- Title
- Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants
- Creator
- Bournazos, Adam M.; Riley, Lisa G.; Beshay, Victoria; Boggs, Kirsten; Bojadzieva, Jasmina; Brown, Natasha J.; Bryen, Samantha J.; Buckley, Michael F.; Chong, Belinda; Davis, Mark R.; Dawes, Ruebena; Delatycki, Martin; Bommireddipalli, Shobhana; Donaldson, L; Downie, L; Edwards, C; Edwards, M; Engel, A; Ewans, LJ; Faiz, F; Fennell, A; Field, M; Freckmann, ML; Ades, Lesley; Gallacher, L; Gear, R; Goel, Himanshu; Goh, S; Goodwin, L; Hanna, B; Harraway, J; Higgins, M; Ho, G; Hopper, BK; Akesson, Lauren S.; Horton, AE; Hunter, MF; Huq, AJ; Josephi-Taylor, S; Joshi, H; Kirk, E; Krzesinski, E; Kumar, KR; Lemckert, F; Leventer, RJ; Al-Shinnag, Mohammad; Lindsey-Temple, SE; Lunke, S; Ma, A; Macaskill, S; Mallawaarachchi, A; Marty, M; Marum, JE; McCarthy, HJ; Menezes, MP; McLean, A; Alexander, Stephen I.; Milnes, D; Mohammad, S; Mowat, D; Niaz, A; Palmer, EE; Patel, C; Patel, SG; Phelan, D; Pinner, JR; Rajagopalan, S; Archibald, Alison D.; Regan, M; Rodgers, J; Rodrigues, M; Roxburgh, RH; Sachdev, R; Roscioli, T; Samarasekera, R; Sandaradura, SA; Savva, E; Schindler, T; Balasubramaniam, Shanti; Shah, M; Sinnerbrink, IB; Smith, JM; Smith, RJ; Springer, A; Stark, Z; Strom, SP; Sue, CM; Tan, K; Tan, TY; Berman, Yemima; Tantsis, E; Tchan, MC; Thompson, BA; Trainer, AH; van Spaendonck-Zwarts, K; Walsh, R; Warwick, L; White, S; White, SM; Williams, MG
- Relation
- Genetics in Medicine Vol. 24, Issue 1, p. 130-145
- Publisher Link
- http://dx.doi.org/10.1016/j.gim.2021.09.001
- Publisher
- Elsevier
- Resource Type
- journal article
- Date
- 2022
- Description
- Purpose: Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). Methods: A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. Results: Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. Conclusion: RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data.
- Subject
- genetic diagnosis; noncoding variant; pre-mRNA splicing; putative splice variant; variant classification
- Identifier
- http://hdl.handle.net/1959.13/1465743
- Identifier
- uon:47363
- Identifier
- ISSN:1098-3600
- Language
- eng
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