TY - JOUR
T1 - Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach
AU - de Bruijn, Suzanne E.
AU - Panneman, Daan M.
AU - Weisschuh, Nicole
AU - Cadena, Elizabeth L.
AU - Boonen, Erica G.M.
AU - Holtes, Lara K.
AU - Astuti, Galuh D.N.
AU - Cremers, Frans P.M.
AU - Leijsten, Nico
AU - Corominas, Jordi
AU - Gilissen, Christian
AU - Skowronska, Anna
AU - Woodley, Jessica
AU - Beggs, Andrew D.
AU - Toulis, Vasileios
AU - Chen, Di
AU - Cheetham, Michael E.
AU - Hardcastle, Alison J.
AU - McLaren, Terri L.
AU - Lamey, Tina M.
AU - Thompson, Jennifer A.
AU - Chen, Fred K.
AU - de Roach, John N.
AU - Urwin, Isabella R.
AU - Sullivan, Lori S.
AU - Roosing, Susanne
N1 - Publisher Copyright:
Copyright © 2024 de Bruijn, Panneman, Weisschuh, Cadena, Boonen, Holtes, Astuti, Cremers, Leijsten, Corominas, Gilissen, Skowronska, Woodley, Beggs, Toulis, Chen, Cheetham, Hardcastle, McLaren, Lamey, Thompson, Chen, de Roach, Urwin, Sullivan, Roosing.
PY - 2024/10/23
Y1 - 2024/10/23
N2 - Introduction: Autosomal dominant retinitis pigmentosa type 17 (adRP, type RP17) is caused by complex structural variants (SVs) affecting a locus on chromosome 17 (chr17q22). The SVs disrupt the 3D regulatory landscape by altering the topologically associating domain (TAD) structure of the locus, creating novel TAD structures (neo-TADs) and ectopic enhancer-gene contacts. Currently, screening for RP17-associated SVs is not included in routine diagnostics given the complexity of the variants and a lack of cost-effective detection methods. The aim of this study was to accurately detect novel RP17-SVs by establishing a systematic and efficient workflow. Methods: Genetically unexplained probands diagnosed with adRP (n = 509) from an international cohort were screened using a smMIPs or genomic qPCR-based approach tailored for the RP17 locus. Suspected copy number changes were validated using high-density SNP-array genotyping, and SV breakpoint characterization was performed by mutation-specific breakpoint PCR, genome sequencing and, if required, optical genome mapping. In silico modeling of novel SVs was performed to predict the formation of neo-TADs and whether ectopic contacts between the retinal enhancers and the GDPD1-promoter could be formed. Results: Using this workflow, potential RP17-SVs were detected in eight probands of which seven were confirmed. Two novel SVs were identified that are predicted to cause TAD rearrangement and retinal enhancer-GDPD1 contact, one from Germany (DE-SV9) and three with the same SV from the United States (US-SV10). Previously reported RP17-SVs were also identified in three Australian probands, one with UK-SV2 and two with SA-SV3. Discussion: In summary, we describe a validated multi-step pipeline for reliable and efficient RP17-SV discovery and expand the range of disease-associated SVs. Based on these data, RP17-SVs can be considered a frequent cause of adRP which warrants the inclusion of RP17-screening as a standard diagnostic test for this disease.
AB - Introduction: Autosomal dominant retinitis pigmentosa type 17 (adRP, type RP17) is caused by complex structural variants (SVs) affecting a locus on chromosome 17 (chr17q22). The SVs disrupt the 3D regulatory landscape by altering the topologically associating domain (TAD) structure of the locus, creating novel TAD structures (neo-TADs) and ectopic enhancer-gene contacts. Currently, screening for RP17-associated SVs is not included in routine diagnostics given the complexity of the variants and a lack of cost-effective detection methods. The aim of this study was to accurately detect novel RP17-SVs by establishing a systematic and efficient workflow. Methods: Genetically unexplained probands diagnosed with adRP (n = 509) from an international cohort were screened using a smMIPs or genomic qPCR-based approach tailored for the RP17 locus. Suspected copy number changes were validated using high-density SNP-array genotyping, and SV breakpoint characterization was performed by mutation-specific breakpoint PCR, genome sequencing and, if required, optical genome mapping. In silico modeling of novel SVs was performed to predict the formation of neo-TADs and whether ectopic contacts between the retinal enhancers and the GDPD1-promoter could be formed. Results: Using this workflow, potential RP17-SVs were detected in eight probands of which seven were confirmed. Two novel SVs were identified that are predicted to cause TAD rearrangement and retinal enhancer-GDPD1 contact, one from Germany (DE-SV9) and three with the same SV from the United States (US-SV10). Previously reported RP17-SVs were also identified in three Australian probands, one with UK-SV2 and two with SA-SV3. Discussion: In summary, we describe a validated multi-step pipeline for reliable and efficient RP17-SV discovery and expand the range of disease-associated SVs. Based on these data, RP17-SVs can be considered a frequent cause of adRP which warrants the inclusion of RP17-screening as a standard diagnostic test for this disease.
KW - gene diagnostics
KW - gene regulation
KW - inherited retinal dystrophies
KW - retinitis pigmentosa
KW - structural variants
UR - http://www.scopus.com/inward/record.url?scp=85208648038&partnerID=8YFLogxK
U2 - 10.3389/fgene.2024.1469686
DO - 10.3389/fgene.2024.1469686
M3 - Article
C2 - 39507620
AN - SCOPUS:85208648038
SN - 1664-8021
VL - 15
JO - Frontiers in Genetics
JF - Frontiers in Genetics
M1 - 1469686
ER -