Journal article
Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants
Genetics in medicine, Vol.24(1), pp.130-145
01/2022
DOI: 10.1016/j.gim.2021.09.001
PMID: 34906502
Abstract
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).
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.
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.
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.
Details
- Title: Subtitle
- Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants
- Creators
- Adam M Bournazos - The University of SydneyLisa G Riley - The University of SydneyShobhana Bommireddipalli - Children's Hospital at WestmeadLesley Ades - The University of SydneyLauren S Akesson - The University of MelbourneMohammad Al-Shinnag - The University of QueenslandStephen I Alexander - The University of SydneyAlison D Archibald - The University of MelbourneShanti Balasubramaniam - The University of SydneyYemima Berman - Royal North Shore HospitalVictoria Beshay - Peter MacCallum Cancer CentreKirsten Boggs - Boston Children's HospitalJasmina Bojadzieva - Austin HealthNatasha J Brown - The University of MelbourneSamantha J Bryen - The University of SydneyMichael F Buckley - New South Wales Department of HealthBelinda Chong - Victorian Clinical Genetics ServicesMark R Davis - Pathwest Laboratory MedicineRuebena Dawes - The University of SydneyMartin Delatycki - The University of MelbourneLiz Donaldson - The Royal Melbourne HospitalLilian Downie - The University of MelbourneCaitlin Edwards - Pathwest Laboratory MedicineMatthew Edwards - The University of SydneyAmanda Engel - Canberra HospitalLisa J Ewans - The University of SydneyFathimath Faiz - Pathwest Laboratory MedicineAndrew Fennell - The University of MelbourneMichael Field - Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, AustraliaMary-Louise Freckmann - Canberra HospitalLyndon Gallacher - The University of MelbourneRussell Gear - Victorian Clinical Genetics ServicesHimanshu Goel - University of Newcastle AustraliaShuxiang Goh - Liverpool HospitalLinda Goodwin - Nepean HospitalBernadette Hanna - Westmead HospitalJames Harraway - Sullivan Nicolaides PathologyMegan Higgins - Royal Brisbane and Women's HospitalGladys Ho - The University of SydneyBruce K Hopper - Forster Genetics, Forster, New South Wales, AustraliaAri E Horton - The University of MelbourneMatthew F Hunter - Monash UniversityAamira J Huq - The University of MelbourneSarah Josephi-Taylor - Children's Hospital at WestmeadHimanshu Joshi - Children's Hospital at WestmeadEdwin Kirk - Sydney Children’s Hospitals NetworkEmma Krzesinski - Monash UniversityKishore R Kumar - Garvan Institute of Medical ResearchFrances Lemckert - The University of SydneyRichard J Leventer - The University of MelbourneSuzanna E Lindsey-Temple - UNSW SydneySebastian Lunke - The University of MelbourneAlan Ma - The University of SydneySteven Macaskill - Peter MacCallum Cancer CentreAmali Mallawaarachchi - Garvan Institute of Medical ResearchMelanie Marty - Victorian Clinical Genetics ServicesJustine E Marum - Victorian Clinical Genetics ServicesHugh J McCarthy - The University of SydneyManoj P Menezes - The University of SydneyAlison McLean - Liverpool HospitalDi Milnes - Royal Brisbane and Women's HospitalShekeeb Mohammad - The University of SydneyDavid Mowat - UNSW SydneyAram Niaz - Children's Medical Research InstituteElizabeth E Palmer - UNSW SydneyChirag Patel - Royal Brisbane and Women's HospitalShilpan G Patel - University of AucklandDean Phelan - Victorian Clinical Genetics ServicesJason R Pinner - UNSW SydneySulekha Rajagopalan - Liverpool HospitalMatthew Regan - Monash UniversityJonathan Rodgers - Royal Brisbane and Women's HospitalMiriam Rodrigues - Auckland City HospitalRichard H Roxburgh - Auckland City HospitalRani Sachdev - Boston Children's HospitalTony Roscioli - UNSW SydneyRuvishani Samarasekera - Children's Hospital at WestmeadSarah A Sandaradura - The University of SydneyElena Savva - Victorian Clinical Genetics ServicesTim Schindler - UNSW SydneyMargit Shah - Children's Hospital at WestmeadIngrid B Sinnerbrink - The University of SydneyJanine M Smith - The University of SydneyRichard J Smith - University of IowaAmanda Springer - Monash UniversityZornitza Stark - The University of MelbourneSamuel P Strom - Temple UniversityCarolyn M Sue - Royal North Shore HospitalKenneth Tan - Monash UniversityTiong Y Tan - The University of MelbourneEsther Tantsis - The University of SydneyMichel C Tchan - The University of SydneyBryony A Thompson - The University of MelbourneAlison H Trainer - The University of MelbourneKarin van Spaendonck-Zwarts - Royal Brisbane and Women's HospitalRebecca Walsh - New South Wales Department of HealthLinda Warwick - Canberra HospitalStephanie White - Royal North Shore HospitalSusan M White - The University of MelbourneMark G Williams - The University of QueenslandMeredith J Wilson - The University of SydneyWui Kwan Wong - The University of SydneyDale C Wright - The University of SydneyPatrick Yap - Northern Hub, Genetic Health Service NZ, Auckland, New ZealandAlison Yeung - The University of MelbourneHelen Young - Austin HospitalKristi J Jones - The University of SydneyBruce Bennetts - The University of SydneySandra T Cooper - The University of SydneyAustralasian Consortium for RNA Diagnostics
- Resource Type
- Journal article
- Publication Details
- Genetics in medicine, Vol.24(1), pp.130-145
- DOI
- 10.1016/j.gim.2021.09.001
- PMID
- 34906502
- NLM abbreviation
- Genet Med
- ISSN
- 1098-3600
- eISSN
- 1530-0366
- Language
- English
- Date published
- 01/2022
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Molecular Physiology and Biophysics; Anatomy and Cell Biology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Otolaryngology; Internal Medicine
- Record Identifier
- 9984256934202771
Metrics
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