Prenatal exome sequencing, a powerful tool for improving the description of prenatal features associated with genetic disorders.

Journal

Prenatal diagnosis

ISSN: 1097-0223

Titre abrégé: Prenat Diagn

Pays: England

ID NLM: 8106540

Informations de publication

Date de publication:
13 Aug 2024

Historique:

revised: 11 05 2024

received: 19 10 2023

accepted: 03 06 2024

medline: 14 8 2024

pubmed: 14 8 2024

entrez: 13 8 2024

Statut: aheadofprint

Résumé

Prenatal exome sequencing (pES) is now commonly used in clinical practice. It can be used to identifiy an additional diagnosis in around 30% of fetuses with structural defects and normal chromosomal microarray analysis (CMA). However, interpretation remains challenging due to the limited prenatal data for genetic disorders. We conducted an ancillary study including fetuses with pathogenic/likely pathogenic variants identified by trio-pES from the "AnDDI-Prenatome" study. The prenatal phenotype of each patient was categorized as typical, uncommon, or unreported based on the comparison of the prenatal findings with documented findings in the literature and public phenotype-genotype databases (ClinVar, HGMD, OMIM, and Decipher). Prenatal phenotypes were typical for 38/56 fetuses (67.9%). For the others, genotype-phenotype associations were challenging due to uncommon prenatal features (absence of recurrent hallmark, rare, or unreported). We report the first prenatal features associated with LINS1 and PGM1 variants. In addition, a double diagnosis was identified in three fetuses. Standardizing the description of prenatal features, implementing longitudinal prenatal follow-up, and large-scale collection of prenatal features are essential steps to improving pES data interpretation.

Identifiants

DOI: 10.1002/pd.6623 PMID: 39138116

pubmed: 39138116

doi: 10.1002/pd.6623

doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

Subventions

Organisme : National Network AnDDI-rares

ID : NCT03964441

Informations de copyright

Références

Liu L, Oza S, Hogan D, et al. Global, regional, and national causes of child mortality in 2000‐13, with projections to inform post‐2015 priorities: an updated systematic analysis. Lancet. 2015;385(9966):430‐440. https://doi.org/10.1016/s0140‐6736(14)61698‐6

Hillman SC, McMullan DJ, Hall G, et al. Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta‐analysis. Ultrasound Obstet Gynecol. 2013;41(6):610‐620. https://doi.org/10.1002/uog.12464

Mellis R, Oprych K, Scotchman E, Hill M, Chitty LS. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: a systematic review and meta‐analysis. Prenat Diagn. 2022;42(6):662‐685. https://doi.org/10.1002/pd.6115

Tran Mau‐Them F, Delanne J, Denommé‐Pichon AS, et al. Prenatal diagnosis by trio exome sequencing in fetuses with ultrasound anomalies: a powerful diagnostic tool. Front Genet. 2023;14:1099995. https://doi.org/10.3389/fgene.2023.1099995

Normand EA, Braxton A, Nassef S, et al. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med. 2018;10(1):74. https://doi.org/10.1186/s13073‐018‐0582‐x

Ferretti L, Mellis R, Chitty LS. Update on the use of exome sequencing in the diagnosis of fetal abnormalities. Eur J Med Genet. 2019;62(8):103663. https://doi.org/10.1016/j.ejmg.2019.05.002

Lefebvre M, Bruel AL, Tisserant E, et al. Genotype‐first in a cohort of 95 fetuses with multiple congenital abnormalities: when exome sequencing reveals unexpected fetal phenotype‐genotype correlations. J Med Genet. 2021;58(6):400‐413. https://doi.org/10.1136/jmedgenet‐2020‐106867

Orphanet [Internet]. [cité 5 mai 2024]. https://www.orpha.net/

Orphadata – Orphanet datasets [Internet]. [cité 5 mai 2024]. https://www.orphadata.com/

Dangiolo SB, Wilson A, Jobanputra V, Anyane‐Yeboa K. Bohring‐Opitz syndrome (BOS) with a new ASXL1 pathogenic variant: review of the most prevalent molecular and phenotypic features of the syndrome. Am J Med Genet. 2015;167A(12):3161‐3166. https://doi.org/10.1002/ajmg.a.37342

Cuddapah VA, Dubbs HA, Adang L, et al. Understanding the phenotypic spectrum of ASXL‐related disease: 10 cases and a review of the literature. Am J Med Genet. 2021;185(6):1700‐1711. https://doi.org/10.1002/ajmg.a.62156

Bohring A, Oudesluijs GG, Grange DK, Zampino G, Thierry P. New cases of Bohring–Opitz syndrome, update, and critical review of the literature. Am J Med Genet. 2006;140A(12):1257‐1263. https://doi.org/10.1002/ajmg.a.31265

Zhao J, Hou Y, Fang F, et al. Novel truncating mutations in ASXL1 identified in two boys with Bohring‐Opitz syndrome. Eur J Med Genet. 2021;64(3):104155. https://doi.org/10.1016/j.ejmg.2021.104155

Loberti L, Bruno LP, Granata S, et al. Natural history of KBG syndrome in a large European cohort. Hum Mol Genet. 2022;31(24):4131‐4142. https://doi.org/10.1093/hmg/ddac167

Tan NB, Pagnamenta AT, Ferla MP, et al. Recurrent de novo missense variants in GNB2 can cause syndromic intellectual disability. J Med Genet. 2022;59(5):511‐516. https://doi.org/10.1136/jmedgenet‐2020‐107462

Schindewolf E, Khalek N, Johnson MP, et al. Expanding the fetal phenotype: prenatal sonographic findings and perinatal outcomes in a cohort of patients with a confirmed 22q11.2 deletion syndrome. American J of Med Genetics Pt A. 2018;176(8):1735‐1741. https://doi.org/10.1002/ajmg.a.38665

Besseau‐Ayasse J, Violle‐Poirsier C, Bazin A, et al. A French collaborative survey of 272 fetuses with 22q11.2 deletion: ultrasound findings, fetal autopsies and pregnancy outcomes. Prenat Diagn. 2014;34(5):424‐430. https://doi.org/10.1002/pd.4321

Jing XY, Zhang YL, Zhen L, Li YL, Li DZ. Prenatal sonographic findings in a cohort of foetuses with a confirmed 22q11.2 microdeletion at a single Chinese Tertiary Centre. J Obstet Gynaecol. 2022;42(7):2935‐2940. https://doi.org/10.1080/01443615.2022.2114324

Probst FJ, James RA, Burrage LC, et al. De novo deletions and duplications of 17q25.3 cause susceptibility to cardiovascular malformations. Orphanet J Rare Dis. 2015;10(1):75. https://doi.org/10.1186/s13023‐015‐0291‐0

Neuhofer CM, Catarino CB, Schmidt H, et al. LINS1‐associated neurodevelopmental disorder. Neurol Genet. 2020;6(5):e500. https://doi.org/10.1212/nxg.0000000000000500

Chen CH, Huang YS, Fang TH. Identification of a novel nonsense homozygous mutation of LINS1 gene in two sisters with intellectual disability, schizophrenia, and anxiety. Biomed J. 2021;44(6):748‐751. https://doi.org/10.1016/j.bj.2021.08.003

Wong SYW, Beamer LJ, Gadomski T, et al. Defining the phenotype and assessing severity in phosphoglucomutase‐1 deficiency. J Pediatr. 2016;175:130‐136. https://doi.org/10.1016/j.jpeds.2016.04.021

Racine C, Denommé‐Pichon AS, Engel C, et al. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet. 2023;61(1):36‐46. https://doi.org/10.1136/jmg‐2023‐109170

Bourgon N, Garde A, Bruel AL, et al. Same performance of exome sequencing before and after fetal autopsy for congenital abnormalities: toward a paradigm shift in prenatal diagnosis? Eur J Hum Genet. 2022;30(8):1‐9. https://doi.org/10.1038/s41431‐022‐01117‐7

Köhler S, Vasilevsky NA, Engelstad M, et al. The human phenotype ontology in 2017. Nucleic Acids Res. 2017;45(D1):D865‐D876. https://doi.org/10.1093/nar/gkw1039

Dhombres F, Morgan P, Chaudhari BP, et al. Prenatal phenotyping: a community effort to enhance the Human Phenotype Ontology. Am J Med Genet Part C: Seminars in Medical Genetics. 2022;190(2):231‐242. https://doi.org/10.1002/ajmg.c.31989