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Gao B, Jiang Y, Han M, Ji X, Zhang D, Wu L, Gao X, Huang S, Zhao C, Su Y, Yang S, Zhang X, Liu N, Han L, Wang L, Ren L, Yang J, Wu J, Yuan Y, Dai P. Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles: A Universal and Dependable Noninvasive Prenatal Diagnosis Method Applied to Autosomal Recessive Nonsyndromic Hearing Loss in At-Risk Families. J Mol Diagn 2024:S1525-1578(24)00085-0. [PMID: 38663495 DOI: 10.1016/j.jmoldx.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/04/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. However, the previous method could not be performed on challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. Here, this study assesses the performance of relative haplotype dosage analysis (RHDO)-based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either GJB2 or SLC26A4 were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of GJB2 and SLC26A4, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.
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Affiliation(s)
- Bo Gao
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yi Jiang
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Ear Institute, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai, China
| | - Mingyu Han
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | - Dejun Zhang
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Lihua Wu
- Department of Otolaryngology, Fujian Medical University ShengLi Clinical College, Fujian Provincial Hospital, Fuzhou, China
| | - Xue Gao
- Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shasha Huang
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Chaoyue Zhao
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Yu Su
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Suyan Yang
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | | | | | | | - Jinyuan Yang
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China
| | | | - Yongyi Yuan
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
| | - Pu Dai
- Department of Otolaryngology Head and Neck Surgery, The 6th Medical Center of Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China; State Key Laboratory of Hearing and Balance Science, Beijing, China; National Clinical Research Center for Otolaryngologic Diseases, Beijing, China; Key Laboratory of Hearing Science, Ministry of Education, Beijing, China; Beijing Key Laboratory of Hearing Impairment Prevention and Treatment, Beijing, China.
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Pacot L, Ye M, Nectoux J, Laurendeau I, Briand-Suleau A, Coustier A, Maillard T, Barbance C, Orhant L, Vaucouleur N, Blanché H, Parfait B, Wolkenstein P, Vidaud M, Vidaud D, Pasmant E. Droplet Digital PCR for Fast and Accurate Characterization of NF1 Locus Deletions: Confirmation of the Predominant Maternal Origin of Type-1 Deletions. J Mol Diagn 2024; 26:150-157. [PMID: 38008284 DOI: 10.1016/j.jmoldx.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/09/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023] Open
Abstract
Neurofibromatosis type-1 is a genetic disorder caused by loss-of-function variants in the tumor-suppressor NF1. Approximately 4% to 11% of neurofibromatosis type-1 patients have a NF1 locus complete deletion resulting from nonallelic homologous recombination between low copy repeats. Codeleted genes probably account for the more severe phenotype observed in NF1-deleted patients. This genotype-phenotype correlation highlights the need for a detailed molecular description. A droplet digital PCR (ddPCR) set along the NF1 locus was designed to delimitate the three recurrent NF1 deletion breakpoints. The ddPCR was tested in 121 samples from nonrelated NF1-deleted patients. Classification based on ddPCR versus multiplex ligation-dependent probe amplification (MLPA) was compared. In addition, microsatellites were analyzed to identify parental origin of deletions. ddPCR identified 77 type-1 (64%), 20 type-2 (16%), 7 type-3 (6%), and 17 atypical deletions (14%). The results were comparable with MLPA, except for three atypical deletions misclassified as type-2 using MLPA, for which the SUZ12 gene was not deleted. A significant maternal bias (25 of 30) in the origin of deletions was identified. This study proposes a fast and efficient ddPCR quantification to allow fine NF1 deletion classification. It indicates that ddPCR can be implemented easily into routine diagnosis to complement the techniques dedicated to NF1 point variant identification. This new tool may help unravel the genetic basis conditioning phenotypic variability in NF1-deleted patients and offer tailored genetic counseling.
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Affiliation(s)
- Laurence Pacot
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Manuela Ye
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Juliette Nectoux
- Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Ingrid Laurendeau
- Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Audrey Briand-Suleau
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Audrey Coustier
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Théodora Maillard
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Cécile Barbance
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Lucie Orhant
- Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Nicolas Vaucouleur
- Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | | | - Béatrice Parfait
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Pierre Wolkenstein
- Department of Dermatology, Hôpital Henri Mondor, Assistance Publique-Hôpital Paris, Créteil, France; INSERM, Clinical Investigation Center 1430, Referral Center of Neurofibromatosis, Hôpital Henri Mondor, Assistance Publique-Hôpital Paris, Faculté de Santé Paris Est Créteil, Créteil, France
| | - Michel Vidaud
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Dominique Vidaud
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France
| | - Eric Pasmant
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France; Fédération de Génétique et Médecine Génomique, DMU BioPhyGen, Assistance Publique-Hôpital Paris, Centre-Université Paris Cité, Hôpital Cochin, Paris, France.
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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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Yang L, Fu J, Cheng J, Zhou B, Chen M, Anuchapreeda S, Fu J. Novel, heterozygous, de novo pathogenic variant (c.4963delA: p.Thr1656Glnfs*42) of the NF1 gene in a Chinese family with neurofibromatosis type 1. BMC Med Genomics 2023; 16:85. [PMID: 37095468 PMCID: PMC10123994 DOI: 10.1186/s12920-023-01514-x] [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: 10/26/2022] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) presents an autosomal dominant, haploinsufficient, and multisystemic disorder with patches of skin café-au-lait spots, lisch nodules in the iris, even tumors in the peripheral nervous system or fibromatous skin. In this study, a Chinese young woman who suffered from NF1 disease with first-trimester spontaneous abortion was recruited. Analysis for whole exome sequencing (WES), Sanger sequencing, short tandem repeat (STR), and co-segregation was carried out. As results, a novel, heterozygous, de novo pathogenic variant (c.4963delA:p.Thr1656Glnfs*42) of the NF1 gene in the proband was identified. This pathogenic variant of the NF1 gene produced a truncated protein that lost more than one-third of the NF1 protein at the C-terminus including half of the CRAL-TRIO lipid-binding domain and nuclear localization signal (NLS), thus leading to pathogenicity (ACMG criteria: PVS1 + PM2 + PM2). Analysis for NF1 conservation in species revealed high conservation in different species. Analysis of NF1 mRNA levels in different human tissues showed low tissue specificity, which may affect multiple organs presenting other symptoms or phenotypes. Moreover, prenatal NF1 gene diagnosis showed both alleles as wild types. Thus, this NF1 novel variant probably underlays the NF1 pathogenesis in this pedigree, which would help for the diagnosis, genetic counseling, and clinical management of this disorder.
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Affiliation(s)
- Lisha Yang
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Jiewen Fu
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Jingliang Cheng
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
| | - Baixu Zhou
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China
- Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
| | - Maomei Chen
- Department of Obstetrics, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, 646000, China
| | - Songyot Anuchapreeda
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Research Center of Pharmaceutical Nanotechnology, Chiang Mai University, Chiang Mai, 50200, Thailand.
| | - Junjiang Fu
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, 3-319, Zhongshan Rd, Luzhou, Sichuan, 646000, China.
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Pacault M, Verebi C, Champion M, Orhant L, Perrier A, Girodon E, Leturcq F, Vidaud D, Férec C, Bienvenu T, Daveau R, Nectoux J. Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation. PLoS One 2023; 18:e0280976. [PMID: 37093806 PMCID: PMC10124834 DOI: 10.1371/journal.pone.0280976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023] Open
Abstract
Non-invasive prenatal diagnosis of single-gene disorders (SGD-NIPD) has been widely accepted, but is mostly limited to the exclusion of either paternal or de novo mutations. Indeed, it is still difficult to infer the inheritance of the maternal allele from cell-free DNA (cfDNA) analysis. Based on the study of maternal haplotype imbalance in cfDNA, relative haplotype dosage (RHDO) was developed to address this challenge. Although RHDO has been shown to be reliable, robust control of statistical error and explicit delineation of critical parameters for assessing the quality of the analysis have not been fully addressed. We present here a universal and adaptable enhanced-RHDO (eRHDO) procedure through an automated bioinformatics pipeline with a didactic visualization of the results, aiming to be applied for any SGD-NIPD in routine care. A training cohort of 43 families carrying CFTR, NF1, DMD, or F8 mutations allowed the characterization and optimal setting of several adjustable data variables, such as minimum sequencing depth, type 1 and type 2 statistical errors, as well as the quality assessment of intermediate steps and final results by block score and concordance score. Validation was successfully performed on a test cohort of 56 pregnancies. Finally, computer simulations were used to estimate the effect of fetal-fraction, sequencing depth and number of informative SNPs on the quality of results. Our workflow proved to be robust, as we obtained conclusive and correctly inferred fetal genotypes in 94.9% of cases, with no false-negative or false-positive results. By standardizing data generation and analysis, we fully describe a turnkey protocol for laboratories wishing to offer eRHDO-based non-invasive prenatal diagnosis for single-gene disorders as an alternative to conventional prenatal diagnosis.
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Affiliation(s)
- Mathilde Pacault
- Laboratoire de Génétique Moléculaire et Histocompatibilité, Brest, France
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Camille Verebi
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | | | - Lucie Orhant
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Alexandre Perrier
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Emmanuelle Girodon
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - France Leturcq
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Dominique Vidaud
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et Histocompatibilité, Brest, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Romain Daveau
- MOABI, Plateforme bio-informatique AP-HP, Département I&D, DSI, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
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6
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Contribution of whole genome sequencing in the molecular diagnosis of mosaic partial deletion of the NF1 gene in neurofibromatosis type 1. Hum Genet 2023; 142:1-9. [PMID: 35941319 DOI: 10.1007/s00439-022-02476-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023]
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disease with complete penetrance but highly variable expressivity. In most patients, Next Generation Sequencing (NGS) technologies allow the identification of a loss-of-function pathogenic variant in the NF1 gene, a negative regulator of the RAS-MAPK pathway. We describe the 5-year diagnosis wandering of a patient with a clear NF1 clinical diagnosis, but no molecular diagnosis using standard molecular technologies. The patient presented with a typical NF1 phenotype but NF1 targeted NGS, NF1 transcript analysis, MLPA, and array comparative genomic hybridization failed to reveal a genetic aberration. After 5 years of unsuccessful investigations, trio WGS finally identified a de novo mosaic (VAF ~ 14%) 24.6 kb germline deletion encompassing the promoter and first exon of NF1. This case report illustrates the relevance of WGS to detect structural variants including copy number variants that would be missed by alternative approaches. The identification of the causal pathogenic variant allowed a tailored genetic counseling with a targeted non-invasive prenatal diagnosis by detecting the deletion in plasmatic cell-free DNA from the proband's pregnant partner. This report clearly highlights the need to make WGS a clinically accessible test, offering a tremendous opportunity to identify a molecular diagnosis for otherwise unsolved cases.
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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: 3] [Impact Index Per Article: 1.5] [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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Molecular Characterization of a Rare Case of Monozygotic Dichorionic Diamniotic Twin Pregnancy after Single Blastocyst Transfer in Preimplantation Genetic Testing (PGT). Int J Mol Sci 2022; 23:ijms231810835. [PMID: 36142745 PMCID: PMC9504855 DOI: 10.3390/ijms231810835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022] Open
Abstract
Preimplantation genetic testing (PGT) is widely used to select unaffected embryos, increasing the odds of having a healthy baby. During the last few decades, it was accepted that monozygotic dichorionic diamniotic twin pregnancies occurred from the embryo splitting before Day 3 postfertilization according to Corner’s dogma. Hence, the occurrence of a dichorionic diamniotic twin pregnancy after a single blastocyst transfer was considered a dizygotic pregnancy resulting from blastocyst transfer and concurrent natural fertilization. In our study, we have provided for the first time molecular proof that a single blastocyst transfer can result in a monozygotic dichorionic diamniotic twin pregnancy, invalidating Corner’s dogma. In this case, we recommend systematically assessing the genetic status of dichorionic twins after single blastocyst transfer using prenatal diagnosis to exclude the risk from a potential concurrent spontaneous pregnancy and to ensure that both fetuses are unaffected. To achieve this goal, we have developed here an innovative noninvasive prenatal diagnosis by exclusion of paternal variants with droplet digital PCR, maximizing the reliability of genetic diagnosis. Further multicentric prospective studies using genetic testing are now required to establish the rate of blastocyst splitting leading to dichorionic pregnancy in PGT and to identify the risk factors.
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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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10
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Wu W, Zhou X, Jiang Z, Zhang D, Yu F, Zhang L, Wang X, Chen S, Xu C. Noninvasive fetal genotyping of single nucleotide variants and linkage analysis for prenatal diagnosis of monogenic disorders. Hum Genomics 2022; 16:28. [PMID: 35897115 PMCID: PMC9327225 DOI: 10.1186/s40246-022-00400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 07/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background High-cost, time-consuming and complex processes of several current approaches limit the use of noninvasive prenatal diagnosis (NIPD) for monogenic disorders in clinical application. Thus, a more cost-effective and easily implementable approach is required. Methods We established a low-cost and convenient test to noninvasively deduce fetal genotypes of the mutation and single nucleotide polymorphisms (SNPs) loci by means of targeted amplification combined with deep sequencing of maternal genomic and plasma DNA. The sequential probability ratio test was performed to detect the allelic imbalance in maternal plasma. This method can be employed to directly examine familial pathogenic mutations in the fetal genome, as well as infer the inheritance of parental haplotypes through a group of selected SNPs linked to the pathogenic mutation. Results The fetal mutations in 17 families with different types of monogenic disorders including hemophilia A, von Willebrand disease type 3, Duchenne muscular dystrophy, hyper-IgM type 1, glutaric acidemia type I, Nagashima-type palmoplantar keratosis, and familial exudative vitreoretinopathy were identified in the study. The mutations included various forms: point mutations, gene inversion, deletions/insertions and duplication. The results of 12 families were verified by sequencing of amniotic fluid samples, the accuracy of the approach in fetal genotyping at the mutation and SNPs loci was 98.85% (172/174 loci), and the no-call rate was 28.98% (71/245 loci). The overall accuracy was 12/12 (100%). Moreover, the approach was successfully applied in plasma samples with a fetal fraction as low as 2.3%. Conclusions We have shown in this study that the approach is a cost-effective, less time consuming and accurate method for NIPD of monogenic disorders. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00400-4.
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Affiliation(s)
- Wenman Wu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China.,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China
| | - Zhengwen Jiang
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Dazhi Zhang
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Feng Yu
- Genesky Diagnostics (Suzhou) Inc., 218 Xinghu St, Suzhou, Jiangsu, People's Republic of China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China. .,Collaborative Innovation Center of Hematology, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China. .,Shanghai Academy of Experimental Medicine, Shanghai, People's Republic of China.
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China.
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, People's Republic of China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China. .,Shanghai Key Laboratory of Embryo Original Disorders, Shanghai, People's Republic of China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China.
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11
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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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12
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Huby T, Le Guillou E, Burin des Roziers C, Pacot L, Briand-Suleau A, Chansavang A, Toussaint A, Duchossoy V, Vaucouleur N, Benoit V, Lodé L, Molac C, North MO, Grotto S, Tsatsaris V, Jouinot A, Cochand-Priollet B, Paepegaey AC, Nectoux J, Groussin L, Pasmant E. Noninvasive Prenatal Diagnosis of a Paternally Inherited MEN1 Pathogenic Splicing Variant. J Clin Endocrinol Metab 2022; 107:e1367-e1373. [PMID: 34897474 DOI: 10.1210/clinem/dgab894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disease caused by mutations in the tumor suppressor gene MEN1. The uncertainty of pathogenicity of MEN1 variants complexifies the selection of the patients likely to benefit from specific care. OBJECTIVE MEN1-mutated patients should be offered tailored tumor screening and genetic counseling. We present a patient with hyperparathyroidism for whom genetic analysis identified a variant of uncertain significance in the MEN1 gene (NM_130799.2): c.654G > T p.(Arg218=). Additional functional genetic tests were performed to classify the variant as pathogenic and allowed prenatal testing. DESIGN Targeted next generation sequencing identified a synonymous variant in the MEN1 gene in a 26-year-old male with symptomatic primary hyperparathyroidism. In silico and in vitro genetic tests were performed to assess variant pathogenicity. RESULTS Genetic testing of the proband's unaffected parents showed the variant occurred de novo. Transcript study showed a splicing defect leading to an in-frame deletion. The classification of the MEN1 variant as pathogenic confirmed the diagnosis of MEN1 and recommended an adapted medical care and follow-up. Pathogenic classification also allowed to propose a genetic counseling to the proband and his wife. Noninvasive prenatal diagnosis was performed with a personalized medicine-based protocol by detection of the paternally inherited variant in maternal plasmatic cell free DNA, using digital PCR. CONCLUSION We showed that functional genetic analysis can help to assess the pathogenicity of a MEN1 variant with crucial consequences for medical care and genetic counseling decisions.
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Affiliation(s)
- Thomas Huby
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Edouard Le Guillou
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Cyril Burin des Roziers
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Laurence Pacot
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Audrey Briand-Suleau
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Albain Chansavang
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
| | - Aurélie Toussaint
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Véronique Duchossoy
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Nicolas Vaucouleur
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Virginie Benoit
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Laurence Lodé
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Clémence Molac
- Maternité Port-Royal, FHU PREMA, AP-HP, Hôpital Cochin, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | - Marie-Odile North
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Sarah Grotto
- Maternité Port-Royal, FHU PREMA, AP-HP, Hôpital Cochin, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | - Vassilis Tsatsaris
- Maternité Port-Royal, FHU PREMA, AP-HP, Hôpital Cochin, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | - Anne Jouinot
- Department of Endocrinology, Hôpital Cochin, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | - Béatrix Cochand-Priollet
- Department of Pathology, Cochin Hospital, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | | | - Juliette Nectoux
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
| | - Lionel Groussin
- Department of Endocrinology, Hôpital Cochin, AP-HP.Centre-Université de Paris, Université de Paris, Paris, France
| | - Eric Pasmant
- Service de Génétique et Biologie Moléculaires, Hôpital Cochin, DMU BioPhyGen, Assistance Publique-Hôpitaux de Paris, AP-HP.Centre-Université de Paris, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université de Paris, CARPEM, Paris, France
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D’Aversa E, Breveglieri G, Boutou E, Balassopoulou A, Voskaridou E, Pellegatti P, Guerra G, Scapoli C, Gambari R, Borgatti M. Droplet Digital PCR for Non-Invasive Prenatal Detection of Fetal Single-Gene Point Mutations in Maternal Plasma. Int J Mol Sci 2022; 23:ijms23052819. [PMID: 35269962 PMCID: PMC8911123 DOI: 10.3390/ijms23052819] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 02/04/2023] Open
Abstract
Non-invasive prenatal testing (NIPT) is based on the detection and characterization of circulating cell-free fetal DNA (ccffDNA) in maternal plasma and aims to identify genetic abnormalities. At present, commercial NIPT kits can detect only aneuploidies, small deletions and insertions and some paternally inherited single-gene point mutations causing genetic diseases, but not maternally inherited ones. In this work, we have developed two NIPT assays, based on the innovative and sensitive droplet digital PCR (ddPCR) technology, to identify the two most common β thalassemia mutations in the Mediterranean area (β+IVSI-110 and β039), maternally and/or paternally inherited, by fetal genotyping. The assays were optimized in terms of amplification efficiency and hybridization specificity, using mixtures of two genomic DNAs with different genotypes and percentages to simulate fetal and maternal circulating cell-free DNA (ccfDNA) at various gestational weeks. The two ddPCR assays were then applied to determine the fetal genotype from 52 maternal plasma samples at different gestational ages. The diagnostic outcomes were confirmed for all the samples by DNA sequencing. In the case of mutations inherited from the mother or from both parents, a precise dosage of normal and mutated alleles was required to determine the fetal genotype. In particular, we identified two diagnostic ranges for allelic ratio values statistically distinct and not overlapping, allowing correct fetal genotype determinations for almost all the analyzed samples. In conclusion, we have developed a simple and sensitive diagnostic tool, based on ddPCR, for the NIPT of β+IVSI-110 and β039 mutations paternally and, for the first time, maternally inherited, a tool, which may be applied to other single point mutations causing monogenic diseases.
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Affiliation(s)
- Elisabetta D’Aversa
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (E.D.); (G.B.); (C.S.); (R.G.)
| | - Giulia Breveglieri
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (E.D.); (G.B.); (C.S.); (R.G.)
| | - Effrossyni Boutou
- Molecular Genetics Laboratory, Thalassemia and Hemoglobinopathies Center, Laiko General Hospital, 11526 Athens, Greece; (E.B.); (A.B.)
| | - Angeliki Balassopoulou
- Molecular Genetics Laboratory, Thalassemia and Hemoglobinopathies Center, Laiko General Hospital, 11526 Athens, Greece; (E.B.); (A.B.)
| | - Ersi Voskaridou
- Thalassemia and Hemoglobinopathies Center, Laiko General Hospital, 11526 Athens, Greece;
| | - Patrizia Pellegatti
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, 44121 Ferrara, Italy; (P.P.); (G.G.)
| | - Giovanni Guerra
- Operative Unit of Laboratory Analysis, University Hospital S. Anna, 44121 Ferrara, Italy; (P.P.); (G.G.)
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (E.D.); (G.B.); (C.S.); (R.G.)
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (E.D.); (G.B.); (C.S.); (R.G.)
- Thal-LAB, Research Laboratory “Elio Zago” on the Pharmacologic and Pharmacogenomic Therapy of Thalassemia, University of Ferrara, 44121 Ferrara, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy; (E.D.); (G.B.); (C.S.); (R.G.)
- Biotechnology Center, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-0532-974441
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14
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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: 6] [Impact Index Per Article: 2.0] [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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15
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Pepe F, Mininni C, Zambrotta E, Pepe G, La Rosa V, La Rosa R, Insalaco G, Monteleone MM. Neurofibromatosis and HIV infection in a pregnant woman. Clin Case Rep 2021; 9:e04686. [PMID: 34466247 PMCID: PMC8385255 DOI: 10.1002/ccr3.4686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 03/22/2021] [Accepted: 04/26/2021] [Indexed: 11/22/2022] Open
Abstract
Although pregnant neurofibromatosis or HIV patient established a high-risk group, this report demonstrated that a careful planning and widespread valuations should be associated with a favorable prognosis for both mother and newborn.
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Affiliation(s)
- Franco Pepe
- Ospedale San MarcoUOC Ostetricia e GinecologiaCataniaItaly
| | | | | | - Gabriele Pepe
- Doctor of Political Science and Health EconomicsCataniaItaly
| | - Valeria La Rosa
- Department of Anesthesia and Intensive CarePoliclinico Universitario “G. Rodolico”CataniaItaly
| | - Rosario La Rosa
- UOC Malattie Infettive, Ospedale San Marco, CataniaUniversity of CataniaCataniaCataniaItaly
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16
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Vodicka R, Bohmova J, Holuskova I, Krejcirikova E, Prochazka M, Vrtel R. Risk Minimization of Hemolytic Disease of the Fetus and Newborn Using Droplet Digital PCR Method for Accurate Fetal Genotype Assessment of RHD, KEL, and RHCE from Cell-Free Fetal DNA of Maternal Plasma. Diagnostics (Basel) 2021; 11:diagnostics11050803. [PMID: 33925253 PMCID: PMC8146004 DOI: 10.3390/diagnostics11050803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/23/2021] [Accepted: 04/25/2021] [Indexed: 11/19/2022] Open
Abstract
The molecular pathology of hemolytic disease of the fetus and newborn (HDFN) is determined by different RHD, RHCE, and KEL genotypes and by blood group incompatibility between the mother and fetus that is caused by erythrocyte antigen presence/absence on the cell surface. In the Czech Republic, clinically significant antierythrocyte alloantibodies include anti-D, anti-K, anti C/c, and anti-E. Deletion of the RHD gene and then three single nucleotide polymorphisms in the RHCE and KEL genes (rs676785, rs609320, and rs8176058) are the most common. The aim of this study is to develop effective and precise monitoring of fetal genotypes from maternal plasma of these polymorphisms using droplet digital (dd)PCR. Fifty-three plasma DNA samples (from 10 to 18 weeks of gestation) were analyzed (10 RHD, 33 RHCE, and 10 KEL). The ddPCR methodology was validated on the basis of the already elaborated and established method of minisequencing and real-time PCR and with newborn phenotype confirmation. The results of ddPCR were in 100% agreement with minisequencing and real-time PCR and also with newborn phenotype. ddPCR can fully replace the reliable but more time-consuming method of minisequencing and real-time PCR RHD examination. Accurate and rapid noninvasive fetal genotyping minimizes the possibility of HDFN developing.
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Affiliation(s)
- Radek Vodicka
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Jana Bohmova
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
- Correspondence: ; Tel.: +42-058-844-4636
| | - Iva Holuskova
- Department of Blood Transfusion, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic;
| | - Eva Krejcirikova
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Martin Prochazka
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
| | - Radek Vrtel
- Department of Medical Genetics, University Hospital and Palacky University Olomouc, 775 20 Olomouc, Czech Republic; (R.V.); (E.K.); (M.P.); (R.V.)
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17
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Bieth E, Nectoux J, Girardet A, Gruchy N, Mittre H, Laurans M, Guenet D, Brouard J, Gerard M. Genetic counseling for cystic fibrosis: A basic model with new challenges. Arch Pediatr 2020; 27 Suppl 1:eS30-eS34. [PMID: 32172934 DOI: 10.1016/s0929-693x(20)30048-8] [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: 10/24/2022]
Abstract
While the goals of genetic counseling for cystic fibrosis - delivering relevant information on the risk of recurrence and nondirectional support of couples at risk in their reproductive choices - have not changed fundamentally, the practice has evolved considerably in the last decade, growing more complex to face new challenges but also proving more effective. Many factors have contributed to this evolution: technical progress in the exploration of the genome (new generation sequencing) and in reproductive medicine, but also societal developments promoting access to genetic information and the professionalization of genetic counselors in France. The prospect of expanded pre-conception screening of at-risk couples makes genetic counselors major actors not only in medical care centers, but also in modern society by contributing to genetic education among citizens. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.
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Affiliation(s)
- E Bieth
- Génétique Médicale, CHU Toulouse, France.
| | - J Nectoux
- Service de génétique et biologie moléculaires, CHU Paris Centre - Hôpital Cochin, Site Cochin, Paris, France
| | - A Girardet
- Génétique Moléculaire, CHU Montpellier, France
| | - N Gruchy
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
| | - H Mittre
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
| | - M Laurans
- CRCM, CHU de Caen, Avenue Côte de Nacre, France
| | - D Guenet
- Laboratoire de Biochimie, Dépistage néonatal, CHU de Caen, Avenue Côte de Nacre, France
| | - J Brouard
- Pédiatrie, CHU de Caen, Avenue Côte de Nacre, France
| | - M Gerard
- Génétique Médicale, CHR Clemenceau, CHU de Caen, Avenue Côte de Nacre, France
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18
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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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19
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Abstract
OBJECTIVES Phacomatoses are a group of neuro-oculo-cutaneous syndromes/ neurocutaneous disorders, involving structures arising from the embryonic ectoderm. Most of phacomatoses including the most common ones:, neurofibromatosis type I and type II (NF1, NF2) and tuberosclerosis complex (TSC), are autosomal dominant genetic disorders with full penetrance and variable expression. As no effective treatment exists, the only way to prevent the disease, is by prenatal genetic diagnosis (either chorionic villus sampling-CVS or amniocentesis-AC) and termination of pregnancy or performing preimplantation genetic testing (PGT). As the risk for an affected offspring is 50% in every pregnancy of an affected parent, prenatal, and preimplantation testing are of great importance. However, those procedures are associated with technical and ethical concerns. This chapter shortly reviews the common phacomatoses emphasizes their genetics and inheritance. We will review the common methods for prenatal and preimplantation diagnoses and discuss its use in common phacomatoses. CONCLUSION Phacomatoses are common autosomal dominant genetic conditions with variable expression. Ante-natal genetic diagnosis is an appropriate approach for family planning in individuals affected by phacomatosis or parents of an affected child.
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20
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Radtke HB, Bergner AL, Goetsch AL, McGowan C, Panzer K, Cannon A. Genetic Counseling for Neurofibromatosis 1, Neurofibromatosis 2, and Schwannomatosis—Practice Resource of the National Society of Genetic Counselors. J Genet Couns 2020; 29:692-714. [DOI: 10.1002/jgc4.1303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 05/06/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Heather B. Radtke
- Department of Pediatrics Medical College of Wisconsin Milwaukee Wisconsin USA
- Children’s Tumor Foundation New York New York USA
| | - Amanda L. Bergner
- Department of Genetics and Development Columbia University New York New York USA
| | - Allison L. Goetsch
- Division of Genetics Birth Defects and Metabolism, Ann and Robert H. Lurie Children’s Hospital of Chicago Chicago Illinois USA
- Department of Pediatrics Northwestern University Chicago Illinois USA
| | - Caroline McGowan
- Division of Genetics and Genomics Boston Children’s Hospital Boston Massachusetts USA
| | - Karin Panzer
- Department of Pediatrics University of Iowa Hospitals and Clinics Iowa City Iowa USA
| | - Ashley Cannon
- Department of Genetics University of Alabama at Birmingham Birmingham Alabama USA
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21
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Bienvenu T, Lopez M, Girodon E. Molecular Diagnosis and Genetic Counseling of Cystic Fibrosis and Related Disorders: New Challenges. Genes (Basel) 2020; 11:E619. [PMID: 32512765 PMCID: PMC7349214 DOI: 10.3390/genes11060619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 11/16/2022] Open
Abstract
Identification of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and its numerous variants opened the way to fantastic breakthroughs in diagnosis, research and treatment of cystic fibrosis (CF). The current and future challenges of molecular diagnosis of CF and CFTR-related disorders and of genetic counseling are here reviewed. Technological advances have enabled to make a diagnosis of CF with a sensitivity of 99% by using next generation sequencing in a single step. The detection of heretofore unidentified variants and ethnic-specific variants remains challenging, especially for newborn screening (NBS), CF carrier testing and genotype-guided therapy. Among the criteria for assessing the impact of variants, population genetics data are insufficiently taken into account and the penetrance of CF associated with CFTR variants remains poorly known. The huge diversity of diagnostic and genetic counseling indications for CFTR studies makes assessment of variant disease-liability critical. This is especially discussed in the perspective of wide genome analyses for NBS and CF carrier screening in the general population, as future challenges.
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Affiliation(s)
| | | | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP.Centre–Université de Paris, 75014 Paris, France; (T.B.); (M.L.)
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22
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Zaitsev SY, Bogolyubova NV, Zhang X, Brenig B. Biochemical parameters, dynamic tensiometry and circulating nucleic acids for cattle blood analysis: a review. PeerJ 2020; 8:e8997. [PMID: 32509445 PMCID: PMC7247529 DOI: 10.7717/peerj.8997] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 03/26/2020] [Indexed: 12/19/2022] Open
Abstract
The animal’s blood is the most complicated and important biological liquid for veterinary medicine. In addition to standard methods that are always in use, recent technologies such as dynamic tensiometry (DT) of blood serum and PCR analysis of particular markers are in progress. The standard and modern biochemical tests are commonly used for general screening and, finally, complete diagnosis of animal health. Interpretation of major biochemical parameters is similar across animal species, but there are a few peculiarities in each case, especially well-known for cattle. The following directions are discussed here: hematological indicators; “total protein” and its fractions; some enzymes; major low-molecular metabolites (glucose, lipids, bilirubin, etc.); cations and anions. As example, the numerous correlations between DT data and biochemical parameters of cattle serum have been obtained and discussed. Changes in the cell-free nucleic acids (cfDNA) circulating in the blood have been studied and analyzed in a variety of conditions; for example, pregnancy, infectious and chronic diseases, and cancer. CfDNA can easily be detected using standard molecular biological techniques like DNA amplification and next-generation sequencing. The application of digital PCR even allows exact quantification of copy number variations which are for example important in prenatal diagnosis of chromosomal aberrations.
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Affiliation(s)
- Sergei Yu Zaitsev
- Department of Physiology and Biochemistry of Farm Animals, Federal Science Center for Animal Husbandry Named After Academy Member L.K. Ernst, Podolsk, Moscow Region, Russian Federation
| | - Nadezhda V Bogolyubova
- Department of Physiology and Biochemistry of Farm Animals, Federal Science Center for Animal Husbandry Named After Academy Member L.K. Ernst, Podolsk, Moscow Region, Russian Federation
| | - Xuying Zhang
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
| | - Bertram Brenig
- Institute of Veterinary Medicine, University of Göttingen, Göttingen, Germany
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23
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Bergougnoux A, Lopez M, Girodon E. The Role of Extended CFTR Gene Sequencing in Newborn Screening for Cystic Fibrosis. Int J Neonatal Screen 2020; 6:23. [PMID: 33073020 PMCID: PMC7422980 DOI: 10.3390/ijns6010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 01/25/2023] Open
Abstract
There has been considerable progress in the implementation of newborn screening (NBS) programs for cystic fibrosis (CF), with DNA analysis being part of an increasing number of strategies. Thanks to advances in genomic sequencing technologies, CFTR-extended genetic analysis (EGA) by sequencing its coding regions has become affordable and has already been included as part of a limited number of core NBS programs, to the benefit of admixed populations. Based on results analysis of existing programs, the values and challenges of EGA are reviewed in the perspective of its implementation on a larger scale. Sensitivity would be increased at best by using EGA as a second tier, but this could be at the expense of positive predictive value, which improves, however, if EGA is applied after testing a variant panel. The increased detection of babies with an inconclusive diagnosis has proved to be a major drawback in programs using EGA. The lack of knowledge on pathogenicity and penetrance associated with numerous variants hinders the introduction of EGA as a second tier, but EGA with filtering for all known CF variants with full penetrance could be a solution. The issue of incomplete knowledge is a real challenge in terms of the implemention of NBS extended to many genetic diseases.
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Affiliation(s)
- Anne Bergougnoux
- Molecular Genetics Laboratory, CHU Montpellier, EA7402 University of Montpellier, 34093 Montpellier CEDEX 5, France;
| | - Maureen Lopez
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
| | - Emmanuelle Girodon
- Molecular Genetics Laboratory, Cochin Hospital, APHP. Centre, University of Paris, 75014 Paris, France;
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24
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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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25
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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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