Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders
© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ..
BACKGROUND: Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression.
METHODS: We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance.
RESULTS: We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs.
CONCLUSION: Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:61 |
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| Enthalten in: |
Journal of medical genetics - 61(2023), 1 vom: 21. Dez., Seite 47-56 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Riquin, Kevin [VerfasserIn] |
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| Links: |
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| Themen: |
Central Nervous System Diseases |
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| Anmerkungen: |
Date Completed 25.12.2023 Date Revised 25.12.2023 published: Electronic Citation Status MEDLINE |
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| doi: |
10.1136/jmg-2023-109263 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM359952828 |
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| 520 | |a © Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ. | ||
| 520 | |a BACKGROUND: Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression | ||
| 520 | |a METHODS: We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance | ||
| 520 | |a RESULTS: We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs | ||
| 520 | |a CONCLUSION: Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols | ||
| 650 | 4 | |a Journal Article | |
| 650 | 4 | |a Central Nervous System Diseases | |
| 650 | 4 | |a Clinical Laboratory Techniques | |
| 650 | 4 | |a Genetic Research | |
| 650 | 4 | |a Genetic Testing | |
| 650 | 4 | |a Genomics | |
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| 700 | 1 | |a Mercier, Sandra |e verfasserin |4 aut | |
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| 700 | 1 | |a Colin, Estelle |e verfasserin |4 aut | |
| 700 | 1 | |a Bonneau, Dominique |e verfasserin |4 aut | |
| 700 | 1 | |a Pasquier, Laurent |e verfasserin |4 aut | |
| 700 | 1 | |a Odent, Sylvie |e verfasserin |4 aut | |
| 700 | 1 | |a Le Guillou Horn, Xavier Maximin |e verfasserin |4 aut | |
| 700 | 1 | |a Le Guyader, Gwenaël |e verfasserin |4 aut | |
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