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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; 26:638-651. [PMID: 38663495 DOI: 10.1016/j.jmoldx.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed 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
- Senior 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
- Senior 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
- Senior 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
- Senior 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
- Senior 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
- Senior 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
- Senior 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
- Senior 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
| | - Na Liu
- MyGenostics Inc., Beijing, China
| | - Lu Han
- MyGenostics Inc., Beijing, China
| | | | - Lina Ren
- MyGenostics Inc., Beijing, China
| | - Jinyuan Yang
- Senior 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
| | - Jian Wu
- MyGenostics Inc., Beijing, China
| | - Yongyi Yuan
- Senior 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
- Senior 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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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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Liautard-Haag C, Durif G, VanGoethem C, Baux D, Louis A, Cayrefourcq L, Lamairia M, Willems M, Zordan C, Dorian V, Rooryck C, Goizet C, Chaussenot A, Monteil L, Calvas P, Miry C, Favre R, Le Boette E, Fradin M, Roux AF, Cossée M, Koenig M, Alix-Panabière C, Guissart C, Vincent MC. Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach. Sci Rep 2022; 12:11423. [PMID: 35794169 PMCID: PMC9259573 DOI: 10.1038/s41598-022-15307-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe field of noninvasive prenatal diagnosis (NIPD) has undergone significant progress over the last decade. Direct haplotyping has been successfully applied for NIPD of few single-gene disorders. However, technical issues remain for triplet-repeat expansions. The objective of this study was to develop an NIPD approach for couples at risk of transmitting dynamic mutations. This method includes targeted enrichment for linked-read libraries and targeted maternal plasma DNA sequencing. We also developed an innovative Bayesian procedure to integrate the Hoobari fetal genotyping model for inferring the fetal haplotype and the targeted gene variant status. Our method of directly resolving parental haplotypes through targeted linked-read sequencing was smoothly performed using blood samples from families with Huntington’s disease or myotonic dystrophy type 1. The Bayesian analysis of transmission of parental haplotypes allowed defining the genotype of five fetuses. The predicted variant status of four of these fetuses was in agreement with the invasive prenatal diagnosis findings. Conversely, no conclusive result was obtained for the NIPD of fragile X syndrome. Although improvements should be made to achieve clinically acceptable accuracy, our study shows that linked-read sequencing and parental haplotype phasing can be successfully used for NIPD of triplet-repeat expansion diseases.Trial registration: NCT04698551_date of first registration: 07/01/2021.
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Chiu R, Rajan-Babu IS, Birol I, Friedman JM. Linked-read sequencing for detecting short tandem repeat expansions. Sci Rep 2022; 12:9352. [PMID: 35672336 PMCID: PMC9174224 DOI: 10.1038/s41598-022-13024-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Detection of short tandem repeat (STR) expansions with standard short-read sequencing is challenging due to the difficulty in mapping multicopy repeat sequences. In this study, we explored how the long-range sequence information of barcode linked-read sequencing (BLRS) can be leveraged to improve repeat-read detection. We also devised a novel algorithm using BLRS barcodes for distance estimation and evaluated its application for STR genotyping. Both approaches were designed for genotyping large expansions (> 1 kb) that cannot be sized accurately by existing methods. Using simulated and experimental data of genomes with STR expansions from multiple BLRS platforms, we validated the utility of barcode and phasing information in attaining better STR genotypes compared to standard short-read sequencing. Although the coverage bias of extremely GC-rich STRs is an important limitation of BLRS, BLRS is an effective strategy for genotyping many other STR loci.
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Affiliation(s)
- Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical and Molecular Genetics, King's College London, Strand, London, WC2R 2LS, UK
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 4S6, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.
| | - Jan M Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,BC Children's Hospital Research Institute, Vancouver, BC, V5Z 4H4, Canada
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