here we report on the development and validation of, and early clinical experience with, a new approach for non-invasive prenatal sequencing for a panel of causative genes for frequent dominant monogenic diseases. Cell-free DNA (cfDNA) extracted from maternal plasma was barcoded, enriched, and then analyzed by next-generation sequencing (NGS) for targeted regions. Low-level fetal variants were identified by a statistical analysis adjusted for NGS read count and fetal fraction. Pathogenic or likely pathogenic variants were confirmed by a secondary amplicon-based test on cfDNA. Clinical tests were performed on 422 pregnancies with or without abnormal ultrasound findings or family history. Follow-up studies on cases with available outcome results confirmed 20 true-positive, 127 true-negative, zero false-positive, and zero-false negative results. The initial clinical study demonstrated that this non-invasive test can provide valuable molecular information for the detection of a wide spectrum of dominant monogenic diseases, complementing current screening for aneuploidies or carrier screening for recessive disorders.
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Affiliation(s)
- Jinglan Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | | | | | | | | | | | - Anne K McCombs
- Office of Clinical Research, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xiaoyan Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Statistics, Rice University, Houston, TX, USA
| | - Hui Mei
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Zhao Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shashikant Kulkarni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kwong Wai Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Hong Kong, China
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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26
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Gagliano SA, Sengupta S, Sidore C, Maschio A, Cucca F, Schlessinger D, Abecasis GR. Relative impact of indels versus SNPs on complex disease. Genet Epidemiol 2018; 43:112-117. [PMID: 30565766 PMCID: PMC6330128 DOI: 10.1002/gepi.22175] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/07/2018] [Accepted: 10/29/2018] [Indexed: 11/30/2022]
Abstract
It is unclear whether insertions and deletions (indels) are more likely to influence complex traits than abundant single‐nucleotide polymorphisms (SNPs). We sought to understand which category of variation is more likely to impact health. Using the SardiNIA study as an exemplar, we characterized 478,876 common indels and 8,246,244 common SNPs in up to 5,949 well‐phenotyped individuals from an isolated valley in Sardinia. We assessed association between 120 traits, resulting in 89 nonoverlapping‐associated loci.We evaluated whether indels were enriched among credible sets of potential causal variants. These credible sets included 1,319 SNPs and 88 indels. We did not find indels to be significantly enriched. Indels were the most likely causal variant in seven loci, including one locus associated with monocyte count where an indel with causality and mechanism previously demonstrated (rs200748895:TGCTG/T) had a 0.999 posterior probability. Overall, our results show a very modest and nonsignificant enrichment for common indels in associated loci.
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Affiliation(s)
- Sarah A Gagliano
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Sebanti Sengupta
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Cagliari, Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, US National Institutes of Health, Baltimore, Maryland
| | - Gonçalo R Abecasis
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
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27
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Abstract
As more women with transfusion-dependent thalassemia are seeking pregnancy, ensuring the best outcomes for both the mother and baby requires concerted, collaborative efforts between practitioners and the family. Proactive counseling, early fertility evaluation, recent developments in reproductive technology, and optimal management of iron overload, have resulted in more successful pregnancies and the birth of healthy newborns. With advances in technology for prenatal screening and increased awareness to perform screening for hemoglobinopathies, healthy pregnancy outcomes have become the expectation. Topics that require further study include management that allows fertility preservation, improved non-invasive prenatal diagnosis methods for affected fetuses, the use of chelation therapy during pregnancy, and indications for and duration of anticoagulation.
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28
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Clinical utility of exome sequencing in the prenatal diagnosis of congenital anomalies: A Review. Eur J Obstet Gynecol Reprod Biol 2018; 231:19-24. [PMID: 30317140 DOI: 10.1016/j.ejogrb.2018.10.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/01/2018] [Indexed: 12/25/2022]
Abstract
Advances in prenatal genomics have enabled the assessment of not only the sub-microscopic structure of chromosomes using chromosomal microarray analysis, but also the detection of "pathogenic variants" to the resolution of a single base pair with the use of next generation sequencing. Research is emerging on the additional prenatal diagnostic yield that exome sequencing offers when structural fetal anomalies are detected on ultrasound examination, in particular the identification of monogenic abnormalities defining prognosis and recurrence of anomalies. Primarily assessed using fetal DNA obtained by invasive techniques (amniocytes or chorionic villi), this technology is progressing into a non-invasive approach using maternal plasma. There are several challenges, to be addressed before this technology can be introduced into routine clinical practice. These are primarily technical and interpretational but also relate to service provision; cost-effectiveness; turn-around time; patient acceptability and ethical dilemmas. With adequate pre- and post-test counselling many of these challenges may be overcome and such counselling has to be multi-disciplinary, involving clinical geneticists, genetic scientists, paediatricians, perinatal pathologists and fetal medicine subspecialists. There is therefore a need for obstetricians to have an understanding of the clinical utility, application, advantages and challenges of such technologies before introduction into routine clinical practice.
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29
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Identification of a de novo fetal variant in osteogenesis imperfecta by targeted sequencing-based noninvasive prenatal testing. J Hum Genet 2018; 63:1129-1137. [PMID: 30131598 DOI: 10.1038/s10038-018-0489-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/14/2018] [Accepted: 06/26/2018] [Indexed: 11/08/2022]
Abstract
Noninvasive prenatal testing (NIPT), which involves analysis of circulating cell-free fetal DNA (cffDNA) from maternal plasma, is highly effective for detecting feto-placental chromosome aneuploidy. However, recent studies suggested that coverage-based shallow-depth NIPT cannot accurately detect smaller single or multi-loci genetic variants. To assess the fetal genotype of any locus using maternal plasma, we developed a novel genotyping algorithm named pseudo tetraploid genotyping (PTG). We performed paired-end captured sequencing of the plasma cell-free DNA (cfDNA), in which case a phenotypically healthy woman is suspected to be carrying a fetus with genetic defect. After a series of independent filtering of 111,407 SNPs, we found one variant in COL1A1 graded with high pathogenic potential which might cause osteogenesis imperfecta (OI). Then, we verified this mutation by Sanger sequencing of fetal and parental blood cells. In addition, we evaluated the accuracy and detection rate of the PTG algorithm through direct sequencing of the genomic DNA from maternal and fetal blood cells. Collectively, our study developed an intuitive and cost-effective method for the noninvasive detection of pathogenic mutations, and successfully identified a de novo variant in COL1A1 (c.2596 G > A, p.Gly866Ser) in the fetus implicated in OI.
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30
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Koczok K, Gombos É, Madar L, Török O, Balogh I. Interfering effect of maternal cell contamination on invasive prenatal molecular genetic testing. Prenat Diagn 2018; 38:713-719. [PMID: 29935118 DOI: 10.1002/pd.5319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/07/2018] [Accepted: 06/15/2018] [Indexed: 11/10/2022]
Abstract
OBJECTIVE Fetal samples obtained by invasive techniques are prone to maternal cell contamination (MCC), which may lead to false genotyping results. Our aim was to determine 3 molecular genetic tests' sensitivity to MCC. METHOD By mixing experiments, 1%, 5%, 10%, 20%, 30%, and 40% MCC was simulated, and significant MCC levels were determined for Sanger DNA sequencing, multiplex ligation-dependent probe amplification (MLPA), and pyrosequencing, a next-generation sequencing method. RESULTS For Sanger sequencing, the limit of sensitivity to MCC was 5% to 30%. For MLPA, a higher proportion of MCC (≥40%) was shown to lead to diagnostic uncertainty. In contrast, pyrosequencing proved to be very sensitive to MCC, detecting a proportion as low as 1%. CONCLUSION In the case of Sanger sequencing, sensitivity to MCC was variable, while for MLPA, only high levels of MCC proved to be significant. Although the next-generation sequencing method was sensitive to low-level MCC, if MCC level is determined in parallel, accurate quantification of allelic ratios can help to interpret the diagnostic results. Knowledge of significant MCC levels allows correct prenatal diagnosis even if samples are not purely of fetal origin and repeated sampling can be avoided in many of the cases.
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Affiliation(s)
- Katalin Koczok
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Éva Gombos
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Madar
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Olga Török
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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31
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Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23:94-101. [PMID: 29305293 DOI: 10.1016/j.siny.2017.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.
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32
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Haidar H, Dupras C, Ravitsky V. Non-Invasive Prenatal Testing: Review of Ethical, Legal and Social Implications. BIOÉTHIQUEONLINE 2018. [DOI: 10.7202/1044264ar] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) using cell-free fetal DNA (cffDNA) from maternal blood has recently entered clinical practice in many countries, including Canada. This test can be performed early during pregnancy to detect Down syndrome and other conditions. While NIPT promises numerous benefits, it also has challenging ethical, legal and social implications (ELSI). This paper reviews concerns currently found in the literature on the ELSI of NIPT. We make four observations. First, NIPT seems to exacerbate some of the already existing concerns raised by other prenatal tests (amniocentesis and maternal serum screening) such as threats to women’s reproductive autonomy and the potential for discrimination and stigmatization of disabled individuals and their families. This may be due to the likely upcoming large scale implementation and routinization of NIPT. Second, the distinction between NIPT as a screening test (as it is currently recommended) and as a diagnostic test (potentially in the future), has certain implications for the ELSI discussion. Third, we observed a progressive shift in the literature from initially including mostly conceptual analysis to an increasing number of empirical studies. This demonstrates the contribution of empirical bioethics approaches as the technology is being implemented into clinical use. Finally, we noted an increasing interest in equity and justice concerns regarding access to NIPT as it becomes more widely implemented.
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Affiliation(s)
- Hazar Haidar
- Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
| | - Charles Dupras
- Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
| | - Vardit Ravitsky
- Department of Social and Preventive Medicine, School of Public Health, Université de Montréal, Montreal, Canada
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33
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Jenkins LA, Deans ZC, Lewis C, Allen S. Delivering an accredited non-invasive prenatal diagnosis service for monogenic disorders and recommendations for best practice. Prenat Diagn 2018; 38:44-51. [PMID: 29266293 DOI: 10.1002/pd.5197] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Lucy A. Jenkins
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Zandra C. Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine; Royal Infirmary of Edinburgh; Edinburgh UK
| | - Celine Lewis
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Great Ormond Street Institute of Child Health; London UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's NHS Foundation Trust; Birmingham UK
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34
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Feng C, He Z, Cai B, Peng J, Song J, Yu X, Sun Y, Yuan J, Zhao X, Zhang Y. Non-invasive Prenatal Diagnosis of Chromosomal Aneuploidies and Microdeletion Syndrome Using Fetal Nucleated Red Blood Cells Isolated by Nanostructure Microchips. Theranostics 2018; 8:1301-1311. [PMID: 29507621 PMCID: PMC5835937 DOI: 10.7150/thno.21979] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/08/2017] [Indexed: 11/15/2022] Open
Abstract
Detection of detached fetal nucleated red blood cells (fNRBCs) in the maternal peripheral blood may serve as a prospective testing method competing with the cell-free DNA, in non-invasive prenatal testing (NIPT). Methods: Herein, we introduce a facile and effective lab-on-a-chip method of fNRBCs detection using a capture-releasing material that is composed of biotin-doped polypyrrole nanoparticles. To enhance local topographic interactions between the nano-components and fNRBC, a specific antibody, CD147, coated on the nanostructured substrate led to the isolation of fNRBCs from maternal peripheral blood. Subsequently, an electrical system was employed to release the captured cells using 0.8 V for 15 s. The diagnostic application of fNRBCs for fetal chromosomal disorders (Trisomy 13/21/18/X syndrome, microdeletion syndrome) was demonstrated. Results: Cells captured by nanostructured microchips were identified as fNRBCs. Twelve cases of chromosomal aneuploidies and one case of 18q21 microdeletion syndrome were diagnosed using the fNRBCs released from the microchips. Conclusion: Our method offers effective and accurate analysis of fNRBCs for comprehensive NIPT to monitor fetal cell development.
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Affiliation(s)
- Chun Feng
- Department of Obstetrics and Gynechology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
| | - Zhaobo He
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, Hubei, China
| | - Bo Cai
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, Hubei, China
| | - Jianhong Peng
- Prenatal Diagnostic and Birth Health Clinical Research Center of Hubei Province, Wuhan, Hubei, 430071, China
| | - Jieping Song
- Department of Prenatal Diagnostic Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, 430070, China
| | - Xuechen Yu
- Department of Obstetrics and Gynechology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
| | - Yue Sun
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, Hubei, China
| | - Jing Yuan
- Department of Obstetrics and Gynechology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
| | - Xingzhong Zhao
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yuanzhen Zhang
- Department of Obstetrics and Gynechology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, China
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35
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Chiu EKL, Hui WWI, Chiu RWK. cfDNA screening and diagnosis of monogenic disorders - where are we heading? Prenat Diagn 2018; 38:52-58. [PMID: 29314147 PMCID: PMC5839244 DOI: 10.1002/pd.5207] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/27/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022]
Abstract
Cell‐free fetal DNA analysis for non‐invasive prenatal screening of fetal chromosomal aneuploidy has been widely adopted for clinical use. Fetal monogenic diseases have also been shown to be amenable to non‐invasive detection by maternal plasma DNA analysis. A number of recent technological developments in this area has increased the level of clinical interest, particularly as one approach does not require customized reagents per mutation. The mutational status of the fetus can be assessed by determining which parental haplotype that fetus has inherited based on the detection of haplotype‐associated SNP alleles in maternal plasma. Such relative haplotype dosage analysis requires the input of the parental haplotype information for interpretation of the fetal inheritance pattern from the maternal plasma DNA data. The parental haplotype information can be obtained by direct means, reducing the need to infer haplotypes using DNA from other family members. The technique also allows the assessment of complex mutations and has multiplexing capabilities where a number of genes and mutations can be assessed at the same time. These advantages allow non‐invasive prenatal diagnosis of fetal monogenic diseases to be much more scalable. These applications may drive the next wave of clinical adoption of cell‐free fetal DNA testing. © 2018 The Authors Prenatal Diagnosis Published by John Wiley & Sons Ltd What's already known about this topic?
NIPD for some monogenic diseases is now in clinical service. Current NIPD is based on bespoke mutation‐specific assays, or haplotype inference which requires proband DNA.
What does this study add?
The application of universal haplotype‐based NIPD can be extended to most pregnancies at risk for monogenic diseases. The universal protocol circumvents the need for bespoke assays or access to proband DNA.
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Affiliation(s)
- Eunice Ka Long Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
| | - Winnie Wai In Hui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
| | - Rossa Wai Kwun Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR
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Barrett AN, Xiong L, Tan TZ, Advani HV, Hua R, Laureano-Asibal C, Soong R, Biswas A, Nagarajan N, Choolani M. Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms. PLoS One 2017; 12:e0186771. [PMID: 29084245 PMCID: PMC5662091 DOI: 10.1371/journal.pone.0186771] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/07/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Cell-free DNA from maternal plasma can be used for non-invasive prenatal testing for aneuploidies and single gene disorders, and also has applications as a biomarker for monitoring high-risk pregnancies, such as those at risk of pre-eclampsia. On average, the fractional cell-free fetal DNA concentration in plasma is approximately 15%, but can vary from less than 4% to greater than 30%. Although quantification of cell-free fetal DNA is straightforward in the case of a male fetus, there is no universal fetal marker; in a female fetus measurement is more challenging. We have developed a panel of multiplexed insertion/deletion polymorphisms that can measure fetal fraction in all pregnancies in a simple, targeted sequencing reaction. METHODS A multiplex panel of primers was designed for 35 indels plus a ZFX/ZFY amplicon. cfDNA was extracted from plasma from 157 pregnant women, and maternal genomic DNA was extracted for 20 of these samples for panel validation. Sixty-one samples from pregnancies with a male fetus were subjected to whole genome sequencing on the Ion Proton sequencing platform, and fetal fraction derived from Y chromosome counts was compared to fetal fraction measured using the indel panel. A total of 157 cell-free DNA samples were sequenced using the indel panel, and informativity was assessed, along with the proportion of fetal DNA. RESULTS Using gDNA we optimised the indel panel, removing amplicons giving rise to PCR bias. Good correlation was found between fetal fraction using indels and using whole genome sequencing of the Y chromosome (Spearmans r = 0.69). A median of 12 indels were informative per sample. The indel panel was informative in 157/157 cases (mean fetal fraction 14.4% (±0.58%)). CONCLUSIONS Using our targeted next generation sequencing panel we can readily assess the fetal DNA percentage in male and female pregnancies.
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Affiliation(s)
- Angela N. Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail: (AB); (MC)
| | - Li Xiong
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gynecology & Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Tuan Z. Tan
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Henna V. Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rui Hua
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gynecology & Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Cecille Laureano-Asibal
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Richie Soong
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Arijit Biswas
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail: (AB); (MC)
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Vermeulen C, Geeven G, de Wit E, Verstegen MJ, Jansen RP, van Kranenburg M, de Bruijn E, Pulit SL, Kruisselbrink E, Shahsavari Z, Omrani D, Zeinali F, Najmabadi H, Katsila T, Vrettou C, Patrinos GP, Traeger-Synodinos J, Splinter E, Beekman JM, Kheradmand Kia S, te Meerman GJ, Ploos van Amstel HK, de Laat W. Sensitive Monogenic Noninvasive Prenatal Diagnosis by Targeted Haplotyping. Am J Hum Genet 2017; 101:326-339. [PMID: 28844486 PMCID: PMC5590845 DOI: 10.1016/j.ajhg.2017.07.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 12/11/2022] Open
Abstract
During pregnancy, cell-free DNA (cfDNA) in maternal blood encompasses a small percentage of cell-free fetal DNA (cffDNA), an easily accessible source for determination of fetal disease status in risk families through non-invasive procedures. In case of monogenic heritable disease, background maternal cfDNA prohibits direct observation of the maternally inherited allele. Non-invasive prenatal diagnostics (NIPD) of monogenic diseases therefore relies on parental haplotyping and statistical assessment of inherited alleles from cffDNA, techniques currently unavailable for routine clinical practice. Here, we present monogenic NIPD (MG-NIPD), which requires a blood sample from both parents, for targeted locus amplification (TLA)-based phasing of heterozygous variants selectively at a gene of interest. Capture probes-based targeted sequencing of cfDNA from the pregnant mother and a tailored statistical analysis enables predicting fetal gene inheritance. MG-NIPD was validated for 18 pregnancies, focusing on CFTR, CYP21A2, and HBB. In all cases we could predict the inherited alleles with >98% confidence, even at relatively early stages (8 weeks) of pregnancy. This prediction and the accuracy of parental haplotyping was confirmed by sequencing of fetal material obtained by parallel invasive procedures. MG-NIPD is a robust method that requires standard instrumentation and can be implemented in any clinic to provide families carrying a severe monogenic disease with a prenatal diagnostic test based on a simple blood draw.
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38
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Kane SC, Reidy KL, Norris F, Nisbet DL, Kornman LH, Palma-Dias R. Chorionic villus sampling in the cell-free DNA aneuploidy screening era: careful selection criteria can maximise the clinical utility of screening and invasive testing. Prenat Diagn 2017; 37:399-408. [DOI: 10.1002/pd.5026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 01/19/2017] [Accepted: 02/12/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Stefan C. Kane
- Pregnancy Research Centre; Department of Maternal Fetal Medicine, The Royal Women's Hospital; Parkville VIC Australia
- The University of Melbourne; Department of Obstetrics and Gynaecology, The Royal Women's Hospital; Parkville VIC Australia
- Ultrasound Department; Pauline Gandel Women's Imaging Centre, The Royal Women's Hospital; Parkville VIC Australia
| | - Karen L. Reidy
- Pregnancy Research Centre; Department of Maternal Fetal Medicine, The Royal Women's Hospital; Parkville VIC Australia
- Ultrasound Department; Pauline Gandel Women's Imaging Centre, The Royal Women's Hospital; Parkville VIC Australia
| | - Fiona Norris
- Victorian Clinical Genetics Services; Parkville VIC Australia
| | - Deborah L. Nisbet
- Ultrasound Department; Pauline Gandel Women's Imaging Centre, The Royal Women's Hospital; Parkville VIC Australia
- Women's Ultrasound Melbourne; Parkville VIC Australia
- The University of Melbourne; Departments of Medicine and Radiology; Parkville VIC Australia
| | - Louise H. Kornman
- The University of Melbourne; Department of Obstetrics and Gynaecology, The Royal Women's Hospital; Parkville VIC Australia
- Ultrasound Department; Pauline Gandel Women's Imaging Centre, The Royal Women's Hospital; Parkville VIC Australia
- Women's Ultrasound Melbourne; Parkville VIC Australia
| | - Ricardo Palma-Dias
- Pregnancy Research Centre; Department of Maternal Fetal Medicine, The Royal Women's Hospital; Parkville VIC Australia
- The University of Melbourne; Department of Obstetrics and Gynaecology, The Royal Women's Hospital; Parkville VIC Australia
- Ultrasound Department; Pauline Gandel Women's Imaging Centre, The Royal Women's Hospital; Parkville VIC Australia
- Women's Ultrasound Melbourne; Parkville VIC Australia
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39
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Non-invasive prenatal diagnosis of beta-thalassemia by semiconductor sequencing: a feasibility study in the sardinian population. Eur J Hum Genet 2017; 25:600-607. [PMID: 28272531 DOI: 10.1038/ejhg.2017.26] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/18/2017] [Accepted: 01/22/2017] [Indexed: 01/31/2023] Open
Abstract
β-Thalassemia is the most common autosomal recessive single-gene disorder in Sardinia, where approximately 10.3% of the population is a carrier. Prenatal diagnosis is carried out at 12 weeks of gestation via villocentesis and is commonly aimed at ascertaining the presence or absence of the HBB variant c.118C>T, which is the most common in Sardinia. In this study, we describe for the first time the application of semiconductor sequencing to the non-invasive prenatal diagnosis of β-thalassemia in 37 couples at risk for this variant. In particular, by using a haplotyping-based approach with a hidden Markov model (HMM) and a dedicated pipeline, the two parental haplotypes most likely inherited by the foetus could be established in 30 out of 37 cffDNA samples. Specifically, the paternally inherited haplotype was correctly determined in all 30 of the samples, while the maternal haplotype was incorrectly predicted in six of the 30 genotyped samples. The lack of informative SNPs hampered the inference of both parental haplotypes in the remaining seven samples. As shown in previous studies, we have confirmed that the haplotyping-based approach represents a valuable resource, as it improves the detection of both parental haplotypes inherited by the foetus. In general, our results are encouraging, as we have proven that NIPD is also feasible in couples who are at risk for a monogenic disorder and share the same variant.
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40
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Ahmed S, Jafri H, Rashid Y, Mason G, Ehsan Y, Ahmed M. Attitudes towards non-invasive prenatal diagnosis among obstetricians in Pakistan, a developing, Islamic country. Prenat Diagn 2017; 37:289-295. [PMID: 28109006 DOI: 10.1002/pd.5008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/20/2016] [Accepted: 01/13/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Stakeholders' views are essential for informing implementation strategies for non-invasive prenatal testing (NIPT). Little is known about such views in developing countries. We explored attitudes towards NIPT among obstetricians in Pakistan, a developing, Islamic country. METHODS A 35-item questionnaire was distributed and collected at eight events (a national conference and seven workshops in five cities) for obstetric professionals on advances in fetal medicine. RESULTS Responses from 113 obstetrician show positive attitudes towards implementation of NIPT: 95% agreed prevention of genetic conditions was a necessity, and 97% agreed public hospitals should provide prenatal screening tests. However, participants also agreed the availability of NIPT would increase social pressure on women to have prenatal screening tests and to terminate an affected pregnancy (53% and 63%, respectively). Most participants would not offer NIPT for sex determination (55%), although 31% would. The most valued aspects of NIPT were its safety, followed by its utility and then accuracy. CONCLUSION Participants generally supported the implementation of NIPT but raised concerns about social implications. Therefore, national policy is needed to regulate the implementation of NIPT, and pretest information and post-test genetic counselling are needed to mitigate social pressure and support parents to make informed decisions. © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Shenaz Ahmed
- Leeds Institute of Health Sciences, School of Medicine, University of Leeds, Leeds, LS2 9NL, UK
| | | | | | | | | | - Mushtaq Ahmed
- Yorkshire Regional Genetics Service, Leeds NHS Teaching Hospitals Trust, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
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41
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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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Affiliation(s)
- Winnie W I Hui
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peiyong Jiang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Yu K Tong
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing-Shan Lee
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yvonne K Y Cheng
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Maria I New
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, NY
| | - Rezan A Kadir
- Department of Obstetrics and Gynaecology, Royal Free London NHS Foundation Trust, London, UK
- Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free London NHS Foundation Trust, London, UK
| | - K C Allen Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Tak Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Y M Dennis Lo
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
- Centre for Research into Circulating Fetal Nucleic Acids, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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42
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Parks M, Court S, Bowns B, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S. Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage. Eur J Hum Genet 2017; 25:416-422. [PMID: 28120840 PMCID: PMC5386415 DOI: 10.1038/ejhg.2016.195] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.
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Affiliation(s)
- Michael Parks
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samantha Court
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Benjamin Bowns
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Siobhan Cleary
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Hewitt
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Fiona MacDonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
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Whale AS, Devonshire AS, Karlin-Neumann G, Regan J, Javier L, Cowen S, Fernandez-Gonzalez A, Jones GM, Redshaw N, Beck J, Berger AW, Combaret V, Dahl Kjersgaard N, Davis L, Fina F, Forshew T, Fredslund Andersen R, Galbiati S, González Hernández Á, Haynes CA, Janku F, Lacave R, Lee J, Mistry V, Pender A, Pradines A, Proudhon C, Saal LH, Stieglitz E, Ulrich B, Foy CA, Parkes H, Tzonev S, Huggett JF. International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant. Anal Chem 2017; 89:1724-1733. [DOI: 10.1021/acs.analchem.6b03980] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexandra S. Whale
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Alison S. Devonshire
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - George Karlin-Neumann
- Digital Biology Center, Bio-Rad Laboratories, 5731 West Las Positas, Pleasanton, California 94588, United States
| | - Jack Regan
- Digital Biology Center, Bio-Rad Laboratories, 5731 West Las Positas, Pleasanton, California 94588, United States
| | - Leanne Javier
- Digital Biology Center, Bio-Rad Laboratories, 5731 West Las Positas, Pleasanton, California 94588, United States
| | - Simon Cowen
- Statistics
Team, LGC, Queens Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Ana Fernandez-Gonzalez
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Gerwyn M. Jones
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Nicholas Redshaw
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Julia Beck
- Chronix Biomedical, Goetheallee 8, 37073 Goettingen, Germany
| | - Andreas W. Berger
- Department
of Internal Medicine I, Ulm University, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Valérie Combaret
- Laboratoire de Recherche
Translationnelle, Centre Léon-Bérard, Lyon, F-69008, France
| | - Nina Dahl Kjersgaard
- Sjællands Universitetshospital, Klinisk Biokemisk
Afdeling, Molekylærenhed, Sygehusvej 10, 4000 Roskilde, Denmark
| | - Lisa Davis
- Genoptix Inc., 1811 Aston Avenue, Carlsbad, California 92008, United States
| | - Frederic Fina
- Service
de Transfert d’Oncologie Biologique, Laboratoire de Biologie
Médicale, Faculte de médecine Nord, Boulevard Pierre
Dramard, Marseille 13916 cedex 20, France
| | - Tim Forshew
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley Street, London WC1E 6DD, United Kingdom
| | - Rikke Fredslund Andersen
- Department of Clinical Immunology and Biochemistry, Vejle Hospital, Kabbeltoft 25, 7100 Vejle, Denmark
| | - Silvia Galbiati
- Division of Genetics and
Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina
60, 20132 Milano, Italy
| | - Álvaro González Hernández
- Department of Pediatrics and CIMA LAB Diagnostics, Clínica Universidad de Navarra, Avenida Pío XII 36, 31008 Pamplona, Spain
| | - Charles A. Haynes
- Michael Smith Laboratories, University of British Columbia, 301 Michael Smith Building, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Filip Janku
- The University of Texas MD Anderson Cancer Center, Department of Investigational Cancer Therapeutics (Phase
I Clinical Trials Program), 1515 Holcombe Boulevard 0455, Houston, Texas 77030, United States
| | - Roger Lacave
- Solid Tumours Genomics Unit, Tenon Hospital, APHP and Université Pierre et Marie Curie, 4 rue
de la Chine, 75970 Paris, France
| | - Justin Lee
- Johns Hopkins, 1650 Orleans St., Baltimore, Maryland 21287, United States
| | - Vilas Mistry
- Department
of Cancer Studies, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester
Royal Infirmary, Leicester LE2 7LX, United Kingdom
| | - Alexandra Pender
- Lung Cancer Group, Division of Molecular
Pathology, The Institute of Cancer Research, 123 Old Brompton Road, London SW7 3RP, United Kingdom
| | - Anne Pradines
- Institut Claudius Regaud − IUCTO, Laboratoire de Biologie Medicale Oncologique, 1 avenue Irène Joliot-Curie, Toulouse 31059 cedex 9, France
| | - Charlotte Proudhon
- Institut Curie, PSL Research University, SiRIC, Laboratory of Circulating Tumor Biomarkers, 26 rue d’Ulm, 75005 Paris, France
| | - Lao H. Saal
- Department of Oncology and Pathology, Lund University, Scheelevägen 2, MV 404-B2, SE-22381, Lund, Sweden
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children’s Hospital, UCSF Helen Diller Family Comprehensive Cancer Center, 1450 Third Street, San Francisco, California 94158, United States
| | - Bryan Ulrich
- Dana Farber Cancer Institute, Belfer Center for Applied Cancer Science and Department
of Medical Oncology, Boston, Massachusetts 02115, United States
| | - Carole A. Foy
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Helen Parkes
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
| | - Svilen Tzonev
- Digital Biology Center, Bio-Rad Laboratories, 5731 West Las Positas, Pleasanton, California 94588, United States
| | - Jim F. Huggett
- Molecular and Cell Biology Team, LGC, Queens
Road, Teddington, Middlesex TW11 0LY, United Kingdom
- School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom
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44
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Yamada S, Miyake H. Prenatal Diagnosis of the Human Embryo and Fetus. COMPREHENSIVE GYNECOLOGY AND OBSTETRICS 2017. [DOI: 10.1007/978-981-10-2489-4_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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45
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Non-invasive prenatal diagnosis (NIPD) of cystic fibrosis: an optimized protocol using MEMO fluorescent PCR to detect the p.Phe508del mutation. J Cyst Fibros 2016; 16:198-206. [PMID: 28040480 DOI: 10.1016/j.jcf.2016.12.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/24/2016] [Accepted: 12/11/2016] [Indexed: 01/29/2023]
Abstract
BACKGROUND Analysis of cell-free foetal DNA (cff-DNA) in maternal plasma is very promising for early diagnosis of monogenic diseases; in particular, cystic fibrosis (CF). However, NIPD of single-gene disorders has been limited by the availability of suitable technical platforms and the need to set up patient or disease-specific custom-made approaches. METHODS To make research applications more readily accessible to the clinic, we offer a simple assay combining two independent methods to determine the presence or absence of paternally inherited foetal allele p.Phe508del (the most frequent mutation in CF patients worldwide). The first method detects the presence or absence of a p.Phe508del allele by Mutant Enrichment with 3'-Modified Oligonucleotide PCR coupled to Fragment Length Analysis (MEMO-PCR-FLA). The second method detects the p.Phe508del allele with classical Multiplex Fluorescent PCR including five intragenic and extragenic STR markers of the CFTR locus and a specific SRY sequence. RESULTS We collected 24 plasma samples from 23 women carrying foetuses at risk for CF and tested each sample using both methods. Our new procedures were successfully applied to 10 couples where fathers carried the p.Phe508del mutation and mothers were carrying a different mutation in the CFTR gene. These simple tests provided clear positive or negative results from the maternal plasma of the pregnant women. We confirmed the presence of cff-DNA in the studied samples by the identification of a tri-allelic DNA profile using a miniSTR kit. All results were correlated with chorionic villus sampling or amniocentesis analyses. CONCLUSIONS This NIPD approach, easily set up in any clinical laboratory where prenatal diagnosis is routinely performed, offers many advantages over current methods: it is simple, rapid, and cost-effective. It opens up the possibility for testing a large number of couples with offspring at risk for CF.
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Bayefsky MJ, White A, Wakim P, Hull SC, Wasserman D, Chen S, Berkman BE. Views of American OB/GYNs on the ethics of prenatal whole-genome sequencing. Prenat Diagn 2016; 36:1250-1256. [PMID: 27862072 DOI: 10.1002/pd.4968] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 11/07/2016] [Accepted: 11/11/2016] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Given public demand for genetic information, the potential to perform prenatal whole-genome sequencing (PWGS) non-invasively in the future, and decreasing costs of whole-genome sequencing, it is likely that OB/GYN practice will include PWGS. The goal of this project was to explore OB/GYNs' views on the ethical issues surrounding PWGS and their preparedness for counseling patients on its use. METHODS A national survey was administered to 2500 members of American Congress of Obstetricians and Gynecologists. RESULTS A total of 1114 respondents completed the survey (response rate = 45%). OB/GYNs are most concerned with ordering non-medical fetal genetic information, are worried about increasing parental anxiety, and feel it is appropriate to be directive when counseling parents about PWGS. Furthermore, most OB/GYNs have limited knowledge of genetics, rely heavily on genetic counselors and would like more guidance regarding the clinical adoption of PWGS. CONCLUSION OB/GYNs do not completely accept or reject PWGS, but a substantial number have significant ethical and practical concerns. They are most concerned with issues that will directly affect their practices and interactions with patients, such as increasing parental anxiety and costs of care. Professional guidance would be instrumental in directing the adoption of PWGS and alleviating the ethical burden posed by PWGS on individual OB/GYNs. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Michelle J Bayefsky
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Amina White
- University of North Carolina, Department of Obstetrics and Gynecology, Chapel Hill, NC, USA
| | - Paul Wakim
- Biostatistics and Clinical Epidemiology Service, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Sara Chandros Hull
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD, USA.,Bioethics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Wasserman
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Stephanie Chen
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin E Berkman
- Department of Bioethics, Clinical Center, National Institutes of Health, Bethesda, MD, USA.,Bioethics Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; 124:32-46. [DOI: 10.1111/1471-0528.14050] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2016] [Indexed: 12/18/2022]
Affiliation(s)
- FL Mackie
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
| | - K Hemming
- Public Health, Epidemiology and Biostatistics; Institute of Applied Health Sciences; University of Birmingham; Birmingham UK
| | - S Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - RK Morris
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
| | - MD Kilby
- Centre for Women's & Newborn Health and the Institute of Metabolism and Systems Research; University of Birmingham; Birmingham UK
- Fetal Medicine Centre; Birmingham Women's Hospital NHS Foundation Trust; Birmingham UK
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Fundamentals of multiplexing with digital PCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:15-23. [PMID: 27990345 PMCID: PMC5154634 DOI: 10.1016/j.bdq.2016.05.002] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 05/13/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
Abstract
Over the past decade numerous publications have demonstrated how digital PCR (dPCR) enables precise and sensitive quantification of nucleic acids in a wide range of applications in both healthcare and environmental analysis. This has occurred in parallel with the advances in partitioning fluidics that enable a reaction to be subdivided into an increasing number of partitions. As the majority of dPCR systems are based on detection in two discrete optical channels, most research to date has focused on quantification of one or two targets within a single reaction. Here we describe ‘higher order multiplexing’ that is the unique ability of dPCR to precisely measure more than two targets in the same reaction. Using examples, we describe the different types of duplex and multiplex reactions that can be achieved. We also describe essential experimental considerations to ensure accurate quantification of multiple targets.
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Verhoef TI, Hill M, Drury S, Mason S, Jenkins L, Morris S, Chitty LS. Non-invasive prenatal diagnosis (NIPD) for single gene disorders: cost analysis of NIPD and invasive testing pathways. Prenat Diagn 2016; 36:636-42. [PMID: 27107169 PMCID: PMC6680142 DOI: 10.1002/pd.4832] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 04/13/2016] [Accepted: 04/18/2016] [Indexed: 12/29/2022]
Abstract
Objective Evaluate the costs of offering non‐invasive prenatal diagnosis (NIPD) for single gene disorders compared to traditional invasive testing to inform NIPD implementation into clinical practice. Method Total costs of diagnosis using NIPD or invasive testing pathways were compared for a representative set of single gene disorders. Results For autosomal dominant conditions, where NIPD molecular techniques are straightforward, NIPD cost £314 less than invasive testing. NIPD for autosomal recessive and X‐linked conditions requires more complicated technical approaches and total costs were more than invasive testing, e.g. NIPD for spinal muscular atrophy was £1090 more than invasive testing. Impact of test uptake on costs was assessed using sickle cell disorder as an example. Anticipated high uptake of NIPD resulted in an incremental cost of NIPD over invasive testing of £48 635 per 100 pregnancies at risk of sickle cell disorder. Conclusion Total costs of NIPD are dependent upon the complexity of the testing technique required. Anticipated increased demand for testing may have economic implications for prenatal diagnostic services. Ethical issues requiring further consideration are highlighted including directing resources to NIPD when used for information only and restricting access to safe tests if it is not cost‐effective to develop NIPD for rare conditions. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's Already Known About This Topic?Non‐invasive prenatal diagnosis (NIPD) for some single gene disorders has entered clinical practice and NIPD for other conditions is in development. Studies exploring the costs and benefits of implementing NIPD for a range of single gene disorders have not been undertaken.
What Does This Study Add?For single gene disorders where technical approaches are straightforward, NIPD was considerably cheaper than invasive testing, but for conditions that need more technically challenging approaches NIPD was more expensive. The anticipated increase in test uptake following the introduction of NIPD will be a major contributing factor to the cost of a genetic service offering prenatal diagnosis for single gene disorders in clinical practice. Prospective monitoring and audit of uptake following clinical implementation is required to allow full consideration of the economic, social and ethical issues that will arise.
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Affiliation(s)
- Talitha I Verhoef
- Department of Applied Health Research, University College London, London, UK
| | - Melissa Hill
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
| | - Suzanne Drury
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Sarah Mason
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Stephen Morris
- Department of Applied Health Research, University College London, London, UK
| | - Lyn S Chitty
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Genetics and Genomic Medicine, UCL Institute of Child Health, London, UK
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