Comprehensive variant calling from whole‐genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia
Article Swipe
Thomas J. Nicholas
,
Najla Al‐Sweel
,
Andrew Farrell
,
Rong Mao
,
Pınar Bayrak‐Toydemir
,
Christine E. Miller
,
Dawn Bentley
,
Rachel Palmquist
,
Barry Moore
,
Edgar J. Hernández
,
Michael J. Cormier
,
E. D. Fredrickson
,
Katherine Noble
,
Shawn Rynearson
,
Carson Holt
,
Mary Anne Karren
,
Joshua L. Bonkowsky
,
Martin Tristani‐Firouzi
,
Mark Yandell
,
Gábor Marth
,
Aaron R. Quinlan
,
Luca Brunelli
,
Reha M. Toydemir
,
Brian J. Shayota
,
John C. Carey
,
Steven E. Boyden
,
Sabrina Malone Jenkins
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1002/mgg3.1888
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1002/mgg3.1888
Background Genetic disorders contribute to significant morbidity and mortality in critically ill newborns. Despite advances in genome sequencing technologies, a majority of neonatal cases remain unsolved. Complex structural variants (SVs) often elude conventional genome sequencing variant calling pipelines and will explain a portion of these unsolved cases. Methods As part of the Utah NeoSeq project, we used a research‐based, rapid whole‐genome sequencing (WGS) protocol to investigate the genomic etiology for a newborn with a left‐sided congenital diaphragmatic hernia (CDH) and cardiac malformations, whose mother also had a history of CDH and atrial septal defect. Results Using both a novel, alignment‐free and traditional alignment‐based variant callers, we identified a maternally inherited complex SV on chromosome 8, consisting of an inversion flanked by deletions. This complex inversion, further confirmed using orthogonal molecular techniques, disrupts the ZFPM2 gene, which is associated with both CDH and various congenital heart defects. Conclusions Our results demonstrate that complex structural events, which often are unidentifiable or not reported by clinically validated testing procedures, can be discovered and accurately characterized with conventional, short‐read sequencing and underscore the utility of WGS as a first‐line diagnostic tool.
Related Topics
Concepts
Congenital diaphragmatic hernia
Chromosomal inversion
Whole genome sequencing
Genetics
Genome
Computational biology
Exome sequencing
Biology
Chromosomal rearrangement
DNA sequencing
Chromosome
Medicine
Gene
Karyotype
Mutation
Fetus
Pregnancy
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/mgg3.1888
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mgg3.1888
- OA Status
- gold
- Cited By
- 8
- References
- 67
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4210243964
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4210243964Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1002/mgg3.1888Digital Object Identifier
- Title
-
Comprehensive variant calling from whole‐genome sequencing identifies a complex inversion that disrupts
ZFPM2 in familial congenital diaphragmatic herniaWork title - Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-02-04Full publication date if available
- Authors
-
Thomas J. Nicholas, Najla Al‐Sweel, Andrew Farrell, Rong Mao, Pınar Bayrak‐Toydemir, Christine E. Miller, Dawn Bentley, Rachel Palmquist, Barry Moore, Edgar J. Hernández, Michael J. Cormier, E. D. Fredrickson, Katherine Noble, Shawn Rynearson, Carson Holt, Mary Anne Karren, Joshua L. Bonkowsky, Martin Tristani‐Firouzi, Mark Yandell, Gábor Marth, Aaron R. Quinlan, Luca Brunelli, Reha M. Toydemir, Brian J. Shayota, John C. Carey, Steven E. Boyden, Sabrina Malone JenkinsList of authors in order
- Landing page
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https://doi.org/10.1002/mgg3.1888Publisher landing page
- PDF URL
-
https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mgg3.1888Direct link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/mgg3.1888Direct OA link when available
- Concepts
-
Congenital diaphragmatic hernia, Chromosomal inversion, Whole genome sequencing, Genetics, Genome, Computational biology, Exome sequencing, Biology, Chromosomal rearrangement, DNA sequencing, Chromosome, Medicine, Gene, Karyotype, Mutation, Fetus, PregnancyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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8Total citation count in OpenAlex
- Citations by year (recent)
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2025: 1, 2024: 1, 2023: 2, 2022: 4Per-year citation counts (last 5 years)
- References (count)
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67Number 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.identified | 107 |
| abstract_inverted_index.inversion, | 125 |
| abstract_inverted_index.maternally | 109 |
| abstract_inverted_index.orthogonal | 129 |
| abstract_inverted_index.sequencing | 18, 35, 62, 176 |
| abstract_inverted_index.structural | 28, 153 |
| abstract_inverted_index.underscore | 178 |
| abstract_inverted_index.Conclusions | 147 |
| abstract_inverted_index.demonstrate | 150 |
| abstract_inverted_index.investigate | 66 |
| abstract_inverted_index.procedures, | 166 |
| abstract_inverted_index.significant | 6 |
| abstract_inverted_index.techniques, | 131 |
| abstract_inverted_index.traditional | 102 |
| abstract_inverted_index.conventional | 33 |
| abstract_inverted_index.first‐line | 185 |
| abstract_inverted_index.left‐sided | 75 |
| abstract_inverted_index.short‐read | 175 |
| abstract_inverted_index.characterized | 172 |
| abstract_inverted_index.conventional, | 174 |
| abstract_inverted_index.diaphragmatic | 77 |
| abstract_inverted_index.technologies, | 19 |
| abstract_inverted_index.malformations, | 82 |
| abstract_inverted_index.unidentifiable | 158 |
| abstract_inverted_index.whole‐genome | 61 |
| abstract_inverted_index.alignment‐free | 100 |
| abstract_inverted_index.alignment‐based | 103 |
| abstract_inverted_index.research‐based, | 59 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 90 |
| corresponding_author_ids | https://openalex.org/A5058850998, https://openalex.org/A5050614507 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 27 |
| corresponding_institution_ids | https://openalex.org/I223532165 |
| sustainable_development_goals[0].id | https://metadata.un.org/sdg/3 |
| sustainable_development_goals[0].score | 0.8500000238418579 |
| sustainable_development_goals[0].display_name | Good health and well-being |
| citation_normalized_percentile.value | 0.72313482 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |