Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridia Article Swipe
Hildegard Nikki Hall
,
David Parry
,
Mihail Halachev
,
Kathleen A. Williamson
,
Kevin Donnelly
,
Jose Campos Parada
,
Shipra Bhatia
,
Jeffrey T. Joseph
,
Simon Holden
,
Trine Prescott
,
Pierre Bitoun
,
Edwin P. Kirk
,
Ruth Newbury‐Ecob
,
Katherine Lachlan
,
Juan Bernar
,
Veronica van Heyningen
,
David Fitzpatrick
,
Alison Meynert
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1136/jmg-2023-109181
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1136/jmg-2023-109181
Background Classic aniridia is a highly penetrant autosomal dominant disorder characterised by congenital absence of the iris, foveal hypoplasia, optic disc anomalies and progressive opacification of the cornea. >90% of cases of classic aniridia are caused by heterozygous, loss-of-function variants affecting the PAX6 locus. Methods Short-read whole genome sequencing was performed on 51 (39 affected) individuals from 37 different families who had screened negative for mutations in the PAX6 coding region. Results Likely causative mutations were identified in 22 out of 37 (59%) families. In 19 out of 22 families, the causative genomic changes have an interpretable deleterious impact on the PAX6 locus. Of these 19 families, 1 has a novel heterozygous PAX6 frameshift variant missed on previous screens, 4 have single nucleotide variants (SNVs) (one novel) affecting essential splice sites of PAX6 5′ non-coding exons and 2 have deep intronic SNV (one novel) resulting in gain of a donor splice site. In 12 out of 19, the causative variants are large-scale structural variants; 5 have partial or whole gene deletions of PAX6 , 3 have deletions encompassing critical PAX6 cis -regulatory elements, 2 have balanced inversions with disruptive breakpoints within the PAX6 locus and 2 have complex rearrangements disrupting PAX6 . The remaining 3 of 22 families have deletions encompassing FOXC1 (a known cause of atypical aniridia). Seven of the causative variants occurred de novo and one cosegregated with familial aniridia. We were unable to establish inheritance status in the remaining probands. No plausibly causative SNVs were identified in PAX6 cis -regulatory elements. Conclusion Whole genome sequencing proves to be an effective diagnostic test in most individuals with previously unexplained aniridia.
Related Topics
Concepts
Aniridia
PAX6
Genetics
Biology
Locus (genetics)
Proband
Breakpoint
Frameshift mutation
Exon
Gene
Mutation
Chromosome
Transcription factor
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1136/jmg-2023-109181
- https://jmg.bmj.com/content/jmedgenet/early/2023/11/30/jmg-2023-109181.full.pdf
- OA Status
- hybrid
- Cited By
- 4
- References
- 51
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4389207608
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4389207608Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1136/jmg-2023-109181Digital Object Identifier
- Title
-
Short-read whole genome sequencing identifies causative variants in most individuals with previously unexplained aniridiaWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2023Year of publication
- Publication date
-
2023-11-30Full publication date if available
- Authors
-
Hildegard Nikki Hall, David Parry, Mihail Halachev, Kathleen A. Williamson, Kevin Donnelly, Jose Campos Parada, Shipra Bhatia, Jeffrey T. Joseph, Simon Holden, Trine Prescott, Pierre Bitoun, Edwin P. Kirk, Ruth Newbury‐Ecob, Katherine Lachlan, Juan Bernar, Veronica van Heyningen, David Fitzpatrick, Alison MeynertList of authors in order
- Landing page
-
https://doi.org/10.1136/jmg-2023-109181Publisher landing page
- PDF URL
-
https://jmg.bmj.com/content/jmedgenet/early/2023/11/30/jmg-2023-109181.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
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https://jmg.bmj.com/content/jmedgenet/early/2023/11/30/jmg-2023-109181.full.pdfDirect OA link when available
- Concepts
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Aniridia, PAX6, Genetics, Biology, Locus (genetics), Proband, Breakpoint, Frameshift mutation, Exon, Gene, Mutation, Chromosome, Transcription factorTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
4Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2, 2024: 2Per-year citation counts (last 5 years)
- References (count)
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51Number of works referenced by this work
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-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.families | 59, 207 |
| abstract_inverted_index.intronic | 140 |
| abstract_inverted_index.negative | 63 |
| abstract_inverted_index.occurred | 223 |
| abstract_inverted_index.previous | 117 |
| abstract_inverted_index.screened | 62 |
| abstract_inverted_index.screens, | 118 |
| abstract_inverted_index.variants | 39, 123, 159, 222 |
| abstract_inverted_index.affected) | 54 |
| abstract_inverted_index.affecting | 40, 127 |
| abstract_inverted_index.aniridia. | 231, 271 |
| abstract_inverted_index.anomalies | 21 |
| abstract_inverted_index.autosomal | 7 |
| abstract_inverted_index.causative | 73, 91, 158, 221, 245 |
| abstract_inverted_index.deletions | 170, 176, 209 |
| abstract_inverted_index.different | 58 |
| abstract_inverted_index.effective | 262 |
| abstract_inverted_index.elements, | 182 |
| abstract_inverted_index.elements. | 253 |
| abstract_inverted_index.essential | 128 |
| abstract_inverted_index.establish | 236 |
| abstract_inverted_index.families, | 89, 106 |
| abstract_inverted_index.families. | 83 |
| abstract_inverted_index.mutations | 65, 74 |
| abstract_inverted_index.penetrant | 6 |
| abstract_inverted_index.performed | 50 |
| abstract_inverted_index.plausibly | 244 |
| abstract_inverted_index.probands. | 242 |
| abstract_inverted_index.remaining | 203, 241 |
| abstract_inverted_index.resulting | 144 |
| abstract_inverted_index.variants; | 163 |
| abstract_inverted_index.Background | 0 |
| abstract_inverted_index.Conclusion | 254 |
| abstract_inverted_index.Short-read | 45 |
| abstract_inverted_index.aniridia). | 217 |
| abstract_inverted_index.congenital | 12 |
| abstract_inverted_index.diagnostic | 263 |
| abstract_inverted_index.disrupting | 199 |
| abstract_inverted_index.disruptive | 188 |
| abstract_inverted_index.frameshift | 113 |
| abstract_inverted_index.identified | 76, 248 |
| abstract_inverted_index.inversions | 186 |
| abstract_inverted_index.non-coding | 134 |
| abstract_inverted_index.nucleotide | 122 |
| abstract_inverted_index.previously | 269 |
| abstract_inverted_index.sequencing | 48, 257 |
| abstract_inverted_index.structural | 162 |
| abstract_inverted_index.-regulatory | 181, 252 |
| abstract_inverted_index.breakpoints | 189 |
| abstract_inverted_index.deleterious | 97 |
| abstract_inverted_index.hypoplasia, | 18 |
| abstract_inverted_index.individuals | 55, 267 |
| abstract_inverted_index.inheritance | 237 |
| abstract_inverted_index.large-scale | 161 |
| abstract_inverted_index.progressive | 23 |
| abstract_inverted_index.unexplained | 270 |
| abstract_inverted_index.cosegregated | 228 |
| abstract_inverted_index.encompassing | 177, 210 |
| abstract_inverted_index.heterozygous | 111 |
| abstract_inverted_index.characterised | 10 |
| abstract_inverted_index.heterozygous, | 37 |
| abstract_inverted_index.interpretable | 96 |
| abstract_inverted_index.opacification | 24 |
| abstract_inverted_index.rearrangements | 198 |
| abstract_inverted_index.loss-of-function | 38 |
| cited_by_percentile_year.max | 97 |
| cited_by_percentile_year.min | 94 |
| corresponding_author_ids | https://openalex.org/A5083173934 |
| countries_distinct_count | 5 |
| institutions_distinct_count | 18 |
| corresponding_institution_ids | https://openalex.org/I4210158898, https://openalex.org/I98677209 |
| citation_normalized_percentile.value | 0.74009678 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |