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MacCarrick G, Aradhya S, Bailey M, Chu D, Hunt A, Izzo E, Krakow D, Mackenzie W, Poll S, Raggio C, Shediac R, White KK, McLaughlin HM, Seratti G. Clinical utility of comprehensive gene panel testing for common and rare causes of skeletal dysplasia and other skeletal disorders: Results from the largest cohort to date. Am J Med Genet A 2024; 194:e63646. [PMID: 38702915 DOI: 10.1002/ajmg.a.63646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
Molecular genetics enables more precise diagnoses of skeletal dysplasia and other skeletal disorders (SDs). We investigated the clinical utility of multigene panel testing for 5011 unrelated individuals with SD in the United States (December 2019-April 2022). Median (range) age was 8 (0-90) years, 70.5% had short stature and/or disproportionate growth, 27.4% had a positive molecular diagnosis (MDx), and 30 individuals received two MDx. Genes most commonly contributing to MDx were FGFR3 (16.9%), ALPL (13.0%), and COL1A1 (10.3%). Most of the 112 genes associated with ≥1 MDx were primarily involved in signal transduction (n = 35), metabolism (n = 23), or extracellular matrix organization (n = 17). There were implications associated with specific care/treatment options for 84.4% (1158/1372) of MDx-positive individuals; >50% were linked to conditions with targeted therapy approved or in clinical development, including osteogenesis imperfecta, achondroplasia, hypophosphatasia, and mucopolysaccharidosis. Forty individuals with initially inconclusive results became MDx-positive following family testing. Follow-up mucopolysaccharidosis enzyme activity testing was positive in 14 individuals (10 of these were not MDx-positive). Our findings showed that inclusion of metabolic genes associated with SD increased the clinical utility of a gene panel and confirmed that integrated use of comprehensive gene panel testing with orthogonal testing reduced the burden of inconclusive results.
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Affiliation(s)
- Gretchen MacCarrick
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Mitch Bailey
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Dorna Chu
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Abigail Hunt
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Emanuela Izzo
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Deborah Krakow
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - William Mackenzie
- Department of Orthopaedic Surgery, Nemours Children's Hospital, Wilmington, Delaware, USA
| | - Sarah Poll
- Invitae Corporation, San Francisco, California, USA
| | - Cathleen Raggio
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, New York, USA
| | - Renée Shediac
- BioMarin Pharmaceutical Inc, Novato, California, USA
| | - Klane K White
- Department of Pediatric Orthopedic Surgery, Children's Hospital Colorado, Aurora, Colorado, USA
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Busse E, Lee B, Nagamani SCS. Genetic Evaluation for Monogenic Disorders of Low Bone Mass and Increased Bone Fragility: What Clinicians Need to Know. Curr Osteoporos Rep 2024; 22:308-317. [PMID: 38600318 DOI: 10.1007/s11914-024-00870-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
PURPOSE OF REVIEW The purpose of this review is to outline the principles of clinical genetic testing and to provide practical guidance to clinicians in navigating genetic testing for patients with suspected monogenic forms of osteoporosis. RECENT FINDINGS Heritability assessments and genome-wide association studies have clearly shown the significant contributions of genetic variations to the pathogenesis of osteoporosis. Currently, over 50 monogenic disorders that present primarily with low bone mass and increased risk of fractures have been described. The widespread availability of clinical genetic testing offers a valuable opportunity to correctly diagnose individuals with monogenic forms of osteoporosis, thus instituting appropriate surveillance and treatment. Clinical genetic testing may identify the appropriate diagnosis in a subset of patients with low bone mass, multiple or unusual fractures, and severe or early-onset osteoporosis, and thus clinicians should be aware of how to incorporate such testing into their clinical practices.
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Affiliation(s)
- Emily Busse
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Houston, TX, USA.
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
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Strong A, Behr M, Lott C, Clark AJ, Mentch F, Da Silva RP, Rux DR, Campbell R, Skraban C, Wang X, Anari JB, Sinder B, Cahill PJ, Sleiman P, Hakonarson H. Molecular diagnosis and novel genes and phenotypes in a pediatric thoracic insufficiency cohort. Sci Rep 2023; 13:991. [PMID: 36653407 PMCID: PMC9849333 DOI: 10.1038/s41598-023-27641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023] Open
Abstract
Thoracic insufficiency syndromes are a genetically and phenotypically heterogeneous group of disorders characterized by congenital abnormalities or progressive deformation of the chest wall and/or vertebrae that result in restrictive lung disease and compromised respiratory capacity. We performed whole exome sequencing on a cohort of 42 children with thoracic insufficiency to elucidate the underlying molecular etiologies of syndromic and non-syndromic thoracic insufficiency and predict extra-skeletal manifestations and disease progression. Molecular diagnosis was established in 24/42 probands (57%), with 18/24 (75%) probands having definitive diagnoses as defined by laboratory and clinical criteria and 6/24 (25%) probands having strong candidate genes. Gene identified in cohort patients most commonly encoded components of the primary cilium, connective tissue, and extracellular matrix. A novel association between KIF7 and USP9X variants and thoracic insufficiency was identified. We report and expand the genetic and phenotypic spectrum of a cohort of children with thoracic insufficiency, reinforce the prevalence of extra-skeletal manifestations in thoracic insufficiency syndromes, and expand the phenotype of KIF7 and USP9X-related disease to include thoracic insufficiency.
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Affiliation(s)
- Alanna Strong
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Meckenzie Behr
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Carina Lott
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Abigail J Clark
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frank Mentch
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Renata Pellegrino Da Silva
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Danielle R Rux
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert Campbell
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Cara Skraban
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Xiang Wang
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jason B Anari
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Benjamin Sinder
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patrick J Cahill
- Division of Orthopedics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Patrick Sleiman
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
- Endowed Chair in Genomic Research, Division of Pulmonary Medicine, The Joseph Stokes, Jr. Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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Lv S, Zhao J, Liu L, Wang C, Yue H, Zhang H, Li S, Zhang Z. Exploring and expanding the phenotype and genotype diversity in seven Chinese families with spondylo-epi-metaphyseal dysplasia. Front Genet 2022; 13:960504. [PMID: 36118854 PMCID: PMC9473317 DOI: 10.3389/fgene.2022.960504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Spondylo-epi-metaphyseal dysplasia (SEMD) is a heterogeneous group of disorders with different modes of inheritance and is characterized by disproportionate or proportionate short stature. To date, more than 30 disease-causing genes have been identified, and different types of SEMD exhibit greatly overlapping clinical features, which usually complicate the diagnosis. This study was performed to expand the clinical and molecular spectrum of SEMD among Chinese subjects and to explore their potential phenotype–genotype relations. We enrolled seven families including 11 affected patients with SEMD, and their clinical, radiographic, and genetic data were carefully analyzed. All the seven probands showed different degrees of short stature, and each of them exhibited additional specific skeletal manifestations; four probands had extraosseous manifestations. X-rays of the seven probands showed common features of SEMD, including vertebral deformities, irregular shape of the epiphysis, and disorganization of the metaphysis. Seven variants were identified in TRPV4 (c.694C> T, p.Arg232Cys), COL2A1 (c.654 + 1G > C; c.3266_3268del, p.Gly1089del), CCN6 (c.396 T> G, p.Cys132Trp; c.721 T>C, p.Cys241Arg), SBDS (c.258 + 2T> C), and ACAN (c.1508C> A, p.Thr503Lys) genes, and two of them were novel. Two families with TRPV4 variants showed considerable intrafamily and interfamily heterogeneities. In addition, we reported one case of SEMD with a severe phenotype caused by ACAN gene mutation. Our study expands the phenotype and genetic spectrum of SEMD and provides evidence for the phenotype–genotype relations, aiding future molecular and clinical diagnosis as well as procreative management of SEMD.
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Affiliation(s)
| | | | | | | | | | | | - Shanshan Li
- *Correspondence: Shanshan Li, ; Zhenlin Zhang,
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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Ma Y, Peng H, Hsiang F, Fang H, Du D, Jiang C, Wang Y, Chen C, Zhang C, Gao Y. Case Report: Diagnosis of Mucopolysaccharidosis Type IVA With Compound Heterozygous Galactosamine-6 Sulfatase Variants and Biopsy of Replaced Femoral Heads. Front Pediatr 2022; 10:914889. [PMID: 35859948 PMCID: PMC9289150 DOI: 10.3389/fped.2022.914889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION Mucopolysaccharidosis Type IVA (MPS IVA) or Morquio A Syndrome, is a rare metabolic disorder caused by compromised galactosamine-6 sulfatase (GALNS) encoded by GALNS gene (NM_000512.5), leading to keratin sulfate (KS), and chondroitin-6-sulfate accumulation in various organs. We present a 17-year-old woman with progressive bilateral hip pain and radiographic evidence of spondyloepiphyseal dysplasia. METHODS Diagnosis of MPS IVA was made based on whole-exome sequencing (WES) of blood samples collected from the patient and family members, high urinary glycosaminoglycan excretion, supportive clinical manifestations, radiographic examinations, including whole-body X-rays, cervical MRI, and pelvic CT. The patient underwent bilateral total hip arthroplasties sequentially, at a 1-month interval. Femoral heads were preserved for the micro-CT (μCT) analysis and the osteochondral histology examination. RESULTS The patient presented with multiple skeletal deformities, including vertebras and long bone deformities. WES disclosed compound heterozygous variants at exon 11 (c.1156C>T) and exon 12 (c.1288C>G) of the GALNS (NM_000512.5). The μCT analysis revealed significant bone quantity loss and microarchitectural change in both weight-bearing area (WBA) and non-weight-bearing area (NWBA) of the femoral heads, while histological analysis showed structural abnormity of articular cartilage in the WBA of the femoral heads. CONCLUSION We have found compound heterozygous variants of GALNS. This is also the first study to report the microarchitectural and histological changes of both subchondral bone and articular cartilage of the femoral head in a patient with MPS IVA.
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Affiliation(s)
- Yiyang Ma
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Hao Peng
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Fuchou Hsiang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Haoyu Fang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Dajiang Du
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Chenyi Jiang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Yehui Wang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Chun Chen
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Changqing Zhang
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
| | - Yun Gao
- Department of Orthopedic Surgery, Shanghai Sixth People's Hospital, Shanghai, China
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