Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants

被引：71

作者：

Bournazos, Adam M. ^{[1
,2
]}

Riley, Lisa G. ^{[2
,3
,4
]}

Bommireddipalli, Shobhana ^{[1
]}

Ades, Lesley ^{[2
,5
]}

Akesson, Lauren S. ^{[6
,7
,8
,9
,10
,11
]}

Al-Shinnag, Mohammad ^{[12
,13
]}

Alexander, Stephen, I ^{[2
,14
]}

Archibald, Alison D. ^{[6
,10
]}

Balasubramaniam, Shanti ^{[15
,16
,17
]}

Berman, Yemima ^{[18
,19
]}

Beshay, Victoria ^{[11
]}

Boggs, Kirsten ^{[5
,20
,21
]}

Bojadzieva, Jasmina ^{[22
]}

Brown, Natasha J. ^{[6
,10
]}

Bryen, Samantha J. ^{[1
,2
]}

Buckley, Michael F. ^{[23
]}

Chong, Belinda ^{[10
]}

Davis, Mark R. ^{[24
]}

Dawes, Ruebena ^{[1
,2
]}

Delatycki, Martin ^{[6
,10
]}

Donaldson, Liz ^{[25
]}

Downie, Lilian ^{[6
,25
,26
]}

Edwards, Caitlin ^{[24
]}

Edwards, Matthew ^{[27
]}

Engel, Amanda ^{[28
]}

Ewans, Lisa J. ^{[29
,30
]}

Faiz, Fathimath ^{[24
]}

Fennell, Andrew ^{[6
,31
]}

Field, Michael ^{[32
]}

Freckmann, Mary-Louise ^{[33
]}

Gallacher, Lyndon ^{[6
,10
]}

Gear, Russell ^{[10
]}

Goel, Himanshu ^{[32
,34
]}

Goh, Shuxiang ^{[35
]}

Goodwin, Linda ^{[36
]}

Hanna, Bernadette ^{[37
]}

Harraway, James ^{[38
]}

Higgins, Megan ^{[12
]}

Ho, Gladys ^{[2
,39
]}

Hopper, Bruce K. ^{[40
]}

Horton, Ari E. ^{[6
,31
,41
,42
,43
]}

Hunter, Matthew F. ^{[31
,44
]}

Huq, Aamira J. ^{[7
,25
]}

Josephi-Taylor, Sarah ^{[5
,37
]}

Joshi, Himanshu ^{[1
]}

Kirk, Edwin ^{[23
,45
]}

Krzesinski, Emma ^{[31
,44
]}

Kumar, Kishore R. ^{[46
,47
]}

Lemckert, Frances ^{[1
,2
]}

Leventer, Richard J. ^{[6
,26
,48
]}

机构：

[1] Childrens Hosp Westmead, Kids Neurosci Ctr, Kids Res, Locked Bag 4001, Westmead, NSW 2145, Australia

[2] Univ Sydney, Fac Med & Hlth, Dept Child & Adolescent Hlth, Westmead, NSW, Australia

[3] Sydney Childrens Hosp Network, Kids Res, Rare Dis Funct Genom, Westmead, NSW, Australia

[4] Childrens Med Res Inst, Locked Bag 4001, Westmead, NSW 2145, Australia

[5] Childrens Hosp Westmead, Dept Clin Genet, Westmead, NSW, Australia

[6] Univ Melbourne, Dept Paediat, Parkville, Vic, Australia

[7] Univ Melbourne, Dept Med, Parkville, Vic, Australia

[8] Univ Melbourne, Dept Pathol, Parkville, Vic, Australia

[9] Royal Melbourne Hosp, Dept Genom Med, Parkville, Vic, Australia

[10] Murdoch Childrens Res Inst, Victorian Clin Genet Serv, Parkville, Vic, Australia

[11] Peter MacCallum Canc Ctr, Melbourne, Vic, Australia

[12] Royal Brisbane & Womens Hosp, Genet Hlth Queensland, Herston, Qld, Australia

[13] Univ Queensland, Herston, Qld, Australia

[14] Childrens Hosp Westmead, Dept Pediat Nephrol, Westmead, NSW, Australia

[15] Childrens Hosp Westmead, Genet Metab Disorders Serv, Westmead, NSW, Australia

[16] Childrens Hosp Westmead, Western Sydney Genet Program, Westmead, NSW, Australia

[17] Univ Sydney, Fac Med & Hlth, Specialty Genom Med, Westmead, NSW, Australia

[18] Royal North Shore Hosp, Dept Clin Genet, St Leonards, NSW, Australia

[19] Royal North Shore Hosp, Northern Clin Sch, St Leonards, NSW, Australia

[20] Australian Genom Hlth Alliance, Parkville, Vic, Australia

[21] Sydney Childrens Hosp Randwick, Ctr Clin Genet, Randwick, NSW, Australia

[22] Austin Hlth, Dept Clin Genet, Heidelberg, Vic, Australia

[23] NSW Hlth Pathol, Randwick, NSW, Australia

[24] QEII Med Ctr, Dept Diagnost Genom, PathWest Lab Med, Nedlands, WA, Australia

[25] Royal Melbourne Hosp, Parkville, Vic, Australia

[26] Murdoch Childrens Res Inst, Parkville, Vic, Australia

[27] Western Sydney Univ, Sch Med, Dept Paediat, Penrith, NSW, Australia

[28] Canberra Hosp, ACT Genet Serv, ACT Hlth, Garran, ACT, Australia

[29] Royal Prince Alfred Hosp, Dept Med Genom, Camperdown, NSW, Australia

[30] Univ Sydney, Cent Clin Sch, Camperdown, NSW, Australia

[31] Monash Hlth, Monash Genet, Clayton, Vic, Australia

[32] Genet Learning Disabil Serv, Hunter Genet, Waratah, NSW, Australia

[33] Canberra Hosp, Dept Clin Genet, Garran, ACT, Australia

[34] Univ Newcastle, Callaghan, NSW, Australia

[35] Liverpool Hosp, Dept Clin Genet, Liverpool, NSW, Australia

[36] Nepean Hosp, Dept Clin Genet, Kingswood, NSW, Australia

[37] Westmead Hosp, Dept Genom Med, Westmead, NSW, Australia

[38] Sullivan Nicolaides Pathol, Bowen Hills, Qld, Australia

[39] Childrens Hosp Westmead, Dept Mol Genet, Westmead, NSW, Australia

[40] Forster Genet, Forster, NSW, Australia

[41] Monash Hlth, Monash Heart, Clayton, Vic, Australia

[42] Monash Hlth, Monash Childrens Hosp, Clayton, Vic, Australia

[43] Monash Cardiovasc Res Ctr, Clayton, Vic, Australia

[44] Monash Univ, Dept Paediat, Clayton, Vic, Australia

[45] Sydney Childrens Hosp, Ctr Clin Genet, Randwick, NSW, Australia

[46] Univ Sydney, Royal North Shore Hosp, Fac Med & Hlth, Kolling Inst,Dept Neurogenet, St Leonards, NSW, Australia

[47] Garvan Inst Med Res, Kinghorn Ctr Clin Genom, Translat Genom, Darlinghurst, NSW, Australia

[48] Royal Childrens Hosp, Dept Neurol, Parkville, Vic, Australia

[49] Univ New South Wales, Fac Med & Hlth, Sch Womens & Childrens Hlth, Kensington, NSW, Australia

[50] Garvan Inst Med Res, Div Genom & Epigenet, Darlinghurst, NSW, Australia

来源：

GENETICS IN MEDICINE | 2022年 / 24卷 / 01期

基金：

英国医学研究理事会;

关键词：

Genetic diagnosis; Noncoding variant; Pre-mRNA splicing; Putative splice variant; Variant classification; ENCODE DATA; GENOMICS;

D O I：

10.1016/j.gim.2021.09.001

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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. (C) 2021 Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics.

引用

页码：130 / 145

页数：16

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