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De Pace R, Maroofian R, Paimboeuf A, Zamani M, Zaki MS, Sadeghian S, Azizimalamiri R, Galehdari H, Zeighami J, Williamson CD, Fleming E, Zhou D, Gannon JL, Thiffault I, Roze E, Suri M, Zifarelli G, Bauer P, Houlden H, Severino M, Patten SA, Farrow E, Bonifacino JS. Biallelic BORCS8 variants cause an infantile-onset neurodegenerative disorder with altered lysosome dynamics. Brain 2024; 147:1751-1767. [PMID: 38128568 PMCID: PMC11068110 DOI: 10.1093/brain/awad427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/30/2023] [Accepted: 12/02/2023] [Indexed: 12/23/2023] Open
Abstract
BLOC-one-related complex (BORC) is a multiprotein complex composed of eight subunits named BORCS1-8. BORC associates with the cytosolic face of lysosomes, where it sequentially recruits the small GTPase ARL8 and kinesin-1 and -3 microtubule motors to promote anterograde transport of lysosomes toward the peripheral cytoplasm in non-neuronal cells and the distal axon in neurons. The physiological and pathological importance of BORC in humans, however, remains to be determined. Here, we report the identification of compound heterozygous variants [missense c.85T>C (p.Ser29Pro) and frameshift c.71-75dupTGGCC (p.Asn26Trpfs*51)] and homozygous variants [missense c.196A>C (p.Thr66Pro) and c.124T>C (p.Ser42Pro)] in BORCS8 in five children with a severe early-infantile neurodegenerative disorder from three unrelated families. The children exhibit global developmental delay, severe-to-profound intellectual disability, hypotonia, limb spasticity, muscle wasting, dysmorphic facies, optic atrophy, leuko-axonopathy with hypomyelination, and neurodegenerative features with prevalent supratentorial involvement. Cellular studies using a heterologous transfection system show that the BORCS8 missense variants p.Ser29Pro, p.Ser42Pro and p.Thr66Pro are expressed at normal levels but exhibit reduced assembly with other BORC subunits and reduced ability to drive lysosome distribution toward the cell periphery. The BORCS8 frameshift variant p.Asn26Trpfs*51, on the other hand, is expressed at lower levels and is completely incapable of assembling with other BORC subunits and promoting lysosome distribution toward the cell periphery. Therefore, all the BORCS8 variants are partial or total loss-of-function alleles and are thus likely pathogenic. Knockout of the orthologous borcs8 in zebrafish causes decreased brain and eye size, neuromuscular anomalies and impaired locomotion, recapitulating some of the key traits of the human disease. These findings thus identify BORCS8 as a novel genetic locus for an early-infantile neurodegenerative disorder and highlight the critical importance of BORC and lysosome dynamics for the development and function of the central nervous system.
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Affiliation(s)
- Raffaella De Pace
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child, Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Adeline Paimboeuf
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 83151-61355, Iran
- Department of Molecular Genetics, Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 61556-89467, Iran
| | - Maha S Zaki
- Human Genetics and Genome Research Institute, Clinical Genetics Department, National Research Centre, Cairo 12622, Egypt
| | - Saeid Sadeghian
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 61357-33184, Iran
| | - Reza Azizimalamiri
- Department of Pediatric Neurology, Golestan Medical, Educational, and Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 61357-33184, Iran
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 83151-61355, Iran
| | - Jawaher Zeighami
- Department of Molecular Genetics, Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz 61556-89467, Iran
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child, Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emily Fleming
- Department of Genetics, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Department of Genetics, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Jennifer L Gannon
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Division of Clinical Genetics, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Department of Genetics, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pathology, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emmanuel Roze
- Sorbonne Université, CNRS, INSERM, Institut du Cerveau (ICM), and Assistance Publique-Hôpitaux de Paris, Department of Neurology, Hôpital de la Pitié-Salpêtrière, Paris 75013, France
| | - Mohnish Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, City Hospital Campus, Nottingham NG5 1PB, UK
| | | | | | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Shunmoogum A Patten
- Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
- Départementde Neurosciences, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Emily Farrow
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child, Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Cohen ASA, Berrios CD, Zion TN, Barrett CM, Moore R, Boillat E, Belden B, Farrow EG, Thiffault I, Zuccarelli BD, Pastinen T. Genomic Answers for Kids: Toward more equitable access to genomic testing for rare diseases in rural populations. Am J Hum Genet 2024; 111:825-832. [PMID: 38636509 PMCID: PMC11080604 DOI: 10.1016/j.ajhg.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Next-generation sequencing has revolutionized the speed of rare disease (RD) diagnoses. While clinical exome and genome sequencing represent an effective tool for many RD diagnoses, there is room to further improve the diagnostic odyssey of many RD patients. One recognizable intervention lies in increasing equitable access to genomic testing. Rural communities represent a significant portion of underserved and underrepresented individuals facing additional barriers to diagnosis and treatment. Primary care providers (PCPs) at local clinics, though sometimes suspicious of a potential benefit of genetic testing for their patients, have significant constraints in pursuing it themselves and rely on referrals to specialists. Yet, these referrals are typically followed by long waitlists and significant delays in clinical assessment, insurance clearance, testing, and initiation of diagnosis-informed care management. Not only is this process time intensive, but it also often requires multiple visits to urban medical centers for which distance may be a significant barrier to rural families. Therefore, providing early, "direct-to-provider" (DTP) local access to unrestrictive genomic testing is likely to help speed up diagnostic times and access to care for RD patients in rural communities. In a pilot study with a PCP clinic in rural Kansas, we observed a minimum 5.5 months shortening of time to diagnosis through the DTP exome sequencing program as compared to rural patients receiving genetic testing through the "traditional" PCP-referral-to-specialist scheme. We share our experience to encourage future partnerships beyond our center. Our efforts represent just one step in fostering greater diversity and equity in genomic studies.
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Affiliation(s)
- Ana S A Cohen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA.
| | - Courtney D Berrios
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Tricia N Zion
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Cassandra M Barrett
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Riley Moore
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emelia Boillat
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Bradley Belden
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA
| | - Britton D Zuccarelli
- Salina Pediatric Care, Salina Regional Health Center, Salina, KS 67401, USA; Department of Pediatrics, University of Kansas School of Medicine - Salina Campus, Salina, KS 67401, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA; UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO 64108, USA; Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO 64108, USA
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Marchant RG, Bryen SJ, Bahlo M, Cairns A, Chao KR, Corbett A, Davis MR, Ganesh VS, Ghaoui R, Jones KJ, Kornberg AJ, Lek M, Liang C, MacArthur DG, Oates EC, O'Donnell-Luria A, O'Grady GL, Osei-Owusu IA, Rafehi H, Reddel SW, Roxburgh RH, Ryan MM, Sandaradura SA, Scott LW, Valkanas E, Weisburd B, Young H, Evesson FJ, Waddell LB, Cooper ST. Genome and RNA sequencing boost neuromuscular diagnoses to 62% from 34% with exome sequencing alone. Ann Clin Transl Neurol 2024; 11:1250-1266. [PMID: 38544359 DOI: 10.1002/acn3.52041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/24/2024] [Indexed: 05/15/2024] Open
Abstract
OBJECTIVE Most families with heritable neuromuscular disorders do not receive a molecular diagnosis. Here we evaluate diagnostic utility of exome, genome, RNA sequencing, and protein studies and provide evidence-based recommendations for their integration into practice. METHODS In total, 247 families with suspected monogenic neuromuscular disorders who remained without a genetic diagnosis after standard diagnostic investigations underwent research-led massively parallel sequencing: neuromuscular disorder gene panel, exome, genome, and/or RNA sequencing to identify causal variants. Protein and RNA studies were also deployed when required. RESULTS Integration of exome sequencing and auxiliary genome, RNA and/or protein studies identified causal or likely causal variants in 62% (152 out of 247) of families. Exome sequencing alone informed 55% (83 out of 152) of diagnoses, with remaining diagnoses (45%; 69 out of 152) requiring genome sequencing, RNA and/or protein studies to identify variants and/or support pathogenicity. Arrestingly, novel disease genes accounted for <4% (6 out of 152) of diagnoses while 36.2% of solved families (55 out of 152) harbored at least one splice-altering or structural variant in a known neuromuscular disorder gene. We posit that contemporary neuromuscular disorder gene-panel sequencing could likely provide 66% (100 out of 152) of our diagnoses today. INTERPRETATION Our results emphasize thorough clinical phenotyping to enable deep scrutiny of all rare genetic variation in phenotypically consistent genes. Post-exome auxiliary investigations extended our diagnostic yield by 81% overall (34-62%). We present a diagnostic algorithm that details deployment of genomic and auxiliary investigations to obtain these diagnoses today most effectively. We hope this provides a practical guide for clinicians as they gain greater access to clinical genome and transcriptome sequencing.
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Affiliation(s)
- Rhett G Marchant
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Samantha J Bryen
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Melanie Bahlo
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Anita Cairns
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Department, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Katherine R Chao
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alastair Corbett
- Neurology Department, Repatriation General Hospital Concord, Concord, New South Wales, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, WA, Australia
| | - Vijay S Ganesh
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Neuromuscular Division, Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Roula Ghaoui
- Department of Neurology, Central Adelaide Local Health Network/Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Genetics & Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Kristi J Jones
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Clinical Genetics, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Andrew J Kornberg
- Department of Neurology, Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Monkol Lek
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Christina Liang
- Department of Neurology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
- Neurogenetics, Northern Clinical School, Kolling Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Daniel G MacArthur
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Centre for Population Genomics, Garvan Institute of Medical Research/University of New South Wales, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Emily C Oates
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Randwick, New South Wales, Australia
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gina L O'Grady
- Starship Children's Health, Auckland District Health Board, Auckland, New Zealand
| | - Ikeoluwa A Osei-Owusu
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Haloom Rafehi
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Stephen W Reddel
- Neurology Department, Repatriation General Hospital Concord, Concord, New South Wales, Australia
- Brain and Mind Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard H Roxburgh
- Department of Neurology, Auckland District Health Board, Auckland, New Zealand
- Centre of Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Monique M Ryan
- Department of Neurology, Royal Children's Hospital Melbourne, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
- Neurosciences Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah A Sandaradura
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Clinical Genetics, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Liam W Scott
- Functional Neuromics, Children's Medical Research Institute, Westmead, New South Wales, Australia
- Population Health and Immunity, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Elise Valkanas
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA
| | - Ben Weisburd
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Helen Young
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Department of Neurology, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Paediatrics, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Frances J Evesson
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Leigh B Waddell
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Sandra T Cooper
- Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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5
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Bhat S, Rousseau J, Michaud C, Lourenço CM, Stoler JM, Louie RJ, Clarkson LK, Lichty A, Koboldt DC, Reshmi SC, Sisodiya SM, Hoytema van Konijnenburg EMM, Koop K, van Hasselt PM, Démurger F, Dubourg C, Sullivan BR, Hughes SS, Thiffault I, Tremblay ES, Accogli A, Srour M, Blunck R, Campeau PM. Mono-allelic KCNB2 variants lead to a neurodevelopmental syndrome caused by altered channel inactivation. Am J Hum Genet 2024; 111:761-777. [PMID: 38503299 PMCID: PMC11023922 DOI: 10.1016/j.ajhg.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/21/2024] Open
Abstract
Ion channels mediate voltage fluxes or action potentials that are central to the functioning of excitable cells such as neurons. The KCNB family of voltage-gated potassium channels (Kv) consists of two members (KCNB1 and KCNB2) encoded by KCNB1 and KCNB2, respectively. These channels are major contributors to delayed rectifier potassium currents arising from the neuronal soma which modulate overall excitability of neurons. In this study, we identified several mono-allelic pathogenic missense variants in KCNB2, in individuals with a neurodevelopmental syndrome with epilepsy and autism in some individuals. Recurrent dysmorphisms included a broad forehead, synophrys, and digital anomalies. Additionally, we selected three variants where genetic transmission has not been assessed, from two epilepsy studies, for inclusion in our experiments. We characterized channel properties of these variants by expressing them in oocytes of Xenopus laevis and conducting cut-open oocyte voltage clamp electrophysiology. Our datasets indicate no significant change in absolute conductance and conductance-voltage relationships of most disease variants as compared to wild type (WT), when expressed either alone or co-expressed with WT-KCNB2. However, variants c.1141A>G (p.Thr381Ala) and c.641C>T (p.Thr214Met) show complete abrogation of currents when expressed alone with the former exhibiting a left shift in activation midpoint when expressed alone or with WT-KCNB2. The variants we studied, nevertheless, show collective features of increased inactivation shifted to hyperpolarized potentials. We suggest that the effects of the variants on channel inactivation result in hyper-excitability of neurons, which contributes to disease manifestations.
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Affiliation(s)
- Shreyas Bhat
- Center for Interdisciplinary Research on Brain and Learning (CIRCA), Department of Physics and Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, Canada
| | - Justine Rousseau
- Centre de Recherche Du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Coralie Michaud
- Centre de Recherche Du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | | | - Joan M Stoler
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Angie Lichty
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Daniel C Koboldt
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA
| | - Shalini C Reshmi
- Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, OH, USA; Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | | | - Klaas Koop
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Peter M van Hasselt
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Université de Rennes, CNRS, IGDR, UMR 6290 Rennes, France
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Susan S Hughes
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Departments of Pediatrics and of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Elisabeth Simard Tremblay
- Department of Neurology and Neurosurgery, McGill University Health Centre, Montréal, QC, Canada; Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montréal, QC, Canada
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montréal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montral, QC H3A 1B1, Canada
| | - Myriam Srour
- Department of Pediatrics, Division of Pediatric Neurology, McGill University, Montréal, QC, Canada; Department of Human Genetics, Faculty of Medicine, McGill University, Montral, QC H3A 1B1, Canada
| | - Rikard Blunck
- Center for Interdisciplinary Research on Brain and Learning (CIRCA), Department of Physics and Department of Pharmacology and Physiology, Université de Montréal, Montréal, QC, Canada.
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6
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Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads. medRxiv 2024:2024.03.22.24304756. [PMID: 38585974 PMCID: PMC10996739 DOI: 10.1101/2024.03.22.24304756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvements in germline SV detection. However, current long-read SV detection methods do not generalize well to the analysis of somatic SVs in tumor genomes with complex rearrangements, heterogeneity, and aneuploidy. Here, we present Severus: a method for the accurate detection of different types of somatic SVs using a phased breakpoint graph approach. To benchmark various short- and long-read SV detection methods, we sequenced five tumor/normal cell line pairs with Illumina, Nanopore, and PacBio sequencing platforms; on this benchmark Severus showed the highest F1 scores (harmonic mean of the precision and recall) as compared to long-read and short-read methods. We then applied Severus to three clinical cases of pediatric cancer, demonstrating concordance with known genetic findings as well as revealing clinically relevant cryptic rearrangements missed by standard genomic panels.
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Affiliation(s)
- Ayse Keskus
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tanveer Ahmad
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Byunggil Yoo
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Anton Goretsky
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Ataberk Donmez
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Lisa A. Lansdon
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabel Rodriguez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Jimin Park
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Yuelin Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Xiwen Cui
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Samuel Sacco
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Jyoti Shetty
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yongmei Zhao
- Sequencing Facility Bioinformatics Group, Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bao Tran
- Sequencing Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | | | | | | | | | | | - Erin K. Molloy
- Department of Computer Science, University of Maryland, College Park, MD, USA
| | - Irina Pushel
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Erin Guest
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Tomi Pastinen
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kishwar Shafin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Salem Malikic
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chi-Ping Day
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | - Cenk Sahinalp
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Midhat S. Farooqi
- Children’s Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | | | - Mikhail Kolmogorov
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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7
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LeMaster C, Schwendinger-Schreck C, Ge B, Cheung W, Johnston JJ, Pastinen T, Smail C. Mapping structural variants to rare disease genes using long-read whole genome sequencing and trait-relevant polygenic scores. medRxiv 2024:2024.03.15.24304216. [PMID: 38562793 PMCID: PMC10984062 DOI: 10.1101/2024.03.15.24304216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent studies have revealed the pervasive landscape of rare structural variants (rSVs) present in human genomes. rSVs can have extreme effects on the expression of proximal genes and, in a rare disease context, have been implicated in patient cases where no diagnostic single nucleotide variant (SNV) was found. Approaches for integrating rSVs to date have focused on targeted approaches in known Mendelian rare disease genes. This approach is intractable for rare diseases with many causal loci or patients with complex, multi-phenotype syndromes. We hypothesized that integrating trait-relevant polygenic scores (PGS) would provide a substantial reduction in the number of candidate disease genes in which to assess rSV effects. We further implemented a method for ranking PGS genes to define a set of core/key genes where a rSV has the potential to exert relatively larger effects on disease risk. Among a subset of patients enrolled in the Genomic Answers for Kids (GA4K) rare disease program (N=497), we used PacBio HiFi long-read whole genome sequencing (lrWGS) to identify rSVs intersecting genes in trait-relevant PGSs. Illustrating our approach in Autism (N=54 cases), we identified 1,827 deletions, 158 duplications, 619 insertions, and 14 inversions overlapping putative core/key PGS genes. Additionally, by integrating genomic constraint annotations from gnomAD, we observed that rare duplications overlapping putative core/key PGS genes were frequently in higher constraint regions compared to controls (P = 2×10-04). This difference was not observed in the lowest-ranked gene set (P = 0.18). Overall, our study provides a framework for the annotation of long-read rSVs from lrWGS data and prioritization of disease-linked genomic regions for downstream functional validation of rSV impacts. To enable reuse by other researchers, we have made SV allele frequencies and gene associations freely available.
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Affiliation(s)
- C LeMaster
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - C Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - B Ge
- McGill University, Montreal, Quebec, Canada
| | - W Cheung
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - J J Johnston
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - T Pastinen
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
| | - C Smail
- Genomic Medicine Center, Children's Mercy Research Institute and Children's Mercy Kansas City, Kansas City, MO, USA
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8
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Pucel J, Briere LC, Reuter C, Gochyyev P, LeBlanc K. Exome and genome sequencing in a heterogeneous population of patients with rare disease: Identifying predictors of a diagnosis. Genet Med 2024; 26:101115. [PMID: 38436216 DOI: 10.1016/j.gim.2024.101115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024] Open
Abstract
PURPOSE Exome (ES) and genome sequencing (GS) are increasingly being utilized for individuals with rare and undiagnosed diseases; however, guidelines on their use remain limited. This study aimed to identify factors associated with diagnosis by ES and/or GS in a heterogeneous population of patients with rare and undiagnosed diseases. METHODS In this case control study, we reviewed data from 400 diagnosed and 400 undiagnosed randomly selected participants in the Undiagnosed Diseases Network, all of whom had undergone ES and/or GS. We analyzed factors associated with receiving a diagnosis by ES and/or GS. RESULTS Factors associated with a decreased odds of being diagnosed included adult symptom onset, singleton sequencing, and having undergone ES and/or GS before acceptance to the Undiagnosed Diseases Network (48%, 51%, and 32% lower odds, respectively). Factors that increased the odds of being diagnosed by ES and/or GS included having primarily neurological symptoms and having undergone prior chromosomal microarray testing (44% and 59% higher odds, respectively). CONCLUSION We identified several factors that were associated with receiving a diagnosis by ES and/or GS. This will ideally inform the utilization of ES and/or GS and help manage expectations of individuals and families undergoing these tests.
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Affiliation(s)
- Jenna Pucel
- MGH Institute of Health Professions, Boston, MA.
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Cardiovascular Medicine, Stanford University, Palo Alto, CA
| | | | - Kimberly LeBlanc
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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9
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Porubsky D, Eichler EE. A 25-year odyssey of genomic technology advances and structural variant discovery. Cell 2024; 187:1024-1037. [PMID: 38290514 DOI: 10.1016/j.cell.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/20/2023] [Accepted: 01/02/2024] [Indexed: 02/01/2024]
Abstract
This perspective focuses on advances in genome technology over the last 25 years and their impact on germline variant discovery within the field of human genetics. The field has witnessed tremendous technological advances from microarrays to short-read sequencing and now long-read sequencing. Each technology has provided genome-wide access to different classes of human genetic variation. We are now on the verge of comprehensive variant detection of all forms of variation for the first time with a single assay. We predict that this transition will further transform our understanding of human health and biology and, more importantly, provide novel insights into the dynamic mutational processes shaping our genomes.
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Affiliation(s)
- David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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10
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Groza C, Schwendinger-Schreck C, Cheung WA, Farrow EG, Thiffault I, Lake J, Rizzo WB, Evrony G, Curran T, Bourque G, Pastinen T. Pangenome graphs improve the analysis of structural variants in rare genetic diseases. Nat Commun 2024; 15:657. [PMID: 38253606 PMCID: PMC10803329 DOI: 10.1038/s41467-024-44980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal and graph genomes. We leverage standard reference genomes, public assemblies (n = 94) and a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n = 574 assemblies) to build a graph genome representing a unified SV callset in GA4K, identify common variation and prioritize SVs that are more likely to cause genetic disease (MAF < 0.01). Using graphs, we obtain a higher level of reproducibility than the standard reference approach. We observe over 200,000 SV alleles unique to GA4K, including nearly 1000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate a novel diagnostic SV in KMT2E, demonstrating use of personal assemblies coupled with pangenome graphs for rare disease genomics. The community may interrogate our pangenome with additional assemblies to discover new SVs within the allele frequency spectrum relevant to genetic diseases.
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Affiliation(s)
- Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, QC, Canada
| | | | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Hospital and Research Institute, KC, MO, USA
| | - Emily G Farrow
- Genomic Medicine Center, Children's Mercy Hospital and Research Institute, KC, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital and Research Institute, KC, MO, USA
| | | | - William B Rizzo
- Child Health Research Institute, Department of Pediatrics, Nebraska Medical Center, Omaha, NE, USA
| | - Gilad Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO, USA
| | - Guillaume Bourque
- Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada.
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan.
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada.
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital and Research Institute, KC, MO, USA.
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11
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Smail C, Ge B, Keever-Keigher MR, Schwendinger-Schreck C, Cheung W, Johnston JJ, Barrett C, Feldman K, Cohen AS, Farrow EG, Thiffault I, Grundberg E, Pastinen T. Complex trait associations in rare diseases and impacts on Mendelian variant interpretation. medRxiv 2024:2024.01.10.24301111. [PMID: 38260377 PMCID: PMC10802745 DOI: 10.1101/2024.01.10.24301111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Emerging evidence implicates common genetic variation - aggregated into polygenic scores (PGS) - impacting the onset and phenotypic presentation of rare diseases. In this study, we quantified individual polygenic liability for 1,151 previously published PGS in a cohort of 2,374 probands enrolled in the Genomic Answers for Kids (GA4K) rare disease study, revealing widespread associations between rare disease phenotypes and PGSs for common complex diseases and traits, blood protein levels, and brain and other organ morphological measurements. We observed increased polygenic burden in probands with variants of unknown significance (VUS) compared to unaffected carrier parents. We further observed an enrichment in overlap between diagnostic and candidate rare disease genes and large-effect PGS genes. Overall, our study supports and expands on previous findings of complex trait associations in rare disease phenotypes and provides a framework for identifying novel candidate rare disease genes and in understanding variable penetrance of candidate Mendelian disease variants.
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Affiliation(s)
- Craig Smail
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Bing Ge
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Marissa R. Keever-Keigher
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Warren Cheung
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J. Johnston
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Cassandra Barrett
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | - Keith Feldman
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Health Outcomes and Health Services Research, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Ana S.A. Cohen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Emily G. Farrow
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Elin Grundberg
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
- UKMC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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12
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Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA. Characterization and visualization of tandem repeats at genome scale. Nat Biotechnol 2024:10.1038/s41587-023-02057-3. [PMID: 38168995 DOI: 10.1038/s41587-023-02057-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Tandem repeat (TR) variation is associated with gene expression changes and numerous rare monogenic diseases. Although long-read sequencing provides accurate full-length sequences and methylation of TRs, there is still a need for computational methods to profile TRs across the genome. Here we introduce the Tandem Repeat Genotyping Tool (TRGT) and an accompanying TR database. TRGT determines the consensus sequences and methylation levels of specified TRs from PacBio HiFi sequencing data. It also reports reads that support each repeat allele. These reads can be subsequently visualized with a companion TR visualization tool. Assessing 937,122 TRs, TRGT showed a Mendelian concordance of 98.38%, allowing a single repeat unit difference. In six samples with known repeat expansions, TRGT detected all expansions while also identifying methylation signals and mosaicism and providing finer repeat length resolution than existing methods. Additionally, we released a database with allele sequences and methylation levels for 937,122 TRs across 100 genomes.
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Affiliation(s)
| | - Adam English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Harriet Dashnow
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | | | - Tom Mokveld
- Pacific Biosciences of California, Menlo Park, CA, USA
| | | | | | | | - Matt C Danzi
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron Wenger
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Khi Pin Chua
- Pacific Biosciences of California, Menlo Park, CA, USA
| | - Verónica Martínez-Cerdeño
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
- MIND Institute, UC Davis School of Medicine, Sacramento, CA, USA
| | - Trevor D Bartley
- Institute for Pediatric Regenerative Medicine, Shriner's Hospital for Children and UC Davis School of Medicine, Sacramento, CA, USA
- Department of Pathology & Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Aaron R Quinlan
- Departments of Human Genetics and Biomedical Informatics, University of Utah, Salt Lake City, UT, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
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13
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Farrow E, Jay A, Means J, Younger S, Biswell R, Koseva B, Thiffault I, Pastinen T, Pappas K, Toriello H. Case of CLPB deficiency solved by HiFi long read genome sequencing and RNAseq. Am J Med Genet A 2023; 191:2908-2912. [PMID: 37548286 DOI: 10.1002/ajmg.a.63365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/03/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Affiliation(s)
- Emily Farrow
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | | | - John Means
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Scott Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Rebecca Biswell
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Kara Pappas
- Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Helga Toriello
- College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
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14
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Henly M, Phillips KG, Smith SL, Kloza EM, Brucker DL. Referral networks for pediatric patients with genetic conditions: The perspective of occupational therapists. J Genet Couns 2023; 32:982-992. [PMID: 37062897 DOI: 10.1002/jgc4.1706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/28/2023] [Accepted: 03/12/2023] [Indexed: 04/18/2023]
Abstract
Families of children with developmental delays but no diagnosed genetic condition may benefit from connection to genetic systems of care. This work examines the role of occupational therapy as a space for families of pediatric patients to gain access to genetic services. Between September 2021 and February 2022, we interviewed 20 occupational therapists in New England who work primarily with pediatric patients. We transcribed the interviews and used a grounded theory approach to identify and code recurring themes. The data reveal several barriers to linking pediatric patients to genetic systems of care, including lack of insurance coverage, wait times for appointments and test results, hesitant primary care providers, and familial and cultural stigma of disability. We discuss the unique role of occupational therapists as professionals who spend substantial time with patients, often in their everyday environments, to bridge these barriers. We also address challenges associated with occupational therapists facilitating connections to genetics services, including their lack of specialized knowledge of genetics and barriers fully integrating with others on the medical team.
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Affiliation(s)
- Megan Henly
- Institute on Disability, University of New Hampshire, New Hampshire, Durham, USA
| | - Kimberly G Phillips
- Institute on Disability, University of New Hampshire, New Hampshire, Durham, USA
| | - Sarah L Smith
- Department of Occupational Therapy, University of New Hampshire, New Hampshire, Durham, USA
| | - Edward M Kloza
- Women & Infants Hospital of Rhode Island, Rhode Island, Providence, USA
| | - Debra L Brucker
- Institute on Disability, University of New Hampshire, New Hampshire, Durham, USA
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15
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Abstract
Selecting the ideal test to evaluate an individual with a suspected genetic disorder can be challenging. While several clinical testing options are available, no single test yet captures all potentially causative genetic variants. Thus, clinicians may order testing in a stepwise fashion, and what to order after non-diagnostic testing can be challenging to determine. Here, we provide an overview of commonly used clinical genetic tests, guidance on when they are best used, and what they may miss. We conclude with a discussion of how new technologies might be used to identify challenging variants and simplify clinical testing in the future.
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Affiliation(s)
- Arthur L Lenahan
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Audrey E Squire
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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16
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Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YHH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, Stergachis AB. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition. bioRxiv 2023:2023.09.26.559521. [PMID: 37808736 PMCID: PMC10557686 DOI: 10.1101/2023.09.26.559521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes (NBEA, PDK3, MAB21L1, and RB1) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes.
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Affiliation(s)
- Mitchell R. Vollger
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kiara C. Eldred
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Elliott Swanson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | - Yong-Han H. Cheng
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | - Jane Ranchalis
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Yizi Mao
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Elizabeth E. Blue
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Ulrike Schwarze
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Katherine M. Munson
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
| | | | | | - Aimee Allworth
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Sirisak Chanprasert
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Ian Glass
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Martha Horike-Pyne
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | | | - Kathleen A. Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | | | | | - Sam Sheppeard
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Stephanie M. Sherman
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Samuel Strohbehn
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
| | - Amy L. Yuen
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | | | - Thomas A. Reh
- University of Washington School of Medicine, Department of Biological Structure, Seattle, WA, USA
| | - Peter H. Byers
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- University of Washington School of Medicine, Department of Laboratory Medicine and Pathology, Seattle, WA, USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Fuki M. Hisama
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Gail P. Jarvik
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yasemin Sancak
- University of Washington School of Medicine, Department of Pharmacology, Seattle, WA, USA
| | - Katrina M. Dipple
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- University of Washington, Department of Pediatrics, Seattle, WA, USA
| | - Andrew B. Stergachis
- University of Washington School of Medicine, Department of Genome Sciences, Seattle, WA, USA
- University of Washington School of Medicine, Department of Medicine, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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17
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Berntsson SG, Matsson H, Kristoffersson A, Niemelä V, van Duyvenvoorde HA, Richel-van Assenbergh C, van der Klift HM, Casar-Borota O, Frykholm C, Landtblom AM. Case report: a novel deep intronic splice-altering variant in DMD as a cause of Becker muscular dystrophy. Front Genet 2023; 14:1226766. [PMID: 37795243 PMCID: PMC10546389 DOI: 10.3389/fgene.2023.1226766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
We present the case of a male patient who was ultimately diagnosed with Becker muscular dystrophy (BMD; MIM# 300376) after the onset of muscle weakness in his teens progressively led to significant walking difficulties in his twenties. A genetic diagnosis was pursued but initial investigation revealed no aberrations in the dystrophin gene (DMD), although immunohistochemistry and Western blot analysis suggested the diagnosis of dystrophinopathy. Eventually, after more than 10 years, an RNA analysis captured abnormal splicing where 154 nucleotides from intron 43 were inserted between exon 43 and 44 resulting in a frameshift and a premature stop codon. Normal splicing of the DMD gene was also observed. Additionally, a novel variant c.6291-13537A>G in DMD was confirmed in the genomic DNA of the patient. The predicted function of the variant aligns with the mRNA results. To conclude, we here demonstrate that mRNA analysis can guide the diagnosis of non-coding genetic variants in DMD.
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Affiliation(s)
| | - Hans Matsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Clinical Genetics, Rudbeck Laboratory, Uppsala University Hospital, Uppsala, Sweden
| | - Anna Kristoffersson
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
| | - Valter Niemelä
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
| | | | | | | | - Olivera Casar-Borota
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Department of Clinical Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Carina Frykholm
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Clinical Genetics, Rudbeck Laboratory, Uppsala University Hospital, Uppsala, Sweden
| | - Anne-Marie Landtblom
- Department of Medical Sciences, Neurology, Uppsala University, Uppsala, Sweden
- Department of Clinical Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health, Linköping University, Linköping, Sweden
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18
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Kolesnikov A, Cook D, Nattestad M, McNulty B, Gorzynski J, Goenka S, Ashley EA, Jain M, Miga KH, Paten B, Chang PC, Carroll A, Shafin K. Local read haplotagging enables accurate long-read small variant calling. bioRxiv 2023:2023.09.07.556731. [PMID: 37745389 PMCID: PMC10515762 DOI: 10.1101/2023.09.07.556731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Biosciences (PacBio) and Oxford nanopore technologies (ONT) are introducing newer platforms and data types. It has been demonstrated that variant calling methods based on deep neural networks can use local haplotyping information with long-reads to improve the genotyping accuracy. However, using local haplotype information creates an overhead as variant calling needs to be performed multiple times which ultimately makes it difficult to extend to new data types and platforms as they get introduced. In this work, we have developed a local haplotype approximate method that enables state-of-the-art variant calling performance with multiple sequencing platforms including PacBio Revio system, ONT R10.4 simplex and duplex data. This addition of local haplotype approximation makes DeepVariant a universal variant calling solution for long-read sequencing platforms.
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Affiliation(s)
| | - Daniel Cook
- Google Inc, 1600 Amphitheatre Pkwy, Mountain View, CA
| | | | - Brandy McNulty
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
| | | | | | | | - Miten Jain
- Northeastern university, Boston, MA, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California, USA
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19
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Kane NJ, Cohen ASA, Berrios C, Jones B, Pastinen T, Hoffman MA. Committing to genomic answers for all kids: Evaluating inequity in genomic research enrollment. Genet Med 2023; 25:100895. [PMID: 37194653 PMCID: PMC10524770 DOI: 10.1016/j.gim.2023.100895] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
PURPOSE Persistent inequities in genomic medicine and research contribute to health disparities. This analysis uses a context-specific and equity-focused strategy to evaluate enrollment patterns for Genomic Answers for Kids (GA4K), a large, metropolitan-wide genomic study on children. METHODS Electronic health records for 2247 GA4K study participants were used to evaluate the distribution of individuals by demographics (race, ethnicity, and payor type) and location (residential address). Addresses were geocoded to produce point density and 3-digit zip code maps showing local and regional enrollment patterns. Health system reports and census data were used to compare participant characteristics with reference populations at different spatial scales. RESULTS Racial and ethnic minoritized and populations with low-income were underrepresented in the GA4K study cohort. Geographic variation demonstrates inequity in enrollment and participation among children from historically segregated and socially disadvantaged communities. CONCLUSION Our findings illustrate inequity in enrollment related to both GA4K study design and structural inequalities, which we suspect may exist for similar US-based studies. Our methods provide a scalable framework for continually evaluating and improving study design to ensure equitable participation in and benefits from genomic research and medicine. The use of high-resolution, place-based data represents a novel and practical means of identifying and characterizing inequities and targeting community engagement.
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Abstract
DNA sequencing has revolutionized medicine over recent decades. However, analysis of large structural variation and repetitive DNA, a hallmark of human genomes, has been limited by short-read technology, with read lengths of 100-300 bp. Long-read sequencing (LRS) permits routine sequencing of human DNA fragments tens to hundreds of kilobase pairs in size, using both real-time sequencing by synthesis and nanopore-based direct electronic sequencing. LRS permits analysis of large structural variation and haplotypic phasing in human genomes and has enabled the discovery and characterization of rare pathogenic structural variants and repeat expansions. It has also recently enabled the assembly of a complete, gapless human genome that includes previously intractable regions, such as highly repetitive centromeres and homologous acrocentric short arms. With the addition of protocols for targeted enrichment, direct epigenetic DNA modification detection, and long-range chromatin profiling, LRS promises to launch a new era of understanding of genetic diversity and pathogenic mutations in human populations.
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Affiliation(s)
- Peter E Warburton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; ,
- Center for Advanced Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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21
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Thewamit R, Khongkhatithum C, Thampratankul L, Kamolvisit W, Khongkrapan A, Wattanasirichaigoon D. Case report: Severe nonketotic hyperglycinemia in a neonate without apparent seizures but concomitant cleft palate and cerebral sinovenous thrombosis. Front Pediatr 2023; 11:1155035. [PMID: 37614902 PMCID: PMC10442541 DOI: 10.3389/fped.2023.1155035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Nonketotic hyperglycinemia (NKH) is in most cases a fatal inborn error of metabolism which usually presents during the neonatal period as encephalopathy and refractory seizures. The reported congenital anomalies associated with NKH included corpus callosal agenesis, club foot, cleft palate, and congenital heart disease. Here, we report a newborn who presented with encephalopathy without overt seizures, cerebral venous sinus thrombosis, and cleft palate. Electroencephalography showed a burst suppression pattern, which suggests the etiology could be due to a metabolic or genetic disorder. The amino acid analysis of plasma and cerebrospinal fluid showed elevated glycine. Whole exome sequencing identified a heterozygous c.492C > G; p.Tyr164Ter variant in exon 4 of the GLDC gene inherited from the patient's father. Further long-read whole genome sequencing revealed an exon 1-2 deletion in the GLDC gene inherited from the patient's mother. Additional analyses revealed no pathogenic variants of the cleft palate-related genes. The cleft palate may be an associated congenital anomaly in NKH. Regarding cerebral venous sinus thrombosis, we found a heterozygous variant (p.Arg189Trp) of the PROC gene, which is a common cause of thrombophilia among Thai newborns. A neonate with NKH could present with severe encephalopathy without seizures. A close follow up for clinical changes and further next generation sequencing are crucial for definite diagnosis in neonates with encephalopathy of unclear cause.
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Affiliation(s)
- Rapeepat Thewamit
- Division of Neurology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chaiyos Khongkhatithum
- Division of Neurology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Lunliya Thampratankul
- Division of Neurology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wuttichart Kamolvisit
- Division of Medical Genetics and Metabolism, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Arthaporn Khongkrapan
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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22
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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23
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Cheung WA, Johnson AF, Rowell WJ, Farrow E, Hall R, Cohen ASA, Means JC, Zion TN, Portik DM, Saunders CT, Koseva B, Bi C, Truong TK, Schwendinger-Schreck C, Yoo B, Johnston JJ, Gibson M, Evrony G, Rizzo WB, Thiffault I, Younger ST, Curran T, Wenger AM, Grundberg E, Pastinen T. Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort. Nat Commun 2023; 14:3090. [PMID: 37248219 DOI: 10.1038/s41467-023-38782-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, and structural variants. Recent algorithmic development enables simultaneous detection of CpG methylation for analysis of regulatory element activity directly in HiFi reads. We present a comprehensive haplotype resolved 5-base HiFi genome sequencing dataset from a rare disease cohort of 276 samples in 152 families to identify rare (~0.5%) hypermethylation events. We find that 80% of these events are allele-specific and predicted to cause loss of regulatory element activity. We demonstrate heritability of extreme hypermethylation including rare cis variants associated with short (~200 bp) and large hypermethylation events (>1 kb), respectively. We identify repeat expansions in proximal promoters predicting allelic gene silencing via hypermethylation and demonstrate allelic transcriptional events downstream. On average 30-40 rare hypermethylation tiles overlap rare disease genes per patient, providing indications for variation prioritization including a previously undiagnosed pathogenic allele in DIP2B causing global developmental delay. We propose that use of HiFi genome sequencing in unsolved rare disease cases will allow detection of unconventional diseases alleles due to loss of regulatory element activity.
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Affiliation(s)
- Warren A Cheung
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Adam F Johnson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | - Emily Farrow
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | | | - Ana S A Cohen
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - John C Means
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tricia N Zion
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Boryana Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Chengpeng Bi
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tina K Truong
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Carl Schwendinger-Schreck
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Byunggil Yoo
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Jeffrey J Johnston
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Margaret Gibson
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Gilad Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY, USA
| | - William B Rizzo
- Child Health Research Institute, Department of Pediatrics, Nebraska Medical Center, Omaha, NE, USA
| | - Isabelle Thiffault
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Scott T Younger
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | - Tom Curran
- Children's Mercy Research Institute, Kansas City, MO, USA
| | | | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
| | - Tomi Pastinen
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, USA.
- Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA.
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Zion TN, Berrios CD, Cohen ASA, Bartik L, Cross LA, Engleman KL, Fleming EA, Gadea RN, Hughes SS, Jenkins JL, Kussmann J, Lawson C, Schwager C, Strenk ME, Welsh H, Rush ET, Amudhavalli SM, Sullivan BR, Zhou D, Gannon JL, Heese BA, Moore R, Boillat E, Biswell RL, Louiselle DA, Puckett LMB, Beyer S, Neal SH, Sierant V, McBeth M, Belden B, Walter AM, Gibson M, Cheung WA, Johnston JJ, Thiffault I, Farrow EG, Grundberg E, Pastinen T. Insurance denials and diagnostic rates in a pediatric genomic research cohort. Genet Med 2023; 25:100020. [PMID: 36718845 PMCID: PMC10584034 DOI: 10.1016/j.gim.2023.100020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/29/2023] Open
Abstract
PURPOSE This study aimed to assess the amount and types of clinical genetic testing denied by insurance and the rate of diagnostic and candidate genetic findings identified through research in patients who faced insurance denials. METHODS Analysis consisted of review of insurance denials in 801 patients enrolled in a pediatric genomic research repository with either no previous genetic testing or previous negative genetic testing result identified through cross-referencing with insurance prior-authorizations in patient medical records. Patients and denials were also categorized by type of insurance coverage. Diagnostic findings and candidate genetic findings in these groups were determined through review of our internal variant database and patient charts. RESULTS Of the 801 patients analyzed, 147 had insurance prior-authorization denials on record (18.3%). Exome sequencing and microarray were the most frequently denied genetic tests. Private insurance was significantly more likely to deny testing than public insurance (odds ratio = 2.03 [95% CI = 1.38-2.99] P = .0003). Of the 147 patients with insurance denials, 53.7% had at least 1 diagnostic or candidate finding and 10.9% specifically had a clinically diagnostic finding. Fifty percent of patients with clinically diagnostic results had immediate medical management changes (5.4% of all patients experiencing denials). CONCLUSION Many patients face a major barrier to genetic testing in the form of lack of insurance coverage. A number of these patients have clinically diagnostic findings with medical management implications that would not have been identified without access to research testing. These findings support re-evaluation of insurance carriers' coverage policies.
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Affiliation(s)
- Tricia N Zion
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO.
| | - Courtney D Berrios
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Ana S A Cohen
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Lauren Bartik
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; University of Kansas Medical Center, School of Professional Health Sciences, Kansas City, MO
| | - Laura A Cross
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Kendra L Engleman
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Emily A Fleming
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Randi N Gadea
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Susan S Hughes
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Janda L Jenkins
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jennifer Kussmann
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Caitlin Lawson
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Caitlin Schwager
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Meghan E Strenk
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Holly Welsh
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Eric T Rush
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO
| | - Shivarajan M Amudhavalli
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Bonnie R Sullivan
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Dihong Zhou
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Jennifer L Gannon
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Bryce A Heese
- Division of Clinical Genetics, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO
| | - Riley Moore
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Emelia Boillat
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Rebecca L Biswell
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Daniel A Louiselle
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Laura M B Puckett
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Shanna Beyer
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Shelby H Neal
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Victoria Sierant
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Macy McBeth
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Bradley Belden
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Adam M Walter
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Margaret Gibson
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Warren A Cheung
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Jeffrey J Johnston
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Isabelle Thiffault
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Emily G Farrow
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Elin Grundberg
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
| | - Tomi Pastinen
- Department of Pediatrics, Children's Mercy Kansas City, Kansas City, MO; Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO
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Perrier S, Guerrero K, Tran LT, Michell-Robinson MA, Legault G, Brais B, Sylvain M, Dorman J, Demos M, Köhler W, Pastinen T, Thiffault I, Bernard G. Solving inherited white matter disorder etiologies in the neurology clinic: Challenges and lessons learned using next-generation sequencing. Front Neurol 2023; 14:1148377. [PMID: 37077564 PMCID: PMC10108901 DOI: 10.3389/fneur.2023.1148377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/23/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionRare neurodevelopmental disorders, including inherited white matter disorders or leukodystrophies, often present a diagnostic challenge on a genetic level given the large number of causal genes associated with a range of disease subtypes. This study aims to demonstrate the challenges and lessons learned in the genetic investigations of leukodystrophies through presentation of a series of cases solved using exome or genome sequencing.MethodsEach of the six patients had a leukodystrophy associated with hypomyelination or delayed myelination on MRI, and inconclusive clinical diagnostic genetic testing results. We performed next generation sequencing (case-based exome or genome sequencing) to further investigate the genetic cause of disease.ResultsFollowing different lines of investigation, molecular diagnoses were obtained for each case, with patients harboring pathogenic variants in a range of genes including TMEM106B, GJA1, AGA, POLR3A, and TUBB4A. We describe the lessons learned in reaching the genetic diagnosis, including the importance of (a) utilizing proper multi-gene panels in clinical testing, (b) assessing the reliability of biochemical assays in supporting diagnoses, and (c) understanding the limitations of exome sequencing methods in regard to CNV detection and region coverage in GC-rich areas.DiscussionThis study illustrates the importance of applying a collaborative diagnostic approach by combining detailed phenotyping data and metabolic results from the clinical environment with advanced next generation sequencing analysis techniques from the research environment to increase the diagnostic yield in patients with genetically unresolved leukodystrophies.
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Affiliation(s)
- Stefanie Perrier
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Kether Guerrero
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Luan T. Tran
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Mackenzie A. Michell-Robinson
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Geneviève Legault
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
| | - Bernard Brais
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Michel Sylvain
- Division of Pediatric Neurology, Centre Mère-Enfant Soleil du CHU de Québec - Université Laval, Québec City, QC, Canada
| | - James Dorman
- John H. Stroger Jr. Hospital of Cook County, Chicago, IL, United States
- Department of Neurological Sciences, Rush Medical College, Chicago, IL, United States
| | - Michelle Demos
- Division of Neurology, Department of Pediatrics, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Wolfgang Köhler
- Leukodystrophy Center, University of Leipzig Medical Center, Leipzig, Germany
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, United States
- University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO, United States
- Isabelle Thiffault
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Department of Pediatrics, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, QC, Canada
- *Correspondence: Geneviève Bernard
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Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
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27
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Scott ER, Yang Y, Botton MR, Seki Y, Hoshitsuki K, Harting J, Baybayan P, Cody N, Nicoletti P, Moriyama T, Chakraborty S, Yang JJ, Edelmann L, Schadt EE, Korlach J, Scott SA. Long-read HiFi sequencing of NUDT15: Phased full-gene haplotyping and pharmacogenomic allele discovery. Hum Mutat 2022; 43:1557-1566. [PMID: 36057977 PMCID: PMC9875722 DOI: 10.1002/humu.24457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
To determine the phase of NUDT15 sequence variants for more comprehensive star (*) allele diplotyping, we developed a novel long-read single-molecule real-time HiFi amplicon sequencing method. A 10.5 kb NUDT15 amplicon assay was validated using reference material positive controls and additional samples for specimen type and blinded accuracy assessment. Triplicate NUDT15 HiFi sequencing of two reference material samples had nonreference genotype concordances of >99.9%, indicating that the assay is robust. Notably, short-read genome sequencing of a subset of samples was unable to determine the phase of star (*) allele-defining NUDT15 variants, resulting in ambiguous diplotype results. In contrast, long-read HiFi sequencing phased all variants across the NUDT15 amplicons, including a *2/*9 diplotype that previously was characterized as *1/*2 in the 1000 Genomes Project v3 data set. Assay throughput was also tested using 8.5 kb amplicons from 100 Ashkenazi Jewish individuals, which identified a novel NUDT15 *1 suballele (c.-121G>A) and a rare likely deleterious coding variant (p.Pro129Arg). Both novel alleles were Sanger confirmed and assigned as *1.007 and *20, respectively, by the PharmVar Consortium. Taken together, NUDT15 HiFi amplicon sequencing is an innovative method for phased full-gene characterization and novel allele discovery, which could improve NUDT15 pharmacogenomic testing and subsequent phenotype prediction.
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Affiliation(s)
- Erick R Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yao Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mariana R Botton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Yoshinori Seki
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keito Hoshitsuki
- School of Pharmacy, University of Pittsburgh, Pennsylvania, Pittsburgh, USA
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - John Harting
- Pacific Biosciences, Menlo Park, California, USA
| | | | - Neal Cody
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Paola Nicoletti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
| | | | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Sema4, Stamford, Connecticut, USA
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28
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Conlin LK, Aref-Eshghi E, McEldrew DA, Luo M, Rajagopalan R. Long-read sequencing for molecular diagnostics in constitutional genetic disorders. Hum Mutat 2022; 43:1531-1544. [PMID: 36086952 PMCID: PMC9561063 DOI: 10.1002/humu.24465] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/11/2022]
Abstract
Long-read sequencing (LRS) has been around for more than a decade, but widespread adoption of the technology has been slow due to the perceived high error rates and high sequencing cost. This is changing due to the recent advancements to produce highly accurate sequences and the reducing costs. LRS promises significant improvement over short read sequencing in four major areas: (1) better detection of structural variation (2) better resolution of highly repetitive or nonunique regions (3) accurate long-range haplotype phasing and (4) the detection of base modifications natively from the sequencing data. Several successful applications of LRS have demonstrated its ability to resolve molecular diagnoses where short-read sequencing fails to identify a cause. However, the argument for increased diagnostic yield from LRS remains to be validated. Larger cohort studies may be required to establish the realistic boundaries of LRS's clinical utility and analytical validity, as well as the development of standards for clinical applications. We discuss the limitations of the current standard of care, and contrast with the applications and advantages of two major LRS platforms, PacBio and Oxford Nanopore, for molecular diagnostics of constitutional disorders, and present a critical argument about the potential of LRS in diagnostic settings.
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Affiliation(s)
- Laura K. Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Erfan Aref-Eshghi
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Deborah A. McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
| | - Minjie Luo
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ramakrishnan Rajagopalan
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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Sanford Kobayashi E, Batalov S, Wenger AM, Lambert C, Dhillon H, Hall RJ, Baybayan P, Ding Y, Rego S, Wigby K, Friedman J, Hobbs C, Bainbridge MN. Approaches to long-read sequencing in a clinical setting to improve diagnostic rate. Sci Rep 2022; 12:16945. [PMID: 36210382 PMCID: PMC9548499 DOI: 10.1038/s41598-022-20113-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 09/08/2022] [Indexed: 12/29/2022] Open
Abstract
Over the past decade, advances in genetic testing, particularly the advent of next-generation sequencing, have led to a paradigm shift in the diagnosis of molecular diseases and disorders. Despite our present collective ability to interrogate more than 90% of the human genome, portions of the genome have eluded us, resulting in stagnation of diagnostic yield with existing methodologies. Here we show how application of a new technology, long-read sequencing, has the potential to improve molecular diagnostic rates. Whole genome sequencing by long reads was able to cover 98% of next-generation sequencing dead zones, which are areas of the genome that are not interpretable by conventional industry-standard short-read sequencing. Through the ability of long-read sequencing to unambiguously call variants in these regions, we discovered an immunodeficiency due to a variant in IKBKG in a subject who had previously received a negative genome sequencing result. Additionally, we demonstrate the ability of long-read sequencing to detect small variants on par with short-read sequencing, its superior performance in identifying structural variants, and thirdly, its capacity to determine genomic methylation defects in native DNA. Though the latter technical abilities have been demonstrated, we demonstrate the clinical application of this technology to successfully identify multiple types of variants using a single test.
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Affiliation(s)
- Erica Sanford Kobayashi
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.50956.3f0000 0001 2152 9905Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Serge Batalov
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Aaron M. Wenger
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Christine Lambert
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Harsharan Dhillon
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Richard J. Hall
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Primo Baybayan
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | - Yan Ding
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Seema Rego
- Rady Institute for Genomic Medicine, San Diego, CA USA
| | - Kristen Wigby
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA
| | - Jennifer Friedman
- Rady Institute for Genomic Medicine, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA ,grid.266100.30000 0001 2107 4242Department of Neuroscience, University of California San Diego and Rady Children’s Hospital, San Diego, CA USA
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30
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Jahn A, Rump A, Widmann TJ, Heining C, Horak P, Hutter B, Paramasivam N, Uhrig S, Gieldon L, Drukewitz S, Kübler A, Bermudez M, Hackmann K, Porrmann J, Wagner J, Arlt M, Franke M, Fischer J, Kowalzyk Z, William D, Weth V, Oster S, Fröhlich M, Hüllein J, Valle González C, Kreutzfeldt S, Mock A, Heilig CE, Lipka DB, Möhrmann L, Hanf D, Teleanu V, Allgäuer M, Ruhnke L, Kutz O, Knurr A, Laßmann A, Endris V, Neumann O, Penzel R, Beck K, Richter D, Winter U, Wolf S, Pfütze K, Geörg C, Meißburger B, Buchhalter I, Augustin M, Aulitzky WE, Hohenberger P, Kroiss M, Schirmacher P, Schlenk RF, Keilholz U, Klauschen F, Folprecht G, Bauer S, Siveke JT, Brandts CH, Kindler T, Boerries M, Illert AL, von Bubnoff N, Jost PJ, Metzeler KH, Bitzer M, Schulze-Osthoff K, von Kalle C, Brors B, Stenzinger A, Weichert W, Hübschmann D, Fröhling S, Glimm H, Schröck E, Klink B. Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers. Ann Oncol 2022:S0923-7534(22)01859-2. [PMID: 35988656 DOI: 10.1016/j.annonc.2022.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 07/04/2022] [Accepted: 07/18/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Germline variant evaluation in precision oncology opens new paths towards the identification of patients with genetic tumor risk syndromes and the exploration of therapeutic relevance. Here, we present the results of germline variant analysis and their clinical implications in a precision oncology study for patients with predominantly rare cancers. PATIENTS AND METHODS Matched tumor and control genome/exome and RNA sequencing was performed for 1,485 patients with rare cancers (79%) and/or young adults (77% younger than 51 years) in the NCT/DKTK MASTER trial, a German multicenter, prospective observational precision oncology study. Clinical and therapeutic relevance of prospective pathogenic germline variant (PGV) evaluation was analyzed and compared to other precision oncology studies. RESULTS Ten percent of patients (n=157) harbored PGVs in 35 genes associated with autosomal dominant cancer predisposition, whereof up to 75% were unknown before study participation. Another five percent of patients (n=75) were heterozygous carriers for recessive genetic tumor risk syndromes. Particularly high PGV yields were found in patients with gastrointestinal stromal tumors (GISTs) (28%, 11/40), and more specific in wild-type GISTS (50%, n=10/20), leiomyosarcomas (21%, n=19/89), and hepatopancreaticobiliary cancers (16%, n=16/97). Forty-five percent of PGVs (n=100/221) supported treatment recommendations, and its implementation led to a clinical benefit in 40% of patients (n=10/25). A comparison of different precision oncology studies revealed variable PGV yields and considerable differences in germline variant analysis workflows. We therefore propose a detailed workflow for germline variant evaluation. CONCLUSIONS Genetic germline testing in patients with rare cancers can identify the very first patient in a hereditary cancer family and can lead to clinical benefit in a broad range of entities. Its routine implementation in precision oncology accompanied by the harmonization of germline variant evaluation workflows will increase clinical benefit and boost research.
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Lansdon LA, Cadieux-Dion M, Herriges JC, Johnston J, Yoo B, Alaimo JT, Thiffault I, Miller N, Cohen ASA, Repnikova EA, Zhang L, Farooqi MS, Farrow EG, Saunders CJ. Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies. Clin Chem 2022; 68:1177-1183. [DOI: 10.1093/clinchem/hvac113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/31/2022] [Indexed: 01/02/2023]
Abstract
Abstract
Background
Laboratories utilizing next-generation sequencing align sequence data to a standardized human reference genome (HRG). Several updated versions, or builds, have been released since the original HRG in 2001, including the Genome Reference Consortium Human Build 38 (GRCh38) in 2013. However, most clinical laboratories still use GRCh37, which was released in 2009. We report our laboratory’s clinical validation of GRCh38.
Methods
Migration to GRCh38 was validated by comparing the coordinates (lifting over) of 9443 internally curated variants from GRCh37 to GRCh38, globally comparing protein coding sequence variants aligned with GRCh37 vs GRCh38 from 917 exomes, assessing genes with known discrepancies, comparing coverage differences, and establishing the analytic sensitivity and specificity of variant detection using Genome in a Bottle data.
Results
Eight discrepancies, due to strand swap or reference base, were observed. Three clinically relevant variants had the GRCh37 alternate allele as the reference allele in GRCh38. A comparison of 88 295 calls between builds identified 8 disease-associated genes with sequence differences: ABO, BNC2, KIZ, NEFL, NR2E3, PTPRQ, SHANK2, and SRD5A2. Discrepancies in coding regions in GRCh37 were resolved in GRCh38.
Conclusions
There were a small number of clinically significant changes between the 2 genome builds. GRCh38 provided improved detection of nucleotide changes due to the resolution of discrepancies present in GRCh37. Implementation of GRCh38 results in more accurate and consistent reporting.
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Affiliation(s)
- Lisa A Lansdon
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Maxime Cadieux-Dion
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - John C Herriges
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Jeffrey Johnston
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Byunggil Yoo
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Joseph T Alaimo
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Isabelle Thiffault
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Neil Miller
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Bionano Genomics, Inc. , 9540 Towne Centre Dr., Suite 100, San Diego, CA , USA
| | - Ana S A Cohen
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Elena A Repnikova
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Lei Zhang
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
| | - Midhat S Farooqi
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
| | - Emily G Farrow
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
- Department of Pediatrics Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
| | - Carol J Saunders
- Department of Pathology and Laboratory Medicine, Children’s Mercy—Kansas City , 2401 Gillham Rd., Kansas City, MO , USA
- Genomic Medicine Center, Children’s Mercy Research Institute—Kansas City , 2420 Pershing Rd. Suite 100, Kansas City, MO , USA
- School of Medicine, University of Missouri-Kansas City , 2411 Holmes St., Kansas City, MO , USA
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McQuerry JA, Mclaird M, Hartin SN, Means JC, Johnston J, Pastinen T, Younger ST. Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients. Sci Rep 2022; 12:7576. [PMID: 35534523 PMCID: PMC9085742 DOI: 10.1038/s41598-022-11589-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Clinical whole genome sequencing has enabled the discovery of potentially pathogenic noncoding variants in the genomes of rare disease patients with a prior history of negative genetic testing. However, interpreting the functional consequences of noncoding variants and distinguishing those that contribute to disease etiology remains a challenge. Here we address this challenge by experimentally profiling the functional consequences of rare noncoding variants detected in a cohort of undiagnosed rare disease patients at scale using a massively parallel reporter assay. We demonstrate that this approach successfully identifies rare noncoding variants that alter the regulatory capacity of genomic sequences. In addition, we describe an integrative analysis that utilizes genomic features alongside patient clinical data to further prioritize candidate variants with an increased likelihood of pathogenicity. This work represents an important step towards establishing a framework for the functional interpretation of clinically detected noncoding variants.
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Affiliation(s)
- Jasmine A McQuerry
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Merry Mclaird
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Samantha N Hartin
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - John C Means
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Jeffrey Johnston
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Scott T Younger
- Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
- Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO, 64110, USA.
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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