101
|
Trans-ancestry mutational landscape of hepatocellular carcinoma genomes. Nat Genet 2014; 46:1267-73. [PMID: 25362482 DOI: 10.1038/ng.3126] [Citation(s) in RCA: 574] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 10/03/2014] [Indexed: 11/08/2022]
Abstract
Diverse epidemiological factors are associated with hepatocellular carcinoma (HCC) prevalence in different populations. However, the global landscape of the genetic changes in HCC genomes underpinning different epidemiological and ancestral backgrounds still remains uncharted. Here a collection of data from 503 liver cancer genomes from different populations uncovered 30 candidate driver genes and 11 core pathway modules. Furthermore, a collaboration of two large-scale cancer genome projects comparatively analyzed the trans-ancestry substitution signatures in 608 liver cancer cases and identified unique mutational signatures that predominantly contribute to Asian cases. This work elucidates previously unexplored ancestry-associated mutational processes in HCC development. A combination of hotspot TERT promoter mutation, TERT focal amplification and viral genome integration occurs in more than 68% of cases, implicating TERT as a central and ancestry-independent node of hepatocarcinogenesis. Newly identified alterations in genes encoding metabolic enzymes, chromatin remodelers and a high proportion of mTOR pathway activations offer potential therapeutic and diagnostic opportunities.
Collapse
|
102
|
Wit JM, Mullis PE. Genetics of growth. Horm Res Paediatr 2014; 80:379-80. [PMID: 24356245 DOI: 10.1159/000355402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Jan M Wit
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | | |
Collapse
|
103
|
Couthouis J, Raphael AR, Daneshjou R, Gitler AD. Targeted exon capture and sequencing in sporadic amyotrophic lateral sclerosis. PLoS Genet 2014; 10:e1004704. [PMID: 25299611 PMCID: PMC4191946 DOI: 10.1371/journal.pgen.1004704] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/25/2014] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive degeneration of motor neurons, ultimately leading to paralysis and death. Approximately 10% of ALS cases are familial, with the remaining 90% of cases being sporadic. Genetic studies in familial cases of ALS have been extremely informative in determining the causative mutations behind ALS, especially as the same mutations identified in familial ALS can also cause sporadic disease. However, the cause of ALS in approximately 30% of familial cases and in the majority of sporadic cases remains unknown. Sporadic ALS cases represent an underutilized resource for genetic information about ALS; therefore, we undertook a targeted sequencing approach of 169 known and candidate ALS disease genes in 242 sporadic ALS cases and 129 matched controls to try to identify novel variants linked to ALS. We found a significant enrichment in novel and rare variants in cases versus controls, indicating that we are likely identifying disease associated mutations. This study highlights the utility of next generation sequencing techniques combined with functional studies and rare variant analysis tools to provide insight into the genetic etiology of a heterogeneous sporadic disease. Amyotrophic lateral sclerosis (ALS), also known as Charcot disease or Lou Gehrig's disease, is one of the most common neuromuscular diseases worldwide. This disease is characterized by a progressive degeneration of motor neurons, leading to patient death within a few years after onset. Despite the fact that most ALS cases are sporadic, most of the ALS genetic studies have focused on familial forms, leading to the genetic determination of cause for 70% of cases of familial ALS but for only 10% of sporadic ALS cases. This, coupled with the dearth of families available for study, suggests that researchers should begin tapping into the relatively untouched reservoir of available sporadic samples to identify novel genetic causes of sporadic ALS. Here we take advantage of high-throughput target sequencing techniques to test four different hypotheses about the genetic causes of ALS in sporadic ALS and uncover new candidate genes and pathways implicated in ALS.
Collapse
Affiliation(s)
- Julien Couthouis
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Alya R. Raphael
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Roxana Daneshjou
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Aaron D. Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| |
Collapse
|
104
|
Bao R, Huang L, Andrade J, Tan W, Kibbe WA, Jiang H, Feng G. Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing. Cancer Inform 2014; 13:67-82. [PMID: 25288881 PMCID: PMC4179624 DOI: 10.4137/cin.s13779] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 12/21/2022] Open
Abstract
The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.
Collapse
Affiliation(s)
- Riyue Bao
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Lei Huang
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Jorge Andrade
- Center for Research Informatics, The University of Chicago, Chicago, IL, USA
| | - Wei Tan
- IBM Thomas J. Watson Research Center, Yorktown Heights, New York, USA
| | - Warren A Kibbe
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
| | - Hongmei Jiang
- Department of Statistics, Northwestern University, Evanston, IL, USA
| | - Gang Feng
- Biomedical Informatics Center (NUBIC), Clinical and Translational Sciences Institute (NUCATS), Northwestern University, Chicago, IL, USA
| |
Collapse
|
105
|
Abstract
Epigenetic control of gene expression programs is essential for normal organismal development and cellular function. Abrogation of epigenetic regulation is seen in many human diseases, including cancer and neuropsychiatric disorders, where it can affect disease etiology and progression. Abnormal epigenetic profiles can serve as biomarkers of disease states and predictors of disease outcomes. Therefore, epigenetics is a key area of clinical investigation in diagnosis, prognosis, and treatment. In this review, we give an overarching view of epigenetic mechanisms of human disease. Genetic mutations in genes that encode chromatin regulators can cause monogenic disease or are incriminated in polygenic, multifactorial diseases. Environmental stresses can also impact directly on chromatin regulation, and these changes can increase the risk of, or directly cause, disease. Finally, emerging evidence suggests that exposure to environmental stresses in older generations may predispose subsequent generations to disease in a manner that involves the transgenerational inheritance of epigenetic information.
Collapse
Affiliation(s)
- Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | | |
Collapse
|
106
|
Dong S, Han J, Chen H, Liu T, Huen M, Yang Y, Guo C, Huang J. The Human SRCAP Chromatin Remodeling Complex Promotes DNA-End Resection. Curr Biol 2014; 24:2097-2110. [DOI: 10.1016/j.cub.2014.07.081] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/15/2014] [Accepted: 07/31/2014] [Indexed: 11/30/2022]
|
107
|
FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet 2014; 94:809-17. [PMID: 24906018 DOI: 10.1016/j.ajhg.2014.05.003] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Indexed: 01/08/2023] Open
Abstract
Inherited monogenic disease has an enormous impact on the well-being of children and their families. Over half of the children living with one of these conditions are without a molecular diagnosis because of the rarity of the disease, the marked clinical heterogeneity, and the reality that there are thousands of rare diseases for which causative mutations have yet to be identified. It is in this context that in 2010 a Canadian consortium was formed to rapidly identify mutations causing a wide spectrum of pediatric-onset rare diseases by using whole-exome sequencing. The FORGE (Finding of Rare Disease Genes) Canada Consortium brought together clinicians and scientists from 21 genetics centers and three science and technology innovation centers from across Canada. From nation-wide requests for proposals, 264 disorders were selected for study from the 371 submitted; disease-causing variants (including in 67 genes not previously associated with human disease; 41 of these have been genetically or functionally validated, and 26 are currently under study) were identified for 146 disorders over a 2-year period. Here, we present our experience with four strategies employed for gene discovery and discuss FORGE's impact in a number of realms, from clinical diagnostics to the broadening of the phenotypic spectrum of many diseases to the biological insight gained into both disease states and normal human development. Lastly, on the basis of this experience, we discuss the way forward for rare-disease genetic discovery both in Canada and internationally.
Collapse
|
108
|
Longoni M, Marangi G, Zollino M. Utility and Challenges of Next Generation Sequencing in Pediatric Disorders. CURRENT PEDIATRICS REPORTS 2014. [DOI: 10.1007/s40124-014-0039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
109
|
Kleefstra T, Schenck A, Kramer JM, van Bokhoven H. The genetics of cognitive epigenetics. Neuropharmacology 2014; 80:83-94. [PMID: 24434855 DOI: 10.1016/j.neuropharm.2013.12.025] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 12/29/2013] [Accepted: 12/30/2013] [Indexed: 01/31/2023]
Abstract
Cognitive disorders (CDs) are a heterogeneous group of disorders for which the genetic foundations are rapidly being uncovered. The large number of CD-associated gene mutations presents an opportunity to identify common mechanisms of disease as well as molecular processes that are of key importance to human cognition. Given the disproportionately high number of epigenetic genes associated with CD, epigenetic regulation of gene transcription is emerging as a process of major importance in cognition. The cognate protein products of these genes often co-operate in shared protein complexes or pathways, which is reflected in similarities between the neurodevelopmental phenotypes corresponding to these mutant genes. Here we provide an overview of the genes associated with CDs, and highlight some of the epigenetic regulatory complexes involving multiple CD genes. Such common gene networks may provide a handle for designing therapeutic interventions applicable to a number of cognitive disorders with variable genetic etiology.
Collapse
Affiliation(s)
- Tjitske Kleefstra
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Annette Schenck
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Jamie M Kramer
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Radboud University Medical Center, Department of Human Genetics, Nijmegen Center for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands; Radboud University Medical Center, Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| |
Collapse
|
110
|
Exome sequencing greatly expedites the progressive research of Mendelian diseases. Front Med 2014; 8:42-57. [PMID: 24384736 DOI: 10.1007/s11684-014-0303-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/30/2013] [Indexed: 12/23/2022]
Abstract
The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.
Collapse
|
111
|
Guo MH, Shen Y, Walvoord EC, Miller TC, Moon JE, Hirschhorn JN, Dauber A. Whole exome sequencing to identify genetic causes of short stature. Horm Res Paediatr 2014; 82:44-52. [PMID: 24970356 PMCID: PMC4130218 DOI: 10.1159/000360857] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 02/24/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND/AIMS Short stature is a common reason for presentation to pediatric endocrinology clinics. However, for most patients, no cause for the short stature can be identified. As genetics plays a strong role in height, we sought to identify known and novel genetic causes of short stature. METHODS We recruited 14 children with severe short stature of unknown etiology. We conducted whole exome sequencing of the patients and their family members. We used an analysis pipeline to identify rare non-synonymous genetic variants that cause the short stature. RESULTS We identified a genetic cause of short stature in 5 of the 14 patients. This included cases of floating-harbor syndrome, Kenny-Caffey syndrome, the progeroid form of Ehlers-Danlos syndrome, as well as 2 cases of the 3-M syndrome. For the remaining patients, we have generated lists of candidate variants. CONCLUSIONS Whole exome sequencing can help identify genetic causes of short stature in the context of defined genetic syndromes, but may be less effective in identifying novel genetic causes of short stature in individual families. Utilized in the clinic, whole exome sequencing can provide clinically relevant diagnoses for these patients. Rare syndromic causes of short stature may be underrecognized and underdiagnosed in pediatric endocrinology clinics.
Collapse
Affiliation(s)
- Michael H. Guo
- Department of Genetics, Harvard Medical School, Boston, MA, USA,Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Yiping Shen
- Shanghai Children's Medical Center, Jiaotong University School of Medicine, Shanghai, China,Departments of Laboratory Medicine and Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Emily C. Walvoord
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Timothy C. Miller
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
| | - Jennifer E. Moon
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
| | - Joel N Hirschhorn
- Department of Genetics, Harvard Medical School, Boston, MA, USA,Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Andrew Dauber
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| |
Collapse
|
112
|
Nagasaki K, Asami T, Sato H, Ogawa Y, Kikuchi T, Saitoh A, Ogata T, Fukami M. Long-term follow-up study for a patient with Floating-Harbor syndrome due to a hotspot SRCAP mutation. Am J Med Genet A 2013; 164A:731-5. [PMID: 24375913 DOI: 10.1002/ajmg.a.36314] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
Floating-Harbor syndrome (FHS) is a rare autosomal dominant disorder characterized by short stature, skeletal malformations, speech delay, and dysmorphic facial appearance. Recently, mutations in SRCAP encoding a coactivator for cAMP-response element binding protein (CREB)-binding protein have been identified in small number of patients with FHS. Here, we report on long-term follow-up data of a male patient with a SRCAP mutation. The patient presented with mild hypothyroidism and renal hypouricemia, in addition to several FHS-compatible features including growth impairment, cognitive disability, facial dysmorphisms, and hypertension. He showed delayed bone age from infancy to 9 years of age and markedly accelerated bone age with the formation of cone-shaped epiphyses and early epiphysial fusions after the onset of puberty. His pubertal sexual development was almost age appropriate. Two-year treatment with growth hormone (GH) did not significantly improve the growth velocity. Molecular analysis identified a de novo heterozygous nonsense mutation (p.R2444X) in the last exon of SRCAP, which has been most common mutation detected in patients from other ethnic groups. These results indicate that perturbed skeletal maturation from infancy through adolescence is a characteristic feature in patients with SRCAP mutations. Furthermore, our data imply that GH therapy exerted only a marginal effect on the growth of this patient, and that renal hypouricemia may be a novel complication of FHS.
Collapse
Affiliation(s)
- Keisuke Nagasaki
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan; Division of Pediatrics, Department of Homeostatic Regulation and Development, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | | | | | | | | | | | | |
Collapse
|
113
|
Au PYB, Racher HE, Graham JM, Kramer N, Lowry RB, Parboosingh JS, Innes AM. De novo exon 1 missense mutations of SKI and Shprintzen-Goldberg syndrome: two new cases and a clinical review. Am J Med Genet A 2013; 164A:676-84. [PMID: 24357594 DOI: 10.1002/ajmg.a.36340] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 10/06/2013] [Indexed: 01/21/2023]
Abstract
Shprintzen-Goldberg syndrome (OMIM #182212) is a connective tissue disorder characterized by craniosynostosis, distinctive craniofacial features, skeletal abnormalities, marfanoid body habitus, aortic dilatation, and intellectual disability. Mutations in exon 1 of SKI have recently been identified as being responsible for approximately 90% of reported individuals diagnosed clinically with Shprintzen-Goldberg syndrome. SKI is a known regulator of TGFβ signaling. Therefore, like Marfan syndrome and Loeys-Dietz syndrome, Shprintzen-Goldberg syndrome is likely caused by deregulated TGFβ signals, explaining the considerable phenotypic overlap between these three disorders. We describe two additional patients with exon 1 SKI mutations and review the clinical features and literature of Shprintzen-Goldberg syndrome.
Collapse
Affiliation(s)
- P Y Billie Au
- Department of Medical Genetics, Alberta Children's Hospital, University of Calgary, Alberta, Canada
| | | | | | | | | | | | | | | |
Collapse
|
114
|
The promise of whole-exome sequencing in medical genetics. J Hum Genet 2013; 59:5-15. [DOI: 10.1038/jhg.2013.114] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 09/29/2013] [Accepted: 10/11/2013] [Indexed: 12/14/2022]
|
115
|
Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 2013; 14:681-91. [PMID: 23999272 DOI: 10.1038/nrg3555] [Citation(s) in RCA: 502] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Work over the past 25 years has resulted in the identification of genes responsible for ~50% of the estimated 7,000 rare monogenic diseases, and it is predicted that most of the remaining disease-causing genes will be identified by the year 2020, and probably sooner. This marked acceleration is the result of dramatic improvements in DNA-sequencing technologies and the associated analyses. We examine the rapid maturation of rare-disease genetic analysis and successful strategies for gene identification. We highlight the impact of discovering rare-disease-causing genes, from clinical diagnostics to insights gained into biological mechanisms and common diseases. Last, we explore the increasing therapeutic opportunities and challenges that the resulting expansion of the 'atlas' of human genetic pathology will bring.
Collapse
Affiliation(s)
- Kym M Boycott
- Department of Pediatrics, University of Ottawa and Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, Ontario K1H 8L1, Canada
| | | | | | | |
Collapse
|
116
|
Dyment D, Smith A, Alcantara D, Schwartzentruber J, Basel-Vanagaite L, Curry C, Temple I, Reardon W, Mansour S, Haq M, Gilbert R, Lehmann O, Vanstone M, Beaulieu C, Majewski J, Bulman D, O’Driscoll M, Boycott K, Innes A. Mutations in PIK3R1 cause SHORT syndrome. Am J Hum Genet 2013; 93:158-66. [PMID: 23810382 PMCID: PMC3710754 DOI: 10.1016/j.ajhg.2013.06.005] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/14/2013] [Accepted: 06/04/2013] [Indexed: 11/24/2022] Open
Abstract
SHORT syndrome is a rare, multisystem disease characterized by short stature, anterior-chamber eye anomalies, characteristic facial features, lipodystrophy, hernias, hyperextensibility, and delayed dentition. As part of the FORGE (Finding of Rare Disease Genes) Canada Consortium, we studied individuals with clinical features of SHORT syndrome to identify the genetic etiology of this rare disease. Whole-exome sequencing in a family trio of an affected child and unaffected parents identified a de novo frameshift insertion, c.1906_1907insC (p.Asn636Thrfs*18), in exon 14 of PIK3R1. Heterozygous mutations in exon 14 of PIK3R1 were subsequently identified by Sanger sequencing in three additional affected individuals and two affected family members. One of these mutations, c.1945C>T (p.Arg649Trp), was confirmed to be a de novo mutation in one affected individual and was also identified and shown to segregate with the phenotype in an unrelated family. The other mutation, a de novo truncating mutation (c.1971T>G [p.Tyr657*]), was identified in another affected individual. PIK3R1 is involved in the phosphatidylinositol 3 kinase (PI3K) signaling cascade and, as such, plays an important role in cell growth, proliferation, and survival. Functional studies on lymphoblastoid cells with the PIK3R1 c.1906_1907insC mutation showed decreased phosphorylation of the downstream S6 target of the PI3K-AKT-mTOR pathway. Our findings show that PIK3R1 mutations are the major cause of SHORT syndrome and suggest that the molecular mechanism of disease might involve downregulation of the PI3K-AKT-mTOR pathway.
Collapse
Affiliation(s)
- David A. Dyment
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Amanda C. Smith
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Diana Alcantara
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | | | - Lina Basel-Vanagaite
- Department of Pediatric Genetics, Schneider Children’s Medical Center of Israel, Petah-Tikva 49100, Israel
| | - Cynthia J. Curry
- Genetic Medicine Central California, Fresno, CA 93701, USA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 93701, USA
| | - I. Karen Temple
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton SO16 5YA, UK
| | - William Reardon
- Our Lady’s Hospital for Sick Children, Crumlin, Dublin 12, Ireland
| | - Sahar Mansour
- South West Thames Regional Genetics Service, St. George’s Hospital Medical School, London SW17 0RE, UK
| | - Mushfequr R. Haq
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Rodney Gilbert
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Ordan J. Lehmann
- Department of Ophthalmology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Megan R. Vanstone
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Chandree L. Beaulieu
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Dennis E. Bulman
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Mark O’Driscoll
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
| | - Kym M. Boycott
- Department of Genetics, Children’s Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - A. Micheil Innes
- Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary, AB T2N 4N1, Canada
| |
Collapse
|
117
|
Kehrer M, Beckmann A, Wyduba J, Finckh U, Dufke A, Gaiser U, Tzschach A. Floating-Harbor syndrome: SRCAP mutations are not restricted to exon 34. Clin Genet 2013; 85:498-9. [PMID: 23763483 DOI: 10.1111/cge.12199] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 05/17/2013] [Accepted: 05/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- M Kehrer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | | | | | | | | | | | | |
Collapse
|
118
|
The SWI/SNF genetic blockade: effects in cell differentiation, cancer and developmental diseases. Oncogene 2013; 33:2681-9. [PMID: 23752187 DOI: 10.1038/onc.2013.227] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 04/17/2013] [Accepted: 04/17/2013] [Indexed: 12/26/2022]
Abstract
Our rapidly growing knowledge about cancer genetics attests to the widespread occurrence of alterations at genes encoding different components of the SWI/SNF complex. This reveals an important new feature that sustains cancer development: the blockade of chromatin remodeling. Here, we provide an overview of our current knowledge on the gene alterations of chromatin-remodeling factors, and how they relate to cancer and human developmental diseases. We also consider the functional repercussions, particularly how the inactivation of the SWI/SNF complex impairs the appropriate cell response to nuclear receptor signaling, which, in turn, prevents cell differentiation and sustains cell growth independently of the environment.
Collapse
|
119
|
Nikkel SM, Dauber A, de Munnik S, Connolly M, Hood RL, Caluseriu O, Hurst J, Kini U, Nowaczyk MJM, Afenjar A, Albrecht B, Allanson JE, Balestri P, Ben-Omran T, Brancati F, Cordeiro I, da Cunha BS, Delaney LA, Destrée A, Fitzpatrick D, Forzano F, Ghali N, Gillies G, Harwood K, Hendriks YMC, Héron D, Hoischen A, Honey EM, Hoefsloot LH, Ibrahim J, Jacob CM, Kant SG, Kim CA, Kirk EP, Knoers NVAM, Lacombe D, Lee C, Lo IFM, Lucas LS, Mari F, Mericq V, Moilanen JS, Møller ST, Moortgat S, Pilz DT, Pope K, Price S, Renieri A, Sá J, Schoots J, Silveira EL, Simon MEH, Slavotinek A, Temple IK, van der Burgt I, de Vries BBA, Weisfeld-Adams JD, Whiteford ML, Wierczorek D, Wit JM, Yee CFO, Beaulieu CL, White SM, Bulman DE, Bongers E, Brunner H, Feingold M, Boycott KM. The phenotype of Floating-Harbor syndrome: clinical characterization of 52 individuals with mutations in exon 34 of SRCAP. Orphanet J Rare Dis 2013; 8:63. [PMID: 23621943 PMCID: PMC3659005 DOI: 10.1186/1750-1172-8-63] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/16/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Floating-Harbor syndrome (FHS) is a rare condition characterized by short stature, delays in expressive language, and a distinctive facial appearance. Recently, heterozygous truncating mutations in SRCAP were determined to be disease-causing. With the availability of a DNA based confirmatory test, we set forth to define the clinical features of this syndrome. METHODS AND RESULTS Clinical information on fifty-two individuals with SRCAP mutations was collected using standardized questionnaires. Twenty-four males and twenty-eight females were studied with ages ranging from 2 to 52 years. The facial phenotype and expressive language impairments were defining features within the group. Height measurements were typically between minus two and minus four standard deviations, with occipitofrontal circumferences usually within the average range. Thirty-three of the subjects (63%) had at least one major anomaly requiring medical intervention. We did not observe any specific phenotype-genotype correlations. CONCLUSIONS This large cohort of individuals with molecularly confirmed FHS has allowed us to better delineate the clinical features of this rare but classic genetic syndrome, thereby facilitating the development of management protocols.
Collapse
|
120
|
Frese KS, Katus HA, Meder B. Next-generation sequencing: from understanding biology to personalized medicine. BIOLOGY 2013; 2:378-98. [PMID: 24832667 PMCID: PMC4009863 DOI: 10.3390/biology2010378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 01/21/2013] [Accepted: 02/04/2013] [Indexed: 12/11/2022]
Abstract
Within just a few years, the new methods for high-throughput next-generation sequencing have generated completely novel insights into the heritability and pathophysiology of human disease. In this review, we wish to highlight the benefits of the current state-of-the-art sequencing technologies for genetic and epigenetic research. We illustrate how these technologies help to constantly improve our understanding of genetic mechanisms in biological systems and summarize the progress made so far. This can be exemplified by the case of heritable heart muscle diseases, so-called cardiomyopathies. Here, next-generation sequencing is able to identify novel disease genes, and first clinical applications demonstrate the successful translation of this technology into personalized patient care.
Collapse
Affiliation(s)
- Karen S Frese
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Hugo A Katus
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, Heidelberg 69120, Germany.
| |
Collapse
|
121
|
Ku CS, Polychronakos C, Tan EK, Naidoo N, Pawitan Y, Roukos DH, Mort M, Cooper DN. A new paradigm emerges from the study of de novo mutations in the context of neurodevelopmental disease. Mol Psychiatry 2013; 18:141-53. [PMID: 22641181 DOI: 10.1038/mp.2012.58] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of de novo point mutations (new germline mutations arising from the gametes of the parents) remained largely static until the arrival of next-generation sequencing technologies, which made both whole-exome sequencing (WES) and whole-genome sequencing (WGS) feasible in practical terms. Single nucleotide polymorphism genotyping arrays have been used to identify de novo copy-number variants in a number of common neurodevelopmental conditions such as schizophrenia and autism. By contrast, as point mutations and microlesions occurring de novo are refractory to analysis by these microarray-based methods, little was known about either their frequency or impact upon neurodevelopmental disease, until the advent of WES. De novo point mutations have recently been implicated in schizophrenia, autism and mental retardation through the WES of case-parent trios. Taken together, these findings strengthen the hypothesis that the occurrence of de novo mutations could account for the high prevalence of such diseases that are associated with a marked reduction in fecundity. De novo point mutations are also known to be responsible for many sporadic cases of rare dominant mendelian disorders such as Kabuki syndrome, Schinzel-Giedion syndrome and Bohring-Opitz syndrome. These disorders share a common feature in that they are all characterized by intellectual disability. In summary, recent WES studies of neurodevelopmental and neuropsychiatric disease have provided new insights into the role of de novo mutations in these disorders. Our knowledge of de novo mutations is likely to be further accelerated by WGS. However, the collection of case-parent trios will be a prerequisite for such studies. This review aims to discuss recent developments in the study of de novo mutations made possible by technological advances in DNA sequencing.
Collapse
Affiliation(s)
- C S Ku
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
| | | | | | | | | | | | | | | |
Collapse
|
122
|
Berdasco M, Esteller M. Genetic syndromes caused by mutations in epigenetic genes. Hum Genet 2013; 132:359-83. [PMID: 23370504 DOI: 10.1007/s00439-013-1271-x] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 01/18/2013] [Indexed: 12/21/2022]
Abstract
The orchestrated organization of epigenetic factors that control chromatin dynamism, including DNA methylation, histone marks, non-coding RNAs (ncRNAs) and chromatin-remodeling proteins, is essential for the proper function of tissue homeostasis, cell identity and development. Indeed, deregulation of epigenetic profiles has been described in several human pathologies, including complex diseases (such as cancer, cardiovascular and neurological diseases), metabolic pathologies (type 2 diabetes and obesity) and imprinting disorders. Over the last decade it has become increasingly clear that mutations of genes involved in epigenetic mechanism, such as DNA methyltransferases, methyl-binding domain proteins, histone deacetylases, histone methylases and members of the SWI/SNF family of chromatin remodelers are linked to human disorders, including Immunodeficiency Centromeric instability Facial syndrome 1, Rett syndrome, Rubinstein-Taybi syndrome, Sotos syndrome or alpha-thalassemia/mental retardation X-linked syndrome, among others. As new members of the epigenetic machinery are described, the number of human syndromes associated with epigenetic alterations increases. As recent examples, mutations of histone demethylases and members of the non-coding RNA machinery have recently been associated with Kabuki syndrome, Claes-Jensen X-linked mental retardation syndrome and Goiter syndrome. In this review, we describe the variety of germline mutations of epigenetic modifiers that are known to be associated with human disorders, and discuss the therapeutic potential of epigenetic drugs as palliative care strategies in the treatment of such disorders.
Collapse
Affiliation(s)
- María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908 L'Hospitalet de LLobregat, Barcelona, Catalonia, Spain
| | | |
Collapse
|
123
|
Doucette L, Green J, Black C, Schwartzentruber J, Johnson GJ, Galutira D, Young TL. Molecular genetics of achromatopsia in Newfoundland reveal genetic heterogeneity, founder effects and the first cases of Jalili syndrome in North America. Ophthalmic Genet 2013; 34:119-29. [PMID: 23362848 DOI: 10.3109/13816810.2013.763993] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Achromatopsia (ACHM) is a severe retinal disorder characterized by an inability to distinguish colors, impaired visual acuity, photophobia and nystagmus. This rare autosomal recessive disorder of the cone photoreceptors is best known for its increased frequency due to founder effect in the Pingelapese population of the Pacific islands. Sixteen patients from Newfoundland, Canada were sequenced for mutations in the four known achromatopsia genes CNGA3, CNGB3, GNAT2, and PDE6C. The majority (n = 12) of patients were either homozygotes or compound heterozygotes for known achromatopsia alleles, two in CNGB3 (p.T383fsX and p.T296YfsX9) and three in CNGA3 (p.R283Q, p.R427C and p.L527R). Haplotype reconstruction showed that recurrent mutations p.T383fsX and p.L527R were due to a founder effect. Aggregate data from exome sequencing, segregation analysis and archived medical records support a rediagnosis of Jalili syndrome in affected siblings (n = 4) from Family 0094, which to our knowledge is the first family identified with Jalili Syndrome in North America.
Collapse
Affiliation(s)
- Lance Doucette
- Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | | | | | | | | | | | | |
Collapse
|
124
|
Reschen M, Kini U, Hood RL, Boycott KM, Hurst J, O'Callaghan CA. Floating-Harbor syndrome and polycystic kidneys associated with SRCAP mutation. Am J Med Genet A 2012; 158A:3196-200. [PMID: 23165645 DOI: 10.1002/ajmg.a.35635] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/25/2012] [Indexed: 11/11/2022]
Abstract
Floating-Harbor syndrome (FHS) is a rare genetic disorder recently shown to be caused by mutations in the Snf2-related CREB-binding protein activator protein gene (SRCAP). It comprises three key clinical features of characteristic facies, expressive and receptive speech impairment and short stature. We report on a patient with this syndrome associated with early adult-onset hypertension and bilateral polycystic kidneys. Family screening for polycystic kidney disease was negative and mutations in polycystic kidney disease 1 and 2 genes (PKD1 and PKD2) were absent. Sequencing of the SRCAP gene demonstrated a de novo mutation matching one of the known FHS-associated mutations. The patient required treatment with anti-hypertensives and will require lifelong renal monitoring. We suggest this patient's presentation may be due to the pleiotropic effects of SRCAP mutations. Further, the protein encoded by SRCAP is known to interact with CREB-binding protein, the product of the gene mutated in Rubinstein-Taybi syndrome, which is associated with renal abnormalities. A literature review of the renal findings in patients with Floating-Harbor syndrome identified another patient with possible polycystic kidneys, two patients with early onset hypertension, and a young patient with a ruptured intracranial aneurysm, which can be a feature of classic adult polycystic kidney disease. Collectively, these findings suggest that all patients with Floating-Harbor syndrome should undergo regular blood pressure monitoring and screening for polycystic kidneys by ultrasound at the time of the FHS diagnosis with imaging to be repeated during adulthood if a childhood ultrasound was negative.
Collapse
|
125
|
Lynch DC, Dyment DA, Huang L, Nikkel SM, Lacombe D, Campeau PM, Lee B, Bacino CA, Michaud JL, Bernier FP, Parboosingh JS, Innes AM. Identification of novel mutations confirms PDE4D as a major gene causing acrodysostosis. Hum Mutat 2012; 34:97-102. [PMID: 23033274 DOI: 10.1002/humu.22222] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 09/10/2012] [Indexed: 11/09/2022]
Abstract
Acrodysostosis is characterized by nasal hypoplasia, peripheral dysostosis, variable short stature, and intellectual impairment. Recently, mutations in PRKAR1A were reported in patients with acrodysostosis and hormone resistance. Subsequently, mutations in a phosphodiesterase gene (PDE4D) were identified in seven sporadic cases. We sequenced PDE4D in seven acrodysostosis patients from five families. Missense mutations were identified in all cases. Families showed de novo inheritance except one family with three affected children whose father was subsequently found to have subtle features of acrodysostosis. There were no recurrent mutations. Short stature and endocrine resistance are rare in this series; however, cognitive involvement and obesity were frequent. This last finding is relevant given PDE4D is insulin responsive and potentially involved in lipolysis. PDE4D encodes a cyclic AMP regulator and places PDE4D-related acrodysostosis within the same family of diseases as pseudohypoparathyroidism, pseudopseudohypoparathyroidism, PRKAR1A-related acrodysostosis and brachydactyly-mental retardation syndrome; all characterized by cognitive impairment and short distal extremities.
Collapse
Affiliation(s)
- Danielle C Lynch
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
126
|
Le Goff C, Mahaut C, Bottani A, Doray B, Goldenberg A, Moncla A, Odent S, Nitschke P, Munnich A, Faivre L, Cormier-Daire V. Not all floating-harbor syndrome cases are due to mutations in exon 34 of SRCAP. Hum Mutat 2012; 34:88-92. [PMID: 22965468 DOI: 10.1002/humu.22216] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 08/27/2012] [Indexed: 01/19/2023]
Abstract
Floating-Harbor syndrome (FHS) is a rare disorder characterized by short stature, delayed bone age, speech delay, and dysmorphic facial features. We report here the molecular analysis of nine cases, fulfilling the diagnostic criteria for FHS. Using exome sequencing, we identified SRCAP as the disease gene in two cases and subsequently found SRCAP truncating mutations in 6/9 cases. All mutations occurred de novo and were located in exon 34, in accordance with the recent report of Hood et al. However, the absence of SRCAP mutations in 3/9 cases supported genetic heterogeneity of FH syndrome. Importantly, no major clinical differences were observed supporting clinical homogeneity in this series of FHS patients.
Collapse
Affiliation(s)
- Carine Le Goff
- Department of Genetics, INSERM U781, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine, Hôpital Necker, Paris, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
127
|
Jones WD, Dafou D, McEntagart M, Woollard WJ, Elmslie FV, Holder-Espinasse M, Irving M, Saggar AK, Smithson S, Trembath RC, Deshpande C, Simpson MA. De novo mutations in MLL cause Wiedemann-Steiner syndrome. Am J Hum Genet 2012; 91:358-64. [PMID: 22795537 DOI: 10.1016/j.ajhg.2012.06.008] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/25/2012] [Accepted: 06/18/2012] [Indexed: 01/28/2023] Open
Abstract
Excessive growth of terminal hair around the elbows (hypertrichosis cubiti) has been reported both in isolation and in association with a variable spectrum of associated phenotypic features. We identified a cohort of six individuals with hypertrichosis cubiti associated with short stature, intellectual disability, and a distinctive facial appearance, consistent with a diagnosis of Wiedemann-Steiner syndrome (WSS). Utilizing a whole-exome sequencing approach, we identified de novo mutations in MLL in five of the six individuals. MLL encodes a histone methyltransferase that regulates chromatin-mediated transcription through the catalysis of methylation of histone H3K4. Each of the five mutations is predicted to result in premature termination of the protein product. Furthermore, we demonstrate that transcripts arising from the mutant alleles are subject to nonsense-mediated decay. These findings define the genetic basis of WSS, provide additional evidence for the role of haploinsufficency of histone-modification enzymes in multiple-congenital-anomaly syndromes, and further illustrate the importance of the regulation of histone modification in development.
Collapse
Affiliation(s)
- Wendy D Jones
- South West Thames Regional Genetics Service, St George's Hospital, University of London, London SW17 0RE, UK
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
128
|
Rabbani B, Mahdieh N, Hosomichi K, Nakaoka H, Inoue I. Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders. J Hum Genet 2012; 57:621-32. [DOI: 10.1038/jhg.2012.91] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
129
|
Jarinova O, Ekker M. Regulatory variations in the era of next-generation sequencing: Implications for clinical molecular diagnostics. Hum Mutat 2012; 33:1021-30. [DOI: 10.1002/humu.22083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/06/2012] [Indexed: 01/05/2023]
|
130
|
Shalev SA, Spiegel R, Borochowitz ZU. A distinctive autosomal recessive syndrome of severe disproportionate short stature with short long bones, brachydactyly, and hypotrichosis in two consanguineous Arab families. Eur J Med Genet 2012; 55:256-64. [PMID: 22440536 DOI: 10.1016/j.ejmg.2012.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 02/22/2012] [Indexed: 11/20/2022]
Abstract
Disproportionate short stature is a heterogeneous group of hereditary disorders, which are classified according to their mode of inheritance, their clinical skeletal and non-skeletal manifestations, and their radiological characteristics. Herein, we inform on eight individuals with severe disproportionate short stature from two unrelated consanguineous families of Arab-Muslim ancestry. The adult height of the affected individuals is between 112 cm and 127 cm, and is due to pre- and post-natal growth retardation, which probably manifests as early as the second trimester of pregnancy. At a young age, the phenotype is characterized by a short stature, a relatively large head, and a long triangular face, and this phenotype later evolves to one with in which the head is relatively small, the mandible is large and pointy. The affected individuals have normal cognitive abilities and lack any neurological deficits. Other typical features include a prominent nose, a voice with an unusual high-pitched sound, relatively small ears, clinodactyly, brachydactyly, small hands, hypoplastic fingernails, a waddling gait, and sparse hair post-pubertally. Typical skeletal changes include short long bones, especially the femurs and humeri, with mild metaphyseal changes and very short femoral necks. After due consideration of the other hereditary causes of disproportionate short stature and close examination of the pedigrees of the two families, we concluded that these eight individuals have the same hitherto unreported form of severe disproportionate short stature that is inherited in the autosomal recessive mode.
Collapse
|