All-in-one whole exome sequencing strategy with simultaneous copy number variant, single nucleotide variant and absence-of-heterozygosity analysis in fetuses with structural ultrasound anomalies: A 1-year experience.
Journal
Prenatal diagnosis
ISSN: 1097-0223
Titre abrégé: Prenat Diagn
Pays: England
ID NLM: 8106540
Informations de publication
Date de publication:
04 2023
04 2023
Historique:
revised:
06
01
2023
received:
07
10
2022
accepted:
11
01
2023
medline:
18
4
2023
pubmed:
18
1
2023
entrez:
17
1
2023
Statut:
ppublish
Résumé
We performed a 1-year evaluation of a novel strategy of simultaneously analyzing single nucleotide variants (SNVs), copy number variants (CNVs) and copy-number-neutral Absence-of-Heterozygosity from Whole Exome Sequencing (WES) data for prenatal diagnosis of fetuses with ultrasound (US) anomalies and a non-causative QF-PCR result. After invasive diagnostics, whole exome parent-offspring trio-sequencing with exome-wide CNV analysis was performed in pregnancies with fetal US anomalies and a non-causative QF-PCR result (WES-CNV). On request, additional SNV-analysis, restricted to (the) requested gene panel(s) only (with the option of whole exome SNV-analysis afterward) was performed simultaneously (WES-CNV/SNV) or as rapid SNV-re-analysis, following a normal CNV analysis. In total, 415 prenatal samples were included. Following a non-causative QF-PCR result, WES-CNV analysis was initially requested for 74.3% of the chorionic villus (CV) samples and 45% of the amniotic fluid (AF) samples. In case WES-CNV analysis did not reveal a causative aberration, SNV-re-analysis was requested in 41.7% of the CV samples and 17.5% of the AF samples. All initial analyses could be finished within 2 weeks after sampling. For SNV-re-analysis during pregnancy, turn-around-times (TATs) varied between one and 8 days. We show a highly efficient all-in-one WES-based strategy, with short TATs, and the option of rapid SNV-re-analysis after a normal CNV result.
Substances chimiques
Nucleotides
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
527-543Informations de copyright
© 2023 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
Références
de Ligt J, Willemsen MH, van Bon BWM, et al. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med. 2012;367(20):1921-1929. https://doi.org/10.1056/nejmoa1206524
Guadagnolo D, Mastromoro G, Di Palam F, Pizzuti A, Marchionni E. Prenatal exome sequencing: Background, current practice and future perspectives - a systemic review. Diagnostics (Basel). 2021;11(2):224. https://doi.org/10.3390/diagnostics11020224
Deden C, Neveling K, Zafeiropopoulou D, et al. Rapid whole exome sequencing in pregnancies to identify the underlying genetic cause in fetuses with congenital anomalies detected by ultrasound imaging. Prenat Diagn. 2020;40(8):972-983. https://doi.org/10.1002/pd.5717
Lord J, McMullan DJ, Eberhardt RY, et al. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): a cohort study. Lancet. 2019;393(10173):747-757.
Petrovski S, Aggarwal V, Giordano JL, et al. Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study. Lancet. 2019;393(10173):758-767. https://doi.org/10.1016/s0140-6736(18)32042-7
Han J, Yang YD, He Y, et al. Rapid prenatal diagnosis of skeletal dysplasia using medical trio exome sequencing: Benefit for prenatal counseling and pregnancy management. Prenat Diagn. 2020;40(5):577-584. https://doi.org/10.1002/pd.5653
Qi Q, Jiang Y, Zhou X, et al. Simultaneous detection of CNVs and SNVs improves the diagnostic yield of fetuses with ultrasound anomalies and normal karyotypes. Genes. 2020;11(12):1397. https://doi.org/10.3390/genes11121397
Plagnol V, Curtis J, Epstein M, et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28(21):2747-2754. https://doi.org/10.1093/bioinformatics/bts526
Krumm N, Sudmant PH, Ko A, et al. NHLBI Exome Sequencing Project. Copy number variation detection and genotyping from exome sequence data. Genome Res. 2012;22:1525-1532.
de Ligt J, Boone PM, Pfundt R, et al. Platform comparison of detecting copy number variants with microarrays and whole-exome sequencing. Genom Data. 2014;2:144-146. https://doi.org/10.1016/j.gdata.2014.06.009
Lelieveld SH, Reijnders MRF, Pfundt R, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19(9):1194-1196. https://doi.org/10.1038/nn.4352
Yauy K, de Leeuw N, Yntema HG, Pfundt R, Gilissen C. Accurate detection of clinically relevant uniparental disomy from exome sequencing data. Genet Med. 2020;22(4):803-808. https://doi.org/10.1038/s41436-019-0704-x
van der Schoot V, Haer-Wigman L, Feenstra I, et al. Lessons learned from unsolicited findings in clinical exome sequencing of 16,482 individuals. Eur J Hum Genet. 2022;30(2):170-177. https://doi.org/10.1038/s41431-021-00964-0
McGowan-Jordan J, Hastings RJ, Moore S. An International system for human cytogenomic nomenclature (2020). Repr Cytogenet Genome Res. 2020;160(7-8). (ISSN 1424-8581).
Wapner RJ, Martin CL, Levy B, et al. Chromosomal microarray versus karyotyping for prenatal diagnosis. N Engl J Med. 2012;367(23):2175-2184. https://doi.org/10.1056/nejmoa1203382