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Türkyılmaz A, Cimbek EA, Kardeş H, Çebi AH, Acar Arslan E, Karagüzel G. A triple molecular diagnosis in a Turkish individual with hypotrichosis, deafness, and diabetes. Clin Dysmorphol 2024; 33:118-120. [PMID: 38818819 DOI: 10.1097/mcd.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
| | - Emine Ayça Cimbek
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | - Hakan Kardeş
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | | | - Elif Acar Arslan
- Department of Pediatric Neurology, Marmara University, Faculty of Medicine, İstanbul, Türkiye
| | - Gülay Karagüzel
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
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2
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Bozkurt-Yozgatli T, Pehlivan D, Gibbs RA, Sezerman U, Posey JE, Lupski JR, Coban-Akdemir Z. Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders. BMC Med Genomics 2024; 17:85. [PMID: 38622594 PMCID: PMC11020671 DOI: 10.1186/s12920-024-01852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Multilocus pathogenic variants (MPVs) are genetic changes that affect multiple gene loci or regions of the genome, collectively leading to multiple molecular diagnoses. MPVs may also contribute to intrafamilial phenotypic variability between affected individuals within a nuclear family. In this study, we aim to gain further insights into the influence of MPVs on a disease manifestation in individual research subjects and explore the complexities of the human genome within a familial context. METHODS We conducted a systematic reanalysis of exome sequencing data and runs of homozygosity (ROH) regions of 47 sibling pairs previously diagnosed with various neurodevelopmental disorders (NDD). RESULTS We found siblings with MPVs driven by long ROH regions in 8.5% of families (4/47). The patients with MPVs exhibited significantly higher FROH values (p-value = 1.4e-2) and larger total ROH length (p-value = 1.8e-2). Long ROH regions mainly contribute to this pattern; the siblings with MPVs have a larger total size of long ROH regions than their siblings in all families (p-value = 6.9e-3). Whereas the short ROH regions in the siblings with MPVs are lower in total size compared to their sibling pairs with single locus pathogenic variants (p-value = 0.029), and there are no statistically significant differences in medium ROH regions between sibling pairs (p-value = 0.52). CONCLUSION This study sheds light on the significance of considering MPVs in families with affected sibling pairs and the role of ROH as an adjuvant tool in explaining clinical variability within families. Identifying individuals carrying MPVs may have implications for disease management, identification of possible disease risks to different family members, genetic counseling and exploring personalized treatment approaches.
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Affiliation(s)
- Tugce Bozkurt-Yozgatli
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Davut Pehlivan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ugur Sezerman
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Zeynep Coban-Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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3
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Rodrigues Alves Barbosa V, Maroilley T, Diao C, Colvin-James L, Perrier R, Tarailo-Graovac M. Single variant, yet "double trouble": TSC and KBG syndrome because of a large de novo inversion. Life Sci Alliance 2024; 7:e202302115. [PMID: 38253421 PMCID: PMC10803213 DOI: 10.26508/lsa.202302115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Despite the advances in high-throughput sequencing, many rare disease patients remain undiagnosed. In particular, the patients with well-defined clinical phenotypes and established clinical diagnosis, yet missing or partial genetic diagnosis, may hold a clue to more complex genetic mechanisms of a disease that could be missed by available clinical tests. Here, we report a patient with a clinical diagnosis of Tuberous sclerosis, combined with unusual secondary features, but negative clinical tests including TSC1 and TSC2 Short-read whole-genome sequencing combined with advanced bioinformatics analyses were successful in uncovering a de novo pericentric 87-Mb inversion with breakpoints in TSC2 and ANKRD11, which explains the TSC clinical diagnosis, and confirms a second underlying monogenic disorder, KBG syndrome. Our findings illustrate how complex variants, such as large inversions, may be missed by clinical tests and further highlight the importance of well-defined clinical diagnoses in uncovering complex molecular mechanisms of a disease, such as complex variants and "double trouble" effects.
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Affiliation(s)
- Victoria Rodrigues Alves Barbosa
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Tatiana Maroilley
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Catherine Diao
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Leslie Colvin-James
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Renee Perrier
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Maja Tarailo-Graovac
- https://ror.org/03yjb2x39 Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- https://ror.org/03yjb2x39 Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
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4
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Wigby KM, Brockman D, Costain G, Hale C, Taylor SL, Belmont J, Bick D, Dimmock D, Fernbach S, Greally J, Jobanputra V, Kulkarni S, Spiteri E, Taft RJ. Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders. NPJ Genom Med 2024; 9:15. [PMID: 38409289 PMCID: PMC10897481 DOI: 10.1038/s41525-024-00396-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.
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Affiliation(s)
- Kristen M Wigby
- University of California, Davis, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | | | | | | | | | - John Belmont
- Genetics & Genomics Services Inc, Houston, TX, USA
| | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | - John Greally
- Albert Einstein College of Medicine, Bronx, NY, USA
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5
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Abolhassani A, Fattahi Z, Beheshtian M, Fadaee M, Vazehan R, Ahangari F, Dehdahsi S, Faraji Zonooz M, Parsimehr E, Kalhor Z, Peymani F, Mozaffarpour Nouri M, Babanejad M, Noudehi K, Fatehi F, Zamanian Najafabadi S, Afroozan F, Yazdan H, Bozorgmehr B, Azarkeivan A, Sadat Mahdavi S, Nikuei P, Fatehi F, Jamali P, Ashrafi MR, Karimzadeh P, Habibi H, Kahrizi K, Nafissi S, Kariminejad A, Najmabadi H. Clinical application of next generation sequencing for Mendelian disease diagnosis in the Iranian population. NPJ Genom Med 2024; 9:12. [PMID: 38374194 PMCID: PMC10876633 DOI: 10.1038/s41525-024-00393-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Next-generation sequencing (NGS) has been proven to be one of the most powerful diagnostic tools for rare Mendelian disorders. Several studies on the clinical application of NGS in unselected cohorts of Middle Eastern patients have reported a high diagnostic yield of up to 48%, correlated with a high level of consanguinity in these populations. We evaluated the diagnostic utility of NGS-based testing across different clinical indications in 1436 patients from Iran, representing the first study of its kind in this highly consanguineous population. A total of 1075 exome sequencing and 361 targeted gene panel sequencing were performed over 8 years at a single clinical genetics laboratory, with the majority of cases tested as proband-only (91.6%). The overall diagnostic rate was 46.7%, ranging from 24% in patients with an abnormality of prenatal development to over 67% in patients with an abnormality of the skin. We identified 660 pathogenic or likely pathogenic variants, including 241 novel variants, associated with over 342 known genetic conditions. The highly consanguineous nature of this cohort led to the diagnosis of autosomal recessive disorders in the majority of patients (79.1%) and allowed us to determine the shared carrier status of couples for suspected recessive phenotypes in their deceased child(ren) when direct testing was not possible. We also highlight the observations of recessive inheritance of genes previously associated only with dominant disorders and provide an expanded genotype-phenotype spectrum for multiple less-characterized genes. We present the largest mutational spectrum of known Mendelian disease, including possible founder variants, throughout the Iranian population, which can serve as a unique resource for clinical genomic studies locally and beyond.
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Affiliation(s)
- Ayda Abolhassani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zohreh Fattahi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Mahsa Fadaee
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Raheleh Vazehan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Ahangari
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Shima Dehdahsi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Elham Parsimehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Zahra Kalhor
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Peymani
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Mojgan Babanejad
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Noudehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Fatemeh Fatehi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Fariba Afroozan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hilda Yazdan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Bita Bozorgmehr
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Azita Azarkeivan
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran
| | | | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
- Nasle Salem Genetic Counseling Center, Bandar Abbas, Iran
| | - Farzad Fatehi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Payman Jamali
- Genetic Counseling Center, Shahroud Welfare Organization, Semnan, Iran
| | | | - Parvaneh Karimzadeh
- Pediatric Neurology Department, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haleh Habibi
- Hamedan University of Medical Science, Hamedan, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Department of Neurology, Neuromuscular Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Najmabadi
- Kariminejad - Najmabadi Pathology & Genetics Center, Tehran, Iran.
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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6
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Aubry RL, Innes AM, Haber RM. Syndromic or non-syndromic congenital ichthyosis? A case report of two brothers with ichthyosis but microphthalmia and blindness in only one brother. SAGE Open Med Case Rep 2024; 12:2050313X241231386. [PMID: 38333515 PMCID: PMC10851717 DOI: 10.1177/2050313x241231386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
We present the cases of two brothers with ichthyosis, born to consanguineous parents, with the eldest having extracutaneous manifestations in the form of microphthalmia and corneal opacities causing complete blindness. Initially, we were faced with the question of whether the phenotype in this family was due to the effects of a single pleiotropic, presumably autosomal recessive gene manifesting as a syndromic form of ichthyosis, or whether there were multiple causal genes, and the ichthyosis was non-syndromic. Ultimately, clinical follow-up of the family, combined with research-based exome sequencing established a diagnosis of NIPAL4 autosomal recessive congenital ichthyosis in both brothers, but the ocular abnormalities causing blindness in the older brother were due to coexisting autosomal recessively inherited loss of function mutations in peroxidasin, the latter finding also seen in a sister unaffected by ichthyosis.
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Affiliation(s)
- Rachel L Aubry
- Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - A. Micheil Innes
- Department of Medical Genetics, Alberta Children’s Hospital, Calgary, AB, Canada
| | - Richard M Haber
- Richmond Road Diagnostic and Treatment Centre (RRDTC), Calgary, AB, Canada
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7
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Rezende RC, Menezes de Andrade NL, Branco Dantas NC, de Polli Cellin L, Victorino Krepischi AC, Lerario AM, de Lima Jorge AA. Exome Sequencing Identifies Multiple Genetic Diagnoses in Children with Syndromic Growth Disorders. J Pediatr 2024; 265:113841. [PMID: 37995928 DOI: 10.1016/j.jpeds.2023.113841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVE To evaluate the presence of multiple genetic diagnoses in syndromic growth disorders. STUDY DESIGN We carried out a cross-sectional study to evaluate 115 patients with syndromic tall (n = 24) or short stature (n = 91) of unknown cause from a tertiary referral center for growth disorders. Exome sequencing was performed to assess germline single nucleotide, InDel, and copy number variants. All variants were classified according to ACMG/AMP guidelines. The main outcome measured was the frequency of multiple genetic diagnoses in a cohort of children with syndromic growth disorders. RESULTS The total diagnostic yield of the cohort was 54.8% (63/115). Six patients had multiple genetic diagnoses (tall stature group = 2; short stature group = 4). The proportion of multiple diagnoses within total cases was 5.2% (6/115), and within solved cases was 9.5% (6/63). No characteristics were significantly more frequent when compared with patients with single or multiple genetic findings. Among patients with multiple diagnoses, 3 had syndromes with overlapping clinical features, and the others had syndromes with distinct phenotypes. CONCLUSION Recognition of multiple genetic diagnoses as a possibility in complex cases of syndromic growth disorders opens a new perspective on treatment and genetic counseling for affected patients, defying the medical common sense of trying to fit all findings into one diagnosis.
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Affiliation(s)
- Raissa Carneiro Rezende
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Nathalia Liberatoscioli Menezes de Andrade
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Naiara Castelo Branco Dantas
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Laurana de Polli Cellin
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Antonio Marcondes Lerario
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Alexander Augusto de Lima Jorge
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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Hauschild LA, Seixas Maia da Silva T, Winckler PB, Moreira Cardoso-Júnior L, Saute JAM, Donis KC. Co-Occurrence of Myotonic Dystrophy Type 1 and Limb-Girdle Muscular Dystrophy Type 2B: A Case Report. Mol Syndromol 2024; 15:58-62. [PMID: 38357254 PMCID: PMC10862322 DOI: 10.1159/000533219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 07/24/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Myotonic dystrophy type 1 (DM1) is an autosomal dominant neuromuscular disease whose pattern of weakness is predominantly distal. Limb-girdle muscular dystrophy type 2B/R2-dysferlin-related (LGMD2B/R2) is another neuromuscular disease, which presents an autosomal recessive inheritance and is marked by proximal muscle weakness. Even if uncommon, comorbid inherited pathologies must be considered in cases of atypical presentations, especially in those with family history of consanguinity. Case Presentation Herein, we report the unique case of a patient diagnosed with both DM1 and LGMD2B/R2: a 38-year-old woman in follow-up of DM1 in a neuromuscular disease service presenting prominent proximal weakness. The patient's parents were consanguineous, and creatine kinase levels were elevated. A multi-gene panel test was performed and revealed the diagnosis of LGMD2B/R2. Conclusion Genetic diseases with atypical presentations should raise the possibility of a second disorder, prompting an appropriate investigation. Overlooking a second diagnosis can implicate in not offering adequate genetic counseling, support, or specific treatment.
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Affiliation(s)
- Lucas Augusto Hauschild
- Faculty of Medicine, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Pablo Brea Winckler
- Neurology Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | | | - Jonas Alex Morales Saute
- Faculty of Medicine, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Neurology Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Internal Medicine Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Karina Carvalho Donis
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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Hizem S, Maamouri R, Zaouak A, Rejeb I, Karoui S, Sebai M, Jilani H, Elaribi Y, Fenniche S, Cheour M, Bilan F, Ben Jemaa L. Absent meibomian glands and cone dystrophy in ADULT syndrome: identification by whole exome sequencing of pathogenic variants in two causal genes TP63 and CNGB3. Ophthalmic Genet 2024; 45:84-94. [PMID: 37158316 DOI: 10.1080/13816810.2023.2206891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/20/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Ectrodactyly is a rare congenital limb malformation characterized by a deep median cleft of the hand and/or foot due to the absence of central rays. It could be isolated or depicts a part of diverse syndromic forms. Heterozygous pathogenic variants in the TP63 gene are responsible for at least four rare syndromic human disorders associated with ectrodactyly. Among them, ADULT (Acro-Dermato-Ungual-Lacrimal-Tooth) syndrome is characterized by ectodermal dysplasia, excessive freckling, nail dysplasia, and lacrimal duct obstruction, in addition to ectrodactyly and/or syndactyly. Ophthalmic findings are very common in TP63-related disorders, consisting mainly of lacrimal duct hypoplasia. Absent meibomian glands have also been well documented in EEC3 (Ectrodactyly Ectodermal dysplasia Cleft lip/palate) syndrome but not in ADULT syndrome. METHODS We report a case of syndromic ectrodactyly consistent with ADULT syndrome, with an additional ophthalmic manifestation of agenesis of meibomian glands. The proband, as well as her elder sister, presented with congenital cone dystrophy.The molecular investigation was performed in the proband using Whole Exome Sequencing. Family segregation of the identified variants was confirmed by Sanger sequencing. RESULTS Two clinically relevant variants were found in the proband: the novel de novo heterozygous missense c.931A > G (p.Ser311Gly) in the TP63 gene classified as pathogenic, and the homozygous nonsense pathogenic c.1810C > T (p.Arg604Ter) in the CNGB3 gene. The same homozygous CNGB3 variation was also found in the sister, explaining the cone dystrophy in both cases. CONCLUSIONS Whole Exome Sequencing allowed dual molecular diagnoses: de novo TP63-related syndromic ectrodactyly and familial CNGB3-related congenital cone dystrophy.
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Affiliation(s)
- Syrine Hizem
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Human genetics laboratory, LR99ES10- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Rym Maamouri
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Ophthalmology, Habib Thameur hospital, Tunis, Tunisia
| | - Anissa Zaouak
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Imen Rejeb
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Maternal and Child health laboratory, LR22SP01- Mongi Slim Hospital, Tunis, Tunisia
| | - Sana Karoui
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Maternal and Child health laboratory, LR22SP01- Mongi Slim Hospital, Tunis, Tunisia
| | - Molka Sebai
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Human genetics laboratory, LR99ES10- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Houweyda Jilani
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Yasmina Elaribi
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sami Fenniche
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Dermatology, Genodermatosis and Cancers Laboratory LR12SP03, Habib Thameur Hospital, Tunis, Tunisia
| | - Monia Cheour
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Ophthalmology, Habib Thameur hospital, Tunis, Tunisia
| | - Frédéric Bilan
- Laboratoire de Génétique, Service de Génétique, CHU Poitiers, Poitiers, France
| | - Lamia Ben Jemaa
- Department of congenital and hereditary diseases, Mongi Slim hospital, La Marsa, Tunisia
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Maternal and Child health laboratory, LR22SP01- Mongi Slim Hospital, Tunis, Tunisia
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10
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Racine C, Denommé-Pichon AS, Engel C, Tran Mau-Them F, Bruel AL, Vitobello A, Safraou H, Sorlin A, Nambot S, Delanne J, Garde A, Colin E, Moutton S, Thevenon J, Jean-Marçais N, Willems M, Geneviève D, Pinson L, Perrin L, Laffargue F, Lespinasse J, Lacaze E, Molin A, Gerard M, Lambert L, Benigni C, Patat O, Bourgeois V, Poe C, Chevarin M, Couturier V, Garret P, Philippe C, Duffourd Y, Faivre L, Thauvin-Robinet C. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet 2023; 61:36-46. [PMID: 37586840 DOI: 10.1136/jmg-2023-109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Wide access to clinical exome/genome sequencing (ES/GS) enables the identification of multiple molecular diagnoses (MMDs), being a long-standing but underestimated concept, defined by two or more causal loci implicated in the phenotype of an individual with a rare disease. Only few series report MMDs rates (1.8% to 7.1%). This study highlights the increasing role of MMDs in a large cohort of individuals addressed for congenital anomalies/intellectual disability (CA/ID). METHODS From 2014 to 2021, our diagnostic laboratory rendered 880/2658 positive ES diagnoses for CA/ID aetiology. Exhaustive search on MMDs from ES data was performed prospectively (January 2019 to December 2021) and retrospectively (March 2014 to December 2018). RESULTS MMDs were identified in 31/880 individuals (3.5%), responsible for distinct (9/31) or overlapping (22/31) phenotypes, and potential MMDs in 39/880 additional individuals (4.4%). CONCLUSION MMDs are frequent in CA/ID and remain a strong challenge. Reanalysis of positive ES data appears essential when phenotypes are partially explained by the initial diagnosis or atypically enriched overtime. Up-to-date clinical data, clinical expertise from the referring physician, strong interactions between clinicians and biologists, and increasing gene discoveries and improved ES bioinformatics tools appear all the more fundamental to enhance chances of identifying MMDs. It is essential to provide appropriate patient care and genetic counselling.
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Affiliation(s)
- Caroline Racine
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Camille Engel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Frederic Tran Mau-Them
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Hana Safraou
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Estelle Colin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Marjolaine Willems
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - David Geneviève
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
- INSERM U1183, Université de Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Laurence Perrin
- Genetic Department, Robert-Debré Hospital Department of Genetics, Paris, France
| | - Fanny Laffargue
- Service de Génétique médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - James Lespinasse
- Unité de Génétique médicale, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Elodie Lacaze
- Department of Medical Genetics, Hospital Group Le Havre, Le Havre, France
| | - Arnaud Molin
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | - Marion Gerard
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | | | | | - Olivier Patat
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, France
| | - Valentin Bourgeois
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Charlotte Poe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Martin Chevarin
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Victor Couturier
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Philippine Garret
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christophe Philippe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Yannis Duffourd
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
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11
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Al Eissa MM, Alotibi RS, Alhaddad B, Aloraini T, Samman MS, AlAsiri A, Abouelhoda M, AlQahtani AS. Reclassifying variations of unknown significance in diseases affecting Saudi Arabia's population reveal new associations. Front Genet 2023; 14:1250317. [PMID: 38028588 PMCID: PMC10646566 DOI: 10.3389/fgene.2023.1250317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Physicians face diagnostic dilemmas upon reports indicating disease variants of unknown significance (VUS). The most puzzling cases are patients with rare diseases, where finding another matched genotype and phenotype to associate their results is challenging. This study aims to prove the value of updating patient files with new classifications, potentially leading to better assessment and prevention. Methodology: We recruited retrospective phenotypic and genotypic data from King Saud Medical City, Riyadh, Kingdom of Saudi Arabia. Between September 2020 and December 2021, 1,080 patients' genetic profiles were tested in a College of American Pathologists accredited laboratory. We excluded all confirmed pathogenic variants, likely pathogenic variants and copy number variations. Finally, we further reclassified 194 VUS using different local and global databases, employing in silico prediction to justify the phenotype-genotype association. Results: Of the 194 VUS, 90 remained VUS, and the other 104 were reclassified as follows: 16 pathogenic, 49 likely pathogenic, nine benign, and 30 likely benign. Moreover, most of these variants had never been observed in other local or international databases. Conclusion: Reclassifying the VUS adds value to understanding the causality of the phenotype if it has been reported in another family or population. The healthcare system should establish guidelines for re-evaluating VUS, and upgrading VUS should reflect on individual/family risks and management strategies.
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Affiliation(s)
- Mariam M. Al Eissa
- Public Health Authority, Public Health Lab, Molecular Genetics Laboratory, Riyadh, Saudi Arabia
- Medical School, AlFaisal University, Riyadh, Saudi Arabia
| | - Raniah S. Alotibi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Bader Alhaddad
- Laboratory Medicine Department, King Fahd University Hospital, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Molecular Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Division of Translational Pathology, Department of Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
- Department of Genetics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Manar S. Samman
- Department of Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City (KFMC), Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Mohamed Abouelhoda
- Chairman Computational Science Department at King Faisal Specialised Hospital and Research Center, KFSHRC, Riyadh, Saudi Arabia
| | - Amerh S. AlQahtani
- Medical Genetics Department, King Saud Medical City, Riyadh, Saudi Arabia
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12
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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: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [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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13
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Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13122377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
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14
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Dahlan R, Bablghaith E. Hereditary thrombotic thrombocytopenic purpura (TTP) with co-occurring autosomal dominant polycystic kidney disease (ADPKD). BMJ Case Rep 2022; 15:e250378. [PMID: 36414344 PMCID: PMC9684965 DOI: 10.1136/bcr-2022-250378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Hereditary thrombotic thrombocytopenic purpura (TTP) and autosomal dominant polycystic kidney disease (ADPKD) are two distinct genetic diseases that may affect the kidneys through different mechanisms. ADPKD is a common genetic disorder that leads to exponential formation and growth of cysts replacing all segments of nephrons. Hereditary TTP is a rare autosomal recessive disorder that leads to the disseminated formation of arteriolar platelet-rich thrombi, which produce manifestations of various organs dysfunction. We present a case of a pregnant female with hereditary TTP co-occurring with ADPKD. To our knowledge, this is the first case in the literature describing the co-occurrence of ADPKD and hereditary TTP. We aim to describe the clinical course including the renal and the pregnancy outcomes, describe the consanguinity and family history, and try to explain the potential effect of one disease on the clinical course of the other.
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Affiliation(s)
- Randah Dahlan
- Department of Internal Medicine, Section of Nephrology, King Abdullah Medical City, Mecca, Mecca region, Saudi Arabia
| | - Eman Bablghaith
- Department of Internal Medicine, King Abdullah Medical City, Mecca, Mecca region, Saudi Arabia
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15
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Boycott KM, Hartley T, Kernohan KD, Dyment DA, Howley H, Innes AM, Bernier FP, Brudno M. Care4Rare Canada: Outcomes from a decade of network science for rare disease gene discovery. Am J Hum Genet 2022; 109:1947-1959. [PMID: 36332610 PMCID: PMC9674964 DOI: 10.1016/j.ajhg.2022.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
The past decade has witnessed a rapid evolution in rare disease (RD) research, fueled by the availability of genome-wide (exome and genome) sequencing. In 2011, as this transformative technology was introduced to the research community, the Care4Rare Canada Consortium was launched: initially as FORGE, followed by Care4Rare, and Care4Rare SOLVE. Over what amounted to three eras of diagnosis and discovery, the Care4Rare Consortium used exome sequencing and, more recently, genome and other 'omic technologies to identify the molecular cause of unsolved RDs. We achieved a diagnostic yield of 34% (623/1,806 of participating families), including the discovery of deleterious variants in 121 genes not previously associated with disease, and we continue to study candidate variants in novel genes for 145 families. The Consortium has made significant contributions to RD research, including development of platforms for data collection and sharing and instigating a Canadian network to catalyze functional characterization research of novel genes. The Consortium was instrumental to implementing genome-wide sequencing as a publicly funded test for RD diagnosis in Canada. Despite the successes of the past decade, the challenge of solving all RDs remains enormous, and the work is far from over. We must leverage clinical and 'omic data for secondary use, develop tools and policies to support safe data sharing, continue to explore the utility of new and emerging technologies, and optimize research protocols to delineate complex disease mechanisms. Successful approaches in each of these realms is required to offer diagnostic clarity to all families with RDs.
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Affiliation(s)
- Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada,Corresponding author
| | - Taila Hartley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David A. Dyment
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Heather Howley
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Francois P. Bernier
- Department of Medical Genetics and Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
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16
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Santos Simarro F. Advances in clinical genetics and its current challenges. An Pediatr (Barc) 2022; 97:281.e1-281.e5. [PMID: 36115780 DOI: 10.1016/j.anpede.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
The great advances in the development of genomic technologies and their incorporation into routine clinical practice is bringing about a change in which an individual's genetic information is becoming increasingly relevant to their medical care. This is known as genomic medicine. Its implementation is not without barriers, including difficulties in the assessment and interpretation of genomic data, deficient training of professionals and patients in this field, unequal access to units with expertise, and a lack of professional profiles and infrastructures necessary for the incorporation of genomic technologies into routine clinical practice. This article reviews the advances and challenges of genomic medicine.
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Affiliation(s)
- Fernando Santos Simarro
- Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
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17
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Santos Simarro F. Avances en genética clínica y sus retos actuales. An Pediatr (Barc) 2022. [DOI: 10.1016/j.anpedi.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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18
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Rosina E, Pezzani L, Pezzoli L, Marchetti D, Bellini M, Pilotta A, Calabrese O, Nicastro E, Cirillo F, Cereda A, Scatigno A, Milani D, Iascone M. Atypical, Composite, or Blended Phenotypes: How Different Molecular Mechanisms Could Associate in Double-Diagnosed Patients. Genes (Basel) 2022; 13:genes13071275. [PMID: 35886058 PMCID: PMC9319862 DOI: 10.3390/genes13071275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 12/10/2022] Open
Abstract
In the last few years, trio-Whole Exome Sequencing (WES) analysis has revolutionized the diagnostic process for patients with rare genetic syndromes, demonstrating its potential even in non-specific clinical pictures and in atypical presentations of known diseases. Multiple disorders in a single patient have been estimated to occur in approximately 2–7.5% of diagnosed cases, with higher frequency in consanguineous families. Here, we report the clinical and molecular characterisation of eight illustrative patients for whom trio-WES allowed for identifing more than one genetic condition. Double homozygosity represented the causal mechanism in only half of them, whereas the other half showed peculiar multilocus combinations. The paper takes into consideration difficulties and learned lessons from our experience and therefore supports the powerful role of wide analyses for ascertaining multiple genetic diseases in complex patients, especially when a clinical suspicion could account for the majority of clinical signs. It finally makes clear how a patient’s “deep phenotyping” might not be sufficient to suggest the presence of multiple genetic diagnoses but remains essential to validate an unexpected multilocus result from genetic tests.
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Affiliation(s)
- Erica Rosina
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Lidia Pezzani
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Laura Pezzoli
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Daniela Marchetti
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Matteo Bellini
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Alba Pilotta
- Auxo-Endocrinology, Diabetology and Medical Genetic Unit, Department of Paediatrics, ASST Spedali Civili, 25123 Brescia, Italy;
| | - Olga Calabrese
- Medical Genetics Unit, Azienda Ospedaliera Universitaria di Modena, 41125 Modena, Italy;
| | - Emanuele Nicastro
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Francesco Cirillo
- Pediatric Hepatology and Paediatric Liver Transplantation, Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, 90127 Palermo, Italy;
| | - Anna Cereda
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Agnese Scatigno
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Donatella Milani
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
- Correspondence: ; Tel.: +39-02-55032560
| | - Maria Iascone
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
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19
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Chin HL, Gazzaz N, Huynh S, Handra I, Warnock L, Moller-Hansen A, Boerkoel P, Jacobsen JOB, du Souich C, Zhang N, Shefchek K, Prentice LM, Washington N, Haendel M, Armstrong L, Clarke L, Li WL, Smedley D, Robinson PN, Boerkoel CF. The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice. Genet Med 2022; 24:1512-1522. [PMID: 35442193 PMCID: PMC9363005 DOI: 10.1016/j.gim.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Genomic test results, regardless of laboratory variant classification, require clinical practitioners to judge the applicability of a variant for medical decisions. Teaching and standardizing clinical interpretation of genomic variation calls for a methodology or tool. METHODS To generate such a tool, we distilled the Clinical Genome Resource framework of causality and the American College of Medical Genetics/Association of Molecular Pathology and Quest Diagnostic Laboratory scoring of variant deleteriousness into the Clinical Variant Analysis Tool (CVAT). Applying this to 289 clinical exome reports, we compared the performance of junior practitioners with that of experienced medical geneticists and assessed the utility of reported variants. RESULTS CVAT enabled performance comparable to that of experienced medical geneticists. In total, 124 of 289 (42.9%) exome reports and 146 of 382 (38.2%) reported variants supported a diagnosis. Overall, 10.5% (1 pathogenic [P] or likely pathogenic [LP] variant and 39 variants of uncertain significance [VUS]) of variants were reported in genes without established disease association; 20.2% (23 P/LP and 54 VUS) were in genes without sufficient phenotypic concordance; 7.3% (15 P/LP and 13 VUS) conflicted with the known molecular disease mechanism; and 24% (91 VUS) had insufficient evidence for deleteriousness. CONCLUSION Implementation of CVAT standardized clinical interpretation of genomic variation and emphasized the need for collaborative and transparent reporting of genomic variation.
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Affiliation(s)
- Hui-Lin Chin
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada; Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Nour Gazzaz
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada; Department of Pediatrics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Stephanie Huynh
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Iulia Handra
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Lynn Warnock
- Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Ashley Moller-Hansen
- Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Pierre Boerkoel
- MD Undergraduate Program, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christèle du Souich
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Kent Shefchek
- Oregon Clinical and Translational Science Institute, Oregon Health & Science University, Portland, OR
| | - Leah M Prentice
- Provincial Laboratory Medicine Services, Provincial Health Services Authority, Vancouver, British Columbia, Canada
| | | | - Melissa Haendel
- Oregon Clinical and Translational Science Institute, Oregon Health & Science University, Portland, OR
| | - Linlea Armstrong
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Lorne Clarke
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | | | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, London, United Kingdom
| | | | - Cornelius F Boerkoel
- Department of Medical Genetics, Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada; Provincial Medical Genetics Program, Women's Hospital of British Columbia, Vancouver, British Columbia, Canada.
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20
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Pitfalls in Genetic Testing for Consanguineous Pediatric Populations. Case Rep Genet 2022; 2022:9393042. [PMID: 35663206 PMCID: PMC9159873 DOI: 10.1155/2022/9393042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/28/2022] [Indexed: 11/18/2022] Open
Abstract
We describe the diagnostic odyssey of an eight-year-old female born to consanguineous parents. Our patient presented with global developmental delay, regression, microcephaly, spastic diplegia, and leukodystrophy confirmed on brain magnetic resonance imaging (MRI). She was found on whole exome sequencing (WES) to have dual genetic diagnoses. The first was a homozygous pathogenic HERC2 gene partial deletion of exons 43–45 that causes HERC2-related disorder. The second was a homozygous pathogenic variant (c.836 C > T, p.A279 V) in the SUMF1 gene responsible for multiple sulfatase deficiency. This case highlights some of the challenges in diagnosing consanguineous pediatric populations where standard genetic and metabolic testing may not provide answers. Our case further supports the recent American College of Medical Genetics and Genomics (ACMG) recommendation of WES as a first or second-tier test for patients with developmental delay, particularly in a population where the chances of dual diagnosis is high.
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21
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Sabir AH, Singhal J, Man J, Cooper N, Cheung M, Irving M. Autosomal recessive EXT2 syndrome - extending the phenotypic spectrum of an emerging condition, a further case? Clin Dysmorphol 2022; 31:84-90. [PMID: 35045016 DOI: 10.1097/mcd.0000000000000406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ataf H Sabir
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London
- Institute of Cancer and Genomic Sciences, University of Birmingham
- Department of Clinical Genetics, Lavender House, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham
| | - Juhi Singhal
- Department of Medicine, West Hertfordshire Hospitals NHS Trust, Hertfordshire
| | - Jessica Man
- Institute of Cancer and Genomic Sciences, University of Birmingham
| | - Nicola Cooper
- Institute of Cancer and Genomic Sciences, University of Birmingham
- Department of Clinical Genetics, Lavender House, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham
| | - Moira Cheung
- Department of Paediatric Endocrinology, Evelina London Children's Hospital, London
- Guy's King's College and Saint Thomas' Hospitals' Medical and Dental School of King's College London: King's College London, School of Medical Education
| | - Melita Irving
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London
- Guy's King's College and Saint Thomas' Hospitals' Medical and Dental School of King's College London: King's College London, School of Medical Education
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22
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Liu L, Sun L, Chen Y, Wang M, Yu C, Huang Y, Zhao S, Du H, Chen S, Fan X, Tian W, Wu Z, Qiu G, Zhang TJ, Wu N. Delineation of dual molecular diagnosis in patients with skeletal deformity. Orphanet J Rare Dis 2022; 17:139. [PMID: 35346302 PMCID: PMC8962553 DOI: 10.1186/s13023-022-02293-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Skeletal deformity is characterized by an abnormal anatomical structure of bone and cartilage. In our previous studies, we have found that a substantial proportion of patients with skeletal deformity could be explained by monogenic disorders. More recently, complex phenotypes caused by more than one genetic defect (i.e., dual molecular diagnosis) have also been reported in skeletal deformities and may complicate the diagnostic odyssey of patients. In this study, we report the molecular and phenotypic characteristics of patients with dual molecular diagnosis and variable skeletal deformities. Results From 1108 patients who underwent exome sequencing, we identified eight probands with dual molecular diagnosis and variable skeletal deformities. All eight patients had dual diagnosis consisting of two autosomal dominant diseases. A total of 16 variants in 12 genes were identified, 5 of which were of de novo origin. Patients with dual molecular diagnosis presented blended phenotypes of two genetic diseases. Mendelian disorders occurred more than once include Osteogenesis Imperfecta Type I (COL1A1, MIM:166200), Neurofibromatosis, Type I (NF1, MIM:162200) and Marfan Syndrome (FBN1, MIM:154700). Conclusions This study demonstrated the complicated skeletal phenotypes associated with dual molecular diagnosis. Exome sequencing represents a powerful tool to detect such complex conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02293-x.
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Affiliation(s)
- Lian Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Liying Sun
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Yujun Chen
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Muchuan Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Graduate School of Peking Union Medical College, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Chenxi Yu
- Department of Joint Surgery, Shandong Provincial Hospital Affiliated To Shandong First Medical University, Shandong, 250021, China
| | - Yingzhao Huang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Shaoke Chen
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Xin Fan
- The Second Affiliated Hospital of Guangxi Medical University, Nanning, 530000, Guangxi, China
| | - Wen Tian
- Department of Hand Surgery, Beijing Jishuitan Hospital, Beijing, 100035, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | | | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, 100730, China. .,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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23
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Passos-Bueno MR, Costa CIS, Zatz M. Dystrophin genetic variants and autism. DISCOVER MENTAL HEALTH 2022; 2:4. [PMID: 37861890 PMCID: PMC10501027 DOI: 10.1007/s44192-022-00008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/07/2022] [Indexed: 10/21/2023]
Abstract
Loss-of-function variants in the dystrophin gene, a well-known cause of muscular dystrophies, have emerged as a mutational risk mechanism for autism spectrum disorder (ASD), which in turn is a highly prevalent (~ 1%) genetically heterogeneous neurodevelopmental disorder. Although the association of intellectual disability with the dystrophinopathies Duchenne (DMD) and Becker muscular dystrophy (BMD) has been long established, their association with ASD is more recent, and the dystrophin genotype-ASD phenotype correlation is unclear. We therefore present a review of the literature focused on the ASD prevalence among dystrophinopathies, the relevance of the dystrophin isoforms, and most particularly the relevance of the genetic background to the etiology of ASD in these patients. Four families with ASD-DMD/BMD patients are also reported here for the first time. These include a single ASD individual, ASD-discordant and ASD-concordant monozygotic twins, and non-identical ASD triplets. Notably, two unrelated individuals, which were first ascertained because of the ASD phenotype at ages 15 and 5 years respectively, present rare dystrophin variants still poorly characterized, suggesting that some dystrophin variants may compromise the brain more prominently. Whole exome sequencing in these ASD-DMD/BMD individuals together with the literature suggest, although based on preliminary data, a complex and heterogeneous genetic architecture underlying ASD in dystrophinopathies, that include rare variants of large and medium effect. The need for the establishment of a consortia for genomic investigation of ASD-DMD/BMD patients, which may shed light on the genetic architecture of ASD, is discussed.
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Affiliation(s)
- Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Claudia Ismania Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mayana Zatz
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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24
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Herman I, Jolly A, Du H, Dawood M, Abdel-Salam GMH, Marafi D, Mitani T, Calame DG, Coban-Akdemir Z, Fatih JM, Hegazy I, Jhangiani SN, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. Am J Med Genet A 2022; 188:735-750. [PMID: 34816580 PMCID: PMC8837671 DOI: 10.1002/ajmg.a.62565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022]
Abstract
Genomic sequencing and clinical genomics have demonstrated that substantial subsets of atypical and/or severe disease presentations result from multilocus pathogenic variation (MPV) causing blended phenotypes. In an infant with a severe neurodevelopmental disorder, four distinct molecular diagnoses were found by exome sequencing (ES). The blended phenotype that includes brain malformation, dysmorphism, and hypotonia was dissected using the Human Phenotype Ontology (HPO). ES revealed variants in CAPN3 (c.259C > G:p.L87V), MUSK (c.1781C > T:p.A594V), NAV2 (c.1996G > A:p.G666R), and ZC4H2 (c.595A > C:p.N199H). CAPN3, MUSK, and ZC4H2 are established disease genes linked to limb-girdle muscular dystrophy (OMIM# 253600), congenital myasthenia (OMIM# 616325), and Wieacker-Wolff syndrome (WWS; OMIM# 314580), respectively. NAV2 is a retinoic-acid responsive novel disease gene candidate with biological roles in neurite outgrowth and cerebellar dysgenesis in mouse models. Using semantic similarity, we show that no gene identified by ES individually explains the proband phenotype, but rather the totality of the clinically observed disease is explained by the combination of disease-contributing effects of the identified genes. These data reveal that multilocus pathogenic variation can result in a blended phenotype with each gene affecting a different part of the nervous system and nervous system-muscle connection. We provide evidence from this n = 1 study that in patients with MPV and complex blended phenotypes resulting from multiple molecular diagnoses, quantitative HPO analysis can allow for dissection of phenotypic contribution of both established disease genes and novel disease gene candidates not yet proven to cause human disease.
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Affiliation(s)
- Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ghada M. H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ibrahim Hegazy
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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25
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Marwaha S, Knowles JW, Ashley EA. A guide for the diagnosis of rare and undiagnosed disease: beyond the exome. Genome Med 2022; 14:23. [PMID: 35220969 PMCID: PMC8883622 DOI: 10.1186/s13073-022-01026-w] [Citation(s) in RCA: 83] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/10/2022] [Indexed: 02/07/2023] Open
Abstract
AbstractRare diseases affect 30 million people in the USA and more than 300–400 million worldwide, often causing chronic illness, disability, and premature death. Traditional diagnostic techniques rely heavily on heuristic approaches, coupling clinical experience from prior rare disease presentations with the medical literature. A large number of rare disease patients remain undiagnosed for years and many even die without an accurate diagnosis. In recent years, gene panels, microarrays, and exome sequencing have helped to identify the molecular cause of such rare and undiagnosed diseases. These technologies have allowed diagnoses for a sizable proportion (25–35%) of undiagnosed patients, often with actionable findings. However, a large proportion of these patients remain undiagnosed. In this review, we focus on technologies that can be adopted if exome sequencing is unrevealing. We discuss the benefits of sequencing the whole genome and the additional benefit that may be offered by long-read technology, pan-genome reference, transcriptomics, metabolomics, proteomics, and methyl profiling. We highlight computational methods to help identify regionally distant patients with similar phenotypes or similar genetic mutations. Finally, we describe approaches to automate and accelerate genomic analysis. The strategies discussed here are intended to serve as a guide for clinicians and researchers in the next steps when encountering patients with non-diagnostic exomes.
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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Ojha VA, Bahl V, Ramachandra SC, Prashant A. Putrescence to Quintessence: An Atypical Presentation of Multiple Osteoporotic Spinal Fractures Masquerading as Multiple Myeloma. Cureus 2021; 13:e20788. [PMID: 35141056 PMCID: PMC8796275 DOI: 10.7759/cureus.20788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2021] [Indexed: 11/30/2022] Open
Abstract
A 64-year-old male patient presented with multiple osteoporotic spinal fractures of unknown origin. He was provisionally diagnosed with multiple myeloma based on biochemical and radiological findings. The patient presented in a very frail condition with a questionable outcome but showed a remarkable recovery from being frail to relatively fit. His baseline characteristics including magnetic resonance imaging of the dorsolumbar spine, beta 2 microglobulins, and C-reactive protein improved. The diagnosis was later changed to multiple spinal osteoporotic fractures. In this case report, we highlight that, although it is a good practice to have a single working diagnosis, when the diagnosis is challenging, a holistic approach should be followed to prevent medical and diagnostic miscalculations.
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Scholz T, Dufke A, Haack T, Elbracht M, Eggermann T, Roggia C, Riess O, Kurth I, Hempel M. Exomsequenzierung bei Kindern und Jugendlichen mit seltenen Erkrankungen. Monatsschr Kinderheilkd 2021. [DOI: 10.1007/s00112-021-01352-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Strong A, Skraban C, Meyers K, Amaral S, Furth S, Drant S, Hsiao W, Galea L, Gold J, Gold NB, Leonard J, Lopez S, Zackai EH, Pyeritz RE. Expanding the phenotypic spectrum of Mendelian connective tissue disorders to include prominent kidney phenotypes. Am J Med Genet A 2021; 185:3762-3769. [PMID: 34355836 PMCID: PMC9888756 DOI: 10.1002/ajmg.a.62449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/02/2023]
Abstract
Heritable connective tissue disorders are a group of diseases, each rare, characterized by various combinations of skin, joint, musculoskeletal, organ, and vascular involvement. Although kidney abnormalities have been reported in some connective tissue disorders, they are rarely a presenting feature. Here we present three patients with prominent kidney phenotypes who were found by whole exome sequencing to have variants in established connective tissue genes associated with Loeys-Dietz syndrome and congenital contractural arachnodactyly. These cases highlight the importance of considering connective tissue disease in children presenting with structural kidney disease and also serves to expand the phenotype of Loeys-Dietz syndrome and possibly congenital contractural arachnodactyly to include cystic kidney disease and cystic kidney dysplasia, respectively.
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Affiliation(s)
- Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Cara Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kevin Meyers
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sandra Amaral
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Susan Furth
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stacey Drant
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Wendy Hsiao
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lauren Galea
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jessica Gold
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nina B. Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital, Boston, Massachusetts, USA,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacqueline Leonard
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sonya Lopez
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine H. Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Reed E. Pyeritz
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Abstract
PURPOSE OF REVIEW A single genetic diagnosis, especially from the analysis of a limited number of genes, may not signal the end of a diagnostic odyssey. When a patient with a genetic syndrome presents with symptoms that are not usually associated with their disease phenotype, additional genetic testing is warranted. RECENT FINDINGS Although multiple co-existing genetic diagnoses may sound unlikely, many recent studies and case reports have demonstrated that this scenario is more common than expected. Studies involving whole exome and genome sequencing have identified a frequency of multiple genetic diagnoses and have identified clinical findings that make a second diagnosis more likely, which we have seen reflected in recent cases from our own clinic and consult service. These include multisystem disease, consanguinity, well described aneuploidies with rare or new symptoms, and complex structural chromosomal anomalies which may include multiple chromosomes and breakpoints that disrupt gene function. SUMMARY Identifying a second diagnosis can have vast implications for patient management and counseling. Patients can be followed with appropriate medical screening and early interventions to support optimal child development. Furthermore, the patient's family can be impacted by ending the diagnostic odyssey, providing testing for other at-risk family members, and offering prenatal options.
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Affiliation(s)
- Kristin B Linscott
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer A Cassady
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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31
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Muthusamy K, El-Jabali A, Ongie LJ, Dhamija R, Babovic-Vuksanovic D. Neurofibromatosis 1 in the setting of dual diagnosis: Diagnostic and management conundrums. Am J Med Genet A 2021; 188:911-918. [PMID: 34797032 DOI: 10.1002/ajmg.a.62575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/27/2021] [Accepted: 10/29/2021] [Indexed: 11/07/2022]
Abstract
Neurofibromatosis type 1 (NF1) is a common neurocutaneous disorder characterized by development of pigmentary skin changes, neurogenic tumors, and other manifestations involving multiple organ systems. Penetrance is complete, though expressivity is quite variable even among the family members. Given that NF1 is a common hereditary condition, existence of a second genetic disorder in NF1 patients is not unexpected. During comprehensive evaluations of individuals with NF1, we encountered 11 patients with dual diagnosis who contributed to phenotypic complexity and challenges for long-term management. Examples include Prader-Willi Syndrome, Autosomal Dominant Polycystic Kidney Disease, Down syndrome, infantile myofibromatosis, Craniosynostosis, cleft lip and palate, 47,XYY, 22q11.2 duplication, 15q13.3 deletion syndrome, and BRCA2- and ATM- related cancer predisposition syndromes. Presence of dysmorphism, developmental delay, atypical tumors, and family history of other genetic disorders including cancers appears as determinants to consider a second genetic etiology and helps to differentiate from an extreme phenotypic spectrum of NF1. Clinicians should have high index of suspicion to exclude coexisting disorders, as apart from providing comprehensive medical care. This also has potential implications in genetic counseling. Long-term effects of the synergistic mechanisms leading to phenotypic complexity and patient outcomes are yet to be characterized, with follow-up needed.
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Affiliation(s)
- Karthik Muthusamy
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Laura J Ongie
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Radhika Dhamija
- Department of Clinical Genomics, Mayo Clinic, Phoenix, Arizona, USA.,Department of Neurology, Mayo Clinic, Phoenix, Arizona, USA
| | - Dusica Babovic-Vuksanovic
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA.,Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Genome sequencing identifies three molecular diagnoses including a mosaic variant in the COL2A1 gene in an individual with Pol III-related leukodystrophy and Feingold syndrome. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006143. [PMID: 34737199 PMCID: PMC8751417 DOI: 10.1101/mcs.a006143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
Undiagnosed genetic disease imposes a significant burden on families and health-care resources, especially in cases with a complex phenotype. Here we present a child with suspected leukodystrophy in the context of additional features, including hearing loss, clinodactyly, rotated thumbs, tapered fingers, and simplified palmar crease. Trio genome sequencing (GS) identified three molecular diagnoses in this individual: compound heterozygous missense variants associated with polymerase III (Pol III)–related leukodystrophy, a 4-Mb de novo copy-number loss including the MYCN gene associated with Feingold syndrome, and a mosaic single-nucleotide variant associated with COL2A1-related disorders. These variants fully account for the individual's features, but also illustrate the potential for superimposed and unclear contributions of multiple diagnoses to an individual's overall presentation. This report demonstrates the advantage of GS in detection of multiple variant types, including low-level mosaic variants, and emphasizes the need for comprehensive genetic analysis and detailed clinical phenotyping to provide individuals and their families with the maximum benefit for clinical care and genetic counseling.
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33
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van der Werf-'t Lam AS, van Haeringen A, Rinnen T, Robles de Medina RM, Wilde AAM, Hennekam RC, Barge-Schaapveld DQCM. Andersen-Tawil syndrome: Overlapping clinical features with Noonan syndrome? Eur J Med Genet 2021; 65:104382. [PMID: 34748995 DOI: 10.1016/j.ejmg.2021.104382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/28/2021] [Accepted: 11/02/2021] [Indexed: 11/03/2022]
Abstract
Andersen-Tawil syndrome (ATS) and Noonan syndrome (NS) are both autosomal dominantly inherited disorders that share anomalies in the same body systems, i.e. cardiovascular system, skeleton, growth, and face morphology. Here we report a patient meeting clinical diagnostic criteria for NS in whom no variant in one of the genes known to cause NS was found and a pathogenic variant in KCNJ2 (c.653G > C, p.(Arg218Pro)) was demonstrated. Because of manifestations typical for NS and previously not described in ATS (broad neck, low hairline and pectus excavatum), this may indicate there is a phenotypical overlap between ATS and NS, although we cannot exclude that the patient has an additional, hitherto undetected variant in another gene that explains the NS features. Further studies into a functional relation between KCNJ2 and the RAS/MAPK pathway are needed to determine this further.
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Affiliation(s)
| | - A van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - T Rinnen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | | | - A A M Wilde
- Department of Cardiology, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - R C Hennekam
- Department of Paediatrics, Amsterdam University Medical Centre, Amsterdam, the Netherlands
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34
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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35
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Narayanan DL, Udyawar D, Kaur P, Sharma S, Suresh N, Nampoothiri S, do Rosario MC, Somashekar PH, Rao LP, Kausthubham N, Majethia P, Pande S, Ramesh Bhat Y, Shrikiran A, Bielas S, Girisha KM, Shukla A. Multilocus disease-causing genomic variations for Mendelian disorders: role of systematic phenotyping and implications on genetic counselling. Eur J Hum Genet 2021; 29:1774-1780. [PMID: 34276053 PMCID: PMC8633282 DOI: 10.1038/s41431-021-00933-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 04/24/2021] [Accepted: 06/22/2021] [Indexed: 11/09/2022] Open
Abstract
Multilocus disease-causing genomic variations (MGVs) and multiple genetic diagnoses (MGDs) are increasingly being recognised in individuals and families with Mendelian disorders. This can be mainly attributed to the widespread use of genomic tests for the evaluation of these disorders. We conducted a retrospective study of families evaluated over the last 6 years at our centre to identify families with MGVs and MGDs. MGVs were observed in fourteen families. We observed five different consequences: (i) individuals with MGVs presenting as blended phenotypes (ii) individuals with MGVs presenting with distinct phenotypes (iii) individuals with MGVs with age-dependent penetrance (iv) individuals with MGVs with one phenotype obscured by another more predominant phenotype (v) two distinct phenotypes in different individuals in families with MGVs. Consanguinity was present in eight (8/14, 57.1%) of them. Thirteen families had two Mendelian disorders and one had three Mendelian disorders. The risk of recurrence of one or more conditions in these families ranged from 25% to 75%. Our findings underline the importance of the role of a clinical geneticist in systematic phenotyping, challenges in genetic counselling and risk estimation in families with MGVs and MGDs, especially in highly inbred populations.
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Affiliation(s)
- Dhanya Lakshmi Narayanan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Divya Udyawar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Parneet Kaur
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Suvasini Sharma
- Department of Pediatrics (Neurology division), Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Narayanaswamy Suresh
- Department of Pediatrics (Neurology division), Lady Hardinge Medical College and Kalawati Saran Children's Hospital, New Delhi, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, India
| | - Michelle C do Rosario
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Puneeth H Somashekar
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Lakshmi Priya Rao
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Neethukrishna Kausthubham
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Purvi Majethia
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shruti Pande
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Y Ramesh Bhat
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Aroor Shrikiran
- Department of Pediatrics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Stephanie Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India.
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Priolo M, Radio FC, Pizzi S, Pintomalli L, Pantaleoni F, Mancini C, Cordeddu V, Africa E, Mammì C, Dallapiccola B, Tartaglia M. Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype. Genes (Basel) 2021; 12:genes12071009. [PMID: 34208845 PMCID: PMC8303239 DOI: 10.3390/genes12071009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objective, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. Patients and Methods, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. Results, two co-occurring heterozygous truncating variants in CNOT3 and SMAD6 were identified. Heterozygous loss-of-function variants in CNOT3, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the SMAD6 gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. Conclusions, two concomitant truncating variants in CNOT3 and SMAD6 are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Francesca Pantaleoni
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Emilio Africa
- UOC di Neuroradiologia, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
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Unraveling the genetic complexities of combined retinal dystrophy and hearing impairment. Hum Genet 2021; 141:785-803. [PMID: 34148116 PMCID: PMC9035000 DOI: 10.1007/s00439-021-02303-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022]
Abstract
Usher syndrome, the most prevalent cause of combined hereditary vision and hearing impairment, is clinically and genetically heterogeneous. Moreover, several conditions with phenotypes overlapping Usher syndrome have been described. This makes the molecular diagnosis of hereditary deaf–blindness challenging. Here, we performed exome sequencing and analysis on 7 Mexican and 52 Iranian probands with combined retinal degeneration and hearing impairment (without intellectual disability). Clinical assessment involved ophthalmological examination and hearing loss questionnaire. Usher syndrome, most frequently due to biallelic variants in MYO7A (USH1B in 16 probands), USH2A (17 probands), and ADGRV1 (USH2C in 7 probands), was diagnosed in 44 of 59 (75%) unrelated probands. Almost half of the identified variants were novel. Nine of 59 (15%) probands displayed other genetic entities with dual sensory impairment, including Alström syndrome (3 patients), cone-rod dystrophy and hearing loss 1 (2 probands), and Heimler syndrome (1 patient). Unexpected findings included one proband each with Scheie syndrome, coenzyme Q10 deficiency, and pseudoxanthoma elasticum. In four probands, including three Usher cases, dual sensory impairment was either modified/aggravated or caused by variants in distinct genes associated with retinal degeneration and/or hearing loss. The overall diagnostic yield of whole exome analysis in our deaf–blind cohort was 92%. Two (3%) probands were partially solved and only 3 (5%) remained without any molecular diagnosis. In many cases, the molecular diagnosis is important to guide genetic counseling, to support prognostic outcomes and decisions with currently available and evolving treatment modalities.
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Zhu AY, Costain G, Cytrynbaum C, Weksberg R, Cohn RD, Ali A. Novel heterozygous variants in PXDN cause different anterior segment dysgenesis phenotypes in monozygotic twins. Ophthalmic Genet 2021; 42:624-630. [PMID: 33985410 DOI: 10.1080/13816810.2021.1925929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND Since bi-allelic variants in the PXDN gene were first discovered in 2011 to be associated with anterior segment dysgenesis, a spectrum of ophthalmologic and systemic clinical manifestations has been described. This manuscript reports two distinct clinical phenotypes in monozygotic twin sisters, including the previously unreported ocular manifestation of bilateral primary aphakia, associated with novel compound heterozygous variants in the PXDN gene. MATERIALS AND METHODS We used genome sequencing to study a non-consanguineous family with monozygotic twin sister probands: one presenting with bilateral microphthalmia, primary aphakia, total corneal opacification, congenital glaucoma, and complex systemic comorbidities; the other with anterior persistent fetal vasculature in the right eye, and Peters anomaly type 2 with cataract and iris coloboma in the left eye but no systemic issues. These findings were compared to published reports of PXDN-related ocular diseases upon comprehensive review of prior literature. RESULTS In both affected sisters, genome sequencing identified two novel heterozygous variants in trans in the PXDN gene: c.1569_1570insT, predicting p.(Thr524TyrfsTer53), and c.3206 C > A, predicting p.(Ala1069Asp), respectively. No other potentially diagnostic variants were identified in any other genes. CONCLUSIONS This report on two novel compound heterozygous variants in the PXDN gene associated with previously unreported clinical manifestations further expands the genotypic and phenotypic spectrum associated with this gene. Our finding of distinctive clinical phenotypes associated with identical compound heterozygous PXDN variants in monozygotic twins emphasizes the significant clinical variability that can occur, suggesting a potential role for stochastic developmental and/or epigenetic factors in the ultimate pathophysiologic pathway.
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Affiliation(s)
- Angela Y Zhu
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Ophthalmology and Visual Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto and Hospital for Sick Children, Toronto, Ontario, Canada.,Genetics & Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - Cheryl Cytrynbaum
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario, Canada.,Genetics & Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto and Hospital for Sick Children, Toronto, Ontario, Canada.,Genetics & Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ronald D Cohn
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Paediatrics, University of Toronto and Hospital for Sick Children, Toronto, Ontario, Canada.,Genetics & Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - Asim Ali
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Ophthalmology and Visual Sciences, University of Toronto, Toronto, Ontario, Canada
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Haploinsufficiency of PRR12 causes a spectrum of neurodevelopmental, eye, and multisystem abnormalities. Genet Med 2021; 23:1234-1245. [PMID: 33824499 DOI: 10.1038/s41436-021-01129-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Proline Rich 12 (PRR12) is a gene of unknown function with suspected DNA-binding activity, expressed in developing mice and human brains. Predicted loss-of-function variants in this gene are extremely rare, indicating high intolerance of haploinsufficiency. METHODS Three individuals with intellectual disability and iris anomalies and truncating de novo PRR12 variants were described previously. We add 21 individuals with similar PRR12 variants identified via matchmaking platforms, bringing the total number to 24. RESULTS We observed 12 frameshift, 6 nonsense, 1 splice-site, and 2 missense variants and one patient with a gross deletion involving PRR12. Three individuals had additional genetic findings, possibly confounding the phenotype. All patients had developmental impairment. Variable structural eye defects were observed in 12/24 individuals (50%) including anophthalmia, microphthalmia, colobomas, optic nerve and iris abnormalities. Additional common features included hypotonia (61%), heart defects (52%), growth failure (54%), and kidney anomalies (35%). PrediXcan analysis showed that phecodes most strongly associated with reduced predicted PRR12 expression were enriched for eye- (7/30) and kidney- (4/30) phenotypes, such as wet macular degeneration and chronic kidney disease. CONCLUSION These findings support PRR12 haploinsufficiency as a cause for a novel disorder with a wide clinical spectrum marked chiefly by neurodevelopmental and eye abnormalities.
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Gatticchi L, Vešelényiová D, Miertus J, Enrico Maltese P, Manara E, Costantini A, Benedetti S, Ďurovčíková D, Krajcovic J, Bertelli M. Recessive multiple epiphyseal dysplasia and Stargardt disease in two sisters. Mol Genet Genomic Med 2021; 9:e1630. [PMID: 33724725 PMCID: PMC8123746 DOI: 10.1002/mgg3.1630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/22/2020] [Accepted: 02/12/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The rapid spread of genome-wide next-generation sequencing in the molecular diagnosis of rare genetic disorders has produced increasing evidence of multilocus genomic variations in cases with a previously well-characterized molecular diagnosis. Here, we describe two patients with a rare combination of skeletal abnormalities and retinal dystrophy caused by variants in the SLC26A2 and ABCA4 genes, respectively, in a family with parental consanguinity. METHODS Next-generation sequencing and Sanger sequencing were performed to obtain a molecular diagnosis for the retinal and skeletal phenotypes, respectively. RESULTS Genetic testing revealed that the sisters were homozygous for the p.(Cys653Ser) variant in SLC26A2 and heterozygous for the missense p.(Pro68Leu) and splice donor c.6386+2C>G variants in ABCA4. Segregation analysis confirmed the carrier status of the parents. CONCLUSION Despite low frequency of occurrence, the detection of multilocus genomic variations in a single disease gene-oriented approach can provide accurate diagnosis even in cases with high phenotypic complexity. A targeted sequencing approach can detect relationships between observed phenotypes and underlying genotypes, useful for clinical management.
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Affiliation(s)
- Leonardo Gatticchi
- Department of Experimental Medicine, Laboratory of Biochemistry, University of Perugia, Perugia, Italy
| | - Dominika Vešelényiová
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Jan Miertus
- Génius n.o, Trnava, Slovakia.,MAGI's Lab, Genetic Testing Laboratory, Rovereto, Italy
| | | | | | | | | | - Darina Ďurovčíková
- Institute of Genetics and Molecular Medicine, Faculty of Medicine, Slovak Healthcare University, Bratislava, Slovakia
| | - Juraj Krajcovic
- Department of Biology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Matteo Bertelli
- MAGI's Lab, Genetic Testing Laboratory, Rovereto, Italy.,MAGI Euregio, Bolzano, Italy
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von Stülpnagel C, van Baalen A, Borggraefe I, Eschermann K, Hartlieb T, Kiwull L, Pringsheim M, Wolff M, Kudernatsch M, Wiegand G, Striano P, Kluger G. Network for Therapy in Rare Epilepsies (NETRE): Lessons From the Past 15 Years. Front Neurol 2021; 11:622510. [PMID: 33519703 PMCID: PMC7840830 DOI: 10.3389/fneur.2020.622510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/14/2020] [Indexed: 01/14/2023] Open
Abstract
Background: In 2005, Network for Therapy in Rare Epilepsies (NETRE)-was initiated in order to share treatment experiences among clinicians in patients with rare epilepsies. Here we describe the structure of the rapidly growing NETRE and summarize some of the findings of the last 15 years. Methodology/Structure of NETRE: NETRE is organized in distinct groups (currently >270). Starting point is always a patient with a rare epilepsy/ epileptic disorder. This creates a new group, and next, a medical coordinator is appointed. The exchange of experiences is established using a data entry form, which the coordinator sends to colleagues. The primary aim is to exchange experiences (retrospectively, anonymously, MRI results also non-anonymously) of the epilepsy treatment as well as on clinical presentation and comorbidities NETRE is neither financed nor sponsored. Results: Some of the relevant results: (1) first description of FIRES as a new epilepsy syndrome and its further investigation, (2) in SCN2A, the assignment to gain- vs. loss-of-function mutations has a major impact on clinical decisions to use or avoid treatment with sodium channel blockers, (3) the important aspect of avoiding overtreatment in CDKL5 patients, due to loss of effects of anticonvulsants after 12 months, (4) pathognomonic MRI findings in FOXG1 patients, (5) the first description of pathognomonic chewing-induced seizures in SYNGAP1 patients, and the therapeutic effect of statins as anticonvulsant in these patients, (6) the phenomenon of another reflex epilepsy-bathing epilepsy associated with a SYN1 mutation. Of special interest is also a NETRE group following twins with genetic and/or structural epilepsies [including vanishing-twin-syndrome and twin-twin-transfusion syndrome) [= "Early Neuroimpaired Twin Entity" (ENITE)]. Discussion and Perspective: NETRE enables clinicians to quickly exchange information on therapeutic experiences in rare diseases with colleagues at an international level. For both parents and clinicians/scientist this international exchange is both reassuring and helpful. In collaboration with other groups, personalized therapeutic approaches are sought, but the present limitations of currently available therapies are also highlighted. Presently, the PATRE Project (PATient based phenotyping and evaluation of therapy for Rare Epilepsies) is commencing, in which information on therapies will be obtained directly from patients and their caregivers.
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Affiliation(s)
- Celina von Stülpnagel
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics and Epilepsy Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
| | - Andreas van Baalen
- Clinic for Child and Adolescent Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ingo Borggraefe
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics and Epilepsy Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Kirsten Eschermann
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
| | - Till Hartlieb
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Schoen Klinik Vogtareuth, Vogtareuth, Germany
| | - Lorenz Kiwull
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics and Epilepsy Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
- Institute of Social Pediatrics and Adolescent Medicine, Ludwig-Maximilian-University, Munich, Germany
| | - Milka Pringsheim
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Schoen Klinik Vogtareuth, Vogtareuth, Germany
| | - Markus Wolff
- Department of Pediatric Neurology, Vivantes Hospital Neukölln, Berlin, Germany
| | - Manfred Kudernatsch
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
- Clinic for Neurosurgery, Schön Klinik Vogtareuth, Vogtareuth, Germany
| | - Gert Wiegand
- Clinic for Child and Adolescent Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany
- Neuropediatrics Section of the Department of Pediatrics, Asklepios Clinic Hamburg Nord-Heidberg, Hamburg, Germany
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, Istituto die Ricovero e Cura a Carattere Scientifico Istituto Giannina Gaslini, Genova, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genova, Genova, Italy
| | - Gerhard Kluger
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Medical University, Salzburg, Austria
- Center for Pediatric Neurology, Neurorehabilitation and Epileptology, Schoen Klinik Vogtareuth, Vogtareuth, Germany
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Hannah-Shmouni F, Al-Shahoumi R, Brady LI, Wu L, Frei J, Tarnopolsky MA. Dual molecular diagnoses in a neurometabolic specialty clinic. Am J Med Genet A 2020; 185:766-773. [PMID: 33369152 DOI: 10.1002/ajmg.a.62034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 11/08/2022]
Abstract
Reports of patients with concomitant diagnoses of two inherited genetic disorders, sometimes referred to as "double trouble," have appeared intermittently in the medical literature. We report eight additional cases with dual diagnoses of two genetic conditions. All cases had a phenotype atypical for their primary diagnosis, leading to the search for a second genetic diagnosis. These cases highlight the importance of the history, physical examination and continued work-up if the phenotype of the patient falls drastically outside what has been reported with their primary diagnosis. Some of the diagnoses of the patients presented here (e.g., Myotonic Dystrophy Type 1, fascioscapulohumeral muscular dystrophy) would not have been identified by genetic testing done on a next generation sequencing backbone (e.g., panel or exome sequencing). When the clinical picture is atypical or more severe than expected the possibility of a dual diagnosis (double trouble) should be considered. Identification of a second genetic condition can impact management and genetic counseling.
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Affiliation(s)
- Fady Hannah-Shmouni
- Section on Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Rashid Al-Shahoumi
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lauren I Brady
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Lily Wu
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Julia Frei
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
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Muthusamy K, Mrugala MM, Bendok BR, Dhamija R. LZTR1-related spinal schwannomatosis and 7q11.23 duplication syndrome: A complex phenotype with dual diagnosis. Mol Genet Genomic Med 2020; 9:e1560. [PMID: 33269527 PMCID: PMC7963420 DOI: 10.1002/mgg3.1560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 01/25/2023] Open
Abstract
Background Dual diagnoses in genetics practice are not uncommon and patients with dual diagnosis often present with complex and challenging phenotypes. A combination of meticulous phenotyping and molecular genetic techniques are essential in solving these diagnostic odysseys. Methods Clinical features and genetic workup of a patient presenting with incidental schwannomatosis. Results A 19‐year‐old male presented with incidental painless schwannomatosis in the background of macrocephaly, distinctive facies, and learning disability. Comprehensive genetic testing with gene panel and chromosomal microarray led to a dual diagnosis of LZTR1‐related schwannomatosis and 7q11.23 duplication syndrome. Conclusion We emphasize the need for high index of suspicion and comprehensive genetic testing in complex phenotypes. Interrogation of the interplay between the pathogenic variants in multiple genes could improve our understanding of the pathophysiologic pathways and contribute to therapeutic discoveries. A nineteen year old male presented with incidental painless schwannomatosis in the background of macrocephaly, distinctive facies and learning disability. Comprehensive genetic testing with gene panel and chromosomal microarray led to a dual diagnosis of LZTR1 related schwannomatosis and 7q11.23 duplication syndrome. We emphasize the need for high index of suspicion and comprehensive genetic testing in complex phenotypes. Interrogation of the interplay between the pathogenic variants in multiple genes could improve our understanding of the pathophysiologic pathways and contribute to therapeutic discoveries.
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Affiliation(s)
| | - Maciej M Mrugala
- Department of Neurology, Mayo Clinic, Phoenix, AZ, USA.,Department of Neurologic Surgery, Mayo Clinic, Phoenix, AZ, USA.,Department of Radiation Oncology, Mayo Clinic, Phoenix, AZ, USA.,Division of Hematology/Oncology, Department of Internal Medicine, Mayo Clinic, Phoenix, AZ, USA
| | - Bernard R Bendok
- Department of Neurologic Surgery, Mayo Clinic, Phoenix, AZ, USA.,Department of Diagnostic Radiology, Mayo Clinic, Phoenix, AZ, USA.,Department of Otolaryngology-Head and Neck Surgery, Mayo Clinic, Phoenix, AZ, USA
| | - Radhika Dhamija
- Department of Neurology, Mayo Clinic, Phoenix, AZ, USA.,Department of Clinical Genomics, Mayo Clinic, Phoenix, AZ, USA
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Reis LM, Basel D, McCarrier J, Weinberg DV, Semina EV. Compound heterozygous splicing CDON variants result in isolated ocular coloboma. Clin Genet 2020; 98:486-492. [PMID: 32729136 PMCID: PMC8341436 DOI: 10.1111/cge.13824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/20/2022]
Abstract
Ocular coloboma is caused by failure of optic fissure closure during development and recognized as part of the microphthalmia, anophthalmia, and coloboma (MAC) spectrum. While many genes are known to cause colobomatous microphthalmia, relatively few have been reported in coloboma with normal eye size. Genetic analysis including trio exome sequencing and Sanger sequencing was undertaken in a family with two siblings affected with bilateral coloboma of the iris, retina, and choroid. Pathogenic variants in MAC genes were excluded. Trio analysis identified compound heterozygous donor splice site variants in CDON, a cell-surface receptor known to function in the Sonic Hedgehog pathway, c.928 + 1G > A and c.2650 + 1G > T, in both affected individuals. Heterozygous missense and truncating CDON variants are associated with dominant holoprosencephaly (HPE) with incomplete penetrance and Cdon-/- mice display variable HPE and coloboma. A homozygous nonsense allele of uncertain significance was recently identified in a consanguineous patient with coloboma and a second molecular diagnosis. We report the first compound heterozygous variants in CDON as a cause of isolated coloboma. CDON is the first HPE gene identified to cause recessive coloboma. Given the phenotypic overlap, further examination of HPE genes in coloboma is indicated.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226
| | - Donald Basel
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226
| | - Julie McCarrier
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226
| | - David V Weinberg
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226
| | - Elena V Semina
- Department of Pediatrics, Children’s Research Institute, Medical College of Wisconsin and Children’s Wisconsin, Milwaukee, WI 53226
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI 53226
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226
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A systematic review of monogenic etiologies of nonimmune hydrops fetalis. Genet Med 2020; 23:3-12. [PMID: 33082562 PMCID: PMC7796968 DOI: 10.1038/s41436-020-00967-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Hydrops Fetalis (HF), accumulation of fluid in two or more fetal compartments, is life-threatening to the fetus. Genetic etiologies include many chromosomal and monogenic disorders. Despite this, the clinical workup typically evaluates limited genetic targets. To support broader molecular testing of pregnancies with HF, we cataloged the spectrum of monogenic disorders associated with nonimmune hydrops fetalis (NIHF). We performed a systematic literature review under PROSPERO tag CRD42018099495 of cases reporting NIHF meeting strict phenotypic criteria and well-defined genetic diagnosis. We ranked the evidence per gene based on number of reported cases, phenotype and molecular/biochemical diagnosis. We identified 131 genes with strong evidence for an association with NIHF and 46 genes with emerging evidence spanning the spectrum of multisystem syndromes, cardiac disorders, hematologic disorders, and metabolic disorders. Several genes previously implicated with NIHF did not have any reported cases in the literature with both fetal hydrops and molecular diagnosis. Many genes with strong evidence for association with NIHF would not be detected using current sequencing panels. Nonimmune HF has many possible monogenic etiologies, several with treatment implications, but current diagnostic approaches are not exhaustive. Studies are needed to assess if broad sequencing approaches like whole exome sequencing are useful in clinical management of HF.
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Molinari E, Srivastava S, Dewhurst RM, Sayer JA. Use of patient derived urine renal epithelial cells to confirm pathogenicity of PKHD1 alleles. BMC Nephrol 2020; 21:435. [PMID: 33059616 PMCID: PMC7559414 DOI: 10.1186/s12882-020-02094-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background PKHD1 is the main genetic cause of autosomal recessive polycystic kidney disease (ARPKD), a hereditary hepato-renal fibrocystic disorder which is the most important cause of end-stage renal disease during early childhood. ARPKD can also present in adulthood with milder phenotypes. In this study, we describe a 24-year-old woman with atypical polycystic kidney, no family history of renal disease and no obvious extra-renal manifestations who was referred for genetic investigation. Methods We used a combination of next generation sequencing, Sanger sequencing and RNA and microscopy studies performed on urine-derived renal epithelial cells (URECs) to provide a genetic diagnosis of ARPKD. Results A next generation sequencing panel of cystic ciliopathy genes allowed the identification of two heterozygous sequence changes in PKHD1 (c.6900C > T; p.(Asn2300=) and c.7964A > C; p.(His2655Pro)). The pathogenicity of the synonymous PKHD1 variant is not clear and requires RNA studies, which cannot be carried out efficiently on RNA extracted from proband blood, due to the low expression levels of PKHD1 in lymphocytes. Using URECs as a source of kidney-specific RNA, we show that PKHD1 is alternatively spliced around exon 43, both in control and proband URECs. The variant p.(Asn2300=) shifts the expression ratio in favour of a shorter, out-of-frame transcript. To further study the phenotypic consequence of these variants, we investigated the ciliary phenotype of patient URECs, which were abnormally elongated and presented multiple blebs along the axoneme. Conclusions We confirm the power of URECs as a tool for functional studies on candidate variants in inherited renal disease, especially when the expression of the gene of interest is restricted to the kidney and we describe, for the first time, ciliary abnormalities in ARPKD patient cells.
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Affiliation(s)
- Elisa Molinari
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Shalabh Srivastava
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - Rebecca M Dewhurst
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK. .,Renal Services, The Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK. .,NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne, UK.
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A Chinese girl with Turner syndrome and Duchenne muscular dystrophy: diagnosis and management of this “dual diagnosis”. Chin Med J (Engl) 2020; 134:743-745. [PMID: 33031137 PMCID: PMC7989979 DOI: 10.1097/cm9.0000000000001159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Genomic testing in 1019 individuals from 349 Pakistani families results in high diagnostic yield and clinical utility. NPJ Genom Med 2020; 5:44. [PMID: 33083013 PMCID: PMC7536406 DOI: 10.1038/s41525-020-00150-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/06/2020] [Indexed: 11/08/2022] Open
Abstract
We implemented a collaborative diagnostic program in Lahore (Pakistan) aiming to establish the genetic diagnosis, and to asses diagnostic yield and clinical impact in patients with suspected genetic diseases. Local physicians ascertained pediatric patients who had no previous access to genetic testing. More than 1586 genetic tests were performed in 1019 individuals (349 index cases, 670 relatives). Most frequently performed tests were exome/genome sequencing (ES/GS, 284/78 index cases) and specific gene panels (55 index cases). In 61.3% of the patients (n = 214) a genetic diagnosis was established based on pathogenic and likely pathogenic variants. Diagnostic yield was higher in consanguineous families (60.1 vs. 39.5%). In 27 patients, genetic diagnosis relied on additional biochemical testing, allowing rapid assessment of the functional effect of the variants. Remarkably, the genetic diagnosis had a direct impact on clinical management. Most relevant consequences were therapy related such as initiation of the appropriated treatment in a timely manner in 51.9% of the patients (n = 111). Finally, we report 12 candidate genes among 66 cases with no genetic diagnosis. Importantly, three of these genes were validated as 'diagnostic' genes given the strong evidence supporting causality derived from our data repository (CAP2-dilated cardiomyopathy, ITFG2-intellectual disability and USP53-liver cholestasis). The high diagnostic yield, clinical impact, and research findings demonstrate the utility of genomic testing, especially when used as first-line genetic test. For patients with suspected genetic diseases from resource-limited regions, ES can be considered as the test of choice to achieve genetic diagnosis.
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Yang XR, Benson MD, MacDonald IM, Innes AM. A diagnostic approach to syndromic retinal dystrophies with intellectual disability. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:538-570. [PMID: 32918368 DOI: 10.1002/ajmg.c.31834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/20/2022]
Abstract
Inherited retinal dystrophies are a group of monogenic disorders that, as a whole, contribute significantly to the burden of ocular disease in both pediatric and adult patients. In their syndromic forms, retinal dystrophies can be observed in association with intellectual disability, frequently alongside other systemic manifestations. There are now over 80 genes implicated in syndromic retinal dystrophies with intellectual disability. Identifying and accurately characterizing these disorders allows the clinician to narrow the differential diagnosis, evaluate for relevant associated features, arrive at a timely and accurate diagnosis, and address both sight-threatening ocular manifestations and morbidity-causing systemic manifestations. The co-occurrence of retinal dystrophy and intellectual disability in an individual can be challenging to investigate, diagnose, and counsel given the considerable phenotypic and genotypic heterogeneity that exists within this broad group of disorders. We performed a review of the current literature and propose an algorithm to facilitate the evaluation, and clinical and mechanistic classification, of these individuals.
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Affiliation(s)
- Xiao-Ru Yang
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Matthew D Benson
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada
| | - Ian M MacDonald
- Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Hartley T, Lemire G, Kernohan KD, Howley HE, Adams DR, Boycott KM. New Diagnostic Approaches for Undiagnosed Rare Genetic Diseases. Annu Rev Genomics Hum Genet 2020; 21:351-372. [DOI: 10.1146/annurev-genom-083118-015345] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Accurate diagnosis is the cornerstone of medicine; it is essential for informed care and promoting patient and family well-being. However, families with a rare genetic disease (RGD) often spend more than five years on a diagnostic odyssey of specialist visits and invasive testing that is lengthy, costly, and often futile, as 50% of patients do not receive a molecular diagnosis. The current diagnostic paradigm is not well designed for RGDs, especially for patients who remain undiagnosed after the initial set of investigations, and thus requires an expansion of approaches in the clinic. Leveraging opportunities to participate in research programs that utilize new technologies to understand RGDs is an important path forward for patients seeking a diagnosis. Given recent advancements in such technologies and international initiatives, the prospect of identifying a molecular diagnosis for all patients with RGDs has never been so attainable, but achieving this goal will require global cooperation at an unprecedented scale.
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Affiliation(s)
- Taila Hartley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - Gabrielle Lemire
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
| | - Kristin D. Kernohan
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Newborn Screening Ontario, CHEO, Ottawa, Ontario K1H 9M8, Canada
| | - Heather E. Howley
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
| | - David R. Adams
- Office of the Clinical Director, National Human Genome Research Institute and Undiagnosed Diseases Program, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kym M. Boycott
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada;, , , ,
- Department of Genetics, CHEO, Ottawa, Ontario K1H 8L1, Canada
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