Cargando…

Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation

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 th...

Descripción completa

Detalles Bibliográficos
Autores principales: Pacault, Mathilde, Verebi, Camille, Champion, Magali, Orhant, Lucie, Perrier, Alexandre, Girodon, Emmanuelle, Leturcq, France, Vidaud, Dominique, Férec, Claude, Bienvenu, Thierry, Daveau, Romain, Nectoux, Juliette
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124834/
https://www.ncbi.nlm.nih.gov/pubmed/37093806
http://dx.doi.org/10.1371/journal.pone.0280976
_version_ 1785029916149940224
author Pacault, Mathilde
Verebi, Camille
Champion, Magali
Orhant, Lucie
Perrier, Alexandre
Girodon, Emmanuelle
Leturcq, France
Vidaud, Dominique
Férec, Claude
Bienvenu, Thierry
Daveau, Romain
Nectoux, Juliette
author_facet Pacault, Mathilde
Verebi, Camille
Champion, Magali
Orhant, Lucie
Perrier, Alexandre
Girodon, Emmanuelle
Leturcq, France
Vidaud, Dominique
Férec, Claude
Bienvenu, Thierry
Daveau, Romain
Nectoux, Juliette
author_sort Pacault, Mathilde
collection PubMed
description 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.
format Online
Article
Text
id pubmed-10124834
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-101248342023-04-25 Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation Pacault, Mathilde Verebi, Camille Champion, Magali Orhant, Lucie Perrier, Alexandre Girodon, Emmanuelle Leturcq, France Vidaud, Dominique Férec, Claude Bienvenu, Thierry Daveau, Romain Nectoux, Juliette PLoS One Research Article 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. Public Library of Science 2023-04-24 /pmc/articles/PMC10124834/ /pubmed/37093806 http://dx.doi.org/10.1371/journal.pone.0280976 Text en © 2023 Pacault et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Pacault, Mathilde
Verebi, Camille
Champion, Magali
Orhant, Lucie
Perrier, Alexandre
Girodon, Emmanuelle
Leturcq, France
Vidaud, Dominique
Férec, Claude
Bienvenu, Thierry
Daveau, Romain
Nectoux, Juliette
Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title_full Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title_fullStr Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title_full_unstemmed Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title_short Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
title_sort non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10124834/
https://www.ncbi.nlm.nih.gov/pubmed/37093806
http://dx.doi.org/10.1371/journal.pone.0280976
work_keys_str_mv AT pacaultmathilde noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT verebicamille noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT championmagali noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT orhantlucie noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT perrieralexandre noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT girodonemmanuelle noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT leturcqfrance noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT vidauddominique noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT ferecclaude noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT bienvenuthierry noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT daveauromain noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation
AT nectouxjuliette noninvasiveprenataldiagnosisofsinglegenedisorderswithenhancedrelativehaplotypedosageanalysisfordiagnosticimplementation