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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Damiani G. Bayesian cost-effectiveness analysis of Whole genome sequencing versus Whole exome sequencing in a pediatric population with suspected genetic disorders. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2024; 25:999-1011. [PMID: 37975990 PMCID: PMC11283423 DOI: 10.1007/s10198-023-01644-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Genetic diseases are medical conditions caused by sequence or structural changes in an individual's genome. Whole exome sequencing (WES) and whole genome sequencing (WGS) are increasingly used for diagnosing suspected genetic conditions in children to reduce the diagnostic delay and accelerating the implementation of appropriate treatments. While more information is becoming available on clinical efficacy and economic sustainability of WES, the broad implementation of WGS is still hindered by higher complexity and economic issues. The aim of this study is to estimate the cost-effectiveness of WGS versus WES and standard testing for pediatric patients with suspected genetic disorders. A Bayesian decision tree model was set up. Model parameters were retrieved both from hospital administrative datasets and scientific literature. The analysis considered a lifetime time frame and adopted the perspective of the Italian National Health Service (NHS). Bayesian inference was performed using the Markov Chain Monte Carlo simulation method. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI). The present analysis showed that implementing first-line WGS would be a cost-effective strategy, against the majority of the other tested alternatives at a threshold of €30,000-50,000, for diagnosing outpatient pediatric patients with suspected genetic disorders. According to the sensitivity analyses, the findings were robust to most assumption and parameter uncertainty. Lessons learnt from this modeling study reinforces the adoption of first-line WGS, as a cost-effective strategy, depending on actual difficulties for the NHS to properly allocate limited resources.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168, Rome, Italy.
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy.
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, 00146, Rome, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168, Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, 00168, Rome, Italy
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Xu K, Li G, Niu Y, Wu Z, Zhang TJ, Zhang S, Wu N. First copy number variant in trans with single nucleotide variant in CCN6 causing progressive pseudorheumatoid dysplasia revealed by genome sequencing and deep phenotyping in monozygotic twins. Am J Med Genet A 2024:e63801. [PMID: 38958524 DOI: 10.1002/ajmg.a.63801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Biallelic pathogenic variants in CCN6 cause progressive pseudorheumatoid dysplasia (PPD), a rare skeletal dysplasia. The predominant features include noninflammatory progressive joint stiffness and enlargement, which are not unique to this condition. Nearly 100% of the reported variants are single nucleotide variants or small indels, and missing of a second variant has been reported. Genome sequencing (GS) covers various types of variants and deep phenotyping (DP) provides detailed and precise information facilitating genetic data interpretation. The combination of GS and DP improves diagnostic yield, especially in rare and undiagnosed diseases. We identified a novel compound heterozygote involving a disease-causing copy number variant (g.112057664_112064205del) in trans with a single nucleotide variant (c.624dup(p.Cys209MetfsTer21)) in CCN6 in a pair of monozygotic twins, through the methods of GS and DP. The twins had received three nondiagnostic results before. The g.112057664_112064205del variant was missed by all the tests, and the recorded phenotypes were inaccurate or even misleading. The twins were diagnosed with PPD, ending a 13-year diagnostic odyssey. There may be other patients with PPD experiencing underdiagnosis and misdiagnosis due to inadequate genetic testing or phenotyping methods. This case highlights the critical role of GS and DP in facilitating an accurate and timely diagnosis.
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Affiliation(s)
- Kexin Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Mallawaarachchi AC, Fowles L, Wardrop L, Wood A, O'Shea R, Biros E, Harris T, Alexander SI, Bodek S, Boudville N, Burke J, Burnett L, Casauria S, Chadban S, Chakera A, Crafter S, Dai P, De Fazio P, Faull R, Honda A, Huntley V, Jahan S, Jayasinghe K, Jose M, Leaver A, MacShane M, Madelli EO, Nicholls K, Pawlowski R, Rangan G, Snelling P, Soraru J, Sundaram M, Tchan M, Valente G, Wallis M, Wedd L, Welland M, Whitlam J, Wilkins EJ, McCarthy H, Simons C, Quinlan C, Patel C, Stark Z, Mallett AJ. Genomic Testing in Patients with Kidney Failure of an Unknown Cause: A National Australian Study. Clin J Am Soc Nephrol 2024; 19:887-897. [PMID: 38861662 PMCID: PMC11254024 DOI: 10.2215/cjn.0000000000000464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/25/2024] [Indexed: 06/13/2024]
Abstract
Key Points Twenty-five percent of those with unexplained kidney failure have a monogenic cause. Whole genome sequencing with broad gene panel analysis is a feasible diagnostic approach in nephrology. Background The cause of kidney failure is unknown in approximately 10% of patients with stage 5 chronic kidney disease (CKD). For those who first present to nephrology care with kidney failure, standard investigations of serology, imaging, urinalysis, and kidney biopsy are limited differentiators of etiology. We aimed to determine the diagnostic utility of whole genome sequencing (WGS) with analysis of a broad kidney gene panel in patients with kidney failure of unknown cause. Methods We prospectively recruited 100 participants who reached CKD stage 5 at the age of ≤50 years and had an unknown cause of kidney failure after standard investigation. Clinically accredited WGS was performed in this national cohort after genetic counseling. The primary analysis was targeted to 388 kidney-related genes with second-tier, genome-wide, and mitochondrial analysis. Results The cohort was 61% male and the average age of participants at stage 5 CKD was 32 years (9 months to 50 years). A genetic diagnosis was made in 25% of participants. Disease-causing variants were identified across autosomal dominant tubulointerstitial kidney disease (6), glomerular disorders (4), ciliopathies (3), tubular disorders (2), Alport syndrome (4), and mitochondrial disease (1). Most diagnoses (80%) were in autosomal dominant, X-linked, or mitochondrial conditions (UMOD ; COL4A5 ; INF2 ; CLCN5 ; TRPC6 ; COL4A4 ; EYA1 ; HNF1B ; WT1 ; NBEA ; m.3243A>G ). Participants with a family history of CKD were more likely to have a positive result (odds ratio, 3.29; 95% confidence interval, 1.10 to 11.29). Thirteen percent of participants without a CKD family history had a positive result. In those who first presented in stage 5 CKD, WGS with broad analysis of a curated kidney disease gene panel was diagnostically more informative than kidney biopsy, with biopsy being inconclusive in 24 of the 25 participants. Conclusions In this prospectively ascertained Australian cohort, we identified a genetic diagnosis in 25% of patients with kidney failure of unknown cause.
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Affiliation(s)
- Amali C. Mallawaarachchi
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
- Genomic and Inherited Diseases Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Louise Wardrop
- KidGen Collaborative, Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Alasdair Wood
- KidGen Collaborative, Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Rosie O'Shea
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Erik Biros
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- College of Medicine and Dentistry, James Cook University, Townsville, Queensland, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
| | - Trudie Harris
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
| | - Stephen I. Alexander
- Centre for Kidney Research at the Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Department of Nephrology, Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Bodek
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Neil Boudville
- Medical School, University of Western Australia, Crawley, Western Australia, Australia
| | - Jo Burke
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Leslie Burnett
- Genomic and Inherited Diseases Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales, Australia
- St Vincent's Healthcare Clinical Campus, UNSW Sydney, Sydney, New South Wales, Australia
| | - Sarah Casauria
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Steve Chadban
- Renal Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Aron Chakera
- Harry Perkins Institute for Medical Research, University of Western Australia, Crawley, Western Australia, Australia
- Renal Unit, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Sam Crafter
- The Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Pei Dai
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Paul De Fazio
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Randall Faull
- Renal Unit, Royal Adelaide Hospital, Adelaide, South Australia, Australia
- University of Adelaide, Adelaide, South Australia, Australia
| | - Andrew Honda
- The Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Vanessa Huntley
- Adult Genetics Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Sadia Jahan
- The Central and Northern Renal and Transplantation Service, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - Kushani Jayasinghe
- Department of Medicine, Monash University, Melbourne, Victoria, Australia
- Department of Nephrology, Monash Health, Melbourne, Victoria, Australia
- Melbourne Health, Melbourne, Victoria, Australia
| | - Matthew Jose
- Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - Anna Leaver
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Mandi MacShane
- Genetic Services of WA, KEMH, Subiaco, Western Australia, Australia
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | | | - Kathy Nicholls
- Nephrology Unit, Royal Melbourne Hospital, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Rhonda Pawlowski
- Anatomical Pathology, Monash Health, Melbourne, Victoria, Australia
| | - Gopi Rangan
- Department of Renal Medicine, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia
- Michael Stern Laboratory for Polycystic Kidney Disease, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Paul Snelling
- Renal Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Jacqueline Soraru
- Department of Nephrology and Hypertension, Perth Children's Hospital, Nedlands, Western Australia, Australia
- Department of Nephrology and Renal Transplantation, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | | | - Michel Tchan
- Genetic Medicine, Westmead Hospital, Sydney, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Giulia Valente
- Clinical Genetics Service, Austin Health, Melbourne, Victoria, Australia
| | - Mathew Wallis
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, Tasmania, Australia
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Laura Wedd
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
| | - Matthew Welland
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - John Whitlam
- Department of Nephrology, Austin Health, Melbourne, Victoria, Australia
| | - Ella J. Wilkins
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hugh McCarthy
- Centre for Kidney Research at the Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
- Department of Nephrology, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Catherine Quinlan
- Department of Kidney Regeneration, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Nephrology, Royal Children's Hospital, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Zornitza Stark
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew J. Mallett
- KidGen Collaborative, Australian Genomics Health Alliance, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Townsville University Hospital, Townsville, Queensland, Australia
- Australian Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Institute for Molecular Bioscience and Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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McCarthy HJ, Mallett AJ, Sullivan P, Cowley MJ, Mallawaarachchi AC. Beyond DNA sequencing: genetic kidney disorders related to altered splicing. Nephrol Dial Transplant 2024; 39:1056-1059. [PMID: 38289833 DOI: 10.1093/ndt/gfae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Indexed: 02/01/2024] Open
Affiliation(s)
- Hugh J McCarthy
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
- Department of Nephrology, Sydney Children's Hospitals Network, Westmead, NSW, Australia
| | - Andrew J Mallett
- Department of Renal Medicine, Townsville University Hospital, Townsville, QLD, Australia
- College of Medicine & Dentistry, James Cook University, Townsville, QLD, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales Sydney, Kensington, NSW, Australia
| | - Amali C Mallawaarachchi
- School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales Sydney, Kensington, NSW, Australia
- Genomic and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Clinical Genetics Service, Institute of Precision Medicine and Bioinformatics, Royal Prince Alfred Hospital, Sydney, Australia
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Senthivel V, Jolly B, Vr A, Bajaj A, Bhoyar R, Imran M, Vignesh H, Divakar MK, Sharma G, Rai N, Kumar K, Mp J, Krishna M, Shenthar J, Ali M, Abqari S, Nadri G, Scaria V, Naik N, Sivasubbu S. Whole genome sequencing of families diagnosed with cardiac channelopathies reveals structural variants missed by whole exome sequencing. J Hum Genet 2024:10.1038/s10038-024-01265-2. [PMID: 38890497 DOI: 10.1038/s10038-024-01265-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/07/2024] [Accepted: 06/02/2024] [Indexed: 06/20/2024]
Abstract
Cardiac channelopathies are a group of heritable disorders that affect the heart's electrical activity due to genetic variations present in genes coding for ion channels. With the advent of new sequencing technologies, molecular diagnosis of these disorders in patients has paved the way for early identification, therapeutic management and family screening. The objective of this retrospective study was to understand the efficacy of whole-genome sequencing in diagnosing patients with suspected cardiac channelopathies who were reported negative after whole exome sequencing and analysis. We employed a 3-tier analysis approach to identify nonsynonymous variations and loss-of-function variations missed by exome sequencing, and structural variations that are better resolved only by sequencing whole genomes. By performing whole genome sequencing and analyzing 25 exome-negative cardiac channelopathy patients, we identified 3 pathogenic variations. These include a heterozygous likely pathogenic nonsynonymous variation, CACNA1C:NM_000719:exon19:c.C2570G:p. P857R, which causes autosomal dominant long QT syndrome in the absence of Timothy syndrome, a heterozygous loss-of-function variation CASQ2:NM_001232.4:c.420+2T>C classified as pathogenic, and a 9.2 kb structural variation that spans exon 2 of the KCNQ1 gene, which is likely to cause Jervell-Lange-Nielssen syndrome. In addition, we also identified a loss-of-function variation and 16 structural variations of unknown significance (VUS). Further studies are required to elucidate the role of these identified VUS in gene regulation and decipher the underlying genetic and molecular mechanisms of these disorders. Our present study serves as a pilot for understanding the utility of WGS over clinical exomes in diagnosing cardiac channelopathy disorders.
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Affiliation(s)
- Vigneshwar Senthivel
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bani Jolly
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Arvinden Vr
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anjali Bajaj
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rahul Bhoyar
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Harie Vignesh
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
| | - Mohit Kumar Divakar
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Gautam Sharma
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Nitin Rai
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Kapil Kumar
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Jayakrishnan Mp
- Government Medical College, Kozhikode, Kerala, 673008, India
| | - Maniram Krishna
- Tiny Hearts Fetal and Pediatric Clinic, Thanjavur, Tamil Nadu, 613001, India
| | - Jeyaprakash Shenthar
- Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, Karnataka, 560069, India
| | - Muzaffar Ali
- Sri Jayadeva Institute of Cardiovascular Sciences and Research, Bengaluru, Karnataka, 560069, India
| | - Shaad Abqari
- Jawaharlal Nehru Medical College and Hospital, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Gulnaz Nadri
- Jawaharlal Nehru Medical College and Hospital, Aligarh Muslim University, Aligarh, Uttar Pradesh, 202002, India
| | - Vinod Scaria
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nitish Naik
- Department of Cardiology, All India Institute of Medical Sciences, New Delhi, 110029, India.
| | - Sridhar Sivasubbu
- CSIR- Institute of Genomics and Integrative Biology, Mathura Road, Sukhdev Vihar, New Delhi, 110025, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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van der Geest MA, Maeckelberghe ELM, van Gijn ME, Lucassen AM, Swertz MA, van Langen IM, Plantinga M. Systematic reanalysis of genomic data by diagnostic laboratories: a scoping review of ethical, economic, legal and (psycho)social implications. Eur J Hum Genet 2024; 32:489-497. [PMID: 38480795 PMCID: PMC11061183 DOI: 10.1038/s41431-023-01529-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 05/02/2024] Open
Abstract
With the introduction of Next Generation Sequencing (NGS) techniques increasing numbers of disease-associated variants are being identified. This ongoing progress might lead to diagnoses in formerly undiagnosed patients and novel insights in already solved cases. Therefore, many studies suggest introducing systematic reanalysis of NGS data in routine diagnostics. Introduction will, however, also have ethical, economic, legal and (psycho)social (ELSI) implications that Genetic Health Professionals (GHPs) from laboratories should consider before possible implementation of systematic reanalysis. To get a first impression we performed a scoping literature review. Our findings show that for the vast majority of included articles ELSI aspects were not mentioned as such. However, often these issues were raised implicitly. In total, we identified nine ELSI aspects, such as (perceived) professional responsibilities, implications for consent and cost-effectiveness. The identified ELSI aspects brought forward necessary trade-offs for GHPs to consciously take into account when considering responsible implementation of systematic reanalysis of NGS data in routine diagnostics, balancing the various strains on their laboratories and personnel while creating optimal results for new and former patients. Some important aspects are not well explored yet. For example, our study shows GHPs see the values of systematic reanalysis but also experience barriers, often mentioned as being practical or financial only, but in fact also being ethical or psychosocial. Engagement of these GHPs in further research on ELSI aspects is important for sustainable implementation.
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Affiliation(s)
- Marije A van der Geest
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
| | - Els L M Maeckelberghe
- Institute for Medical Education, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marielle E van Gijn
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Anneke M Lucassen
- Faculty of Medicine, Clinical Ethics and Law, University of Southampton, Southampton, UK
- Centre for Personalised Medicine, Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Morris A Swertz
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Irene M van Langen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Mirjam Plantinga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Del Gobbo GF, Wang X, Couse M, Mackay L, Goldsmith C, Marshall AE, Liang Y, Lambert C, Zhang S, Dhillon H, Fanslow C, Rowell WJ, Marshall CR, Kernohan KD, Boycott KM. Long-read genome sequencing reveals a novel intronic retroelement insertion in NR5A1 associated with 46,XY differences of sexual development. Am J Med Genet A 2024; 194:e63522. [PMID: 38131126 DOI: 10.1002/ajmg.a.63522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Despite significant advancements in rare genetic disease diagnostics, many patients with rare genetic disease remain without a molecular diagnosis. Novel tools and methods are needed to improve the detection of disease-associated variants and understand the genetic basis of many rare diseases. Long-read genome sequencing provides improved sequencing in highly repetitive, homologous, and low-complexity regions, and improved assessment of structural variation and complex genomic rearrangements compared to short-read genome sequencing. As such, it is a promising method to explore overlooked genetic variants in rare diseases with a high suspicion of a genetic basis. We therefore applied PacBio HiFi sequencing in a large multi-generational family presenting with autosomal dominant 46,XY differences of sexual development (DSD), for whom extensive molecular testing over multiple decades had failed to identify a molecular diagnosis. This revealed a rare SINE-VNTR-Alu retroelement insertion in intron 4 of NR5A1, a gene in which loss-of-function variants are an established cause of 46,XY DSD. The insertion segregated among affected family members and was associated with loss-of-expression of alleles in cis, demonstrating a functional impact on NR5A1. This case highlights the power of long-read genome sequencing to detect genomic variants that have previously been intractable to detection by standard short-read genomic testing.
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Affiliation(s)
- Giulia F Del Gobbo
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Xueqi Wang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Madeline Couse
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Layla Mackay
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Claire Goldsmith
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Aren E Marshall
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Yijing Liang
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | - Siyuan Zhang
- PacBio of California, Inc, Menlo Park, California, USA
| | | | | | | | | | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Newborn Screening Ontario, Ottawa, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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8
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Dias KR, Shrestha R, Schofield D, Evans CA, O'Heir E, Zhu Y, Zhang F, Standen K, Weisburd B, Stenton SL, Sanchis-Juan A, Brand H, Talkowski ME, Ma A, Ghedia S, Wilson M, Sandaradura SA, Smith J, Kamien B, Turner A, Bakshi M, Adès LC, Mowat D, Regan M, McGillivray G, Savarirayan R, White SM, Tan TY, Stark Z, Brown NJ, Pérez-Jurado LA, Krzesinski E, Hunter MF, Akesson L, Fennell AP, Yeung A, Boughtwood T, Ewans LJ, Kerkhof J, Lucas C, Carey L, French H, Rapadas M, Stevanovski I, Deveson IW, Cliffe C, Elakis G, Kirk EP, Dudding-Byth T, Fletcher J, Walsh R, Corbett MA, Kroes T, Gecz J, Meldrum C, Cliffe S, Wall M, Lunke S, North K, Amor DJ, Field M, Sadikovic B, Buckley MF, O'Donnell-Luria A, Roscioli T. Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort. Genet Med 2024; 26:101076. [PMID: 38258669 DOI: 10.1016/j.gim.2024.101076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
PURPOSE Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively. METHODS ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID. RESULTS The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis. CONCLUSION Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.
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Affiliation(s)
- Kerith-Rae Dias
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Rupendra Shrestha
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Deborah Schofield
- Centre for Economic Impacts of Genomic Medicine, Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Emily O'Heir
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ying Zhu
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Futao Zhang
- Neuroscience Research Australia, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Krystle Standen
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sarah L Stenton
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Sondy Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia; Northern Clinical School, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Meredith Wilson
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia
| | - Sarah A Sandaradura
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - Janine Smith
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Specialty of Genomic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Benjamin Kamien
- Genetic Services of Western Australia, Perth, WA, Australia; School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Anne Turner
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Madhura Bakshi
- Department of Clinical Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | - Lesley C Adès
- Department of Clinical Genetics, Children's Hospital at Westmead, Sydney Children's Hospital Network, Sydney, NSW, Australia; Disciplines of Child and Adolescent Health and Genetic Medicine, University of Sydney, Sydney, NSW 2050, Australia
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Regan
- Monash Genetics, Monash Health, Melbourne, VIC, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, SA, Australia
| | - Emma Krzesinski
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Lauren Akesson
- Melbourne Pathology, Melbourne, VIC, Australia; Department of Pathology, The Royal Melbourne Hospital, Melbourne, VIC, Australia; Melbourne Medical School, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Paul Fennell
- Monash Genetics, Monash Health, Melbourne, VIC, Australia; Department of Paediatrics, Monash University, Melbourne, VIC, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Tiffany Boughtwood
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia
| | - Lisa J Ewans
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia; Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada
| | - Christopher Lucas
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Louise Carey
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Hugh French
- Department of Medical Genomics, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, University of New South Wales Sydney, Sydney, NSW, Australia; Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Sydney, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Corrina Cliffe
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - George Elakis
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Edwin P Kirk
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia; Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Discipline of Paediatrics & Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
| | | | - Janice Fletcher
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Rebecca Walsh
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Thessa Kroes
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia; South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Cliff Meldrum
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Simon Cliffe
- State Wide Service, New South Wales Health Pathology, Sydney, NSW, Australia
| | - Meg Wall
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Kathryn North
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Australian Genomics, Melbourne, VIC, Australia; Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - David J Amor
- Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Michael Field
- The Genetics of Learning Disability Service, Waratah, NSW, Australia
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Tony Roscioli
- Neuroscience Research Australia, Sydney, NSW, Australia; Prince of Wales Clinical School, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia.
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9
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Kaufman O, Donnelly C, Cork E, Fiel MI, Chu J, Ganesh J. Shwachman-Diamond syndrome mimicking mitochondrial hepatopathy. JPGN REPORTS 2024; 5:213-217. [PMID: 38756125 PMCID: PMC11093899 DOI: 10.1002/jpr3.12064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 05/18/2024]
Abstract
Shwachman-Diamond syndrome (SDS) is a genetic disorder caused by mutations in the Shwachman-Bodian-Diamond syndrome (SBDS) gene. The syndrome is characterized by multiorgan dysfunction primarily involving the bone marrow and exocrine pancreas. Frequently overlooked is the hepatic dysfunction seen in early childhood which tends to improve by adulthood. Here, we report a child who initially presented with failure to thrive and elevated transaminases, and was ultimately diagnosed with SDS. A liver biopsy electron micrograph revealed hepatocytes crowded with numerous small mitochondria, resembling the hepatic architecture from patients with inborn errors of metabolism, including mitochondrial diseases. To our knowledge, this is the first report of the mitochondrial phenotype in an SDS patient. These findings are compelling given the recent cellular and molecular research studies which have identified SBDS as an essential regulator of mitochondrial function and have also implicated SBDS in the maintenance of mitochondrial DNA.
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Affiliation(s)
- Odelya Kaufman
- Department of Genetics and GenomicsMount Sinai HospitalNew YorkNew YorkUSA
| | - Colleen Donnelly
- Department of Genetics and GenomicsMount Sinai HospitalNew YorkNew YorkUSA
| | - Emalyn Cork
- Department of Genetics and GenomicsMount Sinai HospitalNew YorkNew YorkUSA
| | - Maria I. Fiel
- Department of PathologyMount Sinai HospitalNew YorkNew YorkUSA
| | - Jaime Chu
- Division of Pediatric Hepatology at Kravis Children's HospitalMount Sinai HospitalNew YorkNew YorkUSA
| | - Jaya Ganesh
- Department of Genetics and GenomicsMount Sinai HospitalNew YorkNew YorkUSA
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10
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Song P, Tian Y, Chen S, Zhang S, Li X, You Z, Fu J, Xu W, Li Z, Luan J, Zhao Q, Wang C, Pang F. A novel method for simultaneous detection of hematological tumors and infectious pathogens by metagenomic next generation sequencing of plasma. Clin Chim Acta 2024; 557:117874. [PMID: 38484907 DOI: 10.1016/j.cca.2024.117874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/23/2024] [Accepted: 03/11/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is valuable for pathogen identification; however, distinguishing between infectious diseases and conditions with potentially similar clinical manifestations, including malignant tumors, is challenging. Therefore, we developed a method for simultaneous detection of infectious pathogens and cancer in blood samples. METHODS Plasma samples (n = 244) were collected from 150 and 94 patients with infections and hematological malignancies, respectively, and analyzed by mNGS for pathogen detection, alongside human tumor chromosomal copy number variation (CNV) analysis (≥5Mbp or 10Mbp CNV region). Further, an evaluation set, comprising 87 plasma samples, was analyzed by mNGS and human CNV analysis, to validate the feasibility of the method. RESULTS Among 94 patients with hematological malignancy, sensitivity values of CNV detection for tumor diagnosis were 69.15 % and 32.98 % for CNV region 5Mbp and 10Mbp, respectively, with corresponding specificities of 92.62 % and 100 % in the infection group. Area under the ROC curve (AUC) values for 5Mbp and 10Mbp region were 0.825 and 0.665, respectively, which was a significant difference of 0.160 (95 % CI: 0.110-0.210; p < 0.001), highlighting the superiority of 5Mbp output region data. Six patients with high-risk CNV results were identified in the validation study: three with history of tumor treatment, two eventually newly-diagnosed with hematological malignancies, and one with indeterminate final diagnosis. CONCLUSIONS Concurrent CNV analysis alongside mNGS for infection diagnosis is promising for detecting malignant tumors. We recommend adopting a CNV region of 10Mbp over 5Mbp for our model, because of the lower false-positive rate (FPR).
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Affiliation(s)
- Pingping Song
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Yaxian Tian
- Department of Central Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Third People's Hospital, Liaocheng, China
| | - Sheng Zhang
- Department of Pathology, Liaocheng Third People's Hospital, Liaocheng, China
| | - Xuan Li
- The Key Laboratory of Molecular Pharmacology, Liaocheng People's Hospital, Liaocheng, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Zhen Li
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Jing Luan
- Department of Hematology, Liaocheng People's Hospital, Liaocheng, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China.
| | - Feng Pang
- Department of Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, China.
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Mukherjee A, Abraham S, Singh A, Balaji S, Mukunthan KS. From Data to Cure: A Comprehensive Exploration of Multi-omics Data Analysis for Targeted Therapies. Mol Biotechnol 2024:10.1007/s12033-024-01133-6. [PMID: 38565775 DOI: 10.1007/s12033-024-01133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024]
Abstract
In the dynamic landscape of targeted therapeutics, drug discovery has pivoted towards understanding underlying disease mechanisms, placing a strong emphasis on molecular perturbations and target identification. This paradigm shift, crucial for drug discovery, is underpinned by big data, a transformative force in the current era. Omics data, characterized by its heterogeneity and enormity, has ushered biological and biomedical research into the big data domain. Acknowledging the significance of integrating diverse omics data strata, known as multi-omics studies, researchers delve into the intricate interrelationships among various omics layers. This review navigates the expansive omics landscape, showcasing tailored assays for each molecular layer through genomes to metabolomes. The sheer volume of data generated necessitates sophisticated informatics techniques, with machine-learning (ML) algorithms emerging as robust tools. These datasets not only refine disease classification but also enhance diagnostics and foster the development of targeted therapeutic strategies. Through the integration of high-throughput data, the review focuses on targeting and modeling multiple disease-regulated networks, validating interactions with multiple targets, and enhancing therapeutic potential using network pharmacology approaches. Ultimately, this exploration aims to illuminate the transformative impact of multi-omics in the big data era, shaping the future of biological research.
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Affiliation(s)
- Arnab Mukherjee
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Suzanna Abraham
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - Akshita Singh
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India
| | - K S Mukunthan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, India.
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12
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Yun Y, Lee SY. Updates on Genetic Hearing Loss: From Diagnosis to Targeted Therapies. J Audiol Otol 2024; 28:88-92. [PMID: 38695053 PMCID: PMC11065549 DOI: 10.7874/jao.2024.00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 05/05/2024] Open
Abstract
Sensorineural hearing loss (SNHL) is the most common sensory disorder, with a high Mendelian genetic contribution. Considering the genotypic and phenotypic heterogeneity of SNHL, the advent of next-generation sequencing technologies has revolutionized knowledge on its genomic architecture. Nonetheless, the conventional application of panel and exome sequencing in real-world practice is being challenged by the emerging need to explore the diagnostic capability of whole-genome sequencing, which enables the detection of both noncoding and structural variations. Small molecules and gene therapies represent good examples of how breakthroughs in genetic understanding can be translated into targeted therapies for SNHL. For example, targeted small molecules have been used to ameliorate autoinflammatory hearing loss caused by gain-of-function variants of NLRP3 and inner ear proteinopathy with OSBPL2 variants underlying dysfunctional autophagy. Strikingly, the successful outcomes of the first-in-human trial of OTOF gene therapy highlighted its potential in the treatment of various forms of genetic hearing loss. clustered regularly interspaced short palindromic repeats (CRISPR)-based technologies are currently being developed for site-specific genome editing to treat human genetic disorders. These advancements have led to an era of genotype- and mechanism-based precision medicine in SNHL practice.
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Affiliation(s)
- Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
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Seither K, Thompson W, Suhrie K. A Practical Guide to Whole Genome Sequencing in the NICU. Neoreviews 2024; 25:e139-e150. [PMID: 38425198 DOI: 10.1542/neo.25-3-e139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The neonatal period is a peak time for the presentation of genetic disorders that can be diagnosed using whole genome sequencing (WGS). While any one genetic disorder is individually rare, they collectively contribute to significant morbidity, mortality, and health-care costs. As the cost of WGS continues to decline and becomes increasingly available, the ordering of rapid WGS for NICU patients with signs or symptoms of an underlying genetic condition is now feasible. However, many neonatal clinicians are not comfortable with the testing, and unfortunately, there is a dearth of geneticists to facilitate testing for every patient that needs it. Here, we will review the science behind WGS, diagnostic capabilities, limitations of testing, time to consider testing, test initiation, interpretation of results, developing a plan of care that incorporates genomic information, and returning WGS results to families.
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Affiliation(s)
- Katelyn Seither
- Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, and the Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Whitney Thompson
- Division of Neonatal Medicine, and the Department of Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Kristen Suhrie
- Division of Neonatology, Department of Pediatrics, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
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14
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Snyder HE, Jain P, RamachandranNair R, Jones KC, Whitney R. Genetic Advancements in Infantile Epileptic Spasms Syndrome and Opportunities for Precision Medicine. Genes (Basel) 2024; 15:266. [PMID: 38540325 PMCID: PMC10970414 DOI: 10.3390/genes15030266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 06/15/2024] Open
Abstract
Infantile epileptic spasms syndrome (IESS) is a devastating developmental epileptic encephalopathy (DEE) consisting of epileptic spasms, as well as one or both of developmental regression or stagnation and hypsarrhythmia on EEG. A myriad of aetiologies are associated with the development of IESS; broadly, 60% of cases are thought to be structural, metabolic or infectious in nature, with the remainder genetic or of unknown cause. Epilepsy genetics is a growing field, and over 28 copy number variants and 70 single gene pathogenic variants related to IESS have been discovered to date. While not exhaustive, some of the most commonly reported genetic aetiologies include trisomy 21 and pathogenic variants in genes such as TSC1, TSC2, CDKL5, ARX, KCNQ2, STXBP1 and SCN2A. Understanding the genetic mechanisms of IESS may provide the opportunity to better discern IESS pathophysiology and improve treatments for this condition. This narrative review presents an overview of our current understanding of IESS genetics, with an emphasis on animal models of IESS pathogenesis, the spectrum of genetic aetiologies of IESS (i.e., chromosomal disorders, single-gene disorders, trinucleotide repeat disorders and mitochondrial disorders), as well as available genetic testing methods and their respective diagnostic yields. Future opportunities as they relate to precision medicine and epilepsy genetics in the treatment of IESS are also explored.
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Affiliation(s)
- Hannah E. Snyder
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Puneet Jain
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1E8, Canada
| | - Rajesh RamachandranNair
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Kevin C. Jones
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
| | - Robyn Whitney
- Division of Neurology, Department of Paediatrics, McMaster University, Hamilton, ON L8N 3Z5, Canada (R.R.)
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Yeow D, Rudaks LI, Siow SF, Davis RL, Kumar KR. Genetic Testing of Movements Disorders: A Review of Clinical Utility. Tremor Other Hyperkinet Mov (N Y) 2024; 14:2. [PMID: 38222898 PMCID: PMC10785957 DOI: 10.5334/tohm.835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 12/04/2023] [Indexed: 01/16/2024] Open
Abstract
Currently, pathogenic variants in more than 500 different genes are known to cause various movement disorders. The increasing accessibility and reducing cost of genetic testing has resulted in increasing clinical use of genetic testing for the diagnosis of movement disorders. However, the optimal use case(s) for genetic testing at a patient level remain ill-defined. Here, we review the utility of genetic testing in patients with movement disorders and also highlight current challenges and limitations that need to be considered when making decisions about genetic testing in clinical practice. Highlights The utility of genetic testing extends across multiple clinical and non-clinical domains. Here we review different aspects of the utility of genetic testing for movement disorders and the numerous associated challenges and limitations. These factors should be weighed on a case-by-case basis when requesting genetic tests in clinical practice.
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Affiliation(s)
- Dennis Yeow
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Department of Neurology, Prince of Wales Hospital, Randwick, NSW, Australia
- Neuroscience Research Australia, Randwick, NSW, Australia
| | - Laura I. Rudaks
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Sue-Faye Siow
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW, Australia
| | - Ryan L. Davis
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Neurogenetics Research Group, Kolling Institute, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney and Northern Sydney Local Health District, St Leonards, NSW, Australia
| | - Kishore R. Kumar
- Translational Neurogenomics Group, Neurology Department & Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, NSW, Australia
- Concord Clinical School, Sydney Medical School, Faculty of Health & Medicine, University of Sydney, Concord, NSW, Australia
- Rare Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- School of Clinical Medicine, University of New South Wales, Sydney, NSW, Australia
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16
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Nurchis MC, Radio FC, Salmasi L, Heidar Alizadeh A, Raspolini GM, Altamura G, Tartaglia M, Dallapiccola B, Pizzo E, Gianino MM, Damiani G. Cost-Effectiveness of Whole-Genome vs Whole-Exome Sequencing Among Children With Suspected Genetic Disorders. JAMA Netw Open 2024; 7:e2353514. [PMID: 38277144 PMCID: PMC10818217 DOI: 10.1001/jamanetworkopen.2023.53514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024] Open
Abstract
Importance The diagnosis of rare diseases and other genetic conditions can be daunting due to vague or poorly defined clinical features that are not recognized even by experienced clinicians. Next-generation sequencing technologies, such as whole-genome sequencing (WGS) and whole-exome sequencing (WES), have greatly enhanced the diagnosis of genetic diseases by expanding the ability to sequence a large part of the genome, rendering a cost-effectiveness comparison between them necessary. Objective To assess the cost-effectiveness of WGS compared with WES and conventional testing in children with suspected genetic disorders. Design, Setting, and Participants In this economic evaluation, a bayesian Markov model was implemented from January 1 to June 30, 2023. The model was developed using data from a cohort of 870 pediatric patients with suspected genetic disorders who were enrolled and underwent testing in the Ospedale Pediatrico Bambino Gesù, Rome, Italy, from January 1, 2015, to December 31, 2022. The robustness of the model was assessed through probabilistic sensitivity analysis and value of information analysis. Main Outcomes and Measures Overall costs, number of definitive diagnoses, and incremental cost-effectiveness ratios per diagnosis were measured. The cost-effectiveness analyses involved 4 comparisons: first-tier WGS with standard of care; first-tier WGS with first-tier WES; first-tier WGS with second-tier WES; and first-tier WGS with second-tier WGS. Results The ages of the 870 participants ranged from 0 to 18 years (539 [62%] girls). The results of the analysis suggested that adopting WGS as a first-tier strategy would be cost-effective compared with all other explored options. For all threshold levels above €29 800 (US $32 408) per diagnosis that were tested up to €50 000 (US $54 375) per diagnosis, first-line WGS vs second-line WES strategy (ie, 54.6%) had the highest probability of being cost-effective, followed by first-line vs second-line WGS (ie, 54.3%), first-line WGS vs the standard of care alternative (ie, 53.2%), and first-line WGS vs first-line WES (ie, 51.1%). Based on sensitivity analyses, these estimates remained robust to assumptions and parameter uncertainty. Conclusions and Relevance The findings of this economic evaluation encourage the development of policy changes at various levels (ie, macro, meso, and micro) of international health systems to ensure an efficient adoption of WGS in clinical practice and its equitable access.
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Affiliation(s)
- Mario Cesare Nurchis
- School of Economics, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | | | - Luca Salmasi
- Department of Economics and Finance, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Aurora Heidar Alizadeh
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gian Marco Raspolini
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gerardo Altamura
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Tartaglia
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Molecular Genetics and Functional Genomics, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Elena Pizzo
- Department of Applied Health Research, University College London, London, United Kingdom
| | - Maria Michela Gianino
- Department of Public Health Sciences and Paediatrics, Università di Torino, Turin, Italy
| | - Gianfranco Damiani
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
- Department of Health Sciences and Public Health, Section of Hygiene, Università Cattolica del Sacro Cuore, Rome, Italy
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17
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Guo F, Liu R, Pan Y, Collins C, Bean L, Ma Z, Mathur A, Da Silva C, Nallamilli B, Guruju N, Chen-Deutsch X, Yousaf R, Chin E, Balciuniene J, Hegde M. Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test. Genet Med 2024; 26:100995. [PMID: 37838930 DOI: 10.1016/j.gim.2023.100995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023] Open
Abstract
PURPOSE Genome sequencing (GS) is one of the most comprehensive assays that interrogate single-nucleotide variants, copy number variants, mitochondrial variants, repeat expansions, and structural variants in a single assay. Despite the clear technical superiority, the full clinical utility of GS has yet to be determined. METHODS We systematically evaluated 2100 clinical GS index cases performed in our laboratory to explore the diagnostic yield of GS as first-tier and as follow-up testing. RESULTS The overall diagnostic yield was 28% (585/2100). The diagnostic yield for GS as the first-tier test was 26% (294/1146). Among cases with prior non-diagnostic genetic tests, GS provided a diagnosis for 27% (247/910) of cases, including 56 cases with prior exome sequencing (ES). Although re-analysis of previous ES might have resolved the diagnosis in 29 cases, diagnoses for 27 cases would have been missed because of the technical inferiority of ES. Moreover, GS further disclosed additional genetic etiology in 3 out of 44 cases with existing partial diagnosis. CONCLUSION We present the largest-to-date GS data set of a clinically heterogeneous cohort from a single clinical laboratory. Our data demonstrate that GS should be considered as the first-tier genetic test that has the potential to shorten the diagnostic odyssey.
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Affiliation(s)
- Fen Guo
- Revvity Omics, Pittsburgh, PA.
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18
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Riquin K, Isidor B, Mercier S, Nizon M, Colin E, Bonneau D, Pasquier L, Odent S, Le Guillou Horn XM, Le Guyader G, Toutain A, Meyer V, Deleuze JF, Pichon O, Doco-Fenzy M, Bézieau S, Cogné B. Integrating RNA-Seq into genome sequencing workflow enhances the analysis of structural variants causing neurodevelopmental disorders. J Med Genet 2023; 61:47-56. [PMID: 37495270 DOI: 10.1136/jmg-2023-109263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/09/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Molecular diagnosis of neurodevelopmental disorders (NDDs) is mainly based on exome sequencing (ES), with a diagnostic yield of 31% for isolated and 53% for syndromic NDD. As sequencing costs decrease, genome sequencing (GS) is gradually replacing ES for genome-wide molecular testing. As many variants detected by GS only are in deep intronic or non-coding regions, the interpretation of their impact may be difficult. Here, we showed that integrating RNA-Seq into the GS workflow can enhance the analysis of the molecular causes of NDD, especially structural variants (SVs), by providing valuable complementary information such as aberrant splicing, aberrant expression and monoallelic expression. METHODS We performed trio-GS on a cohort of 33 individuals with NDD for whom ES was inconclusive. RNA-Seq on skin fibroblasts was then performed in nine individuals for whom GS was inconclusive and optical genome mapping (OGM) was performed in two individuals with an SV of unknown significance. RESULTS We identified pathogenic or likely pathogenic variants in 16 individuals (48%) and six variants of uncertain significance. RNA-Seq contributed to the interpretation in three individuals, and OGM helped to characterise two SVs. CONCLUSION Our study confirmed that GS significantly improves the diagnostic performance of NDDs. However, most variants detectable by GS alone are structural or located in non-coding regions, which can pose challenges for interpretation. Integration of RNA-Seq data overcame this limitation by confirming the impact of variants at the transcriptional or regulatory level. This result paves the way for new routinely applicable diagnostic protocols.
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Affiliation(s)
- Kevin Riquin
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
| | - Bertrand Isidor
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Sandra Mercier
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Mathilde Nizon
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Estelle Colin
- CHU Angers, Service de Génétique médicale, Angers, France
- UMR CNRS 6214-INSERM 1083, Université d'Angers, Angers, France
| | - Dominique Bonneau
- CHU Angers, Service de Génétique médicale, Angers, France
- UMR CNRS 6214-INSERM 1083, Université d'Angers, Angers, France
| | | | - Sylvie Odent
- Service de Génétique Clinique, ERN ITHACA, Rennes, France
- Institut de Génétique et Développement de Rennes, IGDR UMR 6290 CNRS, INSERM, IGDR Univ Rennes, Rennes, France
| | - Xavier Maximin Le Guillou Horn
- Service de génétique médicale, CHU de Poitiers, Poitiers, France
- LabCom I3M-Dactim mis/LMA CNRS 7348, Université de Poitiers, Poitiers, France
| | | | - Annick Toutain
- UF de Génétique Médicale, Centre Hospitalier Universitaire, Tours, France
- UMR 1253, iBrain, Université de Tours, INSERM, Tours, France
| | - Vincent Meyer
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Université Paris-Saclay, CEA, Evry, France
| | - Olivier Pichon
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Martine Doco-Fenzy
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Stéphane Bézieau
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
| | - Benjamin Cogné
- l'institut du thorax, Nantes Université, CHU de Nantes, CNRS, INSERM, Nantes, France
- Service de Génétique médicale, Nantes Université, CHU de Nantes, Nantes, France
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Curic E, Ewans L, Pysar R, Taylan F, Botto LD, Nordgren A, Gahl W, Palmer EE. International Undiagnosed Diseases Programs (UDPs): components and outcomes. Orphanet J Rare Dis 2023; 18:348. [PMID: 37946247 PMCID: PMC10633944 DOI: 10.1186/s13023-023-02966-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023] Open
Abstract
Over the last 15 years, Undiagnosed Diseases Programs have emerged to address the significant number of individuals with suspected but undiagnosed rare genetic diseases, integrating research and clinical care to optimize diagnostic outcomes. This narrative review summarizes the published literature surrounding Undiagnosed Diseases Programs worldwide, including thirteen studies that evaluate outcomes and two commentary papers. Commonalities in the diagnostic and research process of Undiagnosed Diseases Programs are explored through an appraisal of available literature. This exploration allowed for an assessment of the strengths and limitations of each of the six common steps, namely enrollment, comprehensive clinical phenotyping, research diagnostics, data sharing and matchmaking, results, and follow-up. Current literature highlights the potential utility of Undiagnosed Diseases Programs in research diagnostics. Since participants have often had extensive previous genetic studies, research pipelines allow for diagnostic approaches beyond exome or whole genome sequencing, through reanalysis using research-grade bioinformatics tools and multi-omics technologies. The overall diagnostic yield is presented by study, since different selection criteria at enrollment and reporting processes make comparisons challenging and not particularly informative. Nonetheless, diagnostic yield in an undiagnosed cohort reflects the potential of an Undiagnosed Diseases Program. Further comparisons and exploration of the outcomes of Undiagnosed Diseases Programs worldwide will allow for the development and improvement of the diagnostic and research process and in turn improve the value and utility of an Undiagnosed Diseases Program.
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Affiliation(s)
- Ela Curic
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
| | - Lisa Ewans
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ryan Pysar
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Lorenzo D Botto
- Division of Medical Genetics, Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - William Gahl
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Elizabeth Emma Palmer
- Discipline of Paediatrics and Child Health, Faculty of Medicine and Health, School of Clinical Medicine, University of New South Wales, Bright Alliance Building, Level 8, Randwick, NSW, Australia.
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia.
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20
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Ling X, Wang C, Li L, Pan L, Huang C, Zhang C, Huang Y, Qiu Y, Lin F, Huang Y. Third-generation sequencing for genetic disease. Clin Chim Acta 2023; 551:117624. [PMID: 37923104 DOI: 10.1016/j.cca.2023.117624] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Third-generation sequencing (TGS) has led to a brave new revolution in detecting genetic diseases over the last few years. TGS has been rapidly developed for genetic disease applications owing to its significant advantages such as long read length, rapid detection, and precise detection of complex and rare structural variants. This approach greatly improves the efficiency of disease diagnosis and complements the shortcomings of short-read sequencing. In this paper, we first briefly introduce the working mechanism of one of the most important representatives of TGS, single-molecule real-time (SMRT) sequencing by Pacific Bioscience (PacBio), followed by a review and comparison of the advantages and disadvantages of different sequencing technologies. Finally, we focused on the progress of SMRT sequencing applications in genetic disease detection. Future perspectives on the applications of TGS in other fields were also presented. With the continuous innovation of the SMRT technologies and the expansion of their fields of application, SMRT sequencing has broad clinical application prospects in genetic diseases detection, and is expected to become an important tool for the molecular diagnosis of other diseases.
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Affiliation(s)
- Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Caixia Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yuling Qiu
- NHC Key Laboratory of Thalassemia Medicine, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Thalassemia Research, Guangxi Medical University, Nanning 530021, China
| | - Faquan Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
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Murphy R, Colclough K, Pollin TI, Ikle JM, Svalastoga P, Maloney KA, Saint-Martin C, Molnes J, Misra S, Aukrust I, de Franco E, Flanagan SE, Njølstad PR, Billings LK, Owen KR, Gloyn AL. The use of precision diagnostics for monogenic diabetes: a systematic review and expert opinion. COMMUNICATIONS MEDICINE 2023; 3:136. [PMID: 37794142 PMCID: PMC10550998 DOI: 10.1038/s43856-023-00369-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Monogenic diabetes presents opportunities for precision medicine but is underdiagnosed. This review systematically assessed the evidence for (1) clinical criteria and (2) methods for genetic testing for monogenic diabetes, summarized resources for (3) considering a gene or (4) variant as causal for monogenic diabetes, provided expert recommendations for (5) reporting of results; and reviewed (6) next steps after monogenic diabetes diagnosis and (7) challenges in precision medicine field. METHODS Pubmed and Embase databases were searched (1990-2022) using inclusion/exclusion criteria for studies that sequenced one or more monogenic diabetes genes in at least 100 probands (Question 1), evaluated a non-obsolete genetic testing method to diagnose monogenic diabetes (Question 2). The risk of bias was assessed using the revised QUADAS-2 tool. Existing guidelines were summarized for questions 3-5, and review of studies for questions 6-7, supplemented by expert recommendations. Results were summarized in tables and informed recommendations for clinical practice. RESULTS There are 100, 32, 36, and 14 studies included for questions 1, 2, 6, and 7 respectively. On this basis, four recommendations for who to test and five on how to test for monogenic diabetes are provided. Existing guidelines for variant curation and gene-disease validity curation are summarized. Reporting by gene names is recommended as an alternative to the term MODY. Key steps after making a genetic diagnosis and major gaps in our current knowledge are highlighted. CONCLUSIONS We provide a synthesis of current evidence and expert opinion on how to use precision diagnostics to identify individuals with monogenic diabetes.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand.
- Auckland Diabetes Centre, Te Whatu Ora Health New Zealand, Te Tokai Tumai, Auckland, New Zealand.
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jennifer M Ikle
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
| | - Pernille Svalastoga
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cécile Saint-Martin
- Department of Medical Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Elisa de Franco
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Pål R Njølstad
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Liana K Billings
- Division of Endocrinology, NorthShore University HealthSystem, Skokie, IL, USA
- Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Katharine R Owen
- Oxford Center for Diabetes, Endocrinology & Metabolism, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA.
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
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22
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Tesi B, Boileau C, Boycott KM, Canaud G, Caulfield M, Choukair D, Hill S, Spielmann M, Wedell A, Wirta V, Nordgren A, Lindstrand A. Precision medicine in rare diseases: What is next? J Intern Med 2023; 294:397-412. [PMID: 37211972 DOI: 10.1111/joim.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Molecular diagnostics is a cornerstone of modern precision medicine, broadly understood as tailoring an individual's treatment, follow-up, and care based on molecular data. In rare diseases (RDs), molecular diagnoses reveal valuable information about the cause of symptoms, disease progression, familial risk, and in certain cases, unlock access to targeted therapies. Due to decreasing DNA sequencing costs, genome sequencing (GS) is emerging as the primary method for precision diagnostics in RDs. Several ongoing European initiatives for precision medicine have chosen GS as their method of choice. Recent research supports the role for GS as first-line genetic investigation in individuals with suspected RD, due to its improved diagnostic yield compared to other methods. Moreover, GS can detect a broad range of genetic aberrations including those in noncoding regions, producing comprehensive data that can be periodically reanalyzed for years to come when further evidence emerges. Indeed, targeted drug development and repurposing of medicines can be accelerated as more individuals with RDs receive a molecular diagnosis. Multidisciplinary teams in which clinical specialists collaborate with geneticists, genomics education of professionals and the public, and dialogue with patient advocacy groups are essential elements for the integration of precision medicine into clinical practice worldwide. It is also paramount that large research projects share genetic data and leverage novel technologies to fully diagnose individuals with RDs. In conclusion, GS increases diagnostic yields and is a crucial step toward precision medicine for RDs. Its clinical implementation will enable better patient management, unlock targeted therapies, and guide the development of innovative treatments.
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Affiliation(s)
- Bianca Tesi
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Catherine Boileau
- Département de Génétique, APHP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Guillaume Canaud
- INSERM U1151, Unité de médecine translationnelle et thérapies ciblées, Hôpital Necker-Enfants Malades, Université Paris Cité, AP-HP, Paris, France
| | - Mark Caulfield
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Sue Hill
- Chief Scientific Officer, NHS England, London, UK
| | - Malte Spielmann
- Institute of Human Genetics, University Hospitals Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck, Kiel, Germany
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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23
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Barseghyan H, Pang AWC, Clifford B, Serrano MA, Chaubey A, Hastie AR. Comparative Benchmarking of Optical Genome Mapping and Chromosomal Microarray Reveals High Technological Concordance in CNV Identification and Additional Structural Variant Refinement. Genes (Basel) 2023; 14:1868. [PMID: 37895217 PMCID: PMC10667989 DOI: 10.3390/genes14101868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The recommended practice for individuals suspected of a genetic etiology for disorders including unexplained developmental delay/intellectual disability (DD/ID), autism spectrum disorders (ASD), and multiple congenital anomalies (MCA) involves a genetic testing workflow including chromosomal microarray (CMA), Fragile-X testing, karyotype analysis, and/or sequencing-based gene panels. Since genomic imbalances are often found to be causative, CMA is recommended as first tier testing for many indications. Optical genome mapping (OGM) is an emerging next generation cytogenomic technique that can detect not only copy number variants (CNVs), triploidy and absence of heterozygosity (AOH) like CMA, but can also define the location of duplications, and detect other structural variants (SVs), including balanced rearrangements and repeat expansions/contractions. This study compares OGM to CMA for clinically reported genomic variants, some of these samples also have structural characterization by fluorescence in situ hybridization (FISH). OGM was performed on IRB approved, de-identified specimens from 55 individuals with genomic abnormalities previously identified by CMA (61 clinically reported abnormalities). SVs identified by OGM were filtered by a control database to remove polymorphic variants and against an established gene list to prioritize clinically relevant findings before comparing with CMA and FISH results. OGM results showed 100% concordance with CMA findings for pathogenic variants and 98% concordant for all pathogenic/likely pathogenic/variants of uncertain significance (VUS), while also providing additional insight into the genomic structure of abnormalities that CMA was unable to provide. OGM demonstrates equivalent performance to CMA for CNV and AOH detection, enhanced by its ability to determine the structure of the genome. This work adds to an increasing body of evidence on the analytical validity and ability to detect clinically relevant abnormalities identified by CMA. Moreover, OGM identifies translocations, structures of duplications and complex CNVs intractable by CMA, yielding additional clinical utility.
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Affiliation(s)
- Hayk Barseghyan
- Bionano, San Diego, CA 92121, USA; (H.B.); (A.W.C.P.); (B.C.); (A.C.)
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA
- Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | | | - Benjamin Clifford
- Bionano, San Diego, CA 92121, USA; (H.B.); (A.W.C.P.); (B.C.); (A.C.)
| | | | - Alka Chaubey
- Bionano, San Diego, CA 92121, USA; (H.B.); (A.W.C.P.); (B.C.); (A.C.)
| | - Alex R. Hastie
- Bionano, San Diego, CA 92121, USA; (H.B.); (A.W.C.P.); (B.C.); (A.C.)
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24
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Murphy R, Colclough K, Pollin TI, Ikle JM, Svalastoga P, Maloney KA, Saint-Martin C, Molnes J, Misra S, Aukrust I, de Franco A, Flanagan SE, Njølstad PR, Billings LK, Owen KR, Gloyn AL. A Systematic Review of the use of Precision Diagnostics in Monogenic Diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.15.23288269. [PMID: 37131594 PMCID: PMC10153302 DOI: 10.1101/2023.04.15.23288269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Monogenic forms of diabetes present opportunities for precision medicine as identification of the underlying genetic cause has implications for treatment and prognosis. However, genetic testing remains inconsistent across countries and health providers, often resulting in both missed diagnosis and misclassification of diabetes type. One of the barriers to deploying genetic testing is uncertainty over whom to test as the clinical features for monogenic diabetes overlap with those for both type 1 and type 2 diabetes. In this review, we perform a systematic evaluation of the evidence for the clinical and biochemical criteria used to guide selection of individuals with diabetes for genetic testing and review the evidence for the optimal methods for variant detection in genes involved in monogenic diabetes. In parallel we revisit the current clinical guidelines for genetic testing for monogenic diabetes and provide expert opinion on the interpretation and reporting of genetic tests. We provide a series of recommendations for the field informed by our systematic review, synthesizing evidence, and expert opinion. Finally, we identify major challenges for the field and highlight areas for future research and investment to support wider implementation of precision diagnostics for monogenic diabetes.
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Affiliation(s)
- Rinki Murphy
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Auckland Diabetes Centre, Te Whatu Ora Health New Zealand, Te Tokai Tumai, Auckland, New Zealand
| | - Kevin Colclough
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Toni I Pollin
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jennifer M Ikle
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
| | - Pernille Svalastoga
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kristin A Maloney
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Cécile Saint-Martin
- Department of Medical Genetics, AP-HP Pitié-Salpêtrière Hospital, Sorbonne University, Paris, France
| | - Janne Molnes
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Shivani Misra
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Diabetes and Endocrinology, Imperial College Healthcare NHS Trust, London, UK
| | - Ingvild Aukrust
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - aiElisa de Franco
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Sarah E Flanagan
- Department of Clinical and Biomedical Science, Faculty of Health and Life Sciences, University of Exeter, UK
| | - Pål R Njølstad
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Liana K Billings
- Division of Endocrinology, NorthShore University HealthSystem, Skokie, IL, USA; Department of Medicine, Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Katharine R Owen
- Oxford Center for Diabetes, Endocrinology & Metabolism, University of Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology & Diabetes, Stanford School of Medicine, Stanford, CA, USA
- Stanford Diabetes Research Center, Stanford School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA
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25
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Papadopoulou E, Pepe G, Konitsiotis S, Chondrogiorgi M, Grigoriadis N, Kimiskidis VK, Tsivgoulis G, Mitsikostas DD, Chroni E, Domouzoglou E, Tsaousis G, Nasioulas G. The evolution of comprehensive genetic analysis in neurology: Implications for precision medicine. J Neurol Sci 2023; 447:120609. [PMID: 36905813 DOI: 10.1016/j.jns.2023.120609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Technological advancements have facilitated the availability of reliable and thorough genetic analysis in many medical fields, including neurology. In this review, we focus on the importance of selecting the appropriate genetic test to aid in the accurate identification of disease utilizing currently employed technologies for analyzing monogenic neurological disorders. Moreover, the applicability of comprehensive analysis via NGS for various genetically heterogeneous neurological disorders is reviewed, revealing its efficiency in clarifying a frequently cloudy diagnostic picture and delivering a conclusive and solid diagnosis that is essential for the proper management of the patient. The feasibility and effectiveness of medical genetics in neurology require interdisciplinary cooperation among several medical specialties and geneticists, to select and perform the most relevant test according to each patient's medical history, using the most appropriate technological tools. The prerequisites for a comprehensive genetic analysis are discussed, highlighting the utility of appropriate gene selection, variant annotation, and classification. Moreover, genetic counseling and interdisciplinary collaboration could improve diagnostic yield further. Additionally, a sub-analysis is conducted on the 1,502,769 variation records with submitted interpretations in the Clinical Variation (ClinVar) database, with a focus on neurology-related genes, to clarify the value of suitable variant categorization. Finally, we review the current applications of genetic analysis in the diagnosis and personalized management of neurological patients and the advances in the research and scientific knowledge of hereditary neurological disorders that are evolving the utility of genetic analysis towards the individualization of the treatment strategy.
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Affiliation(s)
| | - Georgia Pepe
- GeneKor Medical SA, Spaton 52, Gerakas 15344, Greece
| | - Spiridon Konitsiotis
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Maria Chondrogiorgi
- Department of Neurology, University of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
| | - Nikolaos Grigoriadis
- Second Department of Neurology, "AHEPA" University Hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Vasilios K Kimiskidis
- First Department of Neurology, "AHEPA" University hospital, Aristotle University of Thessaloniki, St. Kiriakidis 1, Thessaloniki 54636, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, School of Medicine, "Attikon" University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimos D Mitsikostas
- First Department of Neurology, Aeginition Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Elisabeth Chroni
- Department of Neurology, School of Medicine, University of Patras, Rio-Patras, Greece
| | - Eleni Domouzoglou
- Department of Pediatrics, University Hospital of Ioannina, Stavrou Niarchou Avenue, Ioannina 45500, Greece
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26
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Genome-Wide Sequencing Modalities for Children with Unexplained Global Developmental Delay and Intellectual Disabilities—A Narrative Review. CHILDREN 2023; 10:children10030501. [PMID: 36980059 PMCID: PMC10047410 DOI: 10.3390/children10030501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Unexplained global developmental delay (GDD) and intellectual disabilities (ID) together affect nearly 2% of the pediatric population. Establishing an etiologic diagnosis is crucial for disease management, prognostic evaluation, and provision of physical and psychological support for both the patient and the family. Advancements in genome sequencing have allowed rapid accumulation of gene–disorder associations and have accelerated the search for an etiologic diagnosis for unexplained GDD/ID. We reviewed recent studies that utilized genome-wide analysis technologies, and we discussed their diagnostic yield, strengths, and limitations. Overall, exome sequencing (ES) and genome sequencing (GS) outperformed chromosomal microarrays and targeted panel sequencing. GS provides coverage for both ES and chromosomal microarray regions, providing the maximal diagnostic potential, and the cost of ES and reanalysis of ES-negative results is currently still lower than that of GS alone. Therefore, singleton or trio ES is the more cost-effective option for the initial investigation of individuals with GDD/ID in clinical practice compared to a staged approach or GS alone. Based on these updated evidence, we proposed an evaluation algorithm with ES as the first-tier evaluation for unexplained GDD/ID.
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27
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Rezapour A, Souresrafil A, Barzegar M, Sheikhy-Chaman M, Tatarpour P. Economic evaluation of next-generation sequencing techniques in diagnosis of genetic disorders: A systematic review. Clin Genet 2023; 103:513-528. [PMID: 36808726 DOI: 10.1111/cge.14313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 02/23/2023]
Abstract
In recent years, massively parallel sequencing or next generation sequencing (NGS) has considerably changed both the research and diagnostic fields, and rapid developments have led to the combination of NGS techniques in clinical practice, ease of analysis, and detection of genetic mutations. This article aimed at reviewing the economic evaluation studies of the NGS techniques in the diagnosis of genetic diseases. In this systematic review, scientific databases (PubMed, EMBASE, Web of Science, Cochrane, Scopus, and CEA registry) were searched from 2005 to 2022 to identify the related literature on the economic evaluation of NGS techniques in the diagnosis of genetic diseases. Full-text reviews and data extraction were all performed by two independent researchers. The quality of all the articles included in this study was evaluated using the Checklist of Quality of Health Economic Studies (QHES). Out of 20 521 screened abstracts, 36 studies met the inclusion criteria. The mean score of the QHES checklist for the studies was 0.78 (high quality). Seventeen studies were conducted based on modeling. Cost-effectiveness analysis, cost-utility analysis, and cost-minimization analysis were done in 26 studies, 13 studies, and 1 study, respectively. Based on the available evidence and findings, exome sequencing, which is one of the NGS techniques, could have the potential to be used as a cost-effective genomic test to diagnose children with suspected genetic diseases. The results of the present study support the cost-effectiveness of exome sequencing in diagnosing suspected genetic disorders. However, the use of exome sequencing as a first- or second-line diagnostic test is still controversial. Most studies have been conducted in high-income countries, and research on the cost-effectiveness of NGS methods is recommended in low- and middle-income countries.
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Affiliation(s)
- Aziz Rezapour
- Health Management and Economics Research Center, Health Management Research Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Aghdas Souresrafil
- Department of Health Services and Health Promotion, School of Health, Occupational Environment Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Barzegar
- Department of English Language, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Sheikhy-Chaman
- Department of Health Economics, School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Parvin Tatarpour
- School of Health Management and Information Sciences, Iran University of Medical Sciences, Tehran, Iran
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28
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Yao Q, Gorevic P, Shen B, Gibson G. Genetically transitional disease: a new concept in genomic medicine. Trends Genet 2023; 39:98-108. [PMID: 36564319 DOI: 10.1016/j.tig.2022.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Traditional classification of genetic diseases as monogenic and polygenic has lagged far behind scientific progress. In this opinion article, we propose and define a new terminology, genetically transitional disease (GTD), referring to cases where a large-effect mutation is necessary, but not sufficient, to cause disease. This leads to a working disease nosology based on gradients of four types of genetic architecture: monogenic, polygenic, GTD, and mixed. We present four scenarios under which GTD may occur; namely, subsets of traditionally Mendelian disease, modifiable Tier 1 monogenic conditions, variable penetrance, and situations where a genetic mutational spectrum produces qualitatively divergent pathologies. The implications of the new nosology in precision medicine are discussed, in which therapeutic options may target the molecular cause or the disease phenotype.
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Affiliation(s)
- Qingping Yao
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA.
| | - Peter Gorevic
- Division of Rheumatology, Allergy, and Immunology, Stony Brook University Renaissance School of Medicine, Stony Brook, NY, USA
| | - Bo Shen
- Center for Inflammatory Bowel Diseases, New York-Presbyterian/Columbia University Irving Medical Center, New York, NY, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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29
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Fischer J, Alter S. Adding up the desmosomal genes causing syndromes with hair and skin involvement: identification of TUFT1 by state-of-the-art whole-genome sequencing. Br J Dermatol 2023; 188:8-9. [PMID: 36689526 DOI: 10.1093/bjd/ljac073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/05/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Judith Fischer
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Svenja Alter
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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30
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McNeill A. Happy 30th birthday to the European Journal of Human Genetics! Eur J Hum Genet 2022; 30:1095-1096. [PMID: 36221024 PMCID: PMC9554020 DOI: 10.1038/s41431-022-01188-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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