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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579012. [PMID: 38370830 PMCID: PMC10871197 DOI: 10.1101/2024.02.05.579012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing (ES), the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare disease. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery which should in turn increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints, and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks like Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Seth I. Berger
- Center for Genetic Medicine Research, Children’s National Research Institute, 111 Michigan Ave, NW, Washington, DC, 20010, USA
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, 15 Argonaut, Aliso Viejo, CA, 92656, USA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, 200 South Manchester Ave. St 206E, Orange, CA, 92868, USA
| | - Daniel G. Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Megan H. Hawley
- Clinical Operations, Invitae, 485F US-1 Suite 110, Iselin, NJ, 08830, USA
| | - E. Andres Rivera-Munoz
- Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza T605, Houston, TX, 77030, USA
| | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
| | | | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
- Department of Pediatrics, Division of Genetic Medicine, Seattle Children’s Hospital, Seattle, WA, 98195, USA
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02141, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 185 Cambridge St, Boston, MA, 02114, USA
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Lunke S, Bouffler SE, Patel CV, Sandaradura SA, Wilson M, Pinner J, Hunter MF, Barnett CP, Wallis M, Kamien B, Tan TY, Freckmann ML, Chong B, Phelan D, Francis D, Kassahn KS, Ha T, Gao S, Arts P, Jackson MR, Scott HS, Eggers S, Rowley S, Boggs K, Rakonjac A, Brett GR, de Silva MG, Springer A, Ward M, Stallard K, Simons C, Conway T, Halman A, Van Bergen NJ, Sikora T, Semcesen LN, Stroud DA, Compton AG, Thorburn DR, Bell KM, Sadedin S, North KN, Christodoulou J, Stark Z. Integrated multi-omics for rapid rare disease diagnosis on a national scale. Nat Med 2023:10.1038/s41591-023-02401-9. [PMID: 37291213 PMCID: PMC10353936 DOI: 10.1038/s41591-023-02401-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 05/12/2023] [Indexed: 06/10/2023]
Abstract
Critically ill infants and children with rare diseases need equitable access to rapid and accurate diagnosis to direct clinical management. Over 2 years, the Acute Care Genomics program provided whole-genome sequencing to 290 families whose critically ill infants and children were admitted to hospitals throughout Australia with suspected genetic conditions. The average time to result was 2.9 d and diagnostic yield was 47%. We performed additional bioinformatic analyses and transcriptome sequencing in all patients who remained undiagnosed. Long-read sequencing and functional assays, ranging from clinically accredited enzyme analysis to bespoke quantitative proteomics, were deployed in selected cases. This resulted in an additional 19 diagnoses and an overall diagnostic yield of 54%. Diagnostic variants ranged from structural chromosomal abnormalities through to an intronic retrotransposon, disrupting splicing. Critical care management changed in 120 diagnosed patients (77%). This included major impacts, such as informing precision treatments, surgical and transplant decisions and palliation, in 94 patients (60%). Our results provide preliminary evidence of the clinical utility of integrating multi-omic approaches into mainstream diagnostic practice to fully realize the potential of rare disease genomic testing in a timely manner.
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Affiliation(s)
- Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
| | | | - Chirag V Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah A Sandaradura
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Meredith Wilson
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Jason Pinner
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
- Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Christopher P Barnett
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Tasmania, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Tiong Y Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Mary-Louise Freckmann
- Department of Clinical Genetics, The Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Belinda Chong
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dean Phelan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David Francis
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Karin S Kassahn
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Thuong Ha
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Song Gao
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Peer Arts
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Matilda R Jackson
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Australian Genomics, Melbourne, Victoria, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Centre for Cancer Biology, An alliance between SA Pathology and the University of South Australia, Adelaide, South Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stefanie Eggers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simone Rowley
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kirsten Boggs
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Ana Rakonjac
- Australian Genomics, Melbourne, Victoria, Australia
- Sydney Children's Hospitals Network - Westmead, Sydney, New South Wales, Australia
- Sydney Children's Hospitals Network - Randwick, Sydney, New South Wales, Australia
| | - Gemma R Brett
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Michelle G de Silva
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Amanda Springer
- Monash Genetics, Monash Health, Melbourne, Victoria, Australia
- Department of Paediatrics, Monash University, Melbourne, Victoria, Australia
| | - Michelle Ward
- Genetic Services of Western Australia, Perth, Western Australia, Australia
| | - Kirsty Stallard
- Paediatric and Reproductive Genetics Unit, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Cas Simons
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Thomas Conway
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andreas Halman
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tim Sikora
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Liana N Semcesen
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Stroud
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alison G Compton
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - David R Thorburn
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katrina M Bell
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Simon Sadedin
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Kathryn N North
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Christodoulou
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Australian Genomics, Melbourne, Victoria, Australia
- Children's Hospital Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Genomics, Melbourne, Victoria, Australia.
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