Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 and ALYREF as new candidate risk genes Article Swipe
Lu Qiao
,
Le Xu
,
Lan Yu
,
Julia Wynn
,
Rebecca Hernan
,
Xueya Zhou
,
Christiana Farkouh‐Karoleski
,
Usha Krishnan
,
Julie Khlevner
,
Aliva De
,
Annette Zygmunt
,
Timothy M. Crombleholme
,
Foong‐Yen Lim
,
Howard Needelman
,
Robert A. Cusick
,
George B. Mychaliska
,
Brad W. Warner
,
Amy J. Wagner
,
Melissa E. Danko
,
Dai H. Chung
,
Douglas A. Potoka
,
Przemysław Kosiński
,
David J. McCulley
,
Mahmoud Elfiky
,
Kenneth S. Azarow
,
Elizabeth Fialkowski
,
David Schindel
,
Samuel Z. Soffer
,
Jane B. Lyon
,
Jill M. Zalieckas
,
Badri N. Vardarajan
,
Guðrún Aspelund
,
Vincent Duron
,
Frances A. High
,
Xin Sun
,
Patricia K. Donahoe
,
Yufeng Shen
,
Wendy K. Chung
·
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.06.01.21257928
YOU?
·
· 2021
· Open Access
·
· DOI: https://doi.org/10.1101/2021.06.01.21257928
Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (Lon Peptidase 1, Mitochondrial) and ALYREF (Aly/REF Export Factor) as novel candidate CDH genes based on de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 cases and 11,220 ancestry-matched population controls and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in familial cases. Approximately 3% of our CDH cohort was heterozygous with ultra-rare predicted damaging variants in LONP1 who have a range of clinical phenotypes including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium specific deletion of Lonp1 die immediately after birth and have reduced lung growth and branching that may at least partially explain the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.
Related Topics
Concepts
Congenital diaphragmatic hernia
Biology
Proband
Genetics
Population
Phenotype
Gene
Mutation
Fetus
Medicine
Pregnancy
Environmental health
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2021.06.01.21257928
- https://www.medrxiv.org/content/medrxiv/early/2021/06/04/2021.06.01.21257928.full.pdf
- OA Status
- green
- References
- 90
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3166179213
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3166179213Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2021.06.01.21257928Digital Object Identifier
- Title
-
Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 and ALYREF as new candidate risk genesWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2021Year of publication
- Publication date
-
2021-06-04Full publication date if available
- Authors
-
Lu Qiao, Le Xu, Lan Yu, Julia Wynn, Rebecca Hernan, Xueya Zhou, Christiana Farkouh‐Karoleski, Usha Krishnan, Julie Khlevner, Aliva De, Annette Zygmunt, Timothy M. Crombleholme, Foong‐Yen Lim, Howard Needelman, Robert A. Cusick, George B. Mychaliska, Brad W. Warner, Amy J. Wagner, Melissa E. Danko, Dai H. Chung, Douglas A. Potoka, Przemysław Kosiński, David J. McCulley, Mahmoud Elfiky, Kenneth S. Azarow, Elizabeth Fialkowski, David Schindel, Samuel Z. Soffer, Jane B. Lyon, Jill M. Zalieckas, Badri N. Vardarajan, Guðrún Aspelund, Vincent Duron, Frances A. High, Xin Sun, Patricia K. Donahoe, Yufeng Shen, Wendy K. ChungList of authors in order
- Landing page
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https://doi.org/10.1101/2021.06.01.21257928Publisher landing page
- PDF URL
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https://www.medrxiv.org/content/medrxiv/early/2021/06/04/2021.06.01.21257928.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.medrxiv.org/content/medrxiv/early/2021/06/04/2021.06.01.21257928.full.pdfDirect OA link when available
- Concepts
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Congenital diaphragmatic hernia, Biology, Proband, Genetics, Population, Phenotype, Gene, Mutation, Fetus, Medicine, Pregnancy, Environmental healthTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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90Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.small | 32 |
| abstract_inverted_index.trios | 56 |
| abstract_inverted_index.11,220 | 112 |
| abstract_inverted_index.ALYREF | 80 |
| abstract_inverted_index.Export | 82 |
| abstract_inverted_index.cases. | 149 |
| abstract_inverted_index.coding | 51 |
| abstract_inverted_index.cohort | 155 |
| abstract_inverted_index.design | 236 |
| abstract_inverted_index.genes. | 71 |
| abstract_inverted_index.growth | 203 |
| abstract_inverted_index.hernia | 3 |
| abstract_inverted_index.higher | 179 |
| abstract_inverted_index.number | 33 |
| abstract_inverted_index.severe | 7 |
| abstract_inverted_index.Factor) | 83 |
| abstract_inverted_index.anomaly | 9 |
| abstract_inverted_index.disease | 35 |
| abstract_inverted_index.domains | 142 |
| abstract_inverted_index.explain | 211 |
| abstract_inverted_index.further | 41 |
| abstract_inverted_index.genetic | 241 |
| abstract_inverted_index.humans. | 216 |
| abstract_inverted_index.largely | 133 |
| abstract_inverted_index.overall | 60 |
| abstract_inverted_index.reduced | 201 |
| abstract_inverted_index.studies | 242 |
| abstract_inverted_index.through | 126 |
| abstract_inverted_index.variant | 105 |
| abstract_inverted_index.(Aly/REF | 81 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.Although | 17 |
| abstract_inverted_index.analyses | 107 |
| abstract_inverted_index.analysis | 238 |
| abstract_inverted_index.analyzed | 48 |
| abstract_inverted_index.clinical | 170 |
| abstract_inverted_index.controls | 115 |
| abstract_inverted_index.damaging | 64, 161 |
| abstract_inverted_index.deletion | 192 |
| abstract_inverted_index.familial | 148 |
| abstract_inverted_index.findings | 218 |
| abstract_inverted_index.genetics | 21, 44 |
| abstract_inverted_index.membrane | 185 |
| abstract_inverted_index.specific | 191 |
| abstract_inverted_index.variants | 52, 93, 135, 162, 226 |
| abstract_inverted_index.Peptidase | 76 |
| abstract_inverted_index.anomalies | 174 |
| abstract_inverted_index.branching | 205 |
| abstract_inverted_index.candidate | 86 |
| abstract_inverted_index.clustered | 136 |
| abstract_inverted_index.confirmed | 58 |
| abstract_inverted_index.discovery | 97 |
| abstract_inverted_index.including | 172 |
| abstract_inverted_index.inherited | 132, 224 |
| abstract_inverted_index.mortality | 180, 214 |
| abstract_inverted_index.partially | 210 |
| abstract_inverted_index.performed | 103 |
| abstract_inverted_index.predicted | 160 |
| abstract_inverted_index.variants, | 67 |
| abstract_inverted_index.Congenital | 1 |
| abstract_inverted_index.anomalies. | 16, 245 |
| abstract_inverted_index.congenital | 8, 244 |
| abstract_inverted_index.enrichment | 62 |
| abstract_inverted_index.epithelium | 190 |
| abstract_inverted_index.especially | 68 |
| abstract_inverted_index.identified | 73, 117 |
| abstract_inverted_index.phenotypes | 171 |
| abstract_inverted_index.population | 114 |
| abstract_inverted_index.ultra-rare | 104, 131, 159 |
| abstract_inverted_index.accompanied | 13 |
| abstract_inverted_index.association | 106 |
| abstract_inverted_index.constrained | 70 |
| abstract_inverted_index.identified. | 39 |
| abstract_inverted_index.immediately | 196 |
| abstract_inverted_index.individuals | 177 |
| abstract_inverted_index.investigate | 42 |
| abstract_inverted_index.requirement | 182 |
| abstract_inverted_index.segregating | 144 |
| abstract_inverted_index.significant | 61 |
| abstract_inverted_index.contributing | 123 |
| abstract_inverted_index.established, | 29 |
| abstract_inverted_index.heterozygous | 134, 157 |
| abstract_inverted_index.implications | 233 |
| abstract_inverted_index.oxygenation. | 186 |
| abstract_inverted_index.pathogenesis | 24 |
| abstract_inverted_index.Approximately | 150 |
| abstract_inverted_index.diaphragmatic | 2 |
| abstract_inverted_index.Mitochondrial) | 78 |
| abstract_inverted_index.extracorporeal | 184 |
| abstract_inverted_index.proband-parent | 55 |
| abstract_inverted_index.ancestry-matched | 113 |
| cited_by_percentile_year | |
| corresponding_author_ids | https://openalex.org/A5112551457, https://openalex.org/A5018722278 |
| countries_distinct_count | 3 |
| institutions_distinct_count | 38 |
| corresponding_institution_ids | https://openalex.org/I2799503643 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8600000143051147 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.10530793 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |