High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders.
Journal
Human genetics
ISSN: 1432-1203
Titre abrégé: Hum Genet
Pays: Germany
ID NLM: 7613873
Informations de publication
Date de publication:
Jun 2023
Jun 2023
Historique:
received:
21
01
2023
accepted:
05
04
2023
medline:
15
5
2023
pubmed:
20
4
2023
entrez:
19
04
2023
Statut:
ppublish
Résumé
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
Identifiants
pubmed: 37076692
doi: 10.1007/s00439-023-02553-1
pii: 10.1007/s00439-023-02553-1
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
773-783Subventions
Organisme : GIRCI nord ouest
ID : AAP-AE_19-36
Organisme : Recherche Innovation Normandie
ID : RIN2018
Organisme : France Génomique National infrastructure
ID : ANR-10-INBS-09
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
100,000 Genomes Project Pilot Investigators, Smedley D, Smith KR, et al (2021) 100,000 genomes pilot on rare-disease diagnosis in health care—preliminary report. N Engl J Med 385:1868–1880. https://doi.org/10.1056/NEJMoa2035790
Angius A, Uva P, Buers I et al (2016) Bi-allelic mutations in KLHL7 cause a Crisponi/CISS1-like phenotype associated with early-onset retinitis pigmentosa. Am J Hum Genet 99:236–245. https://doi.org/10.1016/j.ajhg.2016.05.026
doi: 10.1016/j.ajhg.2016.05.026
pubmed: 27392078
pmcid: 5005468
Baux D, Van Goethem C, Ardouin O et al (2021) MobiDetails: online DNA variants interpretation. Eur J Hum Genet 29:356–360. https://doi.org/10.1038/s41431-020-00755-z
doi: 10.1038/s41431-020-00755-z
pubmed: 33161418
Beyter D, Ingimundardottir H, Oddsson A et al (2021) Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits. Nat Genet 53:779–786. https://doi.org/10.1038/s41588-021-00865-4
doi: 10.1038/s41588-021-00865-4
pubmed: 33972781
Bruel A-L, Bigoni S, Kennedy J et al (2017) Expanding the clinical spectrum of recessive truncating mutations of KLHL7 to a Bohring-Opitz-like phenotype. J Med Genet 54:830–835. https://doi.org/10.1136/jmedgenet-2017-104748
doi: 10.1136/jmedgenet-2017-104748
pubmed: 29074562
Clarke J, Wu H-C, Jayasinghe L et al (2009) Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 4:265–270. https://doi.org/10.1038/nnano.2009.12
doi: 10.1038/nnano.2009.12
pubmed: 19350039
Colin E, Duffourd Y, Tisserant E et al (2022) OMIXCARE: OMICS technologies solved about 33% of the patients with heterogeneous rare neuro-developmental disorders and negative exome sequencing results and identified 13% additional candidate variants. Front Cell Dev Biol 10:1021785. https://doi.org/10.3389/fcell.2022.1021785
doi: 10.3389/fcell.2022.1021785
pubmed: 36393831
pmcid: 9650323
Coursimault J, Cassinari K, Lecoquierre F et al (2022) Deep intronic NIPBL de novo mutations and differential diagnoses revealed by whole genome and RNA sequencing in Cornelia de Lange syndrome patients. Hum Mutat. https://doi.org/10.1002/humu.24438
doi: 10.1002/humu.24438
pubmed: 35842780
Danis D, Jacobsen JOB, Balachandran P et al (2022) SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing. Genome Med 14:44. https://doi.org/10.1186/s13073-022-01046-6
doi: 10.1186/s13073-022-01046-6
pubmed: 35484572
pmcid: 9047340
De Coster W, De Rijk P, De Roeck A et al (2019) Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome. Genome Res 29:1178–1187. https://doi.org/10.1101/gr.244939.118
doi: 10.1101/gr.244939.118
pubmed: 31186302
pmcid: 6633254
De Coster W, Weissensteiner MH, Sedlazeck FJ (2021) Towards population-scale long-read sequencing. Nat Rev Genet 22:572–587. https://doi.org/10.1038/s41576-021-00367-3
doi: 10.1038/s41576-021-00367-3
pubmed: 34050336
pmcid: 8161719
de Sainte Agathe J-M, Filser M, Isidor B et al (2023) SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation. Hum Genom 17:7. https://doi.org/10.1186/s40246-023-00451-1
doi: 10.1186/s40246-023-00451-1
Deciphering Developmental Disorders Study (2017) Prevalence and architecture of de novo mutations in developmental disorders. Nature 542:433–438. https://doi.org/10.1038/nature21062
doi: 10.1038/nature21062
Dong Z, Yan J, Xu F et al (2019) Genome sequencing explores complexity of chromosomal abnormalities in recurrent miscarriage. Am J Hum Genet 105:1102–1111. https://doi.org/10.1016/j.ajhg.2019.10.003
doi: 10.1016/j.ajhg.2019.10.003
pubmed: 31679651
pmcid: 6904795
Eid J, Fehr A, Gray J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138. https://doi.org/10.1126/science.1162986
doi: 10.1126/science.1162986
pubmed: 19023044
Ellingford JM, Ahn JW, Bagnall RD et al (2022) Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 14:73. https://doi.org/10.1186/s13073-022-01073-3
doi: 10.1186/s13073-022-01073-3
pubmed: 35850704
pmcid: 9295495
Gilissen C, Hehir-Kwa JY, Thung DT et al (2014) Genome sequencing identifies major causes of severe intellectual disability. Nature 511:344–347. https://doi.org/10.1038/nature13394
doi: 10.1038/nature13394
pubmed: 24896178
Hiatt SM, Lawlor JMJ, Handley LH et al (2021) Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders. HGG Adv 2:100023. https://doi.org/10.1016/j.xhgg.2021.100023
doi: 10.1016/j.xhgg.2021.100023
pubmed: 33937879
pmcid: 8087252
Jeffries L, Olivieri JE, Ji W et al (2019) Two siblings with a novel nonsense variant provide further delineation of the spectrum of recessive KLHL7 diseases. Eur J Med Genet 62:103551. https://doi.org/10.1016/j.ejmg.2018.10.003
doi: 10.1016/j.ejmg.2018.10.003
pubmed: 30300710
Kaplanis J, Samocha KE, Wiel L et al (2020) Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 586:757–762. https://doi.org/10.1038/s41586-020-2832-5
doi: 10.1038/s41586-020-2832-5
pubmed: 33057194
pmcid: 7116826
Köhler S, Schulz MH, Krawitz P et al (2009) Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am J Hum Genet 85:457–464. https://doi.org/10.1016/j.ajhg.2009.09.003
doi: 10.1016/j.ajhg.2009.09.003
pubmed: 19800049
pmcid: 2756558
Kovanda A, Zimani AN, Peterlin B (2021) How to design a national genomic project-a systematic review of active projects. Hum Genom 15:20. https://doi.org/10.1186/s40246-021-00315-6
doi: 10.1186/s40246-021-00315-6
Latorre-Pellicer A, Gil-Salvador M, Parenti I et al (2021) Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Sci Rep 11:15459. https://doi.org/10.1038/s41598-021-94958-z
doi: 10.1038/s41598-021-94958-z
pubmed: 34326454
pmcid: 8322329
Lee H, Huang AY, Wang L-K et al (2020) Diagnostic utility of transcriptome sequencing for rare Mendelian diseases. Genet Med 22:490–499. https://doi.org/10.1038/s41436-019-0672-1
doi: 10.1038/s41436-019-0672-1
pubmed: 31607746
Lévy Y (2016) Genomic medicine 2025: France in the race for precision medicine. Lancet 388:2872. https://doi.org/10.1016/S0140-6736(16)32467-9
doi: 10.1016/S0140-6736(16)32467-9
pubmed: 27979406
Mantere T, Kersten S, Hoischen A (2019) Long-read sequencing emerging in medical genetics. Front Genet 10:426. https://doi.org/10.3389/fgene.2019.00426
doi: 10.3389/fgene.2019.00426
pubmed: 31134132
pmcid: 6514244
Olson ND, Wagner J, McDaniel J et al (2022) PrecisionFDA truth challenge V2: calling variants from short and long reads in difficult-to-map regions. Cell Genom 2:100129. https://doi.org/10.1016/j.xgen.2022.100129
doi: 10.1016/j.xgen.2022.100129
pubmed: 35720974
pmcid: 9205427
Pauper M, Kucuk E, Wenger AM et al (2021) Long-read trio sequencing of individuals with unsolved intellectual disability. Eur J Hum Genet 29:637–648. https://doi.org/10.1038/s41431-020-00770-0
doi: 10.1038/s41431-020-00770-0
pubmed: 33257779
Poplin R, Chang P-C, Alexander D et al (2018) A universal SNP and small-indel variant caller using deep neural networks. Nat Biotechnol 36:983–987. https://doi.org/10.1038/nbt.4235
doi: 10.1038/nbt.4235
pubmed: 30247488
Quinodoz M, Peter VG, Bedoni N et al (2021) AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nat Commun 12:518. https://doi.org/10.1038/s41467-020-20584-4
doi: 10.1038/s41467-020-20584-4
pubmed: 33483490
pmcid: 7822856
Richards S, Aziz N, Bale S et al (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17:405–424. https://doi.org/10.1038/gim.2015.30
doi: 10.1038/gim.2015.30
pubmed: 25741868
pmcid: 4544753
Souche E, Beltran S, Brosens E et al (2022) Recommendations for whole genome sequencing in diagnostics for rare diseases. Eur J Hum Genet 30:1017–1021. https://doi.org/10.1038/s41431-022-01113-x
doi: 10.1038/s41431-022-01113-x
pubmed: 35577938
pmcid: 9437083
van El CG, Cornel MC, Borry P et al (2013) Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet 21:580–584. https://doi.org/10.1038/ejhg.2013.46
doi: 10.1038/ejhg.2013.46
pubmed: 23676617
pmcid: 3658192
Walsh T, Casadei S, Munson KM et al (2021) CRISPR-Cas9/long-read sequencing approach to identify cryptic mutations in BRCA1 and other tumour suppressor genes. J Med Genet 58:850–852. https://doi.org/10.1136/jmedgenet-2020-107320
doi: 10.1136/jmedgenet-2020-107320
pubmed: 33060287
Wenger AM, Peluso P, Rowell WJ et al (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 37:1155–1162. https://doi.org/10.1038/s41587-019-0217-9
doi: 10.1038/s41587-019-0217-9
pubmed: 31406327
pmcid: 6776680
Wu Z, Jiang Z, Li T et al (2021) Structural variants in the Chinese population and their impact on phenotypes, diseases and population adaptation. Nat Commun 12:6501. https://doi.org/10.1038/s41467-021-26856-x
doi: 10.1038/s41467-021-26856-x
pubmed: 34764282
pmcid: 8586011
Yépez VA, Gusic M, Kopajtich R et al (2022) Clinical implementation of RNA sequencing for Mendelian disease diagnostics. Genome Med 14:38. https://doi.org/10.1186/s13073-022-01019-9
doi: 10.1186/s13073-022-01019-9
pubmed: 35379322
pmcid: 8981716