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Al-Mutairi DA, Alsabah BH, Pennekamp P, Omran H. Novel pathogenic variants of DNAH5 associated with clinical and genetic spectra of primary ciliary dyskinesia in an Arab population. Front Genet 2024; 15:1396797. [PMID: 39045318 PMCID: PMC11264286 DOI: 10.3389/fgene.2024.1396797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/20/2024] [Indexed: 07/25/2024] Open
Abstract
Introduction: Primary ciliary dyskinesia (PCD) is caused by the dysfunction of motile cilia resulting in insufficient mucociliary clearance of the lungs. This study aimed to map novel PCD variants and determine their pathogenicity in PCD patients in Kuwait. Methods: Herein, we present five PCD individuals belonging to a cohort of 105 PCD individuals recruited from different hospitals in Kuwait. Genomic DNAs from the family members were analysed to screen for pathogenic PCD variants. Transmission electron microscopy (TEM) and immunofluorescence (IF) analyses were performed on the nasal biopsies to detect specific structural abnormalities within the ciliated cells. Results: Genetic screening and functional analyses confirmed that the five PCD individuals carried novel pathogenic variants of DNAH5 causing PCD in three Arabic families. Of these, one multiplex family with two affected individuals showed two novel homozygous missense variants in DNAH5 causing PCD with situs inversus; another multiplex family with two affected individuals showed two newly identified compound heterozygous variants in DNAH5 causing PCD with situs solitus. In addition, novel heterozygous variants were identified in a child with PCD and situs solitus from a singleton family with unrelated parents. TEM analysis demonstrated the lack of outer dynein arms (ODAs) in all analysed samples, and IF analysis confirmed the absence of the dynein arm component of DNAH5 from the ciliary axoneme. Conclusion: The newly identified pathogenic variants of DNAH5 are associated with PCD as well as variable pulmonary clinical manifestations in Arabic families.
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Affiliation(s)
- Dalal A. Al-Mutairi
- Department of Pathology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Petra Pennekamp
- Department of Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Heymut Omran
- Department of Pediatrics, University Hospital Muenster, Muenster, Germany
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Al-Mutairi DA, Jarragh AA, Alsabah BH, Wein MN, Mohammed W, Alkharafi L. A homozygous SP7/OSX mutation causes osteogenesis and dentinogenesis imperfecta with craniofacial anomalies. JBMR Plus 2024; 8:ziae026. [PMID: 38562913 PMCID: PMC10984723 DOI: 10.1093/jbmrpl/ziae026] [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: 11/28/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Osteogenesis imperfecta (OI) is a heterogeneous spectrum of hereditary genetic disorders that cause bone fragility, through various quantitative and qualitative defects of type 1 collagen, a triple helix composed of two α1 and one α2 chains encoded by COL1A1 and COL1A2, respectively. The main extra-skeletal manifestations of OI include blue sclerae, opalescent teeth, and hearing impairment. Moreover, multiple genes involved in osteoblast maturation and type 1 collagen biosynthesis are now known to cause recessive forms of OI. In this study a multiplex consanguineous family of two affected males with OI was recruited for genetic screening. To determine the causative, pathogenic variant(s), genomic DNA from two affected family members were analyzed using whole exome sequencing, autozygosity mapping, and then validated with Sanger sequencing. The analysis led to the mapping of a homozygous variant previously reported in SP7/OSX, a gene encoding for Osterix, a transcription factor that activates a repertoire of genes involved in osteoblast and osteocyte differentiation and function. The identified variant (c.946C > T; p.Arg316Cys) in exon 2 of SP7/OSX results in a pathogenic amino acid change in two affected male siblings and develops OI, dentinogenesis imperfecta, and craniofacial anomaly. On the basis of the findings of the present study, SP7/OSX:c. 946C > T is a rare homozygous variant causing OI with extra-skeletal features in inbred Arab populations.
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Affiliation(s)
- Dalal A Al-Mutairi
- Department of Pathology, Faculty of Medicine, Kuwait University, 13110 Kuwait City, Kuwait
| | - Ali A Jarragh
- Department of Surgery, Faculty of Medicine, Kuwait University, 13110 Kuwait City, Kuwait
| | - Basel H Alsabah
- Zain Specialized Hospital for Ear, Nose and Throat, 70030 Kuwait City, Kuwait
| | - Marc N Wein
- Endocrine Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States
| | - Wasif Mohammed
- Department of Radiology, Al Sabah Hospital, 13041 Kuwait City, Kuwait
| | - Lateefa Alkharafi
- Cleft and Craniofacial Unit, Farwaniya Specialized Dental Center, Ministry of Health, 13001 Kuwait City, Kuwait
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Al-Mutairi DA, Alsabah BH, Alkhaledi BA, Pennekamp P, Omran H. Identification of a novel founder variant in DNAI2 cause primary ciliary dyskinesia in five consanguineous families derived from a single tribe descendant of Arabian Peninsula. Front Genet 2022; 13:1017280. [PMID: 36303540 PMCID: PMC9596166 DOI: 10.3389/fgene.2022.1017280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/23/2022] [Indexed: 11/24/2022] Open
Abstract
Introduction: Primary ciliary dyskinesia (PCD) is caused by dysfunction of motile cilia resulting in insufficient mucociliary clearance of the lungs. The overall aim of this study is to identify disease causing genetic variants for PCD patients in the Kuwaiti population. Methods: A cohort of multiple consanguineous PCD families was identified from Kuwaiti patients and genomic DNA from the family members was analysed for variant screening. Transmission electron microscopy (TEM) and immunofluorescent (IF) analyses were performed on nasal brushings to detect specific structural abnormalities within ciliated cells. Results: All the patients inherited the same founder variant in DNAI2 and exhibited PCD symptoms. TEM analysis demonstrated lack of outer dynein arms (ODA) in all analysed samples. IF analysis confirmed absence of DNAI1, DNAI2, and DNAH5 from the ciliary axoneme. Whole exome sequencing, autozygosity mapping and segregation analysis confirmed that seven patients carry the same homozygous missense variant (DNAI2:c.740G>A; p.Arg247Gln; rs755060592). Conclusion:DNAI2:c.740G>A is the founder variant causing PCD in patients belonging to a particular Arabian tribe which practices consanguineous marriages.
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Affiliation(s)
- Dalal A. Al-Mutairi
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Kuwait City, Kuwait
- *Correspondence: Dalal A. Al-Mutairi,
| | | | | | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
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Autozygosity reveals recessive mutations and novel mechanisms in dominant genes: implications in variant interpretation. Genet Med 2017; 19:1144-1150. [PMID: 28383543 DOI: 10.1038/gim.2017.22] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/24/2017] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The purpose of this study is to describe recessive alleles in strictly dominant genes. Identifying recessive mutations in genes for which only dominant disease or risk alleles have been reported can expand our understanding of the medical relevance of these genes both phenotypically and mechanistically. The Saudi population is enriched for autozygosity, which enhances the homozygous occurrence of alleles, including pathogenic alleles in genes that have been associated only with a dominant inheritance pattern. METHODS Exome sequencing of patients from consanguineous families with likely recessive phenotypes was performed. In one family, the genotype of the deceased children was inferred from their parents due to lack of available samples. RESULTS We describe the identification of 11 recessive variants (5 of which are reported here for the first time) in 11 genes for which only dominant disease or risk alleles have been reported. The observed phenotypes for these recessive variants were novel (e.g., FBN2-related myopathy and CSF1R-related brain malformation and osteopetrosis), typical (e.g., ACTG2-related visceral myopathy), or an apparently healthy state (e.g., PDE11A), consistent with the corresponding mouse knockout phenotypes. CONCLUSION Our results show that, in the era of genomic sequencing and "reverse phenotyping," recessive variants in dominant genes should not be dismissed based on perceived "incompatibility" with the patient's phenotype before careful consideration.Genet Med advance online publication 06 April 2017.
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Kelmemi W, Teeuw ME, Bochdanovits Z, Ouburg S, Jonker MA, Alkuraya F, Hashem M, Kayserili H, van Haeringen A, Sheridan E, Masri A, Cobben JM, Rizzu P, Kostense PJ, Dommering CJ, Henneman L, Bouhamed-Chaabouni H, Heutink P, Ten Kate LP, Cornel MC. Determining the genome-wide kinship coefficient seems unhelpful in distinguishing consanguineous couples with a high versus low risk for adverse reproductive outcome. BMC MEDICAL GENETICS 2015; 16:50. [PMID: 26188928 PMCID: PMC4557855 DOI: 10.1186/s12881-015-0191-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 06/17/2015] [Indexed: 11/25/2022]
Abstract
Background Offspring of consanguineous couples are at increased risk of congenital disorders. The risk increases as parents are more closely related. Individuals that have the same degree of relatedness according to their pedigree, show variable genomic kinship coefficients. To investigate whether we can differentiate between couples with high- and low risk for offspring with congenital disorders, we have compared the genomic kinship coefficient of consanguineous parents with a child affected with an autosomal recessive disorder with that of consanguineous parents with only healthy children, corrected for the degree of pedigree relatedness. Methods 151 consanguineous couples (73 cases and 78 controls) from 10 different ethnic backgrounds were genotyped on the Affymetrix platform and passed quality control checks. After pruning SNPs in linkage disequilibrium, 57,358 SNPs remained. Kinship coefficients were calculated using three different toolsets: PLINK, King and IBDelphi, yielding five different estimates (IBDelphi, PLINK (all), PLINK (by population), King robust (all) and King homo (by population)). We performed a one-sided Mann Whitney test to investigate whether the median relative difference regarding observed and expected kinship coefficients is bigger for cases than for controls. Furthermore, we fitted a mixed effects linear model to correct for a possible population effect. Results Although the estimated degrees of genomic relatedness with the different toolsets show substantial variability, correlation measures between the different estimators demonstrated moderate to strong correlations. Controls have higher point estimates for genomic kinship coefficients. The one-sided Mann Whitney test did not show any evidence for a higher median relative difference for cases compared to controls. Neither did the regression analysis exhibit a positive association between case–control status and genomic kinship coefficient. Conclusions In this case–control setting, in which we compared consanguineous couples corrected for degree of pedigree relatedness, a higher degree of genomic relatedness was not significantly associated with a higher likelihood of having an affected child. Further translational research should focus on which parts of the genome and which pathogenic mutations couples are sharing. Looking at relatedness coefficients by determining genome-wide SNPs does not seem to be an effective measure for prospective risk assessment in consanguineous parents. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0191-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- W Kelmemi
- Laboratory of Human Genetics, Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - M E Teeuw
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - Z Bochdanovits
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - S Ouburg
- Laboratory of Immunogenetics, Medical Microbiology and Infection Control, Research School V-ICI, VU University Medical Center, Amsterdam, The Netherlands
| | - M A Jonker
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - F Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - M Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - H Kayserili
- Medical Genetics Department, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - A van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Juliana Children's Hospital, Hague, The Netherlands
| | - E Sheridan
- Bradford Institute for Health Research, Bradford Royal Infirmary, Bradford, UK.,Department of Genetics, Wellcome Trust Brenner Building, St James's University Hospital, Leeds, UK
| | - A Masri
- Division of Child Neurology, Department of Pediatrics, University of Jordan, Amman, Jordan
| | - J M Cobben
- Department of Pediatric Genetics, AMC University Hospital, Amsterdam, The Netherlands
| | - P Rizzu
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.,Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - P J Kostense
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - C J Dommering
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - L Henneman
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - H Bouhamed-Chaabouni
- Laboratory of Human Genetics, Faculty of Medicine, University of Tunis El Manar, Tunis, Tunisia
| | - P Heutink
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.,Genome Biology of Neurodegenerative Diseases, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - L P Ten Kate
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.,EMGO Institute for Health and Care Research, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands
| | - M C Cornel
- Department of Clinical Genetics, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands. .,EMGO Institute for Health and Care Research, VU University Medical Center, Mail BS7, D450, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands.
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Adams DR, Yuan H, Holyoak T, Arajs KH, Hakimi P, Markello TC, Wolfe LA, Vilboux T, Burton BK, Fajardo KF, Grahame G, Holloman C, Sincan M, Smith ACM, Wells GA, Huang Y, Vega H, Snyder JP, Golas GA, Tifft CJ, Boerkoel CF, Hanson RW, Traynelis SF, Kerr DS, Gahl WA. Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith-Magenis Syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity. Mol Genet Metab 2014; 113:161-70. [PMID: 24863970 PMCID: PMC4219933 DOI: 10.1016/j.ymgme.2014.04.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/05/2014] [Accepted: 04/06/2014] [Indexed: 01/28/2023]
Abstract
The National Institutes of Health Undiagnosed Diseases Program evaluates patients for whom no diagnosis has been discovered despite a comprehensive diagnostic workup. Failure to diagnose a condition may arise from the mutation of genes previously unassociated with disease. However, we hypothesized that this could also co-occur with multiple genetic disorders. Demonstrating a complex syndrome caused by multiple disorders, we report two siblings manifesting both similar and disparate signs and symptoms. They shared a history of episodes of hypoglycemia and lactic acidosis, but had differing exam findings and developmental courses. Clinical acumen and exome sequencing combined with biochemical and functional studies identified three genetic conditions. One sibling had Smith-Magenis Syndrome and a nonsense mutation in the RAI1 gene. The second sibling had a de novo mutation in GRIN2B, which resulted in markedly reduced glutamate potency of the encoded receptor. Both siblings had a protein-destabilizing homozygous mutation in PCK1, which encodes the cytosolic isoform of phosphoenolpyruvate carboxykinase (PEPCK-C). In summary, we present the first clinically-characterized mutation of PCK1 and demonstrate that complex medical disorders can represent the co-occurrence of multiple diseases.
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Affiliation(s)
- David R Adams
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA.
| | - Hongjie Yuan
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, Atlanta, GA, USA
| | - Todd Holyoak
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Katrina H Arajs
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Parvin Hakimi
- Department of Biochemistry, Case Western Reserve University, USA; Department of Pediatrics, Case Western Reserve University, USA
| | - Thomas C Markello
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Wolfe
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Thierry Vilboux
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Barbara K Burton
- Ann and Robert H. Lurie Children's Hospital, Northwestern University, Chicago, IL, USA; Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karin Fuentes Fajardo
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - George Grahame
- Center for Inherited Disorders of Energy Metabolism, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - Conisha Holloman
- University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Murat Sincan
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Ann C M Smith
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Gordon A Wells
- Department of Chemistry, Emory University, Atlanta, GA, USA; Department of Biochemistry, University of Stellenbosch, South Africa
| | - Yan Huang
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Hugo Vega
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - James P Snyder
- Department of Chemistry, Emory University, Atlanta, GA, USA
| | - Gretchen A Golas
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cynthia J Tifft
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Richard W Hanson
- Department of Biochemistry, Case Western Reserve University, USA
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, Atlanta, GA, USA
| | - Douglas S Kerr
- Department of Biochemistry, Case Western Reserve University, USA; Department of Pediatrics, Case Western Reserve University, USA; Center for Inherited Disorders of Energy Metabolism, University Hospitals Case Medical Center, Cleveland, OH, USA
| | - William A Gahl
- Undiagnosed Diseases Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA; Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD, USA
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Linhares ND, Freire MCM, Cardenas RGCCL, Pena HB, Bahia M, Pena SDJ. Exome sequencing identifies a novel homozygous variant in NDRG4 in a family with infantile myofibromatosis. Eur J Med Genet 2014; 57:643-8. [PMID: 25241110 DOI: 10.1016/j.ejmg.2014.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 08/31/2014] [Indexed: 10/24/2022]
Abstract
Infantile myofibromatosis (IM) is a rare disorder characterized by the development of benign tumors in the skin, muscle, bone, and viscera. The incidence is 1/150,000 live births and the disease is the most common cause of fibrous tumors in infancy. Cases which lack visceral involvement generally have a more benign course, usually with spontaneous regression of the tumors. On the other hand, the prognosis tends to be unfavorable when there is involvement of vital organs, which can lead to significant mortality. The identification of rare variants in genes that may cause IM is the first step towards the possibility of targeted treatments; however, the molecular pathogenesis of IM is poorly understood. In the present study, we report the results of exome sequence analysis of two brothers diagnosed with visceral multicentric infantile myofibromatosis, and their healthy consanguineous parents. In the two brothers we identified novel homozygous variants in NDRG4 gene (N-myc downregulated gene family member 4) and in RLTPR gene (RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing). The healthy parents were heterozygous for both variants. Consistent with the phenotype of IM, NDRG4 is a tumor-related gene; its expression has been shown to be decreased in numerous tumor types, suggesting that it might be a tumor suppressor gene. Additionally, studies have demonstrated that NDRG4 may have a role in cell survival and tumor invasion. We thus propose that this homozygous variant in NDRG4 may be the causative variant of the autosomal recessive form of IM in the studied family and that it should be investigated in other cases of autosomal recessive infantile myofibromatosis.
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Affiliation(s)
- Natália D Linhares
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maíra C M Freire
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raony G C C L Cardenas
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Heloísa B Pena
- Laboratório Gene - Núcleo de Genética Médica, Belo Horizonte, Brazil
| | - Magda Bahia
- Divisão de Gastroenterologia Pediátrica, Hospital das Clínicas da UFMG, Belo Horizonte, Brazil
| | - Sergio D J Pena
- Laboratório de Genômica Clínica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Laboratório Gene - Núcleo de Genética Médica, Belo Horizonte, Brazil.
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Jafri H, Hewison J, Sheridan E, Ahmed S. Acceptability of prenatal testing and termination of pregnancy in Pakistan. J Community Genet 2014; 6:29-37. [PMID: 25081227 DOI: 10.1007/s12687-014-0198-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 07/21/2014] [Indexed: 02/06/2023] Open
Abstract
This study aimed to assess acceptability of prenatal testing (PNT) and termination of pregnancy (TOP) for a range of conditions in Pakistani parents with and without a child with a genetic condition. A structured questionnaire assessing acceptability of PNT and TOP for 30 conditions was completed by 400 Pakistani participants: 200 parents with a child with a genetic condition (100 fathers and 100 mothers) and 200 parents without an affected child (100 fathers and 100 mothers). There was a high level of interest in PNT, where over 80 % of parents in all four study groups would want PNT for the majority of the conditions. There was comparatively less interest in TOP for the same conditions (ranging from 5 to 70 % of parents, with mothers of an affected child being most interested). Parents were most likely to be interested in TOP for conditions at the serious end of the continuum. More than half of the participants in each group would consider TOP for anencephaly and quadriplegia. The interest in PNT and TOP for a range of conditions suggests that rapidly developing PNT technologies are likely to be acceptable in Pakistan, a low-middle income level and Muslim country. The comparatively lower level of interest in TOP for the same conditions highlights ethical dilemmas that such technologies are likely to raise.
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Affiliation(s)
- H Jafri
- Genetech Laboratory, 146/1 Shadman Jail Road, Lahore, Pakistan
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9
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Simple, rapid and inexpensive quantitative fluorescent PCR method for detection of microdeletion and microduplication syndromes. PLoS One 2013; 8:e61328. [PMID: 23620743 PMCID: PMC3631209 DOI: 10.1371/journal.pone.0061328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 03/08/2013] [Indexed: 12/14/2022] Open
Abstract
Because of economic limitations, the cost-effective diagnosis of patients affected with rare microdeletion or microduplication syndromes is a challenge in developing countries. Here we report a sensitive, rapid, and affordable detection method that we have called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR). Our procedure is based on the finding of genomic regions with high homology to segments of the critical microdeletion/microduplication region. PCR amplification of both using the same primer pair, establishes competitive kinetics and relative quantification of amplicons, as happens in microsatellite-based Quantitative Fluorescence PCR. We used patients with two common microdeletion syndromes, the Williams-Beuren syndrome (7q11.23 microdeletion) and the 22q11.2 microdeletion syndromes and discovered that MQF-PCR could detect both with 100% sensitivity and 100% specificity. Additionally, we demonstrated that the same principle could be reliably used for detection of microduplication syndromes, by using patients with the Lubs (MECP2 duplication) syndrome and the 17q11.2 microduplication involving the NF1 gene. We propose that MQF-PCR is a useful procedure for laboratory confirmation of the clinical diagnosis of microdeletion/microduplication syndromes, ideally suited for use in developing countries, but having general applicability as well.
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10
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Abstract
Widespread sharing of long, identical-by-descent (IBD) genetic segments is a hallmark of populations that have experienced recent genetic drift. Detection of these IBD segments has recently become feasible, enabling a wide range of applications from phasing and imputation to demographic inference. Here, we study the distribution of IBD sharing in the Wright-Fisher model. Specifically, using coalescent theory, we calculate the variance of the total sharing between random pairs of individuals. We then investigate the cohort-averaged sharing: the average total sharing between one individual and the rest of the cohort. We find that for large cohorts, the cohort-averaged sharing is distributed approximately normally. Surprisingly, the variance of this distribution does not vanish even for large cohorts, implying the existence of "hypersharing" individuals. The presence of such individuals has consequences for the design of sequencing studies, since, if they are selected for whole-genome sequencing, a larger fraction of the cohort can be subsequently imputed. We calculate the expected gain in power of imputation by IBD and subsequently in power to detect an association, when individuals are either randomly selected or specifically chosen to be the hypersharing individuals. Using our framework, we also compute the variance of an estimator of the population size that is based on the mean IBD sharing and the variance in the sharing between inbred siblings. Finally, we study IBD sharing in an admixture pulse model and show that in the Ashkenazi Jewish population the admixture fraction is correlated with the cohort-averaged sharing.
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11
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Ahmed S, Ahmed M, Sharif SM, Sheridan E, Taylor GR. Attitudes towards prenatal testing and termination of pregnancy in British Pakistani parents and relatives of children with recessive conditions in the UK. Prenat Diagn 2012; 32:954-9. [DOI: 10.1002/pd.3940] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/12/2012] [Accepted: 06/20/2012] [Indexed: 11/08/2022]
Affiliation(s)
- S. Ahmed
- Leeds Institute of Health Sciences, School of Medicine; University of Leeds; 101 Clarendon Road Leeds LS2 9LJ UK
| | - M. Ahmed
- Yorkshire Regional Genetics Service; Leeds NHS Teaching Hospitals Trust; UK
| | - S. M. Sharif
- Yorkshire Regional Genetics Service; Leeds NHS Teaching Hospitals Trust; UK
| | - E. Sheridan
- Yorkshire Regional Genetics Service; Leeds NHS Teaching Hospitals Trust; UK
| | - G. R. Taylor
- Translational Genomics; Leeds University and Leeds Teaching Hospital; UK
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