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Resende KKM, Riou MC, Yamaguti PM, Fournier B, Rondeau S, Pacot L, Berdal A, Felizardo R, Mazzeu JF, Cormier-Daire V, Gaucher C, Acevedo AC, de La Dure-Molla M. Oro-dental phenotyping and report of three families with RELT-associated amelogenesis imperfecta. Eur J Hum Genet 2023; 31:1337-1341. [PMID: 37670079 PMCID: PMC10620165 DOI: 10.1038/s41431-023-01440-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 09/07/2023] Open
Abstract
Amelogenesis imperfecta (AI) is a group of rare genetic conditions characterized by quantitative and/or qualitative tooth enamel alterations. AI can manifest as an isolated trait or as part of a syndrome. Recently, five biallelic disease-causing variants in the RELT gene were identified in 7 families with autosomal recessive amelogenesis imperfecta (ARAI). RELT encodes an orphan receptor in the tumor necrosis factor (TNFR) superfamily expressed during tooth development, with unknown function. Here, we report one Brazilian and two French families with ARAI and a distinctive hypomineralized phenotype with hypoplastic enamel, post-eruptive enamel loss, and occlusal attrition. Using Next Generation Sequencing (NGS), four novel RELT variants were identified (c.120+1G>A, p.(?); c.120+1G>T, p.(?); c.193T>C, p.(Cys65Arg) and c.1260_1263dup, p.(Arg422Glyfs*5)). Our findings extend the knowledge of ARAI dental phenotypes and expand the disease-causing variants spectrum of the RELT gene.
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Affiliation(s)
- Kemelly Karolliny Moreira Resende
- Laboratory of Oral Histopathology, Faculty of Health Sciences, University of Brasilia, Brasilia, Brazil
- Oral Care Center for Inherited Diseases, University Hospital of Brasilia, Brasilia, Brazil
| | - Margot Charlotte Riou
- Reference Center of Oral and Dental Rare Diseases (O-Rares), Rothschild Hospital, Public Assistance- Paris Hospitals, Paris, France
- Paris Cité University, Dental Faculty, Paris, France
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne University, UMRS 1138 Inserm, Molecular Oral Physiopathology, Paris, France
| | - Paulo Marcio Yamaguti
- Laboratory of Oral Histopathology, Faculty of Health Sciences, University of Brasilia, Brasilia, Brazil
- Oral Care Center for Inherited Diseases, University Hospital of Brasilia, Brasilia, Brazil
| | - Benjamin Fournier
- Reference Center of Oral and Dental Rare Diseases (O-Rares), Rothschild Hospital, Public Assistance- Paris Hospitals, Paris, France
- Paris Cité University, Dental Faculty, Paris, France
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne University, UMRS 1138 Inserm, Molecular Oral Physiopathology, Paris, France
| | - Sophie Rondeau
- Reference Center for Skeletal Dysplasia, Service de Médecine Génomique des Maladies Rares, Necker Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Paris Cité University, INSERM UMR 1163 IMAGINE Institute, Paris, France
| | - Laurence Pacot
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Ariane Berdal
- Reference Center of Oral and Dental Rare Diseases (O-Rares), Rothschild Hospital, Public Assistance- Paris Hospitals, Paris, France
- Paris Cité University, Dental Faculty, Paris, France
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne University, UMRS 1138 Inserm, Molecular Oral Physiopathology, Paris, France
| | - Rufino Felizardo
- Reference Center of Oral and Dental Rare Diseases (O-Rares), Rothschild Hospital, Public Assistance- Paris Hospitals, Paris, France
- Paris Cité University, Dental Faculty, Paris, France
| | - Juliana Forte Mazzeu
- Laboratory of Clinical Genetics, Faculty of Medicine, University of Brasília, Brasília, Brazil
| | - Valérie Cormier-Daire
- Reference Center for Skeletal Dysplasia, Service de Médecine Génomique des Maladies Rares, Necker Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- Paris Cité University, INSERM UMR 1163 IMAGINE Institute, Paris, France
| | - Céline Gaucher
- Service de Médecine Génomique des Maladies de Système et d'Organe, Fédération de Génétique et de Médecine Génomique, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
- Université Paris Cité, URP2496, F-92120, Montrouge, France
- Department of Odontology, AP-HP, Hôpitaux Universitaire Henri Mondor, Paris, F-94000, France
| | - Ana Carolina Acevedo
- Laboratory of Oral Histopathology, Faculty of Health Sciences, University of Brasilia, Brasilia, Brazil
- Oral Care Center for Inherited Diseases, University Hospital of Brasilia, Brasilia, Brazil
- Paris Cité University, Dental Faculty, Paris, France
- Centre de Recherche des Cordeliers, Université Paris Cité, Sorbonne University, UMRS 1138 Inserm, Molecular Oral Physiopathology, Paris, France
| | - Muriel de La Dure-Molla
- Reference Center of Oral and Dental Rare Diseases (O-Rares), Rothschild Hospital, Public Assistance- Paris Hospitals, Paris, France.
- Paris Cité University, Dental Faculty, Paris, France.
- Paris Cité University, INSERM UMR 1163 IMAGINE Institute, Paris, France.
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2
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Al Mahdi HB, Edris S, Bahieldin A, Al-Aama JY, Elango R, Jamalalail BA, Sabbagh HJ. Identification of Causative Variants Contributing to Nonsyndromic Orofacial Clefts Using Whole-Exome Sequencing in a Saudi Family. Genet Test Mol Biomarkers 2020; 24:723-731. [PMID: 33121284 DOI: 10.1089/gtmb.2019.0233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Objectives: Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations observed across the globe. They are classified into three types: (a) cleft palate, (b) cleft lip, and (c) cleft lip and palate. To identify the potential candidate genes contributing to polygenic diseases such as NSOFC, linkage analyses, genome-wide association studies, and genomic rearrangements can be used. Genomic analyses, based on massively parallel next-generation sequencing technologies, play a vital role in deciphering the genetic bases of NSOFCs. Materials and Methods: In this study, whole exome sequencing was employed to detect genes that likely contributed to the NSOFC phenotype in a consanguineous Saudi family. Results: The exome analysis revealed NRP1 (rs35320960) as one potential candidate gene that is involved in bone differentiation. The RPL27A gene (rs199996172), which plays a crucial role in ribosome biogenesis, also passed all filters to serve as a candidate gene for NSOFC in this family. Rare variants are situated within the 5' UTR of these two genes. Conclusion: The study suggests that rare variants in NRP1 and RPL27A may be associated with NSOFC disease etiology.
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Affiliation(s)
- Hadiah Bassam Al Mahdi
- Princess Al-Jawhara Al-Ibrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Edris
- Princess Al-Jawhara Al-Ibrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Jumana Y Al-Aama
- Princess Al-Jawhara Al-Ibrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Princess Al-Jawhara Al-Ibrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bassam Adnan Jamalalail
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Heba Jafar Sabbagh
- Department of Pediatric Dentistry, Faculty of Dentistry, King Abdulaziz University, Jeddah, Saudi Arabia
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3
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Zahedi Abghari F, Bayat F, Razipour M, Karimipoor M, Taghavi-Basmenj M, Zeinali S, Davoudi-Dehaghani E. Characterization of Niemann-Pick diseases genes mutation spectrum in Iran and identification of a novel mutation in SMPD1 gene. Med J Islam Repub Iran 2020; 33:126. [PMID: 32280632 PMCID: PMC7137857 DOI: 10.34171/mjiri.33.126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Indexed: 02/05/2023] Open
Abstract
Background: Niemann-Pick diseases are rare inherited lipid storage disorders caused by mutations in the SMPD1, NPC1, and NPC2 genes. The aim of this study was to assess the mutation spectrum of a cohort of Iranian Niemann-Pick patients.
Methods: A consanguineous couple with a child suspected of having Niemann-Pick disease type A (died at age 2) was screened for gene mutations in the SMPD1 gene. Sanger sequencing was performed for all exons and exon-intron boundary regions. A literature review on SMPD1, NPC1, and NPC2 genes mutations in Iran was conducted using published original papers on this subject.
Results: A novel frameshift c.762delG (p.Leu256fs*) at a heterozygous state was identified in the parents. According to the review study, identified mutations in 39 Iranian patients were concentrated in exon 2 of the SMPD1 gene and exons 8 and 9 of the NPC1 gene.
Conclusion: Niemann-Pick diseases genes mutation analysis (SMPD1, NPC1, and NPC2) in Iran shows the genetic heterogeneity of these diseases in this country. More studies with larger sample sizes should be conducted to further examine genetic changes associated with Niemann-Pick diseases in Iran.
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Affiliation(s)
- Fateme Zahedi Abghari
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Bayat
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Razipour
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Taghavi-Basmenj
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sirous Zeinali
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elham Davoudi-Dehaghani
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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4
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Levy O, Gath IN. Effects of mating patterns on genealogical trees: Assessment of the high carrier rate of Familial Mediterranean Fever in rural Israeli districts. J Theor Biol 2018; 443:92-99. [PMID: 29382538 DOI: 10.1016/j.jtbi.2018.01.029] [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: 08/28/2017] [Revised: 11/20/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022]
Abstract
We investigate the spread from ancestors to descendants, under a model of sexual reproduction, of hereditary elements distinguishing individuals from their fellow human beings. These hereditary elements, termed labels, are either symbolic, implying a socio-cultural or ethnic self-determined category, or biological, i.e. a DNA sequence (for example founder mutations). The impact of various modes of preferential (assortative) mating on the dissemination of a known ancestral label was studied for both kinds of labels, the symbolic and the biological. For the socio-cultural based labeling, both mathematical modeling and simulation studies were carried out, and disclosed a marked delay in the spread of the labels in future generations, compared to the case where mating was random. The transmission of biological labels (founder mutations) from an ancestor to descendants under various modes and degrees of assortative mating was investigated by simulations and supplemented by an in-depth analysis of allele frequencies of Familial Mediterranean Fever (FMF) in an Israeli Muslim Arab village. The high carrier frequency of FMF in this village was satisfactorily explained solely by the presence of a founder effect and a pronounced high factor of selective mating, causing segregation and consanguinity among its inhabitants. Contribution of further evolutionary mechanisms such as heterozygote advantage, drift, differential reproductive success or selection pressure was not essential to explain these results.
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Affiliation(s)
- Orr Levy
- Faculty of Biomedical Engineering, Technion, Israel Institute of Technology, Haifa, 32000, Israel
| | - Isak Nethanël Gath
- Faculty of Biomedical Engineering, Technion, Israel Institute of Technology, Haifa, 32000, Israel.
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5
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Gialluisi A, Menabò S, Baldazzi L, Casula L, Meloni A, Farci MC, Mariotti S, Balestrino L, Ortolano R, Murru S, Carcassi C, Loche S, Balsamo A, Romeo G. A genetic epidemiology study of congenital adrenal hyperplasia in Italy. Clin Genet 2017. [PMID: 28644547 DOI: 10.1111/cge.13078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Congenital adrenal hyperplasia due to 21-hydroxylase deficiency (21OHD-CAH) is an autosomal recessive disorder affecting steroidogenesis, due to mutations in CYP21A2 (6p21.3). 21OHD-CAH neonatal screening is based on 17-hydroxyprogesterone (17OHP) serum levels, showing high type I error rate and low sensitivity to mild CAH forms. Here, we used an epidemiological approach, which estimates the allelic frequency (q) of an autosomal recessive disorder using the proportion of homozygous patients, the mutational spectrum and the inbreeding coefficient in a sample of affected individuals. We applied this approach to 2 independent Italian cohorts of patients with both clinical and molecular diagnosis of 21OHD-CAH from mainland Italy (N = 240) and Sardinia (N = 53). We inferred q estimates of 2.87% and 1.83%, corresponding to a prevalence of 1/1214 and 1/2986, respectively. CYP21A2 mutational spectra were quite discrepant between the 2 cohorts, with V281L representing 74% of all the mutations detected in Sardinia vs 37% in mainland Italy. These findings provide an updated fine-grained picture of 21OHD-CAH genetic epidemiology in Italy and suggest the need for a screening approach suitable to the detection of the largest number of clinically significant forms of CAH.
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Affiliation(s)
- A Gialluisi
- URT-IGB, IRCCS "Istituto Neurologico Mediterraneo Neuromed", Pozzilli, Italy
| | - S Menabò
- Department of Medical and Surgical Sciences, Pediatric Unit, "S.Orsola-Malpighi" University-Hospital, Bologna, Italy
| | - L Baldazzi
- Department of Women, Children and Urological Diseases, Pediatric Unit, "S.Orsola-Malpighi" University-Hospital, Bologna, Italy
| | - L Casula
- Pediatric Endocrine Unit, Pediatric Hospital Microcitemico "A. Cao," AO Brotzu, Cagliari, Italy
| | - A Meloni
- II Clinica Pediatrica, Pediatric Hospital Microcitemico "A. Cao," AO Brotzu, Cagliari, Italy
| | - M C Farci
- Endocrinology and Diabetology Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - S Mariotti
- Endocrinology and Diabetology Unit, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - L Balestrino
- Medical Genetics Unit, "R.Binaghi" Hospital, Cagliari, Italy
| | - R Ortolano
- Department of Medical and Surgical Sciences, Pediatric Unit, "S.Orsola-Malpighi" University-Hospital, Bologna, Italy
| | - S Murru
- Human Genetics Unit, Pediatric Hospital Microcitemico "A. Cao," AO Brotzu, Cagliari, Italy
| | - C Carcassi
- Medical Genetics Unit and Department of Medical Sciences and Public Health, University of Cagliari, "R.Binaghi" Hospital, Cagliari, Italy
| | - S Loche
- Pediatric Endocrine Unit, Pediatric Hospital Microcitemico "A. Cao," AO Brotzu, Cagliari, Italy
| | - A Balsamo
- Department of Medical and Surgical Sciences, Pediatric Unit, "S.Orsola-Malpighi" University-Hospital, Bologna, Italy
| | - G Romeo
- Medical Genetics Unit, Department of Medical and Surgical Sciences, "S.Orsola-Malpighi" University-Hospital, Bologna, Italy
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6
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Mahmoud SK, Khorrami A, Rafeey M, Ghergherehchi R, Sima MD. Molecular analysis of glycogen storage disease type Ia in Iranian Azeri Turks: identification of a novel mutation. J Genet 2017; 96:19-23. [PMID: 28360385 DOI: 10.1007/s12041-016-0734-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycogen storage diseases (GSDs) are caused by abnormalities in enzymes that are involved in the regulation of gluconeogenesis and glycogenolysis. GSD I, an autosomal recessive metabolic disorder, is the most common GSD and has four subtypes. Here, we examined GSD Ia caused by the defective glucose-6-phosphatase catalytic (G6PC) gene. We investigated the frequency of GSD Ia and clarified its molecular aspect in patients with the main clinical and biochemical characteristics of GSD, including 37 unrelated patients with a mean age of three years at the time of diagnosis. All patients belonged to the Azeri Turkish population. Hypoglycaemia and hypertriglyceridaemia were the most frequent laboratory findings. Mutations were detected by performing direct sequencing. Mutation analysis of the G6PC gene revealed that GSD Ia accounted for 11% in GSD patients with involvement of liver. Three patients were homozygous for R83C mutation. In addition, a novel stop mutation, Y85X, was identified in a patient with the typical features of GSD Ia.
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Affiliation(s)
- Shekari Khaniani Mahmoud
- Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz 5166/15731, Iran.
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7
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Palombo F, Al-Wardy N, Ruscone GAG, Oppo M, Kindi MNA, Angius A, Al Lamki K, Girotto G, Giangregorio T, Benelli M, Magi A, Seri M, Gasparini P, Cucca F, Sazzini M, Al Khabori M, Pippucci T, Romeo G. A novel founder MYO15A frameshift duplication is the major cause of genetic hearing loss in Oman. J Hum Genet 2016; 62:259-264. [PMID: 27734841 DOI: 10.1038/jhg.2016.120] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 12/16/2022]
Abstract
The increased risk for autosomal recessive disorders is one of the most well-known medical implications of consanguinity. In the Sultanate of Oman, a country characterized by one of the highest rates of consanguineous marriages worldwide, prevalence of genetic hearing loss (GHL) is estimated to be 6/10 000. Families of GHL patients have higher consanguinity rates than the general Omani population, indicating a major role for recessive forms. Mutations in GJB2, the most commonly mutated GHL gene, have been sporadically described. We collected 97 DNA samples of GHL probands, affected/unaffected siblings and parents from 26 Omani consanguineous families. Analyzing a first family by whole-exome sequencing, we identified a novel homozygous frameshift duplication (c.1171_1177dupGCCATCT) in MYO15A, the gene linked to the deafness locus DFNB3. This duplication was then found in a total of 8/26 (28%) families, within a 849 kb founder haplotype. Reconstruction of haplotype structure at MYO15A surrounding genomic regions indicated that the founder haplotype branched out in the past two to three centuries from a haplotype present worldwide. The MYO15A duplication emerges as the major cause of GHL in Oman. These findings have major implications for the design of GHL diagnosis and prevention policies in Oman.
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Affiliation(s)
- Flavia Palombo
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Nadia Al-Wardy
- College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Guido Alberto Gnecchi Ruscone
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department BiGeA University of Bologna, Bologna, Italy
| | - Manuela Oppo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | | | - Andrea Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Center for Advanced Studies, Research, and Development in Sardinia (CRS4), Parco Scientifico e Tecnologico della Sardegna, Pula, Italy
| | - Khalsa Al Lamki
- College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - Giorgia Girotto
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Tania Giangregorio
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Matteo Benelli
- Department Laboratory, Careggi University Hospital, Firenze, Italy
| | - Alberto Magi
- Department of Experimental and Clinical Medicine, University of Florence, Firenze, Italy
| | - Marco Seri
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Paolo Gasparini
- Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy.,Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy.,Dipartimento di Scienze Biomediche, University of Sassari, Sassari, Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology & Centre for Genome Biology, Department BiGeA University of Bologna, Bologna, Italy
| | - Mazin Al Khabori
- Department of ENT, Al Nahda Hospital, Ministry of Health, Muscat, Oman
| | - Tommaso Pippucci
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
| | - Giovanni Romeo
- Medical Genetics Unit, Department of Medical and Surgical Sciences, Polyclinic Sant'Orsola-Malpighi, University of Bologna, Bologna, Italy
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8
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Jonker MA, Teeuw ME, Kelmemi W, Kharrat M, Chaabouni-Bouhamed H, Ten Kate LP. Estimating the Total Pathogenic Allele Frequency of Autosomal Recessive Disorders in Case of Consanguinity. Hum Hered 2015; 80:69-78. [PMID: 26540120 DOI: 10.1159/000438862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Estimating the total allele frequency of all pathogenic alleles of an autosomal recessive disease is not possible if only mutational data of a sample of affected individuals are available. However, if the affected individuals come from a population where consanguinity is not uncommon, this total allele frequency can be estimated by additionally using the positive individual inbreeding coefficients or an estimate of the population inbreeding coefficient. In this paper, we propose two estimators. METHODS/RESULTS We propose to estimate the total allele frequency by a conditional maximum likelihood estimator if a part of the affected individuals in the sample comes from consanguineous marriages with known inbreeding coefficients. A simulation study shows that this estimator is unbiased and robust. We propose a second estimator which is based on an estimate of the population inbreeding coefficient. The method is applied to mutational data and individual inbreeding coefficients of Tunisian patients with congenital adrenal hyperplasia. CONCLUSION Additionally using individual inbreeding coefficients or an estimate of the population inbreeding coefficient makes it possible to estimate the total allele frequency. Since consanguinity is commonly practiced in many parts of the world, the estimators proposed in the paper are of practical importance.
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Affiliation(s)
- Marianne A Jonker
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
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9
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Romdhane L, Messaoud O, Bouyacoub Y, Kerkeni E, Naouali C, Cherif Ben Abdallah L, Tiar A, Charfeddine C, Monastiri K, Chabchoub I, Hachicha M, Tadmouri GO, Romeo G, Abdelhak S. Comorbidity in the Tunisian population. Clin Genet 2015; 89:312-9. [PMID: 26010040 DOI: 10.1111/cge.12616] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/19/2015] [Accepted: 05/17/2015] [Indexed: 12/18/2022]
Abstract
Genetic diseases in the Tunisian population represent a real problem of public health as their spectrum encompasses more than 400 disorders. Their frequency and distribution in the country have been influenced by demographic, economic and social features especially consanguinity. In this article, we report on genetic disease association referred to as comorbidity and discuss factors influencing their expressivity. Seventy-five disease associations have been reported among Tunisian families. This comorbidity could be individual or familial. In 39 comorbid associations, consanguinity was noted. Twenty-one founder and 11 private mutations are the cause of 34 primary diseases and 13 of associated diseases. As the information dealing with this phenomenon is fragmented, we proposed to centralize it in this report in order to draw both clinicians' and researcher's attention on the occurrence of such disease associations in inbred populations as it makes genetic counseling and prenatal diagnosis challenging even when mutations are known.
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Affiliation(s)
- L Romdhane
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Department of Biology, Faculty of Science of Bizerte, Université Tunis Carthage, Zarzouna, Tunisia
| | - O Messaoud
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Y Bouyacoub
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - E Kerkeni
- Laboratoire de Pharmacologie, Faculté de Médecine de Monastir, Université de Monastir, Monastir, Tunisia
| | - C Naouali
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - L Cherif Ben Abdallah
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - A Tiar
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - C Charfeddine
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - K Monastiri
- EPS Fattouma Bourguiba, Centre de Maternité & de Néonatologie de Monastir, Service de Réanimation et de Médecine Néonatale, Monastir, Tunisia
| | - I Chabchoub
- Service de Pédiatrie, CHU Hédi Chaker, Sfax, Tunisia
| | - M Hachicha
- Service de Pédiatrie, CHU Hédi Chaker, Sfax, Tunisia
| | - G O Tadmouri
- Faculty of Public Health, Jinan University, Tripoli, Lebanon
| | - G Romeo
- Dipartimento di Scienze Mediche e Chirurgiche Policlinico Sant'Orsola-Malpighi, Unità Operativa di Genetica Medica, Bologna, Italy
| | - S Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
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10
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Jalkh N, Sahbatou M, Chouery E, Megarbane A, Leutenegger AL, Serre JL. Genome-wide inbreeding estimation within Lebanese communities using SNP arrays. Eur J Hum Genet 2014; 23:1364-9. [PMID: 25424710 DOI: 10.1038/ejhg.2014.246] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 08/29/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022] Open
Abstract
Consanguineous marriages have been widely practiced in several global communities with varying rates depending on religion, culture, and geography. In consanguineous marriages, parents pass to their children autozygous segments known as homozygous by descent segments. In this study, single-nucleotide polymorphisms were analyzed in 165 unrelated Lebanese people from Greek Orthodox, Maronite, Shiite and Sunni communities. Runs of homozygosity, total inbreeding levels, remote consanguinity, and population admixture and structure were estimated. The inbreeding coefficient value was estimated to be 1.61% in offspring of unrelated parents over three generations and 8.33% in offspring of first cousins. From these values, remote consanguinity values, resulting from genetic drift or recurrent consanguineous unions, were estimated in offspring of unrelated and first-cousin parents to be 0.61 and 1.2%, respectively. This remote consanguinity value suggests that for any unrelated marriages in Lebanon, the mates could be related as third cousins or as second cousins once removed. Under the assumption that 25% of marriages occur between first cousins, the mean inbreeding value of 2.3% may explain the increased incidence of recessive disease in offspring. Our analysis reveals a common ancestral population in the four Lebanese communities we studied.
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Affiliation(s)
- Nadine Jalkh
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon.,EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
| | | | - Eliane Chouery
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | - André Megarbane
- Unité de Génétique Médicale et Laboratoire associé INSERM à l'Unité UMR_S910, Faculté de Médecine, Université Saint-Joseph, Beirut, Lebanon
| | | | - Jean-Louis Serre
- EA 2493 « pathologie cellulaire & génétique, de la conception à la naissance », Université de Versailles-Saint Quentin en Yvelines, Yvelines, France
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11
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Gialluisi A, Incollu S, Pippucci T, Lepori MB, Zappu A, Loudianos G, Romeo G. The homozygosity index (HI) approach reveals high allele frequency for Wilson disease in the Sardinian population. Eur J Hum Genet 2013; 21:1308-11. [PMID: 23486543 PMCID: PMC3798848 DOI: 10.1038/ejhg.2013.43] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 01/13/2013] [Accepted: 02/07/2013] [Indexed: 12/28/2022] Open
Abstract
Wilson disease (WD) is an autosomal recessive disorder resulting in pathological progressive copper accumulation in liver and other tissues. The worldwide prevalence (P) is about 30/million, while in Sardinia it is in the order of 1/10,000. However, all of these estimates are likely to suffer from an underdiagnosis bias. Indeed, a recent molecular neonatal screening in Sardinia reported a WD prevalence of 1:2707. In this study, we used a new approach that makes it possible to estimate the allelic frequency (q) of an autosomal recessive disorder if one knows the proportion between homozygous and compound heterozygous patients (the homozygosity index or HI) and the inbreeding coefficient (F) in a sample of affected individuals. We applied the method to a set of 178 Sardinian individuals (3 of whom born to consanguineous parents), each with a clinical and molecular diagnosis of WD. Taking into account the geographical provenance of the parents of every patient within Sardinia (to make F computation more precise), we obtained a q=0.0191 (F=7.8 × 10(-4), HI=0.476) and a corresponding prevalence P=1:2732. This result confirms that the prevalence of WD is largely underestimated in Sardinia. On the other hand, the general reliability and applicability of the HI approach to other autosomal recessive disorders is confirmed, especially if one is interested in the genetic epidemiology of populations with high frequency of consanguineous marriages.
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Affiliation(s)
- Alessandro Gialluisi
- Unità Operativa di Genetica Medica, Dipartimento di Scienze Mediche e Chirurgiche Policlinico Sant'Orsola-Malpighi, Bologna, Italy
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Simona Incollu
- Dipartimento delle Scienze Biomediche e Biotecnologie, Università di Cagliari, Cagliari, Italy
| | - Tommaso Pippucci
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Maria Barbara Lepori
- Dipartimento delle Scienze Biomediche e Biotecnologie, Università di Cagliari, Cagliari, Italy
| | - Antonietta Zappu
- Dipartimento delle Scienze Biomediche e Biotecnologie, Università di Cagliari, Cagliari, Italy
| | | | - Giovanni Romeo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- European Genetics Foundation, Bologna, Italy
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12
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Affiliation(s)
- Alessandro Gialluisi
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Tommaso Pippucci
- Unità Operativa di Genetica Medica, Policlinico Sant'Orsola Malpighi, Bologna, Italy
| | - Giovanni Romeo
- 1] Unità Operativa di Genetica Medica, Policlinico Sant'Orsola Malpighi, Bologna, Italy [2] European Genetics Foundation, Bologna, Italy
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13
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Gialluisi A, Dediu D, Francks C, Fisher SE. Persistence and transmission of recessive deafness and sign language: new insights from village sign languages. Eur J Hum Genet 2013; 21:894-6. [PMID: 23321624 DOI: 10.1038/ejhg.2012.292] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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14
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Patrinos GP, Smith TD, Howard H, Al-Mulla F, Chouchane L, Hadjisavvas A, Hamed SA, Li XT, Marafie M, Ramesar RS, Ramos FJ, de Ravel T, El-Ruby MO, Shrestha TR, Sobrido MJ, Tadmouri G, Witsch-Baumgartner M, Zilfalil BA, Auerbach AD, Carpenter K, Cutting GR, Dung VC, Grody W, Hasler J, Jorde L, Kaput J, Macek M, Matsubara Y, Padilla C, Robinson H, Rojas-Martinez A, Taylor GR, Vihinen M, Weber T, Burn J, Qi M, Cotton RGH, Rimoin D. Human Variome Project country nodes: documenting genetic information within a country. Hum Mutat 2012; 33:1513-9. [PMID: 22753370 DOI: 10.1002/humu.22147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 06/04/2012] [Indexed: 11/09/2022]
Abstract
The Human Variome Project (http://www.humanvariomeproject.org) is an international effort aiming to systematically collect and share information on all human genetic variation. The two main pillars of this effort are gene/disease-specific databases and a network of Human Variome Project Country Nodes. The latter are nationwide efforts to document the genomic variation reported within a specific population. The development and successful operation of the Human Variome Project Country Nodes are of utmost importance to the success of Human Variome Project's aims and goals because they not only allow the genetic burden of disease to be quantified in different countries, but also provide diagnosticians and researchers access to an up-to-date resource that will assist them in their daily clinical practice and biomedical research, respectively. Here, we report the discussions and recommendations that resulted from the inaugural meeting of the International Confederation of Countries Advisory Council, held on 12th December 2011, during the 2011 Human Variome Project Beijing Meeting. We discuss the steps necessary to maximize the impact of the Country Node effort for developing regional and country-specific clinical genetics resources and summarize a few well-coordinated genetic data collection initiatives that would serve as paradigms for similar projects.
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Affiliation(s)
- George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.
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15
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Viennas E, Gkantouna V, Ioannou M, Georgitsi M, Rigou M, Poulas K, Patrinos GP, Tzimas G. Population-ethnic group specific genome variation allele frequency data: a querying and visualization journey. Genomics 2012; 100:93-101. [PMID: 22659238 DOI: 10.1016/j.ygeno.2012.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/09/2012] [Accepted: 05/21/2012] [Indexed: 01/28/2023]
Abstract
National/ethnic mutation databases aim to document the genetic heterogeneity in various populations and ethnic groups worldwide. We have previously reported the development and upgrade of FINDbase (www.findbase.org), a database recording causative mutations and pharmacogenomic marker allele frequencies in various populations around the globe. Although this database has recently been upgraded, we continuously try to enhance its functionality by providing more advanced visualization tools that would further assist effective data querying and comparisons. We are currently experimenting in various visualization techniques on the existing FINDbase causative mutation data collection aiming to provide a dynamic research tool for the worldwide scientific community. We have developed an interactive web-based application for population-based mutation data retrieval. It supports sophisticated data exploration allowing users to apply advanced filtering criteria upon a set of multiple views of the underlying data collection and enables browsing the relationships between individual datasets in a novel and meaningful way.
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Affiliation(s)
- Emmanouil Viennas
- Department of Computer Engineering and Informatics, University of Patras, Patras, Greece
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