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Mazzonetto PC, Villela D, Krepischi ACV, Pierry PM, Bonaldi A, Almeida LGD, Paula MG, Bürger MC, de Oliveira AG, Fonseca GGG, Giugliani R, Riegel-Giugliani M, Bertola D, Yamamoto GL, Passos-Bueno MR, Campos GDS, Machado ACD, Mazzeu JF, Perrone E, Zechi-Ceide RM, Kokitsu-Nakata NM, Vieira TP, Steiner CE, Gil-da-Silva-Lopes VL, Vieira DKR, Boy R, de Pina-Neto JM, Scapulatempo-Neto C, Milanezi F, Rosenberg C. Low-pass whole genome sequencing as a cost-effective alternative to chromosomal microarray analysis for low- and middle-income countries. Am J Med Genet A 2024:e63802. [PMID: 38924610 DOI: 10.1002/ajmg.a.63802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Low-pass whole genome sequencing (LP-WGS) has been applied as alternative method to detect copy number variants (CNVs) in the clinical setting. Compared with chromosomal microarray analysis (CMA), the sequencing-based approach provides a similar resolution of CNV detection at a lower cost. In this study, we assessed the efficiency and reliability of LP-WGS as a more affordable alternative to CMA. A total of 1363 patients with unexplained neurodevelopmental delay/intellectual disability, autism spectrum disorders, and/or multiple congenital anomalies were enrolled. Those patients were referred from 15 nonprofit organizations and university centers located in different states in Brazil. The analysis of LP-WGS at 1x coverage (>50kb) revealed a positive testing result in 22% of the cases (304/1363), in which 219 and 85 correspond to pathogenic/likely pathogenic (P/LP) CNVs and variants of uncertain significance (VUS), respectively. The 16% (219/1363) diagnostic yield observed in our cohort is comparable to the 15%-20% reported for CMA in the literature. The use of commercial software, as demonstrated in this study, simplifies the implementation of the test in clinical settings. Particularly for countries like Brazil, where the cost of CMA presents a substantial barrier to most of the population, LP-WGS emerges as a cost-effective alternative for investigating copy number changes in cytogenetics.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | - Roberto Giugliani
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Mariluce Riegel-Giugliani
- Casa dos Raros - House of Rares, Centro de Atenção Integral e Treinamento em Doenças Raras, Porto Alegre, Brazil
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
| | - Débora Bertola
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Guilherme Lopes Yamamoto
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
- Instituto da Criança, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Gabriele da Silva Campos
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Dantas Machado
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Juliana F Mazzeu
- Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
| | - Eduardo Perrone
- Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roseli M Zechi-Ceide
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Nancy M Kokitsu-Nakata
- Department of Clinical Genetics and Molecular Biology, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Carlos Eduardo Steiner
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine - Medical Genetics and Genomic Medicine, School of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Daniela Koeller Rodrigues Vieira
- Municipal Secretary of Health of Angra dos Reis, Rio de Janeiro, Brazil
- National Institute of Women, Children and Adolescents Health Fernandes Figueira/Oswaldo Cruz Foundation (IFF/FIOCRUZ), Rio de Janeiro, Brazil
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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Mazzonetto PC, Villela D, da Costa SS, Krepischi ACV, Milanezi F, Migliavacca MP, Pierry PM, Bonaldi A, Almeida LGD, De Souza CA, Kroll JE, Paula MG, Guarischi-Sousa R, Scapulatempo-Neto C, Rosenberg C. Low-pass whole genome sequencing is a reliable and cost-effective approach for copy number variant analysis in the clinical setting. Ann Hum Genet 2024; 88:113-125. [PMID: 37807935 DOI: 10.1111/ahg.12532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Next generation sequencing technology has greatly reduced the cost and time required for sequencing a genome. An approach that is rapidly being adopted as an alternative method for CNV analysis is the low-pass whole genome sequencing (LP-WGS). Here, we evaluated the performance of LP-WGS to detect copy number variants (CNVs) in clinical cytogenetics. MATERIALS AND METHODS DNA samples with known CNVs detected by chromosomal microarray analyses (CMA) were selected for comparison and used as positive controls; our panel included 44 DNA samples (12 prenatal and 32 postnatal), comprising a total of 55 chromosome imbalances. The selected cases were chosen to provide a wide range of clinically relevant CNVs, the vast majority being associated with intellectual disability or recognizable syndromes. The chromosome imbalances ranged in size from 75 kb to 90.3 Mb, including aneuploidies and two cases of mosaicism. RESULTS All CNVs were successfully detected by LP-WGS, showing a high level of consistency and robust performance of the sequencing method. Notably, the size of chromosome imbalances detected by CMA and LP-WGS were compatible between the two different platforms, which indicates that the resolution and sensitivity of the LP-WGS approach are at least similar to those provided by CMA. DISCUSSION Our data show the potential use of LP-WGS to detect CNVs in clinical diagnosis and confirm the method as an alternative for chromosome imbalances detection. The diagnostic effectiveness and feasibility of LP-WGS, in this technical validation study, were evidenced by a clinically representative dataset of CNVs that allowed a systematic assessment of the detection power and the accuracy of the sequencing approach. Further, since the software used in this study is commercially available, the method can easily be tested and implemented in a routine diagnostic setting.
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Affiliation(s)
- Patricia C Mazzonetto
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
| | | | - Silvia Souza da Costa
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | - Ana C V Krepischi
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | - Carla Rosenberg
- The Human Genome and Stem Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil
- Diagnósticos da América S.A., DASA, São Paulo, Brazil
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3
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Pisareva E, Mihalovičová L, Pastor B, Kudriavtsev A, Mirandola A, Mazard T, Badiou S, Maus U, Ostermann L, Weinmann-Menke J, Neuberger EWI, Simon P, Thierry AR. Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA. Genome Med 2022; 14:135. [PMID: 36443816 PMCID: PMC9702877 DOI: 10.1186/s13073-022-01125-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As circulating DNA (cirDNA) is mainly detected as mononucleosome-associated circulating DNA (mono-N cirDNA) in blood, apoptosis has until now been considered as the main source of cirDNA. The mechanism of cirDNA release into the circulation, however, is still not fully understood. This work addresses that knowledge gap, working from the postulate that neutrophil extracellular traps (NET) may be a source of cirDNA, and by investigating whether NET may directly produce mono-N cirDNA. METHODS We studied (1) the in vitro kinetics of cell derived genomic high molecular weight (gHMW) DNA degradation in serum; (2) the production of extracellular DNA and NET markers such as neutrophil elastase (NE) and myeloperoxidase (MPO) by ex vivo activated neutrophils; and (3) the in vitro NET degradation in serum; for this, we exploited the synergistic analytical information provided by specifically quantifying DNA by qPCR, and used shallow WGS and capillary electrophoresis to perform fragment size analysis. We also performed an in vivo study in knockout mice, and an in vitro study of gHMW DNA degradation, to elucidate the role of NE and MPO in effecting DNA degradation and fragmentation. We then compared the NET-associated markers and fragmentation size profiles of cirDNA in plasma obtained from patients with inflammatory diseases found to be associated with NET formation and high levels of cirDNA (COVID-19, N = 28; systemic lupus erythematosus, N = 10; metastatic colorectal cancer, N = 10; and from healthy individuals, N = 114). RESULTS Our studies reveal that gHMW DNA degradation in serum results in the accumulation of mono-N DNA (81.3% of the remaining DNA following 24 h incubation in serum corresponded to mono-N DNA); "ex vivo" NET formation, as demonstrated by a concurrent 5-, 5-, and 35-fold increase of NE, MPO, and cell-free DNA (cfDNA) concentration in PMA-activated neutrophil culture supernatant, leads to the release of high molecular weight DNA that degrades down to mono-N in serum; NET mainly in the form of gHMW DNA generate mono-N cirDNA (2 and 41% of the remaining DNA after 2 h in serum corresponded to 1-10 kbp fragments and mono-N, respectively) independent of any cellular process when degraded in serum; NE and MPO may contribute synergistically to NET autocatabolism, resulting in a 25-fold decrease in total DNA concentration and a DNA fragment size profile similar to that observed from cirDNA following 8 h incubation with both NE and MPO; the cirDNA size profile of NE KO mice significantly differed from that of the WT, suggesting NE involvement in DNA degradation; and a significant increase in the levels of NE, MPO, and cirDNA was detected in plasma samples from lupus, COVID-19, and mCRC, showing a high correlation with these inflammatory diseases, while no correlation of NE and MPO with cirDNA was found in HI. CONCLUSIONS Our work describes the mechanisms by which NET and cirDNA are linked. In doing so, we demonstrate that NET are a major source of mono-N cirDNA independent of apoptosis and establish a new paradigm of the mechanisms of cirDNA release in normal and pathological conditions. We also demonstrate a link between immune response and cirDNA.
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Affiliation(s)
- Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Lucia Mihalovičová
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovakia
| | - Brice Pastor
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Andrei Kudriavtsev
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Alexia Mirandola
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Thibault Mazard
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
- Department of Medical Oncology, Montpellier Cancer Institute (ICM), Montpellier, France
| | - Stephanie Badiou
- Laboratoire de Biochimie Et Hormonologie, PhyMedExp, Université de Montpellier, INSERM, CNRS, CHU de Montpellier, Montpellier, France
| | - Ulrich Maus
- Division of Experimental Pneumology, Hannover Medical School, and German Center for Lung Research, Partner Site BREATH (Biomedical Research in Endstage and Obstructive Lung Disease), 30625, Hannover, Germany
| | - Lena Ostermann
- Division of Experimental Pneumology, Hannover Medical School, and German Center for Lung Research, Partner Site BREATH (Biomedical Research in Endstage and Obstructive Lung Disease), 30625, Hannover, Germany
| | - Julia Weinmann-Menke
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55101, Mainz, Germany
| | - Elmo W I Neuberger
- Department of Sports Medicine, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France.
- Department of Medical Oncology, Montpellier Cancer Institute (ICM), Montpellier, France.
- Montpellier Cancer Institute (ICM), Montpellier, France.
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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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Han L, Chen C, Guo F, Ye J, Peng Z, Qiu W, Wang Y, Li W, Zhang H, Liang L, Wang Y, Wang H, Ji X, Sun J, Gu X. Noninvasive prenatal diagnosis of cobalamin C (cblC) deficiency through target region sequencing of cell-free DNA in maternal plasma. Prenat Diagn 2019; 40:324-332. [PMID: 31697851 DOI: 10.1002/pd.5601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 09/26/2019] [Accepted: 10/15/2019] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to validate the feasibility of haplotype-based noninvasive prenatal diagnosis (NIPD) of cobalamin C (cblC) deficiency. METHOD This method includes three steps: First, targeted sequencing was performed on 21 families affected by cblC deficiency (including the couples and probands). Second, parental haplotypes linked with the pathogenic variant were determined using the genotypes of trios. Then, the fetal haplotypes were inferred through a parental haplotype assisted hidden Markov model (HMM). The NIPD results were confirmed by using the invasive procedures. RESULTS Twenty-one fetal genotypes were successfully inferred by NIPD including three compound heterozygotes with cblC deficiency, nine heterozygote carriers of cblC deficiency, and nine normal fetuses. The NIPD results were confirmed using the invasive procedures with 100% concordant rate. CONCLUSION This result has shown that haplotype-based NIPD of cblC deficiency has high concordant rate and indicated potential clinical utility as a pregnancy diagnosis method for high-risk carrier couples.
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Affiliation(s)
- Lianshu Han
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Chen
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Fengyu Guo
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Jun Ye
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Wenjuan Qiu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yaoshen Wang
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Huiwen Zhang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huanhuan Wang
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xing Ji
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China.,Wuhan BGI Clinical Laboratory Co, Ltd, BGI-Wuhan, BGI-Shenzhen, Wuhan, China
| | - Xuefan Gu
- Xinhua Hospital, Shanghai Institute for Pediatric Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Fernando MR, Jiang C, Krzyzanowski GD, Somer-Shely T, Ryan WL. A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time. PLoS One 2018; 13:e0208508. [PMID: 30521613 PMCID: PMC6283530 DOI: 10.1371/journal.pone.0208508] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/19/2018] [Indexed: 02/04/2023] Open
Abstract
This study was undertaken to evaluate a novel method for stabilizing and preserving the original proportion of cell-free fetal DNA (cffDNA) in maternal blood for extended periods of time without using crosslinking agents, such as formaldehyde, which compromise DNA integrity and extraction efficiency. Blood was drawn from pregnant donors into K3EDTA and Blood Exo DNA ProTeck® (ProTeck) tubes. Blood drawn into both tubes were aliquoted and stored at three different temperatures. At indicated times sample aliquots were processed for cell-free DNA (cfDNA) extraction. Plasma cfDNA and cffDNA quantified by droplet digital PCR (ddPCR) assay which amplify RASSF1A gene promoter region. ProTeck reagent is formaldehyde free and inhibits blood cell metabolism in blood samples during storage. Cell-free DNA concentration increased over time in blood plasma stored in K3EDTA tubes at 4, 22 and 30°C. Blood stored in ProTeck tubes, cfDNA concentration was stable at 4, 22 and 30°C for 21, 28 and 7 days, respectively. In K3EDTA tubes cffDNA proportion decreases steadily over time whereas in ProTeck tubes cffDNA proportion remained stable. This novel technology stabilizes cffDNA proportion in maternal blood samples at 4, 22 and 30°C for 21, 28 and 7 days, respectively.
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Affiliation(s)
- M. Rohan Fernando
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha NE, United States of America
- Department of Research and Development, CFGenome Omaha NE, United States of America
- * E-mail:
| | - Chao Jiang
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha NE, United States of America
| | - Gary D. Krzyzanowski
- Department of Obstetrics and Gynecology, University of Nebraska Medical Center, Omaha NE, United States of America
- Department of Research and Development, CFGenome Omaha NE, United States of America
| | - Tifany Somer-Shely
- Methodist Physicians Clinic Women’s Center, Elkhorn, NE, United States of America
| | - Wayne L. Ryan
- Department of Research and Development, CFGenome Omaha NE, United States of America
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7
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van Schendel RV, van El CG, Pajkrt E, Henneman L, Cornel MC. Implementing non-invasive prenatal testing for aneuploidy in a national healthcare system: global challenges and national solutions. BMC Health Serv Res 2017; 17:670. [PMID: 28927451 PMCID: PMC5605972 DOI: 10.1186/s12913-017-2618-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 09/13/2017] [Indexed: 02/04/2023] Open
Abstract
Background Since the introduction of non-invasive prenatal testing (NIPT) in 2011, mainly by commercial companies, a growing demand for NIPT from the public and healthcare professionals has been putting pressure on the healthcare systems of various countries. This study identifies the challenges of establishing a responsible implementation of NIPT for aneuploidy in prenatal healthcare, by looking at the Netherlands. Methods A mixed methods approach involving 13 stakeholder interviews, document analysis and (participatory) observations of the Dutch NIPT Consortium meetings were used. The Diffusion of Innovation Theory and a Network of Actors model were used to interpret the findings. Results Implementation of NIPT was facilitated by several factors. The set-up of a national NIPT Consortium enabled discussion and collaboration between stakeholders. Moreover, it led to the plan to offer NIPT through a nationwide research setting (TRIDENT studies), which created a learning phase for careful implementation. The Dutch legal context was perceived as a delaying factor, but eventually gave room for the parties involved to organise themselves and their practices. Conclusions This study shows that implementing advanced technologies with profound effects on prenatal care benefit from a learning phase that allows time to carefully evaluate the technical performance and women’s experiences and to enable public debate. Such a coordinated learning phase, involving all stakeholders, will stimulate the process of responsible and sustainable implementation.
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Affiliation(s)
- Rachèl V van Schendel
- Department of Clinical Genetics, Section of Community Genetics, Amsterdam Public Health research institute, VU University Medical Center, P.O. Box 7057, 1007, MB, Amsterdam, The Netherlands
| | - Carla G van El
- Department of Clinical Genetics, Section of Community Genetics, Amsterdam Public Health research institute, VU University Medical Center, P.O. Box 7057, 1007, MB, Amsterdam, The Netherlands
| | - Eva Pajkrt
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Academic Medical Centre, Amsterdam, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, Section of Community Genetics, Amsterdam Public Health research institute, VU University Medical Center, P.O. Box 7057, 1007, MB, Amsterdam, The Netherlands.
| | - Martina C Cornel
- Department of Clinical Genetics, Section of Community Genetics, Amsterdam Public Health research institute, VU University Medical Center, P.O. Box 7057, 1007, MB, Amsterdam, The Netherlands
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Smith SK, Sousa MS, Essink-Bot ML, Halliday J, Peate M, Fransen M. Socioeconomic Differences in Informed Decisions About Down Syndrome Screening: A Systematic Review and Research Agenda. JOURNAL OF HEALTH COMMUNICATION 2016; 21:868-907. [PMID: 27410478 DOI: 10.1080/10810730.2016.1177145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Supporting pregnant women to make informed choices about Down syndrome screening is widely endorsed. We reviewed the literature on: (a) the association between socioeconomic position and informed choices and decision-making about Down syndrome screening, and (b) the possible mediating variables (e.g., health literacy, numeracy skills, behavioral and communication variables) that might explain the relationship. EMBASE, MEDLINE, PubMed, CINAHL, and PsycINFO were searched from January 1999 to September 2014. The methodological quality of studies was determined by predefined criteria regarding the research aims, study design, study population and setting, measurement tools, and statistical analysis. A total of 33 studies met the inclusion criteria. Women from lower socioeconomic groups experience greater difficulties making informed choices about Down syndrome screening compared to women from higher socioeconomic groups. Most studies focus on individual dimensions of informed decision-making rather than assessing elements in conjunction with one another. Few studies have explored why there are socioeconomic differences in women's ability to make informed screening decisions. Future work is needed to identify mediating variables in this pathway. Systematic evidence-based intervention development to improve communication, understanding, and decision-making about Down syndrome screening is needed to ensure that women have an equal opportunity to make an informed choice about screening regardless of their socioeconomic position.
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Affiliation(s)
- Sian K Smith
- a Psychosocial Research Group, Prince of Wales Clinical School, Faculty of Medicine , University of New South Wales , Sydney , New South Wales , Australia
| | - Mariana S Sousa
- b Centre for Applied Nursing Research, Ingham Institute for Applied Medical Research, School of Nursing and Midwifery , University of Western Sydney , Penrith , New South Wales , Australia
- c Prince of Wales Clinical School , University of New South Wales , Sydney , New South Wales , Australia
| | - Marie-Louise Essink-Bot
- d Department of Public Health, Academic Medical Centre , University of Amsterdam , Amsterdam , The Netherlands
| | - Jane Halliday
- e Murdoch Children's Research Institute , Royal Children's Hospital , Melbourne , Victoria , Australia
- f Department of Paediatrics , University of Melbourne , Parkville , Victoria , Australia
| | - Michelle Peate
- g Department of Obstetrics and Gynaecology, Royal Women's Hospital , University of Melbourne , Parkville , Victoria , Australia
| | - Mirjam Fransen
- d Department of Public Health, Academic Medical Centre , University of Amsterdam , Amsterdam , The Netherlands
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Bolnick AD, Fritz R, Jain C, Kadam L, Bolnick JM, Kilburn BA, Singh M, Diamond MP, Drewlo S, Armant DR. Trophoblast Retrieval and Isolation From the Cervix for Noninvasive, First Trimester, Fetal Gender Determination in a Carrier of Congenital Adrenal Hyperplasia. Reprod Sci 2016; 23:717-22. [PMID: 26919977 PMCID: PMC5933151 DOI: 10.1177/1933719116632922] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Congenital adrenal hyperplasia (CAH) is an autosomal recessive defect in cortisol biosynthesis that elevates fetal androgen levels to cause genital ambiguity and external genital masculinization in newborn females. Introducing dexamethasone in utero by 7 weeks gestation precludes virilization of affected females. However, identification of a male fetus prior to week 7 could avert the necessity of steroid treatment in half of pregnancies at risk of CAH. We recently introduced trophoblast retrieval and isolation from the cervix (TRIC), an approach that noninvasively isolate homogeneous trophoblast cells from pregnant women as early as 5 weeks gestation, using a Papanicolaou test. Here, we have used TRIC to correctly identify male fetal DNA when both parents were carriers of the mutation that produces CAH and previously produced an affected child. Trophoblast cells (1400) obtained by TRIC were assessed using immunocytochemistry with an antibody against the trophoblast-specific β subunit of human chorionic gonadotropin, which labeled 100% (17 of 17) of isolated cells, while none of the excluded maternal cervical cells were labeled. The isolated cells were examined by fluorescent in situ hybridization for chromosomes 18, X, and Y at a clinical cytogenetics laboratory, demonstrating 100% (18 of 18) of cells to be diploid 18/XY. Aliquots of DNA obtained from the isolated cells assayed for SRY and RNASEH genes by TaqMan assays confirmed a male fetus. This case study demonstrates the utility of TRIC to accurately identify fetal gender as a means of reducing the need for prophylactic administration of exogenous steroids in pregnancies at risk of CAH.
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Affiliation(s)
- Alan D Bolnick
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Rani Fritz
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA Department of Physiology, Wayne State University, Detroit, MI, USA
| | - Chandni Jain
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA Department of Physiology, Wayne State University, Detroit, MI, USA
| | - Leena Kadam
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA Department of Physiology, Wayne State University, Detroit, MI, USA
| | - Jay M Bolnick
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Brian A Kilburn
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Manvinder Singh
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - Michael P Diamond
- Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, GA, USA
| | - Sascha Drewlo
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA
| | - D Randall Armant
- Department of Obstetrics & Gynecology, Wayne State University, Detroit, MI, USA Department of Anatomy & Cell Biology, Wayne State University School of Medicine, Detroit, MI, USA Program in Reproductive and Adult Endocrinology, National Institute for Child Health and Human Development, National Institutes of Health, United States Department of Health and Human Services, Bethesda, MD, USA
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Goulart VV, Liao AW, Carvalho MHBD, Brizot MDL, Francisco RPV, Zugaib M. Intrauterine death in singleton pregnancies with trisomy 21, 18, 13 and monosomy X. Rev Assoc Med Bras (1992) 2016; 62:162-70. [DOI: 10.1590/1806-9282.62.02.162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 11/22/2022] Open
Abstract
Summary A retrospective study from November 2004 to May 2012, conducted at the Obstetric Clinic of Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo (HC-FMUSP), which included 92 singleton pregnancies with prenatal diagnosis of trisomy of chromosome 21 (T21), 18, 13 (T13/18) and monosomy X (45X), with diagnosis performed until the 26th week of pregnancy. The aim of the study was to describe the frequency and to investigate predictors of spontaneous fetal death (FD). Diagnosis (T21, n=36; T13/18, n=25; 45X, n=31) was made at a mean gestational age of 18.3±3.7 weeks, through chorionic villus biopsy (n=22,24%), amniocentesis (n=66, 72%) and cordocentesis (n=4, 4%). Major malformations were present in 45 (49%); with hydrops in 32 (35%) fetuses, more frequently in 45X [n=24/31, 77% vs. T21 (n=6/36, 17%) and T13/18 (n=2/25, 8%), p<0.001]. Specialized fetal echocardiography was performed in 60% (55/92). Of these, 60% (33/55) showed changes in heart morphology and/or function. Fetuses with T13/18 had a higher incidence of cardiac anomalies [60 vs. 25% (T21) and 29% (45X), p= 0.01]. FD occurred in 55 (60%) gestations, being more frequent in 45X [n=26/31, 84% vs. T21 (n=13/36, 36%) and T13/18 (n=16/25, 64%), p<0.01]. Stepwise analysis showed a correlation between hydrops and death in fetuses with T21 (LR= 4.29; 95CI=1.9-8.0, p<0.0001). In fetuses with 45X, the presence of echocardiographic abnormalities was associated with lower risk of FD (LR= 0.56; 95CI=0.27- 0.85, p=0.005). No predictive factors were identified in the T13/18 group. Intra- uterine lethality of aneuploid fetuses is high. Occurrence of hydrops increases risk of FD in pregnancies with T21. In pregnancies with 45X, the occurrence of echocardiographic changes reduces this risk.
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Prenatal Evaluation of MicroRNA Expressions in Pregnancies with Down Syndrome. BIOMED RESEARCH INTERNATIONAL 2016; 2016:5312674. [PMID: 27110565 PMCID: PMC4823505 DOI: 10.1155/2016/5312674] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/24/2015] [Accepted: 02/07/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND Currently, the data available on the utility of miRNAs in noninvasive prenatal testing is insufficient in the literature. We evaluated the expression levels of 14 miRNAs located on chromosome 21 in maternal plasma and their utility in noninvasive prenatal testing of Down Syndrome. METHOD A total of 56 patients underwent invasive prenatal testing; 23 cases were carrying Down Syndrome affected fetuses, and 33 control cases carrying unaffected, normal karyotype fetuses were included for comparison. Indications for invasive prenatal testing were advanced maternal age, increased risk of Down Syndrome in screening tests, and abnormal finding in the sonographic examination. In both the study and control groups, all the pregnant women were at 17th and 18th week of gestation. miRNA expression levels were measured using real-time RT-PCR. RESULTS Significantly increased maternal plasma levels of miR-3156 and miR-99a were found in the women carrying a fetus with Down Syndrome. CONCLUSION Our results provide a basis for multicenter studies with larger sample groups and microRNA profiles, particularly with the microRNAs which were found to be variably expressed in our study. Through this clinical research, the utility of microRNAs in noninvasive prenatal testing can be better explored in future studies.
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Alberti A, Salomon LJ, Le Lorc'h M, Couloux A, Bussières L, Goupil S, Malan V, Pelletier E, Hyon C, Vialard F, Rozenberg P, Bouhanna P, Oury JF, Schmitz T, Romana S, Weissenbach J, Vekemans M, Ville Y. Non-invasive prenatal testing for trisomy 21 based on analysis of cell-free fetal DNA circulating in the maternal plasma. Prenat Diagn 2016; 35:471-6. [PMID: 25643828 DOI: 10.1002/pd.4561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 01/04/2015] [Accepted: 01/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVE By-the-book implementation of non-invasive prenatal test and clinical validation for trisomy 21. STUDY DESIGN Publicly funded prospective study of 225 cases. Women at risk for trisomy 21 > 1/250 based on combined ultrasound and serum markers during first or second trimester were eligible following an informed consent. The technique was established from the available literature and performed on 10 mL of venous blood collected prior to chorionic villus sampling or amniocentesis. Investigators were blinded to the fetal karyotype. Results were expressed in Z-scores of the percentage of each chromosome. RESULTS Among 976 eligible cases, 225 were processed: 8 were used for pretesting phase and 23 to build a reference set. One hundred thirty six euploid cases and 47 with trisomy 21 were then run randomly. Eleven cases yielded no result (4.8%). Z-scores were above 3 (7.58+/-2.41) for chromosome 21 in all 47 trisomies and in none of the euploid cases (0.11+/-1.0). Z-scores were within normal range for the other chromosomes in both groups. Using a cut-off of 3, sensitivity and specificity were of 100% 95% CI [94.1, 100] and 100% 95% CI [98, 100], respectively. CONCLUSION Non-invasive prenatal test for trisomy 21 is a robust strategy that can be translated from seminal publications. Publicly funded studies should refine its indications and cost-effectiveness in prenatal screening and diagnosis. © 2015 John Wiley & Sons, Ltd.
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13
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van Schendel RV, Dondorp WJ, Timmermans DRM, van Hugte EJH, de Boer A, Pajkrt E, Lachmeijer AMA, Henneman L. NIPT-based screening for Down syndrome and beyond: what do pregnant women think? Prenat Diagn 2015; 35:598-604. [PMID: 25693726 DOI: 10.1002/pd.4579] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/10/2015] [Accepted: 02/12/2015] [Indexed: 01/23/2023]
Abstract
OBJECTIVE The aim of the study is to study pregnant women's views on noninvasive prenatal testing (NIPT) for Down syndrome and the potential to test for a broader range of conditions. METHODS An online questionnaire available on the Dutch pregnancy fair website was completed by 381 pregnant women. RESULTS Of the women, 51% expressed interest in having NIPT, including 33% of women who had declined first-trimester screening. The majority (73%) thought that the uptake of screening would increase with NIPT. Most women agreed that testing for life-threatening (89%), severe physical (79%), or severe mental (76%) disorders should be offered. A minority (29%) felt that prenatal screening should also be offered for late-onset disorders. Most (41%) preferred to have a free choice from a list of disorders, 31% preferred a 'closed offer', and 26% preferred choosing between packages of disorders. Although most women (76%) thought that screening for a broad range of conditions would avoid much suffering, 39% feared that it would confront couples with choices, the implications of which would be difficult to grasp. CONCLUSION The results suggest that the uptake of screening will increase with NIPT. If NIPT will be offered for a broad range of conditions, it is crucial to find a way that facilitates rather than undermines well-informed decision-making.
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Affiliation(s)
- Rachèl V van Schendel
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Wybo J Dondorp
- Department of Health, Ethics and Society, Faculty of Health, Medicine and Life Sciences, Research Institutes GROW and CAPHRI, Maastricht University, Maastricht, the Netherlands
| | - Danielle R M Timmermans
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands.,Department of Public and Occupational Health, VU University Medical Center, Amsterdam, the Netherlands
| | - Eline J H van Hugte
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Anne de Boer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Eva Pajkrt
- Department of Obstetrics and Gynecology, Fetal Medicine Unit, Academic Medical Center, Amsterdam, the Netherlands
| | - Augusta M A Lachmeijer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, the Netherlands
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15
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Abstract
Cell-free fetal DNA present in maternal circulation has revolutionized non-invasive prenatal diagnosis of genetic diseases. In preeclampsia, the quantity of fetal DNA in maternal plasma has been studied and found to be higher in comparison to healthy pregnant women. Whether the quantity of fetal DNA can be used as a reliable predictive biomarker of preeclampsia is currently uncertain. This is a systematic review on studies quantifying fetal DNA in preeclamptic pregnancies. Using a PubMed search 22 studies were identified. In all of them, elevated levels of fetal DNA in maternal plasma in preeclampsia were found. In some of the studies, the higher concentration of fetal DNA was observed before the onset of clinical symptoms. This shows that fetal DNA levels might have a potential informative value as an early diagnostic biomarker of preeclampsia. However, in most of the studies important data are missing and there is an enormous variability in the reported results between the studies. From the available data it is currently not possible to perform a meta-analysis due to the variation between studies. If once fetal DNA should be used as a marker for determining preeclampsia at early stage, it is necessary to reduce these variations via standardized protocols for the quantification of cell-free fetal DNA as well as its reporting in the publications.
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Affiliation(s)
- Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University , Bratislava , Slovakia
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16
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Non-Invasive Prenatal Diagnosis in the Management of Preimplantation Genetic Diagnosis Pregnancies. J Clin Med 2014; 3:913-22. [PMID: 26237485 PMCID: PMC4449636 DOI: 10.3390/jcm3030913] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/27/2014] [Accepted: 06/25/2014] [Indexed: 11/17/2022] Open
Abstract
Prenatal diagnosis (PD) is recommended in pregnancies after a Preimplantation Genetic Diagnosis (PGD). However, conventional PD entails a risk of fetal loss which makes PGD patients reluctant to undergo obstetric invasive procedures. The presence of circulating fetal DNA in maternal blood allows performing a non-invasive prenatal diagnosis (NIPD) without risk for the pregnancy outcome. This work shows the introduction of NIPD for confirmation of PGD results in eight pregnancies. In those pregnancies referred to PGD for an X-linked disorder (six out of eight), fetal sex determination in maternal blood was performed to confirm fetal sex. One pregnancy referred to PGD for Marfan syndrome and one referred for Huntington disease (HD) were also analyzed. In seven out of eight cases, PGD results were confirmed by NIPD in maternal blood. No results were obtained in the HD pregnancy. NIPD in PGD pregnancies can be a reliable alternative for couples that after a long process feel reluctant to undergo PD due to the risk of pregnancy loss.
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17
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Pregnancy Loss Following Amniocentesis or CVS Sampling-Time for a Reassessment of Risk. J Clin Med 2014; 3:741-6. [PMID: 26237475 PMCID: PMC4449654 DOI: 10.3390/jcm3030741] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/24/2014] [Accepted: 05/29/2014] [Indexed: 11/17/2022] Open
Abstract
Risk of procedure-related pregnancy loss is currently widely quoted in the UK as 1% for amniocentesis and 1.5% for chorionic villus sampling. Published data suggest that these risk figures are out of date and inaccurate, and that new guidelines are required for pre-test counseling. It is our opinion that accurate and evidence-based information concerning miscarriage risk is vital when counseling women, as exaggeration of this risk may deter women from testing, or cause unjustified remorse if a miscarriage ensues. It is also essential that health-care economists are aware of the up-to-date evidence on “procedure-related risk” when applying risk-benefit analysis to assess new technology for non-invasive screening.
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18
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Bolnick JM, Kilburn BA, Bajpayee S, Reddy N, Jeelani R, Crone B, Simmerman N, Singh M, Diamond MP, Armant DR. Trophoblast retrieval and isolation from the cervix (TRIC) for noninvasive prenatal screening at 5 to 20 weeks of gestation. Fertil Steril 2014; 102:135-142.e6. [PMID: 24825422 PMCID: PMC10411519 DOI: 10.1016/j.fertnstert.2014.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/06/2014] [Accepted: 04/07/2014] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To use trophoblast cells accumulating in the endocervical canal at the beginning of pregnancy for noninvasive prenatal testing. DESIGN Prospective, double-blinded test for fetal gender. SETTING Academic medical center. PATIENT(S) Fifty-six women with singleton pregnancies at gestational age 5-20 weeks. INTERVENTION(S) Isolation of fetal cells from resident maternal cells in endocervical specimens using anti-human leukocyte antigen G coupled to magnetic nanoparticles; cell phenotyping immunofluorescently with a panel of trophoblast subtype-specific proteins; DNA integrity assessment with terminal dUTP nick-end labeling (TUNEL); and polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) to detect sex chromosomes in individual cells. MAIN OUTCOME MEASURE(S) Trophoblast phenotype, TUNEL index, and percentage male cells. RESULT(S) The women were given a routine Papanicolaou test; fetal genders were verified from medical records. Recovery after immunomagnetic isolation averaged 746±59 cells across gestational age, with 99% expressing chorionic gonadotropin, whereas the depleted cell fraction expressed none. The isolated cells had an extravillous trophoblast phenotype and intact nuclear DNA (>95%). Fetal gender was determined in 20 specimens without error by PCR. The FISH analysis of isolated cells from male specimens validated their fetal origin. CONCLUSION(S) Noninvasive prenatal testing is feasible beginning at a gestational age of 5 weeks.
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Affiliation(s)
- Jay M Bolnick
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Brian A Kilburn
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Swati Bajpayee
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Nitya Reddy
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Roohi Jeelani
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Barbara Crone
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Neil Simmerman
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Manivinder Singh
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan
| | - Michael P Diamond
- Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, Georgia
| | - D Randall Armant
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan; Anatomy and Cell Biology, C.S. Mott Center for Human Growth and Development, Wayne State University, Detroit, Michigan; Program in Reproductive and Adult Endocrinology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
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Attitudes of pregnant women and male partners towards non-invasive prenatal testing and widening the scope of prenatal screening. Eur J Hum Genet 2014; 22:1345-50. [PMID: 24642832 DOI: 10.1038/ejhg.2014.32] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/31/2014] [Accepted: 01/31/2014] [Indexed: 11/08/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) and its potential to test for multiple disorders has received much attention. This study explores attitudes of women and men towards NIPT, and their views on widening the scope of prenatal testing in a country with a low uptake of prenatal screening (The Netherlands). Five focus groups with low-risk pregnant women (n=28), three focus groups with men (n=19) and 13 interviews with high- and low-risk pregnant women were conducted. Participants felt that current prenatal screening has great disadvantages such as uncertain results and risk of miscarriage from follow-up diagnostics. Characteristics of NIPT (accurate, safe and early testing) could therefore diminish these disadvantages of prenatal screening and help lower the barrier for participation. This suggests that NIPT might allow couples to decide about prenatal testing based mostly on their will to test or not, rather than largely based on fear of miscarriage risk or the uncertainty of results. The lower barrier for participation was also seen as a downside that could lead to uncritical use or pressure to test. Widening the scope of prenatal testing was seen as beneficial for severe disorders, although it was perceived difficult to determine where to draw the line. Participants argued that there should be a limit to the scope of NIPT, avoiding testing for minor abnormalities. The findings suggest that NIPT could enable more meaningful decision-making for prenatal screening. However, to ensure voluntary participation, especially when testing for multiple disorders, safeguards on the basis of informed decision-making will be of utmost importance.
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de Haas M, Finning K, Massey E, Roberts DJ. Anti-D prophylaxis: past, present and future. Transfus Med 2014; 24:1-7. [DOI: 10.1111/tme.12099] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- M. de Haas
- Department of Immunohaematology, Division of Diagnostic Services; Sanquin; Amsterdam the Netherlands
| | - K. Finning
- National Health Service Blood and Transplant; Bristol UK
| | - E. Massey
- National Health Service Blood and Transplant; Bristol UK
| | - D. J. Roberts
- National Health Service Blood and Transplant; Oxford UK
- Radcliffe Department of Medicine, John Radcliffe Hospital; University of Oxford; Oxford UK
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Ogilvie CM, Akolekar R. Procedure-related pregnancy loss following invasive prenatal sampling: time for a new approach to risk assessment and counseling. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/eog.12.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Abstract
Cell-free fetal DNA (cffDNA) is a highly accurate screening test for major aneuploidies. Despite high detection rates and low false-positive rates compared to current screening methods, cffDNA testing is approved for use in only the high-risk population and is expensive for low-risk women because of a lack of insurance coverage. As the technology improves and research demonstrates the efficacy of cffDNA testing in the general population, insurance coverage of this test likely will be extended to all women. At that time, cffDNA testing in most cases will replace current screening methods. Furthermore, cffDNA testing may become a routine diagnostic test, effectively rendering most invasive diagnostic procedures obsolete.
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Additive effect of factors related to assisted conception on the reduction of maternal serum pregnancy-associated plasma protein A concentrations and the increased false-positive rates in first-trimester Down syndrome screening. Fertil Steril 2013; 100:1314-20. [DOI: 10.1016/j.fertnstert.2013.06.045] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/18/2013] [Accepted: 06/23/2013] [Indexed: 11/20/2022]
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24
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Fehrs-Battey A. Opportunities and Challenges Offered by Cell-Free Fetal DNA Testing and Non-Invasive Prenatal Testing. Lab Med 2013. [DOI: 10.1309/lm7un2a4saopvbls] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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25
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Dolled-Filhart MP, Lordemann A, Dahl W, Haraksingh RR, Ou-Yang CW, Lin JCH. Personalizing rare disease research: how genomics is revolutionizing the diagnosis and treatment of rare disease. Per Med 2012; 9:805-819. [DOI: 10.2217/pme.12.97] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A decade after the complete sequencing of the human genome, combined with recent advances in throughput and sequencing costs, the genetics of rare diseases has entered a new era. There has now been an explosion in the identification and mapping of rare diseases, with over 10,000 exomes having been sequenced to date. This article surveys the progress and development of technologies to understand rare disease; it provides a historical overview of traditional techniques such as karyotyping and homozygosity mapping, reviews current methods of whole-exome and -genome sequencing, and provides a future perspective on upcoming developments such as targeted drugs and gene therapy. This article will discuss the implications of these methods for rare disease research, along with a discussion of the success stories that provide great hope and optimism for patients and scientists alike.
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Affiliation(s)
| | - Amanda Lordemann
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - William Dahl
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Rajini Rani Haraksingh
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Chih-Wen Ou-Yang
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Jimmy Cheng-Ho Lin
- Rare Genomics Institute, 4100 Forest Park Avenue, Suite 204, St Louis, MO 63108, USA
- Washington University School of Medicine in St Louis, Genome Technology Access Center (GTAC), Genomics & Pathology Services (GPS), Campus Box 8118, 660 South Euclid Avenue, St Louis, MO 63110, USA
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Getting to know the fetal genome non-invasively: now a reality. Protein Cell 2012; 3:723-5. [PMID: 22941433 DOI: 10.1007/s13238-012-2810-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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