1
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Bhaskar A, Astrof S. A screen of mutants generated and imaged by the International Mouse Phenotyping Consortium identifies 39 novel genes regulating the development of the secondary palate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.09.579685. [PMID: 38405938 PMCID: PMC10888939 DOI: 10.1101/2024.02.09.579685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The International Mouse Phenotyping Consortium (IMPC) has generated thousands of knockout mouse lines, of which a large proportion is embryonic or early neonatal lethal. The IMPC has generated and imaged embryos from lethal lines and made the three-dimensional image data sets publicly available. In this study, we used this resource to screen homozygous null mutants for defects in the development of the secondary palate. Altogether, we analyzed optical sections from 3216 embryos isolated at embryonic day (E) 15.5 and E18.5 from 478 homozygous mutant lines. Through this analysis, we discovered 39 novel genes important for palatal development. These studies provide new insights into the molecular regulation of palatogenesis and craniofacial disease and offer a useful resource for future exploration.
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2
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Saltarelli MA, Quarta A, Chiarelli F. Growth plate extracellular matrix defects and short stature in children. Ann Pediatr Endocrinol Metab 2022; 27:247-255. [PMID: 36567461 PMCID: PMC9816467 DOI: 10.6065/apem.2244120.060] [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: 05/16/2022] [Accepted: 06/29/2022] [Indexed: 12/27/2022] Open
Abstract
Many etiological factors causing short stature have already been identified in humans. In the last few years, the advent of new techniques for the detection of chromosomal and molecular abnormalities has made it possible to better identify patients with genetic causes of growth failure. Some of these factors directly affect the development and growth of the skeleton, since they damage the epiphyseal growth plate, where linear growth occurs, influencing chondrogenesis. In particular, defects in genes involved in the organization and function of the growth plate are responsible for several well-known conditions with short stature. These genes play a pivotal role in various mechanisms involving the extracellular matrix, intracellular signaling, paracrine signaling, endocrine signaling, and epigenetic regulation. In this review, we will discuss the genes involved in extracellular matrix disorders. The identification of genetic defects in linear growth failure is important for clinicians and researchers in order to improve the care of children affected by growth disorders.
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Affiliation(s)
| | - Alessia Quarta
- Department of Pediatrics, University of Chieti, Chieti, Italy
| | - Francesco Chiarelli
- Department of Pediatrics, University of Chieti, Chieti, Italy,Address for correspondence: Francesco Chiarelli Department of Pediatrics, University of Chieti, Via dei Vestini, 5 Chieti, I-66100, Italy
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3
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Girisha KM, Jacob P, SriLakshmi Bhavani G, Shah H, Mortier GR. Report of three patients, including monozygotic twins and review of clinical and mutation profiles. Eur J Med Genet 2022; 65:104521. [PMID: 35568358 DOI: 10.1016/j.ejmg.2022.104521] [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: 03/05/2021] [Revised: 05/03/2022] [Accepted: 05/08/2022] [Indexed: 11/03/2022]
Abstract
Steel syndrome (MIM# 615155) is an autosomal recessive skeletal disorder, characterized by dislocations of the hips and radial heads, carpal coalition, short stature, facial dysmorphism, and scoliosis. Until date 47 patients have been reported. However, disease causing variants have been identified only in twenty Puerto Rican and nine non-Puerto Rican families. Here we report two monozygotic twins and a boy from two families with novel missense variants, c.295G > A p.(Ala99 Thr), c.3056C > A p.(Pro1019His) and c.2521G > A p.(Gly841Arg) in COL27A1. We describe for the first time, cleft palate and delayed carpal bone ossification as features of Steel syndrome. We reviewed clinical features in all mutation-proven Steel syndrome patients. Short stature and dislocation/subluxation of hip joint are consistently observed. Other features include dislocated radial heads, scoliosis, lordosis, carpal coalition, facial dysmorphism, hearing loss, bilateral fifth finger clinodactyly, knee deformities and developmental delay. Seven missense variants and eight null variants are reported in COL27A1 until date. We also looked into the genotype-phenotype correlation in Puerto Rican and non-Puerto Rican patients.
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Affiliation(s)
- Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Prince Jacob
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Hitesh Shah
- Department of Orthopaedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
| | - Geert R Mortier
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium.
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4
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Kim JS, Jeon H, Lee H, Ko JM, Kim Y, Choi M, Nishimura G, Kim OH, Cho TJ. Biallelic novel mutations of the COL27A1 gene in a patient with Steel syndrome. Hum Genome Var 2021; 8:17. [PMID: 33963180 PMCID: PMC8105406 DOI: 10.1038/s41439-021-00149-7] [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: 03/14/2021] [Revised: 03/18/2021] [Accepted: 04/07/2021] [Indexed: 11/09/2022] Open
Abstract
An 11-year-old Korean boy presented with short stature, hip dysplasia, radial head dislocation, carpal coalition, genu valgum, and fixed patellar dislocation and was clinically diagnosed with Steel syndrome. Scrutinizing the trio whole-exome sequencing data revealed novel compound heterozygous mutations of COL27A1 (c.[4229_4233dup]; [3718_5436del], p.[Gly1412Argfs*157];[Gly1240_Lys1812del]) in the proband, which were inherited from heterozygous parents. The maternal mutation was a large deletion encompassing exons 38–60, which was challenging to detect.
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Affiliation(s)
- Jong Seop Kim
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyeran Lee
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yonghwan Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Gen Nishimura
- Center for Intractable Disease, Saitama Medical University Hospital, Saitama, Japan
| | - Ok-Hwa Kim
- Department of Pediatric Radiology, VIC365 Children's Hospital, Incheon, Republic of Korea
| | - Tae-Joon Cho
- Division of Pediatric Orthopaedics, Seoul National University Children's Hospital and Seoul National University College of Medicine, Seoul, Republic of Korea.
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5
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First reported case of Steel syndrome in the European population: A novel homozygous mutation in COL27A1 and review of the literature. Eur J Med Genet 2020; 63:103939. [DOI: 10.1016/j.ejmg.2020.103939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/19/2020] [Accepted: 04/23/2020] [Indexed: 01/01/2023]
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6
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Gonzaga-Jauregui C, Yesil G, Nistala H, Gezdirici A, Bayram Y, Nannuru KC, Pehlivan D, Yuan B, Jimenez J, Sahin Y, Paine IS, Akdemir ZC, Rajamani S, Staples J, Dronzek J, Howell K, Fatih JM, Smaldone S, Schlesinger AE, Ramírez N, Cornier AS, Kelly MA, Haber R, Chim SM, Nieman K, Wu N, Walls J, Poueymirou W, Siao CJ, Sutton VR, Williams MS, Posey JE, Gibbs RA, Carlo S, Tegay DH, Economides AN, Lupski JR. Functional biology of the Steel syndrome founder allele and evidence for clan genomics derivation of COL27A1 pathogenic alleles worldwide. Eur J Hum Genet 2020; 28:1243-1264. [PMID: 32376988 PMCID: PMC7608441 DOI: 10.1038/s41431-020-0632-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 01/20/2023] Open
Abstract
Previously we reported the identification of a homozygous COL27A1 (c.2089G>C; p.Gly697Arg) missense variant and proposed it as a founder allele in Puerto Rico segregating with Steel syndrome (STLS, MIM #615155); a rare osteochondrodysplasia characterized by short stature, congenital bilateral hip dysplasia, carpal coalitions, and scoliosis. We now report segregation of this variant in five probands from the initial clinical report defining the syndrome and an additional family of Puerto Rican descent with multiple affected adult individuals. We modeled the orthologous variant in murine Col27a1 and found it recapitulates some of the major Steel syndrome associated skeletal features including reduced body length, scoliosis, and a more rounded skull shape. Characterization of the in vivo murine model shows abnormal collagen deposition in the extracellular matrix and disorganization of the proliferative zone of the growth plate. We report additional COL27A1 pathogenic variant alleles identified in unrelated consanguineous Turkish kindreds suggesting Clan Genomics and identity-by-descent homozygosity contributing to disease in this population. The hypothesis that carrier states for this autosomal recessive osteochondrodysplasia may contribute to common complex traits is further explored in a large clinical population cohort. Our findings augment our understanding of COL27A1 biology and its role in skeletal development; and expand the functional allelic architecture in this gene underlying both rare and common disease phenotypes.
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Affiliation(s)
| | - Gozde Yesil
- Istanbul Faculty of Medicine Department of Medical Genetics, Istanbul University, 34093, Istanbul, Turkey
| | - Harikiran Nistala
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303, Istanbul, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | | | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Division of Pediatric Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, 06570, Ankara, Turkey
| | - Ingrid S Paine
- 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
| | | | - Jeffrey Staples
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - John Dronzek
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristen Howell
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alan E Schlesinger
- Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Radiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Alberto S Cornier
- Genetics Section, San Jorge Children's Hospital, San Juan, PR, 00912, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA.,Department of Pediatrics, Universidad Central del Caribe School of Medicine, Bayamon, PR, 00960, USA
| | | | - Robert Haber
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Shek Man Chim
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Kristy Nieman
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - Nan Wu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Orthopedic Surgery, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, and Medical Research Center of Orthopedics, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, 100730, Beijing, China
| | | | | | | | - Chia-Jen Siao
- Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Jennifer E Posey
- 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
| | - Simon Carlo
- Mayagüez Medical Center, Mayagüez, PR, 00681, USA.,Ponce Health Sciences University, Ponce, PR, 00716, USA
| | - David H Tegay
- Department of Pediatrics, Division of Medical Genetics, Cohen Children's Medical Center of Northwell Health, New Hyde Park, NY, 11040, USA
| | - Aris N Economides
- Regeneron Genetics Center, Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA.,Regeneron Pharmaceuticals Inc., Tarrytown, NY, 10591, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA. .,Texas Children's Hospital, Houston, TX, 77030, USA.
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7
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Rice SJ, Beier F, Young DA, Loughlin J. Interplay between genetics and epigenetics in osteoarthritis. Nat Rev Rheumatol 2020; 16:268-281. [PMID: 32273577 DOI: 10.1038/s41584-020-0407-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Research into the molecular genetics of osteoarthritis (OA) has been substantially bolstered in the past few years by the implementation of powerful genome-wide scans that have revealed a large number of novel risk loci associated with the disease. This refreshing wave of discovery has occurred concurrently with epigenetic studies of joint tissues that have examined DNA methylation, histone modifications and regulatory RNAs. These epigenetic analyses have involved investigations of joint development, homeostasis and disease and have used both human samples and animal models. What has become apparent from a comparison of these two complementary approaches is that many OA genetic risk signals interact with, map to or correlate with epigenetic mediators. This discovery implies that epigenetic mechanisms, and their effect on gene expression, are a major conduit through which OA genetic risk polymorphisms exert their functional effects. This observation is particularly exciting as it provides mechanistic insight into OA susceptibility. Furthermore, this knowledge reveals avenues for attenuating the negative effect of risk-conferring alleles by exposing the epigenome as an exploitable target for therapeutic intervention in OA.
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Affiliation(s)
- Sarah J Rice
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Frank Beier
- Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada.,Western Bone and Joint Institute, The University of Western Ontario, London, ON, Canada
| | - David A Young
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John Loughlin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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8
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Pölsler L, Schatz UA, Simma B, Zschocke J, Rudnik-Schöneborn S. A Syrian patient with Steel syndrome due to compound heterozygous COL27A1 mutations with colobomata of the eye. Am J Med Genet A 2020; 182:730-734. [PMID: 31913554 PMCID: PMC7079147 DOI: 10.1002/ajmg.a.61478] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/04/2019] [Accepted: 12/22/2019] [Indexed: 01/14/2023]
Abstract
The joint occurrence of short stature, congenital dislocation of the hip, carpal coalition, dislocation of the radial head, cavus deformity, scoliosis, and vertebral anomalies was first described in 1993 by Steel et al. (OMIM #615155) in 23 children from Puerto Rico. The condition is caused by a deficient matrix protein, collagen type XXVII alpha 1 chain, due to bi‐allelic loss of function mutations in the gene COL27A1. Outside of Puerto Rico, only four families have been described, in three of which the patients also had hearing loss. However, structural eye defects have not yet been reported in conjunction with this rare autosomal recessive syndrome. Here, we describe a 9‐year‐old girl born to nonconsanguineous Syrian parents with the characteristic features of Steel syndrome, including short stature, massive malalignment of large joints, kyphoscoliosis, hearing loss, and typical facial dysmorphism. However, she was also born with bilateral colobomata of the irides and choroido‐retinae with unilateral affection of the macula. Whole exome sequencing identified two pathogenic compound heterozygous variants in COL27A1: c.93del, p.(Phe32Leufs*71) and c.3075del, p.(Lys1026Argfs*33). There was no discernible alternative cause for the colobomata. Our findings might indicate an association of this exceptionally rare disorder caused by COL27A1 mutations with developmental defects of the eye from the anophthalmia/microphthalmia/coloboma spectrum.
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Affiliation(s)
- Laura Pölsler
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Ulrich A Schatz
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria.,Institute of Human Genetics, Klinikum rechts der Isar, Technische Universität Munich, Munich, Germany
| | - Burkhard Simma
- Department of Pediatrics and Adolescent Medicine, Academic Teaching Hospital LKH Feldkirch, Feldkich, Austria
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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9
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Amlie-Wolf L, Moyer-Harasink S, Carr AM, Giampietro P, Schneider A, Simon M. Three new patients with Steel syndrome and a Puerto Rican specific COL27A1 mutation. Am J Med Genet A 2020; 182:798-803. [PMID: 31903681 DOI: 10.1002/ajmg.a.61465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 11/09/2022]
Abstract
Steel syndrome was initially described by H. H. Steel in 1993 in Puerto Rico, at which time he described the clinical findings required for diagnosis. The responsible gene, COL27A1, was identified in 2015 (Gonzaga-Jauregui et al., European Journal of Human Genetics, 2015;23:342-346). Eleven patients have previously been described with Steel syndrome and homozygous COL27A1 mutations, with eight having an apparent founder mutation, p.Gly697Arg. We describe three more patients identified at Einstein Medical Center Philadelphia and St. Christopher's Hospital for Children (Philadelphia, PA) diagnosed with Steel syndrome. All three are of Puerto Rican ancestry with the previously described founder mutation and had either hip dislocations or hip dysplasia. Radial head dislocation was only identified in one patient while short stature and scoliosis were noted in two of these patients. There are now 51 patients in the literature with Steel syndrome, including the 3 patients in this article, and 14 patients with a genetically confirmed Steel syndrome diagnosis.
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Affiliation(s)
| | | | - Ann-Marie Carr
- Center for Children with Special Health Care Needs, St. Christopher's Hospital for Children, Philadelphia, Pennsylvania
| | - Philip Giampietro
- Division of Genetics, Rutgers-Robert Wood Johnson Hospital, New Brunswick, New Jersey
| | - Adele Schneider
- Einstein Medical Center Philadelphia Genetics, Philadelphia, Pennsylvania
| | - Mitchell Simon
- Division of General Diagnostic Radiology and the Section of Pediatric Radiology, Rutgers-Robert Wood Johnson Hospital, New Brunswick, New Jersey
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Uttarilli A, Shah H, Shukla A, Girisha KM. A review of skeletal dysplasia research in India. J Postgrad Med 2019; 64:98-103. [PMID: 29692401 PMCID: PMC5954821 DOI: 10.4103/jpgm.jpgm_527_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
We aimed to review the contributions by Indian researchers to the subspecialty of skeletal dysplasias (SDs). Literature search using specific keywords in PubMed was performed to retrieve all the published literature on SDs as on July 6, 2017. All published literature on SDs wherein at least one author was from an Indian institute was included. Publications were grouped into different categories based on the major emphasis of the research paper. Five hundred and forty publications in English language were retrieved and categorized into five different groups. The publications were categorized as reports based on: (i) phenotypes (n = 437), (ii) mutations (n = 51), (iii) novel genes (n = 9), (iv) therapeutic interventions (n = 31), and (v) reviews (n = 12). Most of the publications were single-patient case reports describing the clinical and radiological features of the patients affected with SDs (n = 352). We enlisted all the significant Indian contributions. We have also highlighted the reports in which Indians have contributed to discovery of new genes and phenotypes. This review highlights the substantial Indian contributions to SD research, which is poised to reach even greater heights given the size and structure of our population, technological advances, and expanding national and international collaborations.
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Affiliation(s)
- A Uttarilli
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - H Shah
- Department of Orthopedics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - A Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
| | - K M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, Karnataka, India
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11
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Yue S, Whalen P, Jee YH. Genetic regulation of linear growth. Ann Pediatr Endocrinol Metab 2019; 24:2-14. [PMID: 30943674 PMCID: PMC6449614 DOI: 10.6065/apem.2019.24.1.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
Linear growth occurs at the growth plate. Therefore, genetic defects that interfere with the normal function of the growth plate can cause linear growth disorders. Many genetic causes of growth disorders have already been identified in humans. However, recent genome-wide approaches have broadened our knowledge of the mechanisms of linear growth, not only providing novel monogenic causes of growth disorders but also revealing single nucleotide polymorphisms in genes that affect height in the general population. The genes identified as causative of linear growth disorders are heterogeneous, playing a role in various growth-regulating mechanisms including those involving the extracellular matrix, intracellular signaling, paracrine signaling, endocrine signaling, and epigenetic regulation. Understanding the underlying genetic defects in linear growth is important for clinicians and researchers in order to provide proper diagnoses, management, and genetic counseling, as well as to develop better treatment approaches for children with growth disorders.
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Affiliation(s)
- Shanna Yue
- Pediatric Endocrine, Metabolism and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Philip Whalen
- Pediatric Endocrine, Metabolism and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Youn Hee Jee
- Pediatric Endocrine, Metabolism and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA,Address for correspondence: Youn Hee Jee, MD Pediatric Endocrine, Metabolism and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive MSC 1103, Bethesda, MD 20892-1103, USA Tel: +1-301-435-5834 Fax: +1-301-402-0574 E-mail:
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12
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Uttarilli A, Shah H, Bhavani GS, Upadhyai P, Shukla A, Girisha KM. Phenotyping and genotyping of skeletal dysplasias: Evolution of a center and a decade of experience in India. Bone 2019; 120:204-211. [PMID: 30408610 DOI: 10.1016/j.bone.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/16/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022]
Abstract
Genetic heterogeneity, high burden and the paucity of genetic testing for rare diseases challenge genomic healthcare for these disorders in India. Here we report our experience over the past decade, of establishing the genomic evaluation of skeletal dysplasia at a tertiary university hospital in India. Research or clinical genomic testing was carried out by Sanger sequencing and next-generation sequencing. Close national and international collaborations aided phenotyping and genotyping. We report 508 families (557 affected individuals) with the definitive molecular diagnosis of skeletal dysplasia. Dysostoses multiplex (n = 196), genetic inflammatory/rheumatoid-like osteoarthropathies (n = 114) and osteogenesis imperfecta and decreased bone density (n = 58) were the most common diagnoses. We enumerate the processes, clinical diagnoses and causal variants in the cohort with 48 novel variants in 21 genes. We summarize scientific contributions of the center to the description of clinical and mutation profiles and discovery of new phenotypes and genetic etiology. Our study illustrates the establishment and application of genomic testing tools for genetic disorders of skeleton in a large cohort. We believe this could be a model to emulate for other developing genetic centers.
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Affiliation(s)
- Anusha Uttarilli
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Hitesh Shah
- Pediatric Orthopedics Services, Department of Orthopedics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Priyanka Upadhyai
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India.
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13
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Thuresson AC, Soussi Zander C, Zhao JJ, Halvardson J, Maqbool K, Månsson E, Stenninger E, Holmlund U, Öhrner Y, Feuk L. Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability. Clin Genet 2018; 95:436-439. [PMID: 30525197 PMCID: PMC6392105 DOI: 10.1111/cge.13470] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/26/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Ann-Charlotte Thuresson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cecilia Soussi Zander
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jin J Zhao
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Khurram Maqbool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Else Månsson
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Eric Stenninger
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Ulrika Holmlund
- Department of Pediatrics, Västerås Hospital, Västerås, Sweden
| | - Ylva Öhrner
- Department of Pediatrics, Västerås Hospital, Västerås, Sweden
| | - Lars Feuk
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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14
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Belbin GM, Odgis J, Sorokin EP, Yee MC, Kohli S, Glicksberg BS, Gignoux CR, Wojcik GL, Van Vleck T, Jeff JM, Linderman M, Schurmann C, Ruderfer D, Cai X, Merkelson A, Justice AE, Young KL, Graff M, North KE, Peters U, James R, Hindorff L, Kornreich R, Edelmann L, Gottesman O, Stahl EE, Cho JH, Loos RJ, Bottinger EP, Nadkarni GN, Abul-Husn NS, Kenny EE. Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system. eLife 2017; 6:25060. [PMID: 28895531 PMCID: PMC5595434 DOI: 10.7554/elife.25060] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 08/09/2017] [Indexed: 11/16/2022] Open
Abstract
Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature. We link the gene, COL27A1, with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease. Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations. Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor. This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor. Belbin et al. used this computational technique to identify a mutation that may cause unusually short stature or bone and joint problems in up to 2% of people of Puerto Rican descent. In the experiments, the genomes of about 32,000 New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature. The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and joint problems. People who inherited one copy had an increased likelihood of joint or bone problems. This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth. The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had previously been linked to a disorder called Steel syndrome that was thought to be rare. Belbin et al. showed this condition is actually fairly common in people whose ancestors recently came from Puerto Rico, but may often go undiagnosed by their physicians. The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation.
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Affiliation(s)
- Gillian Morven Belbin
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Jacqueline Odgis
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Elena P Sorokin
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Sumita Kohli
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Benjamin S Glicksberg
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Harris Center for Precision Wellness, Icahn School of Medicine at Mt Sinai, New York, United States
| | - Christopher R Gignoux
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, United States
| | - Tielman Van Vleck
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Janina M Jeff
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Michael Linderman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Douglas Ruderfer
- Broad Institute, Cambridge, United States.,Division of Psychiatric Genomics, Icahn School of Medicine at Mt Sinai, New York, United States.,Center for Statistical Genetics, Icahn School of Medicine at Mt Sinai, New York, United States
| | - Xiaoqiang Cai
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Amanda Merkelson
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Anne E Justice
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Kristin L Young
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Misa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Department of Epidemiology, University of Washington School of Public Health, Seattle, United States
| | - Regina James
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, United States
| | - Lucia Hindorff
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - Ruth Kornreich
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Lisa Edelmann
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Omri Gottesman
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Eli Ea Stahl
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Harris Center for Precision Wellness, Icahn School of Medicine at Mt Sinai, New York, United States.,Broad Institute, Cambridge, United States
| | - Judy H Cho
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Ruth Jf Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Girish N Nadkarni
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Noura S Abul-Husn
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Eimear E Kenny
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, United States.,The Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States.,Center for Statistical Genetics, Icahn School of Medicine at Mt Sinai, New York, United States
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