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Verebi C, Gravrand V, Pacault M, Audrezet MP, Couque N, Vincent MC, Leturcq F, Tsatsaris V, Bienvenu T, Nectoux J. [Towards a generalization of non-invasive prenatal diagnosis of single-gene disorders? Assesment and outlook]. GYNECOLOGIE, OBSTETRIQUE, FERTILITE & SENOLOGIE 2023; 51:463-470. [PMID: 37517661 DOI: 10.1016/j.gofs.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/06/2023] [Accepted: 07/19/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES The screening of fetal aneuploidies and non-invasive prenatal diagnosis of monogenic diseases (NIPD-MD) both rely on the study of free fetal DNA in maternal circulation, but their respective rise was unequal. Development of NIPD-MD has taken longer as it represents a less attractive commercial dynamic for industry, but also because it usually involves the development of tailored tests specific to each pathogenic variant. METHODS We have carried out a review of the literature on the various indications and technologies involved in the use of NIPD-MM. We present its current implementation and its development in France. RESULTS To date, NIPD-MD has been routinely offered in France for several years by the laboratories of the French NIPD-MD network but remains mostly limited to the exclusion of paternal or de novo variants, the exclusion DPNI-MD. Indeed, it is still difficult to study the transmission of maternal variants from circulating free DNA analysis, due to its biological complexity: coexistence and predominance of similar DNA sequences of maternal origin. Different strategies, either direct or indirect, are being evaluated to establish fetal status regardless of the parental origin of the disease or its transmission mode. The emergence of commercial screening solutions for monogenic diseases complements the arsenal of prenatal exploration tools for these diseases. CONCLUSION The multitude of existing technologies and protocols may complicate the information provided during antenatal consultations, but mastery of know-how and knowledge of ethical issues of NIPD-MD will ensure optimal service and better management of pregnancies at risk of transmitting monogenic disease.
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Affiliation(s)
- Camille Verebi
- Service de médecine génomique des maladies de système et d'organe, Fédération de génétique et de médecine génomique, AP-HP centre, université Paris Cité, hôpital Cochin, 27, rue du Faubourg Saint-Jacques, 75014 Paris, France; Université de Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), Inserm UMR1266, « Genetic vulnerability to addictive and psychiatric disorders » team, Paris, France
| | - Victor Gravrand
- Service de médecine génomique des maladies de système et d'organe, Fédération de génétique et de médecine génomique, AP-HP centre, université Paris Cité, hôpital Cochin, 27, rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Mathilde Pacault
- Laboratoire de génétique moléculaire et d'histocompatibilité, centre hospitalier régional universitaire, Brest, France
| | - Marie-Pierre Audrezet
- Laboratoire de génétique moléculaire et d'histocompatibilité, centre hospitalier régional universitaire, Brest, France
| | - Nathalie Couque
- Service de génétique, AP-HP, hôpital Robert-Debré, 75019 Paris, France
| | - Marie-Claire Vincent
- Génétique moléculaire et cytogénomique, centre hospitalier universitaire de Montpellier, 34000 Montpellier, France
| | - France Leturcq
- Service de médecine génomique des maladies de système et d'organe, Fédération de génétique et de médecine génomique, AP-HP centre, université Paris Cité, hôpital Cochin, 27, rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Vassilis Tsatsaris
- Gynécologie-obstétrique, Maternité Port-Royal, AP-HP centre, université Paris Cité, hôpital Cochin, 75014 Paris, France
| | - Thierry Bienvenu
- Service de médecine génomique des maladies de système et d'organe, Fédération de génétique et de médecine génomique, AP-HP centre, université Paris Cité, hôpital Cochin, 27, rue du Faubourg Saint-Jacques, 75014 Paris, France; Université de Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), Inserm UMR1266, « Genetic vulnerability to addictive and psychiatric disorders » team, Paris, France
| | - Juliette Nectoux
- Service de médecine génomique des maladies de système et d'organe, Fédération de génétique et de médecine génomique, AP-HP centre, université Paris Cité, hôpital Cochin, 27, rue du Faubourg Saint-Jacques, 75014 Paris, France.
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Wang J, Wang W, Zhou W, Zhou Y, Zhou L, Wang X, Yu B, Zhang B. Preliminary study of noninvasive prenatal screening for 22q11.2 deletion/duplication syndrome using multiplex dPCR assay. Orphanet J Rare Dis 2023; 18:278. [PMID: 37684689 PMCID: PMC10486099 DOI: 10.1186/s13023-023-02903-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
OBJECTIVE This study aimed to establish a cell-free fetal DNA (cffDNA) assay using multiplex digital PCR (dPCR) for identifying fetuses at increased risk of 22q11.2 deletion/duplication syndrome. METHODS Six detection sites and their corresponding probes were designed for the 22q11.2 recurrent region. A dPCR assay for the noninvasive screening of 22q11.2 deletion/duplication syndrome was established. A total of 130 plasma samples from pregnant women (including 15 samples with fetal 22q11.2 deletion/duplication syndrome) were blindly tested for evaluating the sensitivity and specificity of the established assay. RESULTS DNA with different sizes of 22q11.2 deletion/duplication was detected via dPCR, indicating that the designed probes and detection sites were reasonable and effective. In the retrospective clinical samples, 11 out of 15 samples of pregnant women with 22q11.2 deletion/duplication were detected during the cffDNA assay, and accurate regional localization was achieved. Among the 115 normal samples, 111 were confirmed to be normal. Receiver operating characteristic curves were used for assessing the cut-off values and AUC for these samples. The sensitivity, specificity, and positive as well as negative predictive values were 73.3%, 96.5%, 73.3%, and 96.5%, respectively. CONCLUSION The cffDNA assay based on dPCR technology for the noninvasive detection of 22q11.2 recurrent copy number variants in fetuses detected most affected cases, including smaller but relatively common nested deletions, with a low false-positive rate. It is a potential, efficient and simple method for the noninvasive screening of 22q11.2 deletion/duplication syndrome.
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Affiliation(s)
- Jing Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wei Wang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Wenbo Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Yan Zhou
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Linna Zhou
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China
| | - Xinyue Wang
- Xingzhi Biotechnology Co., LTD, Suzhou, 215000, Jiangsu Province, China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital, Changzhou, 213003, Jiangsu Province, China.
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3
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Shaw J, Scotchman E, Paternoster B, Ramos M, Nesbitt S, Sheppard S, Snowsill T, Chitty LS, Chandler N. Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches. Prenat Diagn 2023; 43:477-488. [PMID: 36760169 DOI: 10.1002/pd.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches. METHODS Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses. RESULTS The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus. CONCLUSIONS ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.
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Affiliation(s)
- Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Maureen Ramos
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sarah Nesbitt
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sophie Sheppard
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | | | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
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Tan Y, Jian H, Zhang R, Wang J, Zhou C, Xiao Y, Liang W, Wang L. Applying amplification refractory mutation system technique to detecting cell-free fetal DNA for single-gene disorders purpose. Front Genet 2023; 14:1071406. [PMID: 37113995 PMCID: PMC10128035 DOI: 10.3389/fgene.2023.1071406] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Non-invasive prenatal diagnosis for single-gene disorders (NIPD) is still in development and deserves further study. The advent of next-generation sequencing technology significantly improved the detection of multiple mutations for non-invasive prenatal diagnosis for single-gene disorder purposes. However, bespoke amplicon-based NGS assays are costly. In this study, we developed a new strategy for non-invasive prenatal screening for single-gene disorders based on a capillary electrophoresis (CE) platform using an amplification refractory mutation system (ARMS)-PCR technique. Allele-specific primers for several disease-correlated mutations were designed, and subsequently, sensitivity and specificity assays were conducted. Assays on simulated two-person DNA mixtures showed that three primers targeting the mutant allele could detect minor DNA components in 1:500 mixtures. All primers showed positive results at 0.01 ng of the template DNA. Cell-free fetal DNA was extracted from a pregnant woman's peripheral blood for the detection of paternally inherited mutations. Our results showed that one primer successfully amplified the mutant allele of fetal DNA in maternal plasma, which was confirmed by genotyping the genomic DNA extracted from amniotic fluid. This study suggested that the ARMS-PCR technique, a fast and cost-effective method, might be a promising method used to target de novo or paternally inherited pathogenic mutations in maternal plasma.
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Affiliation(s)
- Yu Tan
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Hui Jian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- Department of Laboratory Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Cong Zhou
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yuanyuan Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
| | - Li Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
- *Correspondence: Weibo Liang, ; Li Wang,
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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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Shekhawat DS, Sharma C, Singh K, Singh P, Bhardwaj A, Patwa P. Critical appraisal of droplet digital polymerase chain reaction application for noninvasive prenatal testing. Congenit Anom (Kyoto) 2022; 62:188-197. [PMID: 35662261 DOI: 10.1111/cga.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022]
Abstract
Maternal-fetal medicine (FM) is currently a highly demanding branch and is gaining importance as increasing number of genetic disorders rise in incidence. Prenatal testing helps to detect such abnormalities that could affect the health status of the developing fetus like birth defects or genetic disorders. Considering the rising trend of genetic disorders, there is a need for a highly sensitive way of noninvasive prenatal testing (NIPT) that may reduce the incidence of unnecessary invasive procedures and iatrogenic fetal loss. The concept of NIPT for screening of genetic disorders is continuously evolving over the last two decades and multiple techniques have come up to utilize this in the field of FM. The crucial factor which decides the accuracy of NIPS is cell free fetal DNA (cffDNA) that is present in extremely low fraction (10%-15%) in the maternal plasma. Among the available methods, the next generation sequencing (NGS) is considered as the gold standard. However, the higher cost diminishes its utility in low-resource settings. Droplet digital Polymerase chain reaction (ddPCR), a type of digital PCR is a novel technique that is frugal, equally sensitive, less labor intensive, less time-consuming and plain algorithm dependent method for detecting cffDNA fraction. Considering these impressive attributes of ddPCR, we decided to critically review the existing literature on ddPCR for NIPT whilst highlighting the clinical utility, challenges and its advantages over NGS.
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Affiliation(s)
| | - Charu Sharma
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | | | - Pratibha Singh
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | - Abhishek Bhardwaj
- Department of Dermatology, Venereology and Leprology, AIIMS, Jodhpur, India
| | - Payal Patwa
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
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7
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Li YQ, Tan GJ, Zhou YQ. Digital PCR and its applications in noninvasive prenatal testing. Brief Funct Genomics 2022; 21:376-386. [PMID: 35923115 DOI: 10.1093/bfgp/elac024] [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: 02/14/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 11/14/2022] Open
Abstract
In the past decade, digital PCR (dPCR), as a new nucleic acid absolute quantification technology, has been widely used in clinical research. dPCR does not rely on the standard curve and has a higher tolerance to inhibitors. Therefore, it is more accurate than quantitative real-time PCR (qPCR) for the absolute quantification of target sequences. In this article, we aim to review the application of dPCR in noninvasive prenatal testing (NIPT). We focused on the progress of dPCR in screening and identifying fetal chromosome aneuploidies and monogenic mutations. We introduced some common strategies for dPCR in NIPT and analyzed the advantages and disadvantages of different methods. In addition, we compared dPCR with qPCR and next-generation sequencing, respectively, and described their superiority and shortcomings in clinical applications. Finally, we envisaged what the future of dPCR might be in NIPT. Although dPCR can provide reproducible results with improved accuracy due to the digital detection system, it is essential to combine the merits of dPCR and other molecular techniques to achieve more effective and accurate prenatal diagnostic strategies.
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Affiliation(s)
- Yue-Qi Li
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Gong-Jun Tan
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
| | - Yu-Qiu Zhou
- Clinical Laboratory & Zhuhai Institute of Medical Genetics, Zhuhai Centre for Maternity and Child Healthcare & Zhuhai Women and Children's Hospital, Zhuhai City, Guangdong Province, China
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8
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Pacault M, Verebi C, Lopez M, Vaucouleur N, Orhant L, Deburgrave N, Leturcq F, Vidaud D, Girodon E, Bienvenu T, Nectoux J. Non-invasive prenatal diagnosis of single gene disorders by paternal mutation exclusion: 3 years of clinical experience. BJOG 2022; 129:1879-1886. [PMID: 35486001 DOI: 10.1111/1471-0528.17201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 12/24/2021] [Accepted: 01/22/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Cell-free fetal DNA (cffDNA) analysis is performed routinely for aneuploidy screening, RhD genotyping or sex determination. Although applications to single gene disorders (SGD) are being rapidly developed worldwide, only a few laboratories offer cffDNA testing routinely as a diagnosis service for this indication. In a previous report, we described a standardised protocol for non-invasive exclusion of paternal variant in SGD. Three years later, we now report our clinical experience with the protocol. DESIGN Descriptive study. SETTING Multi-centre French. POPULATION Indications for referral included pregnancies at risk of 25% or 50% of paternally inherited SGD, and pregnancies associated with an increased risk of SGD due to a de novo variant, either from strongly suggestive ultrasound findings or from a possible parental germinal mosaicism in the context of a previously affected child. METHODS Non-invasive prenatal diagnosis was performed using custom assays for droplet digital PCR. Feasibility, diagnostic performance and turn-around time were evaluated. RESULTS Mean time for a new assay design and validation was evaluated at 14 days, and mean result reporting time was 6 days. All referred pathogenic variants could be targeted except one located in a complex genomic region. A result was obtained for every 198 referrals except two. CONCLUSION This service was successfully implemented as a routine laboratory practice. It has been widely adopted by French clinicians and patients for paternal variant exclusion in various disorders.
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Affiliation(s)
- Mathilde Pacault
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire, Brest, France
| | - Camille Verebi
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Maureen Lopez
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Nicolas Vaucouleur
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Lucie Orhant
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Nathalie Deburgrave
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - France Leturcq
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Dominique Vidaud
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Emmanuelle Girodon
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des Maladies de Système et d'Organe, Centre Université de Paris - Fédération de Génétique et de Médecine Génomique, Hôpital Cochin, APHP, Paris, France
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Sawakwongpra K, Tangmansakulchai K, Ngonsawan W, Promwan S, Chanchamroen S, Quangkananurug W, Sriswasdi S, Jantarasaengaram S, Ponnikorn S. Droplet-based digital PCR for non-invasive prenatal genetic diagnosis of α and β-thalassemia. Biomed Rep 2021; 15:82. [PMID: 34512970 PMCID: PMC8411484 DOI: 10.3892/br.2021.1458] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022] Open
Abstract
Non-invasive prenatal diagnosis (NIPD) of isolated cell-free DNA from maternal plasma has been applied to detect monogenic diseases in the fetus. Droplet digital PCR (ddPCR) is a sensitive and quantitative technique for NIPD. In the present study, the development and evaluation of ddPCR-based assays for common α and β-thalassemia variants amongst the Asian population was described; specifically, Southeast Asian (SEA) deletion, HbE, and 41/42 (-CTTT). SEA is caused by deletion of a 20 kb region surrounding the α-globin gene, whilst HbE and 41/42 (-CTTT) are caused by point mutations on the β-globin gene. Cell-free DNA samples from 46 singleton pregnant women who were carriers of these mutations were isolated and quantified using ddPCR with specially designed probes for each target allele. Allelic copy number calculation and likelihood ratio tests were used to classify fetal genotypes. Classification performances were evaluated against ground truth fetal genotypes obtained from conventional amniocentesis. Copy number variation analysis of SEA deletion accurately classified fetal genotypes in 20 out of 22 cases with an area under the receiver operating characteristic curve of 0.98 for detecting Hb Bart's hydrops fetalis. For HbE cases, 10 out of 16 samples were correctly classified, and three were inconclusive. For 41/42 (-CTTT) cases, 2 out of 8 were correctly classified, and four were inconclusive. The correct genotype was not rejected in any inconclusive case and may be resolved with additional ddPCR experiments. These results indicate that ddPCR-based analysis of maternal plasma can become an accurate and effective NIPD for SEA deletion α-(0) thalassemia. Although the performance of ddPCR on HbE and 41/42 (-CTTT) mutations were not sufficient for clinical application, these results may serve as a foundation for future works in this field.
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Affiliation(s)
- Kritchakorn Sawakwongpra
- Chulabhorn International College of Medicine, Thammasat University, Khlong Luang, Pathum Thani 12120, Thailand
| | | | | | | | - Sujin Chanchamroen
- Next Generation Genomic, Pathum Wan, Bangkok 10330, Thailand.,SAFE Fertility Center, Pathum Wan, Bangkok 10330, Thailand
| | - Wiwat Quangkananurug
- Next Generation Genomic, Pathum Wan, Bangkok 10330, Thailand.,SAFE Fertility Center, Pathum Wan, Bangkok 10330, Thailand
| | - Sira Sriswasdi
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand.,Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand
| | - Surasak Jantarasaengaram
- Department of Obstetrics and Gynecology, Rajavithi Hospital, Ratchathewi, Bangkok 10400, Thailand
| | - Saranyoo Ponnikorn
- Chulabhorn International College of Medicine, Thammasat University, Khlong Luang, Pathum Thani 12120, Thailand
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Wrobel W, Pach E, Ben-Skowronek I. Advantages and Disadvantages of Different Treatment Methods in Achondroplasia: A Review. Int J Mol Sci 2021; 22:ijms22115573. [PMID: 34070375 PMCID: PMC8197470 DOI: 10.3390/ijms22115573] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023] Open
Abstract
Achondroplasia (ACH) is a disease caused by a missense mutation in the FGFR3 (fibroblast growth factor receptor 3) gene, which is the most common cause of short stature in humans. The treatment of ACH is necessary and urgent because untreated achondroplasia has many complications, both orthopedic and neurological, which ultimately lead to disability. This review presents the current and potential pharmacological treatments for achondroplasia, highlighting the advantages and disadvantages of all the drugs that have been demonstrated in human and animal studies in different stages of clinical trials. The article includes the potential impacts of drugs on achondroplasia symptoms other than short stature, including their effects on spinal canal stenosis, the narrowing of the foramen magnum and the proportionality of body structure. Addressing these effects could significantly improve the quality of life of patients, possibly reducing the frequency and necessity of hospitalization and painful surgical procedures, which are currently the only therapeutic options used. The criteria for a good drug for achondroplasia are best met by recombinant human growth hormone at present and will potentially be met by vosoritide in the future, while the rest of the drugs are in the early stages of clinical trials.
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11
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Yang L, Wu Y, Hu Z, Zhang H, Pu D, Yan H, Zhang S, Jiang H, Liu Q, Yuan Y, Zhang Y, Chen F, Lu Y, Pan S, Lin L, Gao Y. Simultaneous detection of fetal aneuploidy, de novo FGFR3 mutations and paternally derived β-thalassemia by a novel method of noninvasive prenatal testing. Prenat Diagn 2021; 41:440-448. [PMID: 33340121 PMCID: PMC8048498 DOI: 10.1002/pd.5879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVE The aim is to develop a novel noninvasive prenatal testing (NIPT) method that simultaneously performs fetal aneuploidy screening and the detection of de novo and paternally derived mutations. METHODS A total of 68 pregnancies, including 26 normal pregnancies, 7 cases with fetal aneuploidies, 7 cases with fetal achondroplasia or thanatophoric dysplasia, 18 cases with fetal skeletal abnormalities, and 10 cases with β-thalassemia high risk were recruited. Plasma cell-free DNA was amplified by Targeted And Genome-wide simultaneous sequencing (TAGs-seq) to generate around 99% of total reads covering the whole-genome region and around 1% covering the target genes. The reads on the whole-genome region were analyzed for fetal aneuploidy using a binary hypothesis T-score and the reads on target genes were analyzed for point mutations by calculating the minor allelic frequency of loci on FGFR3 and HBB. TAGs-seq results were compared with conventional NIPT and diagnostic results. RESULTS In each sample, TAGs-seq generated 44.7-54 million sequencing reads covering the whole-genome region of 0.1-3× and the target genes of >1000×depth. All cases of fetal aneuploidy and de novo mutations of achondroplasia/thanatophoric dysplasia were identified with high sensitivities and specificities except for one false-negative paternal mutation of β-thalassemia. CONCLUSIONS TAGs-seq is a novel NIPT method that combines the fetal aneuploidy screening and the detection of de novo FGFR3 mutations and paternal HBB mutations.
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Affiliation(s)
- Lin Yang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China.,School of Future Technology, University of Chinese Academy of Sciences, Beijing, China
| | - Yujing Wu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Zhiyang Hu
- Department of Obstetrics, Shenzhen People's Hospital, The Second Clinical Medical School of Jinan University, Shenzhen, China
| | | | | | | | | | | | - Qiang Liu
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Yuying Yuan
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | | | | | - Yanping Lu
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Silin Pan
- Qingdao Women and Children's Hospital, Qingdao University, Qingdao, China
| | - Linhua Lin
- Department of Obstetrics, Shenzhen People's Hospital, The Second Clinical Medical School of Jinan University, Shenzhen, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China.,Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China
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12
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Zednikova I, Pazourkova E, Lassakova S, Vesela B, Korabecna M. Detection of cell-free foetal DNA fraction in female-foetus bearing pregnancies using X-chromosomal insertion/deletion polymorphisms examined by digital droplet PCR. Sci Rep 2020; 10:20036. [PMID: 33208834 PMCID: PMC7676229 DOI: 10.1038/s41598-020-77084-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 10/23/2020] [Indexed: 12/03/2022] Open
Abstract
In families with X-linked recessive diseases, foetal sex is determined prenatally by detection of Y-chromosomal sequences in cell-free foetal DNA (cffDNA) in maternal plasma. The same procedure is used to confirm the cffDNA presence during non-invasive prenatal RhD incompatibility testing but there are no generally accepted markers for the detection of cffDNA fraction in female-foetus bearing pregnancies. We present a methodology allowing the detection of paternal X-chromosomal alleles on maternal background and the confirmation of female sex of the foetus by positive amplification signals. Using digital droplet PCR (ddPCR) we examined X-chromosomal INDEL (insertion/deletion) polymorphisms: rs2307932, rs16397, rs16637, rs3048996, rs16680 in buccal swabs of 50 females to obtain the population data. For all INDELs, we determined the limits of detection for each ddPCR assay. We examined the cffDNA from 63 pregnant women bearing Y-chromosome negative foetuses. The analysis with this set of INDELs led to informative results in 66.67% of examined female-foetus bearing pregnancies. Although the population data predicted higher informativity (74%) we provided the proof of principle of this methodology. We successfully applied this methodology in prenatal diagnostics in a family with Wiscott-Aldrich syndrome and in pregnancies tested for the risk of RhD incompatibility.
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Affiliation(s)
- Iveta Zednikova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourkova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U nemocnice 2, 128 08, Prague, Czech Republic
| | - Sona Lassakova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Barbora Vesela
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
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13
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Ahmadi MH, Amirizadeh N, Rabiee M, Rahimi-Sharbaf F, Pourfathollah AA. Noninvasive Fetal Sex Determination by Real-Time PCR and TaqMan Probes. Rep Biochem Mol Biol 2020; 9:315-323. [PMID: 33649725 DOI: 10.29252/rbmb.9.3.315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Background Noninvasive fetal sex determination by analyzing Y chromosome-specific sequences is very useful in the management of cases related to sex-linked genetic diseases. The aim of this study was to establish a non-invasive fetal sex determination test using Real-Time PCR and specific probes. Methods The study was a prospective observational cohort study conducted from August 2018 to September 2019. Venous blood samples were collected from 25 Iranian pregnant women at weeks 7 to 25 of gestation. Cell-free DNA (cfDNA) was isolated from the plasma of samples and fetal sex was determined by SRY gene analysis using the Real-Time PCR technique. In the absence of SRY detection, the presence of fetal DNA was investigated using cfDNA treated with BstUI enzyme and PCR for the epigenetic marker RASSF1A. Results Of the total samples analyzed, 48% were male and 52% female. The RASSF1A assay performed on SRY negative cases also confirmed the presence of cell-free fetal DNA. Genotype results were in full agreement with neonate gender, and the accuracy of noninvasive fetal sex determination was 100%. Conclusion Fetal sex determination using the strategy applied in this study is noninvasive and highly accurate and can be exploited in the management of sex-linked genetic diseases.
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Affiliation(s)
- Mohammad Hossein Ahmadi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Naser Amirizadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Maryam Rabiee
- Department of Obstetrics and Gynecology, Shahed University, Tehran, Iran
| | - Fatemeh Rahimi-Sharbaf
- Department of Perinatology, Yas Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Pourfathollah
- Department of Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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14
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Ouzegdouh Mammasse Y, Chenet C, Drubay D, Martageix C, Cartron JP, Vainchenker W, Petermann R. A new efficient tool for non-invasive diagnosis of fetomaternal platelet antigen incompatibility. Br J Haematol 2020; 190:787-798. [PMID: 32266719 DOI: 10.1111/bjh.16593] [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: 12/20/2019] [Accepted: 03/02/2020] [Indexed: 12/23/2022]
Abstract
Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is the consequence of platelet destruction by maternal alloantibodies against fetal human platelet antigens (HPA). This may result in intracranial haemorrhages (ICH) or even fetal death. Currently, fetal HPA genotyping is performed using invasive procedures. Here, we carried out a proof-of-concept study for non-invasive prenatal diagnosis of fetal platelet genotyping in four HPA systems (HPA-1, -3, -5 and-15) by droplet digital polymerase chain reaction (ddPCR) using cell-free DNA extracts from the plasma of 47 pregnant women with suspected, or history of, FNAIT. Results showed that 74% (35/47) of pregnant women presented incompatibility in at least one HPA system, and 38% (18/47) of cases presented HPA-1 incompatibility, including nine women with multiple incompatibilities. ICH occurred in one case of profound fetal thrombocytopenia with HPA-15 incompatibility, confirming the need for non-invasive prenatal genotyping in systems other than HPA-1. Fetal HPA genotypes predicted by ddPCR were confirmed in all FNAIT cases after amniocentesis or delivery. Fetal HPA genotyping on maternal plasma based on ddPCR is a fast, safe and reliable non-invasive method. This technique will be useful for the early identification of pregnancies at high risk of FNAIT requiring antenatal management to minimize the risk of fetal/neonatal haemorrhage.
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Affiliation(s)
- Yasmine Ouzegdouh Mammasse
- Institut National de la Transfusion Sanguine (INTS), Département d'Immunologie Plaquettaire, Paris, France
| | - Christophe Chenet
- Institut National de la Transfusion Sanguine (INTS), Département d'Immunologie Plaquettaire, Paris, France
| | - Damien Drubay
- INSERM, U1018, CESP, Faculté de Médecine - Université Paris-Sud - UVSQ, INSERM, Université Paris-Saclay, Villejuif, France.,Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Villejuif, France
| | - Corinne Martageix
- Institut National de la Transfusion Sanguine (INTS), Département d'Immunologie Plaquettaire, Paris, France
| | | | - William Vainchenker
- Institut National de la Transfusion Sanguine (INTS), Département d'Immunologie Plaquettaire, Paris, France.,INSERM, UMR 1287, Gustave Roussy, Villejuif, France.,Université Paris-Saclay, UMR1287, Gustave Roussy, Villejuif, France
| | - Rachel Petermann
- Institut National de la Transfusion Sanguine (INTS), Département d'Immunologie Plaquettaire, Paris, France.,Centre de Recherche des Cordeliers, UMRS 1138, INSERM, Sorbonne Université, Université de Paris, Equipe ETRES (Ethics, Research, Translations), Paris, France
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15
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Louvrier C, Pasmant E, Briand-Suleau A, Cohen J, Nitschké P, Nectoux J, Orhant L, Zordan C, Goizet C, Goutagny S, Lallemand D, Vidaud M, Vidaud D, Kalamarides M, Parfait B. Targeted next-generation sequencing for differential diagnosis of neurofibromatosis type 2, schwannomatosis, and meningiomatosis. Neuro Oncol 2019; 20:917-929. [PMID: 29409008 DOI: 10.1093/neuonc/noy009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Clinical overlap between neurofibromatosis type 2 (NF2), schwannomatosis, and meningiomatosis can make clinical diagnosis difficult. Hence, molecular investigation of germline and tumor tissues may improve the diagnosis. Methods We present the targeted next-generation sequencing (NGS) of NF2, SMARCB1, LZTR1, SMARCE1, and SUFU tumor suppressor genes, using an amplicon-based approach. We analyzed blood DNA from a cohort of 196 patients, including patients with NF2 (N = 79), schwannomatosis (N = 40), meningiomatosis (N = 12), and no clearly established diagnosis (N = 65). Matched tumor DNA was analyzed when available. Forty-seven NF2-/SMARCB1-negative schwannomatosis patients and 27 NF2-negative meningiomatosis patients were also evaluated. Results A NF2 variant was found in 41/79 (52%) NF2 patients. SMARCB1 or LZTR1 variants were identified in 5/40 (12.5%) and 13/40 (∼32%) patients in the schwannomatosis cohort. Potentially pathogenic variants were found in 12/65 (18.5%) patients with no clearly established diagnosis. A LZTR1 variant was identified in 16/47 (34%) NF2/SMARCB1-negative schwannomatosis patients. A SMARCE1 variant was found in 3/39 (∼8%) meningiomatosis patients. No SUFU variant was found in the cohort. NGS was an effective and sensitive method to detect mutant alleles in blood or tumor DNA of mosaic NF2 patients. Interestingly, we identified a 4-hit mechanism resulting in the complete NF2 loss-of-function combined with SMARCB1 and LZTR1 haploinsufficiency in two-thirds of tumors from NF2 patients. Conclusions Simultaneous investigation of NF2, SMARCB1, LZTR1, and SMARCE1 is a key element in the differential diagnosis of NF2, schwannomatosis, and meningiomatosis. The targeted NGS strategy is suitable for the identification of NF2 mosaicism in blood and for the investigation of tumors from these patients.
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Affiliation(s)
- Camille Louvrier
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - Joëlle Cohen
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Patrick Nitschké
- Bioinformatic Platform, INSERM UMR 1163, Université Paris Descartes-Sorbonne, Paris Cité, Imagine Institute, Paris, France
| | - Juliette Nectoux
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Lucie Orhant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Cécile Zordan
- Service de Génétique Médicale, Hôpital Pellegrin, CHU Bordeaux, Bordeaux, France
| | - Cyril Goizet
- Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France.,Laboratoire MRGM, INSERM U1211, Université Bordeaux, Bordeaux, France
| | - Stéphane Goutagny
- Service de Neurochirurgie, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Dominique Lallemand
- Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
| | - Michel Kalamarides
- Service de Neurochirurgie, Hôpital Pitié Salpêtrière, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes-Sorbonne, Paris Cité, Faculté de Pharmacie de Paris, Paris, France
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16
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Yan Y, Wang F, Zhang C, Jin X, Zhang Q, Feng X, Hao S, Gao H, Ma X. Evaluation of droplet digital PCR for non-invasive prenatal diagnosis of phenylketonuria. Anal Bioanal Chem 2019; 411:7115-7126. [PMID: 31485704 DOI: 10.1007/s00216-019-02087-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/02/2019] [Accepted: 08/14/2019] [Indexed: 10/26/2022]
Abstract
This study was carried out to establish a non-invasive prenatal diagnosis method for phenylketonuria (PKU) based on droplet digital PCR (ddPCR) and to evaluate its accuracy by comparison with conventional invasive diagnostic methods. A total of 24 PKU pedigrees that required prenatal diagnosis were studied, in which the genetic mutations in the probands and parents were unambiguous. Prenatal diagnosis of sibling fetuses was performed using traditional invasive prenatal diagnostic methods as a standard. At the same time, cell-free DNA (cfDNA) was extracted from maternal plasma and the fetal genes contained within were typed and quantified using ddPCR method. Invasive prenatal diagnosis determined that 3 of the 24 fetuses were affected, 8 of them were normal, and 13 were heterozygous carriers of pathogenic mutations. Successful non-invasive prenatal diagnosis analysis of PAH gene mutations was performed for 8 of the families using ddPCR method. Non-invasive prenatal diagnosis results were consistent with the results of the invasive prenatal diagnoses and no false positive or false negative results were found. In conclusion, this study is the first to establish non-invasive prenatal diagnosis of PKU based on ddPCR. The method showed high sensitivity and specificity from cfDNA, indicating that ddPCR is a reliable non-invasive prenatal diagnosis tool for PKU diagnosis. Graphical abstract.
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Affiliation(s)
- Yousheng Yan
- National Research Institute for Family Planning, No. 12 Dahuisi Road, Haidian District, Beijing, 100081, China.,Graduate School of Peking Union Medical College, New Building 18, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China.,Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, No. 143, Qili River North Street, Lanzhou, 730050, Gansu, China
| | - Fang Wang
- National Research Institute for Family Planning, No. 12 Dahuisi Road, Haidian District, Beijing, 100081, China.,Graduate School of Peking Union Medical College, New Building 18, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Chuan Zhang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, No. 143, Qili River North Street, Lanzhou, 730050, Gansu, China
| | - Xiaohua Jin
- National Research Institute for Family Planning, No. 12 Dahuisi Road, Haidian District, Beijing, 100081, China.,Graduate School of Peking Union Medical College, New Building 18, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China
| | - Qinhua Zhang
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, No. 143, Qili River North Street, Lanzhou, 730050, Gansu, China
| | - Xuan Feng
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, No. 143, Qili River North Street, Lanzhou, 730050, Gansu, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, No. 143, Qili River North Street, Lanzhou, 730050, Gansu, China
| | - Huafang Gao
- National Research Institute for Family Planning, No. 12 Dahuisi Road, Haidian District, Beijing, 100081, China. .,Graduate School of Peking Union Medical College, New Building 18, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China.
| | - Xu Ma
- National Research Institute for Family Planning, No. 12 Dahuisi Road, Haidian District, Beijing, 100081, China. .,Graduate School of Peking Union Medical College, New Building 18, No. 9 Dongdan Santiao, Dongcheng District, Beijing, 100730, China.
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17
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Prenatal diagnosis of genetic diseases directly using paper-dried cord blood as the starting material for PCR. Anal Bioanal Chem 2019; 411:6825-6835. [PMID: 31410536 DOI: 10.1007/s00216-019-02048-x] [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: 05/25/2019] [Revised: 07/05/2019] [Accepted: 07/22/2019] [Indexed: 10/26/2022]
Abstract
A rapid and low-cost method of diagnosis is becoming important for detecting fetal inherited diseases, including single-gene disorders and chromosomal abnormalities. Here, we demonstrated an innovation that use paper-dried cord blood (PCB) as the starting material for PCR and whole genome amplification without any DNA extraction step at a very low cost. A novel PCR buffer named "DDB buffer" containing ammonium sulfate and glycerol were used instead of the conventional 10× PCR buffer. The amplicons were directly analyzed through microchip electrophoresis and whole genome sequencing. Inhibitory substances in filter paper were effectively inactivated using DDB buffer. Direct PCR amplification of DNA fragments ranging from 100 to 900 bp using filter paper spotted with 0.5 to 5 μL of cord blood and various anticoagulants was successful. We were able to determine fetal single-gene disorders and chromosomal diseases in all 46 chromosomes using PCB samples successfully. Compared with prenatal diagnosis using purified DNA, the proposed method is simple, fast, less prone to cross-contamination at minimal cost. Researchers and clinical and healthcare workers may employ this method for genetic diagnosis using cord blood samples with minimum laboratory resources. This method is very promising for a variety of genetic diagnosis applications in underserved communities at the point of need in developing areas. Graphical abstract.
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18
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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19
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Yang X, Zhou Q, Zhou W, Zhong M, Guo X, Wang X, Fan X, Yan S, Li L, Lai Y, Wang Y, Huang J, Ye Y, Zeng H, Chuan J, Du Y, Ma C, Li P, Song Z, Xu X. A Cell-free DNA Barcode-Enabled Single-Molecule Test for Noninvasive Prenatal Diagnosis of Monogenic Disorders: Application to β-Thalassemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1802332. [PMID: 31179213 PMCID: PMC6548944 DOI: 10.1002/advs.201802332] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Indexed: 05/13/2023]
Abstract
Noninvasive prenatal testing of common aneuploidies has become routine over the past decade, but testing of monogenic disorders remains a challenge in clinical implementation. Most recent studies have inherent limitations, such as complicated procedures, a lack of versatility, and the need for prior knowledge of parental genotypes or haplotypes. To overcome these limitations, a robust and versatile next-generation sequencing-based cell-free DNA (cfDNA) allelic molecule counting system termed cfDNA barcode-enabled single-molecule test (cfBEST) is developed for the noninvasive prenatal diagnosis (NIPD) of monogenic disorders. The accuracy of cfBEST is found to be comparable to that of droplet digital polymerase chain reaction (ddPCR) in detecting low-abundance mutations in cfDNA. The analytical validity of cfBEST is evidenced by a β-thalassemia assay, in which a blind validation study of 143 at-risk pregnancies reveals a sensitivity of 99.19% and a specificity of 99.92% on allele detection. Because the validated cfBEST method can be used to detect maternal-fetal genotype combinations in cfDNA precisely and quantitatively, it holds the potential for the NIPD of human monogenic disorders.
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Affiliation(s)
- Xingkun Yang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Qinghua Zhou
- The Center for Precision Medicine of First Affiliated HospitalBiomedical Translational Research InstituteSchool of PharmacyJinan UniversityGuangzhouGuangdong510632China
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Wanjun Zhou
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Mei Zhong
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Xiaoling Guo
- Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanGuangdong528000China
| | - Xiaofeng Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xin Fan
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Shanhuo Yan
- Qinzhou Maternity & Child Healthcare HospitalQinzhouGuangxi535000China
| | - Liyan Li
- Nanfang HospitalSouthern Medical UniversityGuangzhouGuangdong510515China
| | - Yunli Lai
- Guangxi Zhuang Autonomous Region Women and Children Care HospitalNanningGuangxi530000China
| | - Yongli Wang
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jin Huang
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Yuhua Ye
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
| | - Huaping Zeng
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Jun Chuan
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Yuanping Du
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Chouxian Ma
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Peining Li
- Department of GeneticsYale UniversityNew HavenCT06520USA
| | - Zhuo Song
- Hunan Research Center for Big Data Application in GenomicsGenetalks Inc.ChangshaHunan410152China
| | - Xiangmin Xu
- Department of Medical GeneticsSchool of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong510515China
- Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic DiseasesGuangzhouGuangdong510515China
- Guangdong Key Laboratory of Biological ChipGuangzhouGuangdong510515China
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20
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Validation of Extensive Next-Generation Sequencing Method for Monogenic Disorder Analysis on Cell-Free Fetal DNA: Noninvasive Prenatal Diagnosis. J Mol Diagn 2019; 21:572-579. [PMID: 31028936 DOI: 10.1016/j.jmoldx.2019.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/12/2019] [Accepted: 02/22/2019] [Indexed: 12/29/2022] Open
Abstract
During pregnancy, a percentage of the cell-free DNA circulating in the maternal blood is represented by the cell-free fetal DNA (cffDNA), constituting an accessible source for noninvasive prenatal genetic screening. The coexistence of the maternal DNA, the dominant fraction of cell-free DNA, together with the cffDNA component and the scarcity of the cffDNA itself make applying traditional methods of genetics and molecular biology impossible. Next-generation sequencing methods are widely used to study fetal aneuploidies. However, in monogenic disorders, there have been relatively few studies that analyzed single mutations. We present a method for the analysis of an extended group of gene variants associated with recessive and dominant autosomal disorders using next-generation sequencing. The proposed test should allow a complete analysis of common genetic disorders and pathogen-associated variants for diagnostic use. The analysis of cffDNA for single gene disorders may replace invasive prenatal diagnosis methods, associated with the risk of spontaneous abortion and psychological stress for patients. The proposed test should assess reproductive risk for both genetic family disorders and de novo occurrences of the disease. The application of this method to a case of beta-thalassemia is also discussed.
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21
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Gruber A, Pacault M, El Khattabi LA, Vaucouleur N, Orhant L, Bienvenu T, Girodon E, Vidaud D, Leturcq F, Costa C, Letourneur F, Anselem O, Tsatsaris V, Goffinet F, Viot G, Vidaud M, Nectoux J. Non-invasive prenatal diagnosis of paternally inherited disorders from maternal plasma: detection of NF1 and CFTR mutations using droplet digital PCR. Clin Chem Lab Med 2019; 56:728-738. [PMID: 29613853 DOI: 10.1515/cclm-2017-0689] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND To limit risks of miscarriages associated with invasive procedures of current prenatal diagnosis practice, we aim to develop a personalized medicine-based protocol for non-invasive prenatal diagnosis (NIPD) of monogenic disorders relying on the detection of paternally inherited mutations in maternal blood using droplet digital PCR (ddPCR). METHODS This study included four couples at risk of transmitting paternal neurofibromatosis type 1 (NF1) mutations and four couples at risk of transmitting compound heterozygous CFTR mutations. NIPD was performed between 8 and 15 weeks of gestation, in parallel to conventional invasive diagnosis. We designed specific hydrolysis probes to detect the paternal mutation and to assess the presence of cell-free fetal DNA by ddPCR. Analytical performances of each assay were determined from paternal sample, an then fetal genotype was inferred from maternal plasma sample. RESULTS Presence or absence of the paternal mutant allele was correctly determined in all the studied plasma DNA samples. CONCLUSIONS We report an NIPD protocol suitable for implementation in an experienced laboratory of molecular genetics. Our proof-of-principle results point out a high accuracy for early detection of paternal NF1 and CFTR mutations in cell-free DNA, and open new perspectives for extending the technology to NIPD of many other monogenic diseases.
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Affiliation(s)
- Aurélia Gruber
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Mathilde Pacault
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | | | - Nicolas Vaucouleur
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Lucie Orhant
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Thierry Bienvenu
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - France Leturcq
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Catherine Costa
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Franck Letourneur
- INSERM, U1016, Institut Cochin, CNRS UMR8104, Université Paris Descartes, Paris, France
| | - Olivia Anselem
- Maternité Cochin-Port Royal, HUPC Hôpital Cochin, Paris, France
| | | | | | - Géraldine Viot
- Maternité Cochin-Port Royal, HUPC Hôpital Cochin, Paris, France
| | - Michel Vidaud
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, Paris, France
| | - Juliette Nectoux
- Service de Génétique et Biologie Moléculaires, HUPC Hôpital Cochin, 27 rue du Faubourg Saint Jacques, 75014 Paris, France, Phone: 00 33 1 58 41 16 22, Fax: 00 33 1 58 41 15 80
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22
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Abstract
Achondroplasia is the most common of the skeletal dysplasias that result in marked short stature (dwarfism). Although its clinical and radiologic phenotype has been described for more than 50 years, there is still a great deal to be learned about the medical issues that arise secondary to this diagnosis, the manner in which these are best diagnosed and addressed, and whether preventive strategies can ameliorate the problems that can compromise the health and well being of affected individuals. This review provides both an updated discussion of the care needs of those with achondroplasia and an exploration of the limits of evidence that is available regarding care recommendations, controversies that are currently present, and the many areas of ignorance that remain.
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Affiliation(s)
- Richard M Pauli
- Midwest Regional Bone Dysplasia Clinic, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, 1500 Highland Ave., Madison, WI, 53705, USA.
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23
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Vivanti AJ, Costa JM, Rosefort A, Kleinfinger P, Lohmann L, Cordier AG, Benachi A. Optimal non-invasive diagnosis of fetal achondroplasia combining ultrasonography with circulating cell-free fetal DNA analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 53:87-94. [PMID: 29380944 DOI: 10.1002/uog.19018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/27/2017] [Accepted: 01/17/2018] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To assess the performance of non-invasive prenatal testing (NIPT) for achondroplasia using high-resolution melting (HRM) analysis, and to propose an optimal diagnostic strategy combining ultrasound examination and cell-free fetal DNA (cffDNA) analysis. METHODS In this prospective multicenter study, cffDNA was extracted from blood of pregnant women at risk for fetal achondroplasia (owing to paternal achondroplasia, previous affected child or suspected rhizomelic shortening) and of pregnant low-risk controls. The presence of either one of the two main fibroblast growth factor receptor 3 gene (FGFR3) mutations was determined using HRM combined with confirmation by SNaPshot minisequencing. Results were compared with phenotypes obtained using three-dimensional computed tomography or postnatal examination, and/or molecular diagnosis by an invasive procedure. Fetal biometry (head circumference and femur length) was analyzed in order to develop a strategy in which cffDNA analysis for diagnosis of achondroplasia is offered only in selected cases. RESULTS Eighty-six blood samples from women at risk for fetal achondroplasia and 65 from controls were collected. The overall sensitivity and specificity of NIPT were 1.00 (95% CI, 0.87-1.00) and 1.00 (95% CI, 0.96-1.00), respectively. Critical reduction in femur length of affected fetuses could be observed from 26 weeks' gestation. CONCLUSIONS HRM combined with SNaPshot minisequencing is a reliable method for NIPT for achondroplasia. Its implementation in routine clinical care combined with ultrasonography is an efficient strategy for the non-invasive diagnosis of achondroplasia. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- A J Vivanti
- Service de Gynécologie-Obstétrique, Hôpital Antoine Béclère, AP-HP, Clamart, France
- Université Paris Sud, Orsay, France
| | - J-M Costa
- Laboratoire CERBA, Saint-Ouen l'Aumône, France
| | - A Rosefort
- Service de Gynécologie-Obstétrique, Hôpital Tenon, AP-HP, Paris, France
| | | | - L Lohmann
- Laboratoire CERBA, Saint-Ouen l'Aumône, France
| | - A-G Cordier
- Service de Gynécologie-Obstétrique, Hôpital Antoine Béclère, AP-HP, Clamart, France
- Université Paris Sud, Orsay, France
| | - A Benachi
- Service de Gynécologie-Obstétrique, Hôpital Antoine Béclère, AP-HP, Clamart, France
- Université Paris Sud, Orsay, France
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24
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Ren Y, Zhao J, Li R, Xie Y, Jiang S, Zhou H, Liu H, You Y, Chen F, Wang W, Gao Y, Meng Y, Lu Y. Noninvasive prenatal test for FGFR3-related skeletal dysplasia based on next-generation sequencing and plasma cell-free DNA: Test performance analysis and feasibility exploration. Prenat Diagn 2018; 38:821-828. [PMID: 30048571 DOI: 10.1002/pd.5334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To explore the feasibility and accuracy of a noninvasive prenatal test for fibroblast growth factor receptor 3 (FGFR3)-related skeletal dysplasia based on next-generation sequencing (NGS) of plasma cell-free DNA. METHOD Fragmented genome DNA (gDNA) of fetuses with achondroplasia (ACH) and thanatophoric dysplasia type I (TD I) was mixed with postdelivery maternal plasma cell-free DNA to generate spiked samples of different modeled fetal fractions. Multiplex polymerase chain reaction was used to amplify the 19 FGFR3 loci, and the amplification products were then sequenced by NGS to detect the fetal mutant alleles. Then, maternal plasma samples of pregnant women carrying ACH (n = 4) and TD I fetuses (n = 2), as well as healthy controls (n = 15), were tested by NGS, and the test performance was evaluated. RESULTS Fetal FGFR3 mutations were detected in all artificial mixtures with fetal gDNA concentrations above 3%. In clinical validation, our method identified all fetal FGFR3 mutant alleles from maternal plasma, with no false positive results. The sensitivity and specificity of our method were 100% (95% CI, 54.1%-100%) and 100% (78.2%-100%), respectively. CONCLUSION Our method had a favorable performance for noninvasively detecting fetal FGFR3 mutations in maternal plasma, highlighting its promising value in developing a noninvasive prenatal test for de novo and paternally inherited disorders.
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Affiliation(s)
- Yuan Ren
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Jia Zhao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Ruibing Li
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | | | - Shufang Jiang
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Honghui Zhou
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | | | - Yanqin You
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Ya Gao
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yuanguang Meng
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
| | - Yanping Lu
- Department of Obstetrics and Gynecology, Chinese PLA General Hospital, Beijing, China
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25
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Byrou S, Makrigiorgos GM, Christofides A, Kallikas I, Papasavva T, Kleanthous M. Fast Temperature-Gradient COLD PCR for the enrichment of the paternally inherited SNPs in cell free fetal DNA; an application to non-invasive prenatal diagnosis of β-thalassaemia. PLoS One 2018; 13:e0200348. [PMID: 30044883 PMCID: PMC6059429 DOI: 10.1371/journal.pone.0200348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/25/2018] [Indexed: 11/28/2022] Open
Abstract
Objective To develop a sensitive, specific, simple, cost-effective and reproducible platform for the non-invasive prenatal detection of paternally inherited alleles for β-thalassaemia. The development of such an assay is of major significance in order to replace currently-applied invasive methods containing inherent fetal loss risks. Methods We present a fast Temperature-Gradient Co-amplification at Lower Denaturation Temperature Polymerase Chain Reaction (fast TG COLD PCR) methodology for the detection of the paternally-inherited fetal alleles in maternal plasma. Two single-nucleotide polymorphisms (SNPs), rs7480526 (G/T) and rs968857 (G/A) that are located on the β-globin gene cluster and exhibit a high degree of heterozygosity in the Cypriot population were selected for evaluation. Seventeen maternal plasma samples from pregnancies at risk for β-thalassemia were analysed for the selected SNPs using the novel fast TG COLD PCR assay. Results Using fast TG COLD PCR, the paternally inherited allele in cell free fetal DNA was correctly determined for all the 17 maternal plasma samples tested, showing full agreement with the Chorionic Villus Sampling (CVS) analysis. Conclusions Our findings are encouraging and demonstrate the efficiency and sensitivity of fast TG COLD PCR in detecting the minor paternally-inherited fetal alleles in maternal plasma for the development of a NIPD assay for β-thalassaemia.
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Affiliation(s)
- Stefania Byrou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - G. Mike Makrigiorgos
- Department of Radiation Oncology, Division of Medical Physics & Biophysics, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Thessalia Papasavva
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
- * E-mail:
| | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, Nicosia, Cyprus
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26
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Camunas-Soler J, Lee H, Hudgins L, Hintz SR, Blumenfeld YJ, El-Sayed YY, Quake SR. Noninvasive Prenatal Diagnosis of Single-Gene Disorders by Use of Droplet Digital PCR. Clin Chem 2018; 64:336-345. [DOI: 10.1373/clinchem.2017.278101] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/05/2017] [Indexed: 12/26/2022]
Abstract
Abstract
BACKGROUND
Prenatal diagnosis in pregnancies at risk of single-gene disorders is currently performed using invasive methods such as chorionic villus sampling and amniocentesis. This is in contrast with screening for common aneuploidies, for which noninvasive methods with a single maternal blood sample have become standard clinical practice.
METHODS
We developed a protocol for noninvasive prenatal diagnosis of inherited single-gene disorders using droplet digital PCR from circulating cell-free DNA (cfDNA) in maternal plasma. First, the amount of cfDNA and fetal fraction is determined using a panel of TaqMan assays targeting high-variability single-nucleotide polymorphisms. Second, the ratio of healthy and diseased alleles in maternal plasma is quantified using TaqMan assays targeting the mutations carried by the parents. Two validation approaches of the mutation assay are presented.
RESULTS
We collected blood samples from 9 pregnancies at risk for different single-gene disorders, including common conditions and rare metabolic disorders. We measured cases at risk of hemophilia, ornithine transcarbamylase deficiency, cystic fibrosis, β-thalassemia, mevalonate kinase deficiency, acetylcholine receptor deficiency, and DFNB1 nonsyndromic hearing loss. We correctly differentiated affected and unaffected pregnancies (2 affected, 7 unaffected), confirmed by neonatal testing. We successfully measured an affected pregnancy as early as week 11 and with a fetal fraction as low as 3.7% (0.3).
CONCLUSIONS
Our method detects single-nucleotide mutations of autosomal recessive diseases as early as the first trimester of pregnancy. This is of importance for metabolic disorders in which early diagnosis can affect management of the disease and reduce complications and anxiety related to invasive testing.
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Affiliation(s)
| | - Hojae Lee
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Louanne Hudgins
- Division of Medical Genetics, Department of Pediatrics, Stanford University, Stanford, CA
| | - Susan R Hintz
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Yair J Blumenfeld
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
| | - Yasser Y El-Sayed
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University, Stanford, CA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA
- Department of Applied Physics, Stanford University, Stanford, CA
- Chan Zuckerberg Biohub, San Francisco, CA
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27
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Abstract
PURPOSE OF REVIEW Noninvasive prenatal diagnosis for single gene disorders is coming to fruition in its clinical utility. The presence of cell-free DNA in maternal plasma has been recognized for many years, and a number of applications have developed from this. Noninvasive prenatal diagnosis for single gene disorders has lagged behind due to complexities of technology development, lack of investment and the need for validation samples for rare disorders. RECENT FINDINGS Publications are emerging demonstrating a variety of technical approaches and feasibility of clinical application. Techniques for analysis of cell-free DNA including digital PCR, next-generation sequencing and relative haplotype dosage have been used most often for assay development. Analysis of circulating fetal cells in the maternal blood is still being investigated as a viable alternative and more recently transcervical trophoblast cells. Studies exploring ethical and social issues are generally positive but raise concerns around the routinization of prenatal testing. SUMMARY Further work is necessary to make testing available to all patients with a pregnancy at risk of a single gene disorder, and it remains to be seen if the development of more powerful technologies such as isolation and analysis of single cells will shift the emphasis of noninvasive prenatal diagnosis. As testing becomes possible for a wider range of conditions, more ethical questions will become relevant.
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28
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Zhang H, Liu X, Liu M, Gao T, Huang Y, Liu Y, Zeng W. Gene detection: An essential process to precision medicine. Biosens Bioelectron 2018; 99:625-636. [DOI: 10.1016/j.bios.2017.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/12/2017] [Indexed: 01/08/2023]
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29
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Nectoux J. Current, Emerging, and Future Applications of Digital PCR in Non-Invasive Prenatal Diagnosis. Mol Diagn Ther 2017; 22:139-148. [DOI: 10.1007/s40291-017-0312-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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30
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de Wit MC, Bunnik EM, Go ATJI, de Beaufort ID, Hofstra RMW, Steegers EAP, Galjaard RJH. Amniocentesis is still the best option for advanced genomic testing in case of fetal malformations. Prenat Diagn 2017; 37:1360-1363. [PMID: 29149523 DOI: 10.1002/pd.5187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/05/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022]
Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, The Netherlands
| | - E M Bunnik
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, Rotterdam, The Netherlands
| | - A T J I Go
- Department of Obstetrics and Gynecology, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, The Netherlands
| | - I D de Beaufort
- Department of Medical Ethics and Philosophy of Medicine, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, Rotterdam, The Netherlands
| | - R M W Hofstra
- Department of Clinical Genetics, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, The Netherlands
| | - E A P Steegers
- Department of Obstetrics and Gynecology, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, The Netherlands
| | - R J H Galjaard
- Department of Clinical Genetics, Erasmus Medical Centre and Sophia Children's Hospital, Rotterdam, The Netherlands
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31
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Abstract
PURPOSE OF REVIEW The goal of this review is to evaluate the management options for achondroplasia, the most common non-lethal skeletal dysplasia. This disease is characterized by short stature and a variety of complications, some of which can be quite severe. RECENT FINDINGS Despite several attempts to standardize care, there is still no widely accepted consensus. This is in part due to absence of concrete data on the incidence of sudden unexplained death in infants with achondroplasia and the best investigation for ascertaining which individuals could benefit from foramen magnum decompression surgery. In this review, we identify the different options of care and management for the various orthopedic, neurologic, and respiratory complications. In parallel, several innovative or drug repositioning therapies are being investigated that would restore bone growth but may also prevent complications. Achondroplasia is the most common non-lethal skeletal dysplasia. It is characterized by short stature and a variety of complications, some of which can be quite severe. Despite several attempts to standardize care, there is still no widely accepted consensus. This is in part due to absence of concrete data on the incidence of sudden unexplained death in infants with achondroplasia and the best investigation for ascertaining which individuals could benefit from foramen magnum decompression surgery. In this review, we identify the different options of care and management for the various orthopedic, neurologic, and respiratory complications. In parallel, several innovative or drug repositioning therapies are being investigated that would restore bone growth but may also prevent complications.
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Affiliation(s)
- Sheila Unger
- 0000 0001 0423 4662grid.8515.9Service of Genetic Medicine, Lausanne University Hospital (CHUV), Av. Pierre-Decker 2, 1011 Lausanne, Switzerland
| | - Luisa Bonafé
- 0000 0001 0423 4662grid.8515.9Center for Molecular Diseases, Service of Genetic Medicine, Lausanne University Hospital (CHUV), Av. Pierre-Decker 2, 1011 Lausanne, Switzerland
| | - Elvire Gouze
- 0000 0001 2337 2892grid.10737.32Institute de Biologie Valrose, University. Nice Sophia Antipolis, Batiment Sciences Naturelles; UFR Sciences, Parc Valrose, 28 avenue Valrose, 06108 Nice, Cedex 2 France
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32
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Ding Y, Choo J, deMello AJ. From single-molecule detection to next-generation sequencing: microfluidic droplets for high-throughput nucleic acid analysis. MICROFLUIDICS AND NANOFLUIDICS 2017; 21:58. [PMID: 32214953 PMCID: PMC7087872 DOI: 10.1007/s10404-017-1889-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 02/22/2017] [Indexed: 05/27/2023]
Abstract
Droplet-based microfluidic technologies have proved themselves to be of significant utility in the performance of high-throughput chemical and biological experiments. By encapsulating and isolating reagents within femtoliter-nanoliter droplet, millions of (bio) chemical reactions can be processed in a parallel fashion and on ultra-short timescales. Recent applications of such technologies to genetic analysis have suggested significant utility in low-cost, efficient and rapid workflows for DNA amplification, rare mutation detection, antibody screening and next-generation sequencing. To this end, we describe and highlight some of the most interesting recent developments and applications of droplet-based microfluidics in the broad area of nucleic acid analysis. In addition, we also present a cursory description of some of the most essential functional components, which allow the creation of integrated and complex workflows based on flowing streams of droplets.
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan, 15588 Republic of Korea
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zurich, Switzerland
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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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Butchbach MER. Applicability of digital PCR to the investigation of pediatric-onset genetic disorders. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:9-14. [PMID: 27990344 PMCID: PMC5154671 DOI: 10.1016/j.bdq.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
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