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Salehi Z, Naghizadeh MM, Ezabadi SG, Ebrahimitirtashi A, Abbasi Kasbi N, Khodaie F, Aliyari S, Ashtari F, Baghbanian SM, Nabavi SM, Hosseini S, Razazian N, Shaygannejad V, Majdi-Nasab N, Harirchian MH, Bayati A, Kamali H, Hosseni Nejad Mir N, Beladi Moghadam N, Poursadeghfard M, Mozhdehipanah H, Jalali N, Nahayati MA, Faraji F, Kamyari N, Sahraian MA, Maghbooli Z, Eskandarieh S. Consanguineous marriage among familial multiple sclerosis subjects: A national registry-based study. Heliyon 2024; 10:e32946. [PMID: 38984301 PMCID: PMC11231546 DOI: 10.1016/j.heliyon.2024.e32946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/12/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
Background The rising prevalence of familial multiple sclerosis (MS) in Iran has spurred interest in the potential impact of parental consanguinity on the risk of developing the disease. This study aims to aggregate current knowledge on parental consanguinity and its possible effect on MS risk, particularly among familial MS patients from various regions and ethnicities in Iran. The objective is to enhance the understanding of MS genetics and encourage further research in this field. Materials and methods A cross-sectional study was conducted on clinically definite familial MS (FMS) patients registered in the nationwide MS registry of Iran (NMSRI). Data were extracted and supplemented with structured telephone follow-ups to gather detailed histories of MS in relatives and the familial relationships of the patients' parents. A family penetration score was proposed. Descriptive statistics and inferential statistical tests were used to analyze the data at a significance level of 0.05, adhering to ethical guidelines. Results Out of 19,911 individuals registered in the NMSRI, 2307 FMS patients across 13 provinces were included in the final analysis. Among these, 385 (19.3 %) reported parental consanguinity, with 283 (14.2 %) having parents who were cousins and 102 (5.1 %) having parents who were distant relatives. The data showed no significant association between parental kinship and variables such as MS phenotype, number of affected relatives with MS, hospitalization rates, and expanded disability status scale score. Similarly, MS severity did not differ based on parental consanguinity (P-value >0.05). While the rate of consanguineous marriage was higher among patients with an onset age less than 18 years, there was no statistically significant difference in disease onset age based on parental consanguinity status. Conclusion Our study highlights the complexity of factors influencing MS development, including genetic and environmental components. These results highlight the need for further research to achieve a more comprehensive understanding of MS etiology.
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Affiliation(s)
- Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Sajjad Ghane Ezabadi
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Ebrahimitirtashi
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Naghmeh Abbasi Kasbi
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Faezeh Khodaie
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Aliyari
- Division of Applied Bioinformatics, German Cancer Research Center DKFZ Heidelberg, Heidelberg, Germany
| | - Fereshteh Ashtari
- Isfahan Neurosciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Seyed Massood Nabavi
- Department of Regenerative Medicine, Royan Institute for Stem Cell Technology and Biology, Tehran, Iran
| | - Samaneh Hosseini
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazanin Razazian
- Department of Neurology, School of Medicine, Imam Reza Hospital, Kermanshah University of Medical Sciences, Iran
| | - Vahid Shaygannejad
- Isfahan Neurosciences Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nastaran Majdi-Nasab
- Musculoskeletal Rehabilitation Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hossein Harirchian
- Department of Neurology, School of Medicine, Iranian Center of Neurological Research, Neuroscience Institute, Imam Khomeini Hospital, Tehran University of Medical Sciences, Iran
| | - Asghar Bayati
- Department of Neurology, Shahrekord University of Medical Sciences and Health Services, Shahrekord, Iran
| | - Hoda Kamali
- Neurology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Nahid Hosseni Nejad Mir
- Department of Internal Medicine, School of Medicine, Shohadaye Ashayer Hospital, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Nahid Beladi Moghadam
- Department of Neurology, School of Medicine, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Iran
| | - Maryam Poursadeghfard
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Nazanin Jalali
- Department of Neurology, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Mohammad Ali Nahayati
- Department of Neurology, Ghaem Hospital, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fardin Faraji
- Department of Neurology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Naser Kamyari
- Department of Biostatistics and Epidemiology, School of Health, Abadan University of Medical Sciences, Abadan, Iran
| | - Mohammad Ali Sahraian
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zhila Maghbooli
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sharareh Eskandarieh
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
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Khan MR, Akbari A, Nicholas TJ, Castillo-Madeen H, Ajmal M, Haq TU, Laan M, Quinlan AR, Ahuja JS, Shah AA, Conrad DF. Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP. Andrology 2023:10.1111/andr.13570. [PMID: 38073178 PMCID: PMC11163020 DOI: 10.1111/andr.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/29/2023] [Accepted: 11/30/2023] [Indexed: 06/12/2024]
Abstract
BACKGROUND There are likely to be hundreds of monogenic forms of human male infertility. Whole genome sequencing (WGS) is the most efficient way to make progress in mapping the causative genetic variants, and ultimately improve clinical management of the disease in each patient. Recruitment of consanguineous families is an effective approach to ascertain the genetic forms of many diseases. OBJECTIVES To apply WGS to large consanguineous families with likely hereditary male infertility and identify potential genetic cases. MATERIALS AND METHODS We recruited seven large families with clinically diagnosed male infertility from rural Pakistan, including five with a history of consanguinity. We generated WGS data on 26 individuals (3-5 per family) and analyzed the resulting data with a computational pipeline to identify potentially causal single nucleotide variants, indels, and copy number variants. RESULTS We identified plausible genetic causes in five of the seven families, including a homozygous 10 kb deletion of exon 2 in a well-established male infertility gene (M1AP), and biallelic missense substitutions (SPAG6, CCDC9, TUBA3C) and an in-frame hemizygous deletion (TKTL1) in genes with emerging relevance. DISCUSSION AND CONCLUSION The rate of genetic findings using the current approach (71%) was much higher than what we recently achieved using whole-exome sequencing (WES) of unrelated singleton cases (20%). Furthermore, we identified a pathogenic single-exon deletion in M1AP that would be undetectable by WES. Screening more families with WGS, especially in underrepresented populations, will further reveal the types of variants underlying male infertility and accelerate the use of genetics in the patient management.
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Affiliation(s)
- Muhammad Riaz Khan
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Arvand Akbari
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Thomas J Nicholas
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Helen Castillo-Madeen
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Muhammad Ajmal
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Taqweem Ul Haq
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, USA
| | - Jasvinder S Ahuja
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
| | - Aftab Ali Shah
- Department of Biotechnology, Faculty of Biological Sciences, University of Malakand, Chakdara, Khyber Pakhtunkhwa, Pakistan
| | - Donald F Conrad
- Center for Embryonic Cell & Gene Therapy, Oregon Health & Science University, Portland, Oregon, USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, Oregon, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
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Siddique A, Fatima W, Shahid N. Association of common BRCA1 variants with predisposition to breast tumors in Pakistan. Ann Hum Genet 2023; 87:222-231. [PMID: 37191028 DOI: 10.1111/ahg.12511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 01/19/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
BRCA1 variants are extensively associated with increased risk of breast cancer. Early detection and screening of variants is still rare in developing countries. Here, we investigated six BRCA1 variants in 300 subjects from Pakistani population using tetra amplification-refractory mutation system (T-ARMS) PCR. Our results indicate significant association of BRCA1 variants rs8176237 (AA; OR 8.2, 95% CI 3.02-22.64, p < 0.0001), rs1060915 (CC; OR 4.29, 95% CI 1.94-9.48, p = 0.0003), and rs799912 (TT; OR 3.16, 95% CI 1.44-6.94, p = 0.004) with up to 8-fold increased odds of breast cancer under recessive model. Furthermore, BRCA1 haplotypes AGCACG and AGCCCT were associated with up to 18% breast cancer cases (p < 0.05). Additionally, we found association of these variants with up to 11-fold increased odds of benign breast tumors. Linkage disequilibrium (LD) block-wise analysis revealed haplotypes GCAC and ATAC were associated with significantly increased risk. To our knowledge, this is the first study that identifies the association of these BRCA1 variants with breast tumors in Pakistani population. In conclusion, BRCA1 variants investigated in the present study are associated with high odds of benign- and malignant breast tumors. Studies with bigger sample size may help early detection and screening to reduce the odds of breast cancer.
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Affiliation(s)
- Ayesha Siddique
- Department System Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute for Environmental Research (Biology V), RWTH Aachen University, Aachen, Germany
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Warda Fatima
- Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Naeem Shahid
- Department System Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
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Trajanoska K, Bhérer C, Taliun D, Zhou S, Richards JB, Mooser V. From target discovery to clinical drug development with human genetics. Nature 2023; 620:737-745. [PMID: 37612393 DOI: 10.1038/s41586-023-06388-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 06/29/2023] [Indexed: 08/25/2023]
Abstract
The substantial investments in human genetics and genomics made over the past three decades were anticipated to result in many innovative therapies. Here we investigate the extent to which these expectations have been met, excluding cancer treatments. In our search, we identified 40 germline genetic observations that led directly to new targets and subsequently to novel approved therapies for 36 rare and 4 common conditions. The median time between genetic target discovery and drug approval was 25 years. Most of the genetically driven therapies for rare diseases compensate for disease-causing loss-of-function mutations. The therapies approved for common conditions are all inhibitors designed to pharmacologically mimic the natural, disease-protective effects of rare loss-of-function variants. Large biobank-based genetic studies have the power to identify and validate a large number of new drug targets. Genetics can also assist in the clinical development phase of drugs-for example, by selecting individuals who are most likely to respond to investigational therapies. This approach to drug development requires investments into large, diverse cohorts of deeply phenotyped individuals with appropriate consent for genetically assisted trials. A robust framework that facilitates responsible, sustainable benefit sharing will be required to capture the full potential of human genetics and genomics and bring effective and safe innovative therapies to patients quickly.
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Affiliation(s)
- Katerina Trajanoska
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Claude Bhérer
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Daniel Taliun
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - Sirui Zhou
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada
| | - J Brent Richards
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Department of Epidemiology and Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Vincent Mooser
- Canada Excellence Research Chair in Genomic Medicine, Department of Human Genetics, Faculty of Medicine and Health Sciences, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, Quebec, Canada.
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Marwan M, Dawood M, Ullah M, Shah IU, Khan N, Hassan MT, Karam M, Rawlins LE, Baple EL, Crosby AH, Saleha S. Unravelling the genetic basis of retinal dystrophies in Pakistani consanguineous families. BMC Ophthalmol 2023; 23:205. [PMID: 37165311 PMCID: PMC10170854 DOI: 10.1186/s12886-023-02948-8] [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: 10/19/2022] [Accepted: 04/26/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Retinitis Pigmentosa (RP) is a clinically and genetically progressive retinal dystrophy associated with severe visual impairments and sometimes blindness, the most common syndromic form of which is Usher syndrome (USH). This study aimed to further increase understanding of the spectrum of RP in the Khyber Pakhtunkhwa region of Pakistan. METHODOLOGY Four consanguineous families of Pashtun ethnic group were investigated which were referred by the local collaborating ophthalmologists. In total 42 individuals in four families were recruited and investigated using whole exome and dideoxy sequencing. Among them, 20 were affected individuals including 6 in both family 1 and 2, 5 in family 3 and 3 in family 4. RESULT Pathogenic gene variants were identified in all four families, including two in cone dystrophy and RP genes in the same family (PDE6C; c.480delG, p.Asn161ThrfsTer33 and TULP1; c.238 C > T, p.Gln80Ter) with double-homozygous individuals presenting with more severe disease. Other pathogenic variants were identified in MERTK (c.2194C > T, p.Arg732Ter), RHO (c.448G > A, p.Glu150Lys) associated with non-syndromic RP, and MYO7A (c.487G > A, p.Gly163Arg) associated with USH. In addition, the reported variants were of clinical significance as the PDE6C variant was detected novel, whereas TULP1, MERTK, and MYO7A variants were detected rare and first time found segregating with retinal dystrophies in Pakistani consanguineous families. CONCLUSIONS This study increases knowledge of the genetic basis of retinal dystrophies in families from Pakistan providing information important for genetic testing and diagnostic provision particularly from the Khyber Pakhtunkhwa region.
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Affiliation(s)
- Muhammad Marwan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, 4031, Switzerland
- Department of Ophthalmology, University of Basel, Basel, 4056, Switzerland
| | - Irfan Ullah Shah
- Department of Ophthalmology, KMU Institute of Medical Sciences KIMS, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Taimur Hassan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Muhammad Karam
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan
| | - Lettie E Rawlins
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, UK
| | - Emma L Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Andrew H Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Khyber Pakhtunkhwa, 26000, Pakistan.
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Streață I, Caramizaru A, Riza AL, Șerban-Sosoi S, Pîrvu A, Cara ML, Cucu MG, Dobrescu AM, Shelby ES, Albeanu A, Burada F, Ioana M. Pathogenic Copy Number Variations Involved in the Genetic Etiology of Syndromic and Non-Syndromic Intellectual Disability-Data from a Romanian Cohort. Diagnostics (Basel) 2022; 12:diagnostics12123137. [PMID: 36553144 PMCID: PMC9777762 DOI: 10.3390/diagnostics12123137] [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: 11/08/2022] [Revised: 11/29/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
The investigation of unexplained global developmental delay (GDD)/intellectual disability (ID) is challenging. In low resource settings, patients may not follow a standardized diagnostic process that makes use of the benefits of advanced technologies. Our study aims to explore the contribution of chromosome microarray analysis (CMA) in identifying the genetic etiology of GDD/ID. A total of 371 Romanian patients with syndromic or non-syndromic GDD/ID, without epilepsy, were routinely evaluated in tertiary clinics. A total of 234 males (63.07%) and 137 (36.93%) females, with ages ranging from 6 months to 40 years (median age of 5.5 years), were referred for genetic diagnosis between 2015 and 2022; testing options included CMA and/or karyotyping. Agilent Technologies and Oxford Gene Technology CMA workflows were used. Pathogenic/likely pathogenic copy number variations (pCNVs) were identified in 79 patients (21.29%). Diagnosis yield was comparable between mild ID (17.05%, 22/129) and moderate/severe ID 23.55% (57/242). Higher rates were found in cases where facial dysmorphism (22.97%, 71/309), autism spectrum disorder (ASD) (19.11%, 26/136) and finger anomalies (20%, 27/96) were associated with GDD/ID. GDD/ID plus multiple congenital anomalies (MCA) account for the highest detection rates at 27.42% (17/62). pCNVs represent a significant proportion of the genetic causes of GDD/ID. Our study confirms the utility of CMA in assessing GDD/ID with an uncertain etiology, especially in patients with associated comorbidities.
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Affiliation(s)
- Ioana Streață
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Alexandru Caramizaru
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Anca-Lelia Riza
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Simona Șerban-Sosoi
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Andrei Pîrvu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Monica-Laura Cara
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Mihai-Gabriel Cucu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Amelia Mihaela Dobrescu
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
| | - Ro-NMCA-ID Group
- The Ro-NMCA-ID (RoNetwork Multiple Congenital Abnormalities with ID) Member of European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability (ERN-ITHACA) [EU Framework Partnership Agreement ID: 3HP-HP-FPA ERN-01-2016/739516], 400011 Timisoara, Romania
| | | | | | - Elena-Silvia Shelby
- National University Center for Children’s Neurorehabilitation “Dr. Nicolae Robănescu”, 44 Dumitru Mincă Street, District 4, 041408 Bucharest, Romania
| | - Adriana Albeanu
- Department of Pediatric Neurology, Clinical Emergency Children Hospital Brasov, Nicopole Street No. 45, 500063 Brasov, Romania
| | - Florin Burada
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
- Correspondence: (A.-L.R.); (F.B.)
| | - Mihai Ioana
- Regional Centre of Medical Genetics Dolj, Emergency County Hospital Craiova, 200642 Craiova, Romania
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania
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Susgun S, Kasan K, Yucesan E. Gene Hunting Approaches through the Combination of Linkage Analysis with Whole-Exome Sequencing in Mendelian Diseases: From Darwin to the Present Day. Public Health Genomics 2022; 24:207-217. [PMID: 34237751 DOI: 10.1159/000517102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/27/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND In the context of medical genetics, gene hunting is the process of identifying and functionally characterizing genes or genetic variations that contribute to disease phenotypes. In this review, we would like to summarize gene hunting process in terms of historical aspects from Darwin to now. For this purpose, different approaches and recent developments will be detailed. SUMMARY Linkage analysis and association studies are the most common methods in use for explaining the genetic background of hereditary diseases and disorders. Although linkage analysis is a relatively old approach, it is still a powerful method to detect disease-causing rare variants using family-based data, particularly for consanguineous marriages. As is known that, consanguineous marriages or endogamy poses a social problem in developing countries, however, this same condition also provides a unique opportunity for scientists to identify and characterize pathogenic variants. The rapid advancements in sequencing technologies and their parallel implementation together with linkage analyses now allow us to identify the candidate variants related to diseases in a relatively short time. Furthermore, we can now go one step further and functionally characterize the causative variant through in vitro and in vivo studies and unveil the variant-phenotype relationships on a molecular level more robustly. Key Messages: Herein, we suggest that the combined analysis of linkage and exome analysis is a powerful and precise tool to diagnose clinically rare and recessively inherited conditions.
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Affiliation(s)
- Seda Susgun
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey.,Graduate School of Health Sciences, Istanbul University, Istanbul, Turkey
| | - Koray Kasan
- Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
| | - Emrah Yucesan
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Turkey
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Andres EM, Neely HL, Hafeez H, Yasmin T, Kausar F, Basra MAR, Raza MH. Study of rare genetic variants in TM4SF20, NFXL1, CNTNAP2, and ATP2C2 in Pakistani probands and families with language impairment. Meta Gene 2021; 30. [PMID: 34540591 DOI: 10.1016/j.mgene.2021.100966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Language impairment (LI) is highly heritable and aggregates in families. Genetic investigation of LI has revealed many chromosomal regions and genes of interest, though very few studies have focused on rare variant analysis in non-English speaking or non-European samples. We selected four candidate genes (TM4SF20, NFXL1, CNTNAP2 and ATP2C2) strongly suggested for specific language impairment (SLI), a subtype of LI, and investigated rare protein coding variants through Sanger sequencing of probands with LI ascertained from Pakistan. The probands and their family members completed a speech and language family history questionnaire and a vocabulary measure, the Peabody Picture Vocabulary Test-fourth edition (PPVT-4), translated to Urdu, the national language of Pakistan. Our study aimed to determine the significance of rare variants in these SLI candidate genes through segregation analysis in a novel population with a high rate of consanguinity. In total, we identified 16 rare variants (according to the rare MAF in the global population in gnomAD v2.1.1 database exomes), including eight variants with a MAF <0.5 % in the South Asian population. Most of the identified rare variants aggregated in proband's families, one rare variant (c.*9T>C in CNTNAP2) co-segregated in a small family (PKSLI-64) and another (c.2465C>T in ATP2C2) co-segregated in the proband branch (PKSLI-27). The lack of complete co-segregation of most of the identified rare variants indicates that while these genes could be involved in overall risk for LI, other genes are likely involved in LI in this population. Future investigation of these consanguineous families has the potential to expand our understanding of gene function related to language acquisition and impairment.
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Affiliation(s)
- Erin M Andres
- University of Kansas, Child Language Doctoral Program
| | | | - Huma Hafeez
- School of Chemistry, University of the Punjab
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Spedicati B, Cocca M, Palmisano R, Faletra F, Barbieri C, Francescatto M, Mezzavilla M, Morgan A, Pelliccione G, Gasparini P, Girotto G. Natural human knockouts and Mendelian disorders: deep phenotyping in Italian isolates. Eur J Hum Genet 2021; 29:1272-1281. [PMID: 33727708 PMCID: PMC8384846 DOI: 10.1038/s41431-021-00850-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/30/2020] [Accepted: 02/23/2021] [Indexed: 02/02/2023] Open
Abstract
Whole genome sequencing (WGS) allows the identification of human knockouts (HKOs), individuals in whom loss of function (LoF) variants disrupt both alleles of a given gene. HKOs are a valuable model for understanding the consequences of genes function loss. Naturally occurring biallelic LoF variants tend to be significantly enriched in "genetic isolates," making these populations specifically suited for HKO studies. In this work, a meticulous WGS data analysis combined with an in-depth phenotypic assessment of 947 individuals from three Italian genetic isolates led to the identification of ten biallelic LoF variants in ten OMIM genes associated with known autosomal recessive diseases. Notably, only a minority of the identified HKOs (C7, F12, and GPR68 genes) displayed the expected phenotype. For most of the genes, instead, (ACADSB, FANCL, GRK1, LGI4, MPO, PGAM2, and RP1L1), the carriers showed none or few of the signs and symptoms typically associated with the related diseases. Of particular interest is a case presenting with a FANCL biallelic LoF variant and a positive diepoxybutane test but lacking a full Fanconi anemia phenotypic spectrum. Identifying KO subjects displaying expected phenotypes suggests that the lack of correct genetic diagnoses may lead to inappropriate and delayed treatment. In contrast, the presence of HKOs with phenotypes deviating from the expected patterns underlines how LoF variants may be responsible for broader phenotypic spectra. Overall, these results highlight the importance of in-depth phenotypical characterization to understand the role of LoF variants and the advantage of studying these variants in genetic isolates.
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Affiliation(s)
- Beatrice Spedicati
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Massimiliano Cocca
- grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Roberto Palmisano
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Flavio Faletra
- grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Caterina Barbieri
- grid.18887.3e0000000417581884Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, Italy
| | - Margherita Francescatto
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Massimo Mezzavilla
- grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Anna Morgan
- grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Giulia Pelliccione
- grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Paolo Gasparini
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy ,grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
| | - Giorgia Girotto
- grid.5133.40000 0001 1941 4308Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy ,grid.418712.90000 0004 1760 7415Institute for Maternal and Child Health – I.R.C.C.S. “Burlo Garofolo”, Trieste, Italy
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10
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Ben-Yosef N, Frampton M, Schiff ER, Daher S, Abu Baker F, Safadi R, Israeli E, Segal AW, Levine AP. Genetic analysis of four consanguineous multiplex families with inflammatory bowel disease. Gastroenterol Rep (Oxf) 2021; 9:521-532. [PMID: 34925849 PMCID: PMC8677555 DOI: 10.1093/gastro/goab007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/03/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Family studies support a genetic predisposition to inflammatory bowel diseases (IBD), but known genetic variants only partially explain the disease heritability. Families with multiple affected individuals potentially harbour rare and high-impact causal variants. Long regions of homozygosity due to recent inbreeding may increase the risk of individuals bearing homozygous loss-of-function variants. This study aimed to identify rare and homozygous genetic variants contributing to IBD. Methods Four families with known consanguinity and multiple cases of IBD were recruited. In a family-specific analysis, we utilised homozygosity mapping complemented by whole-exome sequencing. Results We detected a single region of homozygosity shared by Crohn's disease cases from a family of Druze ancestry, spanning 2.6 Mb containing the NOD2 gene. Whole-exome sequencing did not identify any potentially damaging variants within the region, suggesting that non-coding variation may be involved. In addition, affected individuals in the families harboured several rare and potentially damaging homozygous variants in genes with a role in autophagy and innate immunity including LRRK1, WHAMM, DENND3, and C5. Conclusion This study examined the potential contribution of rare, high-impact homozygous variants in consanguineous families with IBD. While the analysis was not designed to achieve statistical significance, our findings highlight genes or loci that warrant further research. Non-coding variants affecting NOD2 may be of importance in Druze patients with Crohn's disease.
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Affiliation(s)
- Noam Ben-Yosef
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Matthew Frampton
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Elena R Schiff
- Institute of Ophthalmology, Moorfields Eye Hospital, University College London, London, UK
| | - Saleh Daher
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Fadi Abu Baker
- Institue of Gastroenterology and Hepatology, Hillel Yaffe Medical Center, Hadera, Israel
| | - Rifaat Safadi
- Institute of Gastroenterology and Liver disease, Hadassah Medical Center, Jerusalem, Israel
| | - Eran Israeli
- Institute of Gastroenterology and Liver disease, E. Wolfson Medical Center, Holon, Israel
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College London, London, UK
- Department of Pathology, University College London, London, UK
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11
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Alshammary AF, Khan IA. Screening of Obese Offspring of First-Cousin Consanguineous Subjects for the Angiotensin-Converting Enzyme Gene with a 287-bp Alu Sequence. J Obes Metab Syndr 2021; 30:63-71. [PMID: 33653971 PMCID: PMC8017326 DOI: 10.7570/jomes20086] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/19/2020] [Accepted: 01/26/2021] [Indexed: 12/22/2022] Open
Abstract
Background Consanguinity, defined as a blood relation between couples, is associated with genetic diseases in their offspring. In Saudi Arabia, obesity is considered a major health problem associated with increased risks of cardiovascular disease, insulin resistance, and type 2 diabetes mellitus. Angiotensin-converting enzyme (ACE) with insertion (I) and deletion (D) polymorphisms of an Alu-287 bp sequence has been implicated in multiple metabolic disorders, including obesity. To date, no studies have been conducted in the Saudi population regarding the ACE gene in consanguineous offspring with obesity. Therefore, the present study aimed to investigate genetic associations in offspring of first cousins, and specifically the relationship between obesity and ACE (Alu-287 bp) was evaluated in the Saudi population. Methods In total, 91 cases of obesity in the offspring of first-cousin couples and 100 control subjects without obesity but with a family history of consanguinity were included. Using genomic DNA, ACE ID polymorphisms between the cases and controls were evaluated by polymerase chain reaction. Results There were strong differences in the height, weight, and body mass index between the cases and controls (P<0.001). A genotype analysis confirmed the strong association with allele frequencies (P<0.001; odds ratio, 4.902; 95% confidence interval, 2.867–8.379) when compared between the cases and controls. One-way analysis of variance showed a positive correlation with height and logistic regression (covariance) that could not be strongly correlated (P>0.05). Conclusion In conclusion, the ACE gene polymorphism was found, through allele frequencies, to be associated with obesity in the offspring of consanguineous first cousins in the Saudi population.
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Affiliation(s)
- Amal F Alshammary
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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12
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Younes N, Syed N, Yadav SK, Haris M, Abdallah AM, Abu-Madi M. A Whole-Genome Sequencing Association Study of Low Bone Mineral Density Identifies New Susceptibility Loci in the Phase I Qatar Biobank Cohort. J Pers Med 2021; 11:jpm11010034. [PMID: 33430342 PMCID: PMC7825795 DOI: 10.3390/jpm11010034] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022] Open
Abstract
Bone density disorders are characterized by a reduction in bone mass density and strength, which lead to an increase in the susceptibility to sudden and unexpected fractures. Despite the serious consequences of low bone mineral density (BMD) and its significant impact on human health, most affected individuals may not know that they have the disease because it is asymptomatic. Therefore, understanding the genetic basis of low BMD and osteoporosis is essential to fully elucidate its pathobiology and devise preventative or therapeutic approaches. Here we sequenced the whole genomes of 3000 individuals from the Qatar Biobank and conducted genome-wide association analyses to identify genetic risk factors associated with low BMD in the Qatari population. Fifteen variants were significantly associated with total body BMD (p < 5 × 10−8). Of these, five variants had previously been reported by and were directionally consistent with previous genome-wide association study data. Ten variants were new: six intronic variants located at six gene loci (MALAT1/TALAM1, FASLG, LSAMP, SAG, FAM189A2, and LOC101928063) and four intergenic variants. This first such study in Qatar provides a new insight into the genetic architecture of low BMD in the Qatari population. Nevertheless, more studies are needed to validate these findings and to elucidate the functional effects of these variants on low BMD and bone fracture susceptibility.
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Affiliation(s)
- Nadin Younes
- Biomedical Research Center, College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar;
| | - Najeeb Syed
- Biomedical Informatics Division, Sidra Medicine, Doha 26999, Qatar; (N.S.); (S.K.Y.); (M.H.)
| | - Santosh K. Yadav
- Biomedical Informatics Division, Sidra Medicine, Doha 26999, Qatar; (N.S.); (S.K.Y.); (M.H.)
| | - Mohammad Haris
- Biomedical Informatics Division, Sidra Medicine, Doha 26999, Qatar; (N.S.); (S.K.Y.); (M.H.)
| | - Atiyeh M. Abdallah
- Department of Biomedical Sciences, College of Health Sciences-QU Health, Doha 2713, Qatar;
- Biomedical and Pharmaceutical Research Unit-QU Health, Qatar University, Doha 2713, Qatar
| | - Marawan Abu-Madi
- Biomedical Research Center, College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar;
- Department of Biomedical Sciences, College of Health Sciences-QU Health, Doha 2713, Qatar;
- Biomedical and Pharmaceutical Research Unit-QU Health, Qatar University, Doha 2713, Qatar
- Correspondence: ; Tel.: +974-4403-7578; Fax: +974-4403-4801
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13
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Clavijo RI. Finding of parental consanguinity in men with infertility facilitates the discovery of specific genetic causes for nonobstructive azoospermia. F S Rep 2020; 1:173. [PMID: 34223238 PMCID: PMC8244363 DOI: 10.1016/j.xfre.2020.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Raul I Clavijo
- Department of Urology, University of California, Davis, Sacramento, California
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14
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Khan A, Miao Z, Umair M, Ullah A, Alshabeeb MA, Bilal M, Ahmad F, Rappold GA, Ansar M, Carapito R. Two Cases of Recessive Intellectual Disability Caused by NDST1 and METTL23 Variants. Genes (Basel) 2020; 11:E1021. [PMID: 32878022 PMCID: PMC7563614 DOI: 10.3390/genes11091021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/03/2022] Open
Abstract
Intellectual disability (ID) is a highly heterogeneous genetic condition with more than a thousand genes described so far. By exome sequencing of two consanguineous families presenting hallmark features of ID, we identified two homozygous variants in two genes previously associated with autosomal recessive ID: NDST1 (c.1966G>A; p.Asp656Asn) and METTL23 (c.310T>C; p.Phe104Leu). The segregation of the variants was validated by Sanger sequencing in all family members. In silico homology modeling of wild-type and mutated proteins revealed substantial changes in the secondary structure of both proteins, indicating a possible effect on function. The identification and validation of new pathogenic NDST1 and METTL23 variants in two cases of autosomal recessive ID further highlight the importance of these genes in proper brain function and development.
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Affiliation(s)
- Amjad Khan
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK;
- Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, No.1878 North Sichuan Road, Hongkou District, Shanghai 200081, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi Arabia;
| | - Amir Ullah
- Nephrology and Dialysis Unit, District Head Quarter Teaching Hospital, Bannu 28100, Pakistan;
| | - Mohammad A. Alshabeeb
- Developmental Medicine Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard-Health Affairs (MNGHA), Riyadh 11481, Saudi Arabia;
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Farooq Ahmad
- Department of Chemistry, Women University Swabi, Khyber Pakhtunkhwa 23430, Pakistan;
| | - Gudrun A. Rappold
- Department of Human Molecular Genetics, Institute of Human Genetics, Ruprecht-Karls-University, 69118 Heidelberg, Germany;
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; (M.B.); (M.A.)
| | - Raphael Carapito
- Laboratoire d’ImmunoRhumatologie Moléculaire, Plateforme GENOMAX, INSERM UMR_S 1109, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), LabEx TRANSPLANTEX, Université de Strasbourg, 67085 Strasbourg, France;
- Service d’Immunologie Biologique, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 1 Place de l’Hôpital, 67091 Strasbourg, France
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15
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Schnappauf O, Zhou Q, Moura NS, Ombrello AK, Michael DG, Deuitch N, Barron K, Stone DL, Hoffmann P, Hershfield M, Applegate C, Bjornsson HT, Beck DB, Witmer PD, Sobreira N, Wohler E, Chiorini JA, Center TAG, Dalgard CL, Center NIS, Kastner DL, Aksentijevich I. Deficiency of Adenosine Deaminase 2 (DADA2): Hidden Variants, Reduced Penetrance, and Unusual Inheritance. J Clin Immunol 2020; 40:917-926. [PMID: 32638197 PMCID: PMC7416912 DOI: 10.1007/s10875-020-00817-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/29/2020] [Indexed: 11/26/2022]
Abstract
PURPOSE Deficiency of adenosine deaminase 2 (DADA2) is an autosomal recessive disorder that manifests with fever, early-onset vasculitis, strokes, and hematologic dysfunction. This study aimed to identify disease-causing variants by conventional Sanger and whole exome sequencing in two families suspected to have DADA2 and non-confirmatory genotypes. ADA2 enzymatic assay confirmed the clinical diagnosis of DADA2. Molecular diagnosis was important to accurately identify other family members at risk. METHODS We used a variety of sequencing technologies, ADA2 enzymatic testing, and molecular methods including qRT-PCR and MLPA. RESULTS Exome sequencing identified heterozygosity for the known pathogenic variant ADA2: c.1358A>G, p.Tyr453Cys in a 14-year-old female with a history of ischemic strokes, livedo, and vasculitis. No second pathogenic variant could be identified. ADA2 enzymatic testing in combination with quantitative RT-PCR suggested a loss-of-function allele. Subsequent genome sequencing identified a canonical splice site variant, c.-47+2T>C, within the 5'UTR of ADA2. Two of her unaffected siblings were found to carry the same two pathogenic variants. A homozygous 800-bp duplication comprising exon 7 of ADA2 was identified in a 5-year-old female with features consistent with Diamond-Blackfan anemia (DBA). The duplication was missed by Sanger sequencing of ADA2, chromosomal microarray, and exome sequencing but was detected by MLPA in combination with long-read PCR sequencing. The exon 7 duplication was also identified in her non-symptomatic father and younger sister. CONCLUSIONS ADA2 pathogenic variants may not be detected by conventional sequencing and genetic testing and may require the incorporation of additional diagnostic methods. A definitive molecular diagnosis is crucial for all family members to make informed treatment decisions.
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Affiliation(s)
- Oskar Schnappauf
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA.
| | - Qing Zhou
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Natalia Sampaio Moura
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Amanda K Ombrello
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Drew G Michael
- Department of Laboratory Medicine, Center for Genetic Medicine Research, Children's National, Washington, DC, USA
| | - Natalie Deuitch
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Karyl Barron
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Deborah L Stone
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Patrycja Hoffmann
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Michael Hershfield
- Department of Medicine and Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Carolyn Applegate
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hans T Bjornsson
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
| | - David B Beck
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - P Dane Witmer
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John A Chiorini
- Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research (NIDCR), Bethesda, MD, USA
| | | | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Nih Intramural Sequencing Center
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Daniel L Kastner
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
| | - Ivona Aksentijevich
- Metabolic, Cardiovascular and Inflammatory Disease Genomics Branch, National Human Genome Research Institute (NHGRI), Bethesda, MD, USA
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16
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Freem L, Summers KM, Gheyas AA, Psifidi A, Boulton K, MacCallum A, Harne R, O’Dell J, Bush SJ, Hume DA. Analysis of the Progeny of Sibling Matings Reveals Regulatory Variation Impacting the Transcriptome of Immune Cells in Commercial Chickens. Front Genet 2019; 10:1032. [PMID: 31803225 PMCID: PMC6870463 DOI: 10.3389/fgene.2019.01032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/25/2019] [Indexed: 01/05/2023] Open
Abstract
There is increasing recognition that the underlying genetic variation contributing to complex traits influences transcriptional regulation and can be detected at a population level as expression quantitative trait loci. At the level of an individual, allelic variation in transcriptional regulation of individual genes can be detected by measuring allele-specific expression in RNAseq data. We reasoned that extreme variants in gene expression could be identified by analysis of inbred progeny with shared grandparents. Commercial chickens have been intensively selected for production traits. Selection is associated with large blocks of linkage disequilibrium with considerable potential for co-selection of closely linked "hitch-hiker alleles" affecting traits unrelated to the feature being selected, such as immune function, with potential impact on the productivity and welfare of the animals. To test this hypothesis that there is extreme allelic variation in immune-associated genes we sequenced a founder population of commercial broiler and layer birds. These birds clearly segregated genetically based upon breed type. Each genome contained numerous candidate null mutations, protein-coding variants predicted to be deleterious and extensive non-coding polymorphism. We mated selected broiler-layer pairs then generated cohorts of F2 birds by sibling mating of the F1 generation. Despite the predicted prevalence of deleterious coding variation in the genomic sequence of the founders, clear detrimental impacts of inbreeding on survival and post-hatch development were detected in only one F2 sibship of 15. There was no effect on circulating leukocyte populations in hatchlings. In selected F2 sibships we performed RNAseq analysis of the spleen and isolated bone marrow-derived macrophages (with and without lipopolysaccharide stimulation). The results confirm the predicted emergence of very large differences in expression of individual genes and sets of genes. Network analysis of the results identified clusters of co-expressed genes that vary between individuals and suggested the existence of trans-acting variation in the expression in macrophages of the interferon response factor family that distinguishes the parental broiler and layer birds and influences the global response to lipopolysaccharide. This study shows that the impact of inbreeding on immune cell gene expression can be substantial at the transcriptional level, and potentially opens a route to accelerate selection using specific alleles known to be associated with desirable expression levels.
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Affiliation(s)
- Lucy Freem
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
| | - Almas A. Gheyas
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Androniki Psifidi
- Department of Clinical Sciences and Services, Royal Veterinary College, University of London, London, United Kingdom
| | - Kay Boulton
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Amanda MacCallum
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Rakhi Harne
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jenny O’Dell
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, QLD, Australia
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17
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Distinct genetic variation and heterogeneity of the Iranian population. PLoS Genet 2019; 15:e1008385. [PMID: 31550250 PMCID: PMC6759149 DOI: 10.1371/journal.pgen.1008385] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Iran, despite its size, geographic location and past cultural influence, has largely been a blind spot for human population genetic studies. With only sparse genetic information on the Iranian population available, we pursued its genome-wide and geographic characterization based on 1021 samples from eleven ethnic groups. We show that Iranians, while close to neighboring populations, present distinct genetic variation consistent with long-standing genetic continuity, harbor high heterogeneity and different levels of consanguinity, fall apart into a cluster of similar groups and several admixed ones and have experienced numerous language adoption events in the past. Our findings render Iran an important source for human genetic variation in Western and Central Asia, will guide adequate study sampling and assist the interpretation of putative disease-implicated genetic variation. Given Iran's internal genetic heterogeneity, future studies will have to consider ethnic affiliations and possible admixture.
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18
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Kornilov SA, Tan M, Aljughaiman A, Naumova OY, Grigorenko EL. Genome-Wide Homozygosity Mapping Reveals Genes Associated With Cognitive Ability in Children From Saudi Arabia. Front Genet 2019; 10:888. [PMID: 31620175 PMCID: PMC6759945 DOI: 10.3389/fgene.2019.00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 08/22/2019] [Indexed: 11/28/2022] Open
Abstract
Recent studies of the genetic foundations of cognitive ability rely on large samples (in extreme, hundreds of thousands) of individuals from relatively outbred populations of mostly European ancestry. Hypothesizing that the genetic foundation of cognitive ability depends on the broader population-specific genetic context, we performed a genome-wide association study and homozygosity mapping of cognitive ability estimates obtained through latent variable modeling in a sample of 354 children from a consanguineous population of Saudi Arabia. Approximately half of the sample demonstrated significantly elevated homozygosity levels indicative of inbreeding, and among those with elevated levels, homozygosity was negatively associated with cognitive ability. Further homozygosity mapping identified a specific run, inclusive of the GRIA4 gene, that survived corrections for multiple testing for association with cognitive ability. The results suggest that in a consanguineous population, a notable proportion of the variance in cognitive ability in the normal range in children might be regulated by population-specific mechanisms such as patterns of elevated homozygosity. This observation has implications for the field's understanding of the etiological bases of intelligence and its variability around the world.
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Affiliation(s)
- Sergey A. Kornilov
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Mei Tan
- Department of Psychology, University of Houston, Houston, TX, USA
| | | | - Oxana Yu Naumova
- Department of Psychology, University of Houston, Houston, TX, USA
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena L. Grigorenko
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
- Child Study Center, Yale University, New Haven, CT, USA
- Moscow State University for Psychology and Education, Moscow, Russia
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19
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Alharbi KK, Al-Sheikh YA, Alsaadi MM, Mani B, Udayaraja GK, Kohailan M, Ali Khan I. Screening for obesity in the offspring of first-cousin consanguineous couples: A Phase-I study in Saudi Arabia. Saudi J Biol Sci 2019; 27:242-246. [PMID: 31889843 PMCID: PMC6933162 DOI: 10.1016/j.sjbs.2019.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/26/2019] [Accepted: 09/01/2019] [Indexed: 01/19/2023] Open
Abstract
Consanguineous or cousin marriages are very common in Saudi Arabia. However, owing to limited studies and insufficient knowledge about genetic diseases/disorders, many couples are unaware of the increased health risks for their offspring. Among the inherited and complex diseases from parents’ consanguinity, obesity is common; therefore, we examined the prevalence of obesity in the offspring of first-cousin consanguineous couples in Saudi Arabia. In this questionnaire-based study, 657 individuals (mean age = 18.7 ± 10.2 years; age range = 2–65 years) who were residing in Riyadh, Saudi Arabia participated. Among them, almost 90% were native Saudis. Participants mean body mass index (BMI) was 24.5 ± 9.1 kg/m2. Sex- stratified demographic details confirmed a significant association between age and BMI (p < .001). We confirmed that adolescents and adults were more prone to develop obesity. Adults and non-Saudi participants were three times more likely to develop obesity if they had first-cousin consanguineous parents than those who did not. Of the 30% of participants who were obese, 100 will be selected for Phase II, in which we plan to perform exome sequencing.
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Affiliation(s)
- Khalid Khalaf Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Yazeed A Al-Sheikh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muslim M Alsaadi
- Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | | | | | - Imran Ali Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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20
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The clinical benefit of array-based comparative genomic hybridization for detection of copy number variants in Czech children with intellectual disability and developmental delay. BMC Med Genomics 2019; 12:111. [PMID: 31337399 PMCID: PMC6651926 DOI: 10.1186/s12920-019-0559-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 07/16/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). METHODS In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). RESULTS In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. In our cohort pathogenic/likely pathogenic microdeletions were more frequent than microduplications (69%; 51/74 vs. 31%; 23/74) ranging in size from 0.395 Mb to 10.676 Mb (microdeletions) and 0.544 Mb to 8.156 Mb (microduplications), but their sizes were not significantly different (P = 0.83). The pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger than benign CNVs (median 0.394 Mb) (P < 0.00001) and likewise the pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger in size than VOUS (median 0.469 Mb) (P < 0.00001). CONCLUSIONS Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.
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Channeling hope: An ethnographic study of how research encounters become meaningful for families suffering from genetic disease in Pakistan. Soc Sci Med 2019; 228:103-110. [PMID: 30904814 PMCID: PMC6481513 DOI: 10.1016/j.socscimed.2019.03.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 11/24/2022]
Abstract
The Pakistani population has become particularly interesting for international genetic research due to its high rates of consanguinity. Based on 5 months fieldwork in Faisalabad among Pakistani genetic researchers from December 2015–January 2016 and February–April 2017 and interviews with 36 families and 14 researchers, this article focuses on research encounters. It demonstrates how genetic research figures in the lives of families affected by genetic medical conditions in light of their everyday struggles with disease, and considers their perspectives on destiny and hope. Through examining the potentials of the research encounter, we ask how research becomes meaningful in the lives of Pakistani families affected by genetic disease: how these families and individuals enable different modes of sharing tragic stories, contemplating hope and contesting logics of consanguinity. International genetic research depends on human raw material. If we wish to understand the precarious lives this research relies on, then the everyday struggles with disease, and the perspectives of families must be methodologically and theoretically engaged. Ethnographic study of genetic research encounters in Pakistan. Illustrates suffering and hopes of families responding to genetic disease. Discusses researcher-participant interaction in genetic research. Calls for a focus on how research participation becomes meaningful for families.
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Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics. Sci Rep 2018; 8:16583. [PMID: 30409984 PMCID: PMC6224454 DOI: 10.1038/s41598-018-34815-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Consanguineous populations of the Arabian Peninsula have been underrepresented in global efforts that catalogue human exome variability. We sequenced 291 whole exomes of unrelated, healthy native Arab individuals from Kuwait to a median coverage of 45X and characterised 170,508 single-nucleotide variants (SNVs), of which 21.7% were ‘personal’. Up to 12% of the SNVs were novel and 36% were population-specific. Half of the SNVs were rare and 54% were missense variants. The study complemented the Greater Middle East Variome by way of reporting many additional Arabian exome variants. The study corroborated Kuwaiti population genetic substructures previously derived using genome-wide genotype data and illustrated the genetic relatedness among Kuwaiti population subgroups, Middle Eastern, European and Ashkenazi Jewish populations. The study mapped 112 rare and frequent functional variants relating to pharmacogenomics and disorders (recessive and common) to the phenotypic characteristics of Arab population. Comparative allele frequency data and carrier distributions of known Arab mutations for 23 disorders seen among Arabs, of putative OMIM-listed causal mutations for 12 disorders observed among Arabs but not yet characterized for genetic basis in Arabs, and of 17 additional putative mutations for disorders characterized for genetic basis in Arab populations are presented for testing in future Arab studies.
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Lahbib S, Leblond CS, Hamza M, Regnault B, Lemée L, Mathieu A, Jaouadi H, Mkaouar R, Youssef-Turki IB, Belhadj A, Kraoua I, Bourgeron T, Abdelhak S. Homozygous 2p11.2 deletion supports the implication of ELMOD3 in hearing loss and reveals the potential association of CAPG with ASD/ID etiology. J Appl Genet 2018; 60:49-56. [PMID: 30284680 DOI: 10.1007/s13353-018-0472-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 09/25/2018] [Accepted: 09/27/2018] [Indexed: 11/30/2022]
Abstract
Autism spectrum disorder (ASD) is a set of neurodevelopmental conditions characterized by early-onset difficulties in social communication and unusually restricted, repetitive behavior and interests. Parental consanguinity may lead to higher risk of ASD and to more severe clinical presentations in the offspring. Studies of ASD families with high inbreeding enable the identification of inherited variants of this disorder particularly those with an autosomal recessive pattern of inheritance. In our study, using copy number variants (CNV) analysis, we identified a rare homozygous deletion in 2p11.2 region that affects ELMOD3, CAPG, and SH2D6 genes in a boy with ASD, intellectual disability (ID), and hearing impairment (HI). This deletion may reveal a new contiguous deletion syndrome in which ELMOD3, known to be implicated in autosomal recessive deafness underlies the HI of the proband and CAPG, member of actin regulatory proteins involved in cytoskeletal dynamic, an important function for brain development and activity, underlies the ASD/ID phenotype. A possible contribution of SH2D6 gene, as a part of a chimeric gene, to the clinical presentation of the patient is discussed. Our result supports the implication of ELMOD3 in hearing loss and highlights the potential clinical relevance of 2p11.2 deletion in autism and/or intellectual disability.
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Affiliation(s)
- Saida Lahbib
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Université Tunis El Manar, Institut Pasteur de Tunis, 1002, Tunis, Tunisia. .,University of Tunis El Manar, Tunis, Tunisia.
| | - Claire S Leblond
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015, Paris, France.,CNRS UMR3571, Genes, Synapses and Cognition, Institut Pasteur, 75015, Paris, France.,Paris Diderot University, Sorbonne Paris Cité, 75013, Paris, France
| | - Mariem Hamza
- Faculty of Medicine of Tunis, University of Tunis El Manar, 1007 La Rabta, Tunis, Tunisia.,Child and Adolescent Psychiatry Department, Mongi Slim Hospital, 2046, Sidi Daoud, Tunisia
| | - Béatrice Regnault
- Plateforme de Génotypage des Eucaryotes, Centre d'Innovation et Recherche Technologique (CITECH), Institut Pasteur, 75015, Paris, France
| | - Laure Lemée
- Plateforme de Génotypage des Eucaryotes, Centre d'Innovation et Recherche Technologique (CITECH), Institut Pasteur, 75015, Paris, France
| | - Alexandre Mathieu
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015, Paris, France.,CNRS UMR3571, Genes, Synapses and Cognition, Institut Pasteur, 75015, Paris, France.,Paris Diderot University, Sorbonne Paris Cité, 75013, Paris, France
| | - Hager Jaouadi
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Université Tunis El Manar, Institut Pasteur de Tunis, 1002, Tunis, Tunisia
| | - Rahma Mkaouar
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Université Tunis El Manar, Institut Pasteur de Tunis, 1002, Tunis, Tunisia
| | - Ilhem Ben Youssef-Turki
- Faculty of Medicine of Tunis, University of Tunis El Manar, 1007 La Rabta, Tunis, Tunisia.,Research Unit UR12 SP24 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, 1007, Tunis, Tunisia
| | - Ahlem Belhadj
- Faculty of Medicine of Tunis, University of Tunis El Manar, 1007 La Rabta, Tunis, Tunisia.,Child and Adolescent Psychiatry Department, Mongi Slim Hospital, 2046, Sidi Daoud, Tunisia
| | - Ichraf Kraoua
- Faculty of Medicine of Tunis, University of Tunis El Manar, 1007 La Rabta, Tunis, Tunisia.,Research Unit UR12 SP24 and Department of Child and Adolescent Neurology, National Institute Mongi Ben Hmida of Neurology, 1007, Tunis, Tunisia
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions Unit, Institut Pasteur, 75015, Paris, France.,CNRS UMR3571, Genes, Synapses and Cognition, Institut Pasteur, 75015, Paris, France.,Paris Diderot University, Sorbonne Paris Cité, 75013, Paris, France
| | - Sonia Abdelhak
- Biomedical Genomics and Oncogenetics Laboratory LR16IPT05, Université Tunis El Manar, Institut Pasteur de Tunis, 1002, Tunis, Tunisia
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24
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Keyfi F, Nasseri M, Nayerabadi S, Alaei A, Mokhtariye A, Varasteh A. Frequency of Inborn Errors of Metabolism in a Northeastern Iranian Sample with High Consanguinity Rates. Hum Hered 2018; 83:71-78. [PMID: 30036870 DOI: 10.1159/000488876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/29/2018] [Indexed: 12/29/2022] Open
Abstract
OBJECTIVE Inborn errors of metabolism (IEMs) are disorders with various manifestations that occur mainly in the pediatric population. In countries where consanguineous marriage is common, the association between consanguinity and IEMs is highly important. No studies have been conducted in Iran examining the impact of consanguinity on IEMs. METHODS In this retrospective study, the incidences of metabolic disorders were evaluated for the years 2006 through 2016 in the North East Iran Regional Diagnostic Laboratory (Pardis Clinical and Genetic Laboratory). A total of 13,327 infants with clinical symptoms were referred and investigated for IEMs. Newborn screening was performed on samples from all patients suspected of having IEMs. RESULTS Of 13,327 infants examined, 60 different IEMs were diagnosed in 1,118. The most frequent disorders among our patients were glucose-6-phosphate dehydrogenase deficiency (G6PDD) (14.04%), methylmalonic and propionic acidurias (MMA/PA) (9.12%), phenylketonuria (PKU) (8%), and isovaleric acidemia (IVA) (6.98%). A significant difference was found in the prevalence of amino acid disorders between the offspring of consanguineous and those of non-consanguineous parents. No statistically significant differences were found between the 2 groups for organic or fatty acids, carnitine or urine cycles, or lysosomal storage disorders. A total of 707 of the 1,118 infants with metabolic diseases (63.24%) were children of consanguineous parents. These findings show that consanguinity can be an important factor in the inheritance of recessive mutations in a homozygous state. CONCLUSION This study found a greater frequency of metabolic diseases in offspring of consanguineous parents than in those of non-consanguineous parents in a population with a high rate of consanguinity.
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Laurin C, Cuellar-Partida G, Hemani G, Smith GD, Yang J, Evans DM. Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices. Behav Genet 2018; 48:67-79. [PMID: 29098496 PMCID: PMC5752821 DOI: 10.1007/s10519-017-9880-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/21/2017] [Indexed: 12/28/2022]
Abstract
We propose a new method, G-REMLadp, to estimate the phenotypic variance explained by parent-of-origin effects (POEs) across the genome. Our method uses restricted maximum likelihood analysis of genome-wide genetic relatedness matrices based on individuals' phased genotypes. Genome-wide SNP data from parent child duos or trios is required to obtain relatedness matrices indexing the parental origin of offspring alleles, as well as offspring phenotype data to partition the trait variation into variance components. To calibrate the power of G-REMLadp to detect non-null POEs when they are present, we provide an analytic approximation derived from Haseman-Elston regression. We also used simulated data to quantify the power and Type I Error rates of G-REMLadp, as well as the sensitivity of its variance component estimates to violations of underlying assumptions. We subsequently applied G-REMLadp to 36 phenotypes in a sample of individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC). We found that the method does not seem to be inherently biased in estimating variance due to POEs, and that substantial correlation between parental genotypes is necessary to generate biased estimates. Our empirical results, power calculations and simulations indicate that sample sizes over 10000 unrelated parent-offspring duos will be necessary to detect POEs explaining < 10% of the variance with moderate power. We conclude that POEs tagged by our genetic relationship matrices are unlikely to explain large proportions of the phenotypic variance (i.e. > 15%) for the 36 traits that we have examined.
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Affiliation(s)
- Charles Laurin
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Gabriel Cuellar-Partida
- Faculty of Medicine, Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - George Davey Smith
- Faculty of Medicine, Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Jian Yang
- Institute for Molecular Bioscience and Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - David M Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Faculty of Medicine, Translational Research Institute, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia.
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26
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Al-Aama JY, Shaik NA, Banaganapalli B, Salama MA, Rashidi O, Sahly AN, Mohsen MO, Shawoosh HA, Shalabi HA, Edreesi MA, Alharthi SE, Wang J, Elango R, Saadah OI. Whole exome sequencing of a consanguineous family identifies the possible modifying effect of a globally rare AK5 allelic variant in celiac disease development among Saudi patients. PLoS One 2017; 12:e0176664. [PMID: 28505210 PMCID: PMC5432167 DOI: 10.1371/journal.pone.0176664] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 04/14/2017] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CD), a multi-factorial auto-inflammatory disease of the small intestine, is known to occur in both sporadic and familial forms. Together HLA and Non-HLA genes can explain up to 50% of CD’s heritability. In order to discover the missing heritability due to rare variants, we have exome sequenced a consanguineous Saudi family presenting CD in an autosomal recessive (AR) pattern. We have identified a rare homozygous insertion c.1683_1684insATT, in the conserved coding region of AK5 gene that showed classical AR model segregation in this family. Sequence validation of 200 chromosomes each of sporadic CD cases and controls, revealed that this extremely rare (EXac MAF 0.000008) mutation is highly penetrant among general Saudi populations (MAF is 0.62). Genotype and allelic distribution analysis have indicated that this AK5 (c.1683_1684insATT) mutation is negatively selected among patient groups and positively selected in the control group, in whom it may modify the risk against CD development [p<0.002]. Our observation gains additional support from computational analysis which predicted that Iso561 insertion shifts the existing H-bonds between 400th and 556th amino acid residues lying near the functional domain of adenylate kinase. This shuffling of amino acids and their H-bond interactions is likely to disturb the secondary structure orientation of the polypeptide and induces the gain-of-function in nucleoside phosphate kinase activity of AK5, which may eventually down-regulates the reactivity potential of CD4+ T-cells against gluten antigens. Our study underlines the need to have population-specific genome databases to avoid false leads and to identify true candidate causal genes for the familial form of celiac disease.
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Affiliation(s)
- Jumana Yousuf Al-Aama
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed A. Salama
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Omran Rashidi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed N. Sahly
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed O. Mohsen
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Harbi A. Shawoosh
- Department of Pediatrics, King Fahd Armed Forces Hospital, Jeddah, Saudi Arabia
| | | | - Mohammad Al Edreesi
- Division of Gastroenterology, Department of Pediatrics, Dhahran Health Center, Saudi Aramco Medical Services Organization, Dhahran, Saudi Arabia
| | - Sameer E. Alharthi
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jun Wang
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ramu Elango
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (RE); (OIS)
| | - Omar I. Saadah
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Division of Pediatric Gastroenterology, Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (RE); (OIS)
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Cruz-Aguilar M, Galaviz-Hernández C, Hiebert-Froese J, Sosa-Macías M, Zenteno JC. A Nonsense ALMS1 Mutation Underlies Alström Syndrome in an Extended Mennonite Kindred Settled in North Mexico. Genet Test Mol Biomarkers 2017; 21:397-401. [PMID: 28402684 DOI: 10.1089/gtmb.2016.0391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
AIM Alström syndrome (AS) is a rare autosomal recessive multisystem disease caused by biallelic mutations in ALMS1, a gene encoding a widely expressed centrosomal/basal body protein. Although more than 200 pathogenic mutations in ALMS1 have been identified to date in AS patients from various ethnic populations, there are very few reports of ALMS1 founder mutations in isolated populations. Our aim was to describe the molecular characterization of a cohort of AS patients from an extended inbred Mennonite kindred settled in Mexico. METHODS Genetic study included polymerase chain reaction amplification and direct nucleotide sequencing of the entire ALMS1 gene in DNA from seven related AS patients. RESULTS A homozygous single-nucleotide c.10480C>T substitution in exon 16, predicting a p.Q3494* nonsense mutation, was identified in all affected subjects. CONCLUSIONS To our knowledge, this is the first demonstration of a high prevalence of AS in Mennonites, a population group maintaining high levels of consanguineous marriage in their communities. Our findings provide an example of genetic isolation and consanguinity causing a high prevalence of AS and offer the opportunity for early clinical interventions and for genetic counseling of at-risk couples in this community.
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Affiliation(s)
- Marisa Cruz-Aguilar
- 1 Genetics Department-Research Unit, Institute of Ophthalmology , "Conde de Valenciana," Mexico City, Mexico
| | | | | | | | - Juan Carlos Zenteno
- 1 Genetics Department-Research Unit, Institute of Ophthalmology , "Conde de Valenciana," Mexico City, Mexico .,4 Department of Biochemistry, Faculty of Medicine, National Autonomous University of Mexico (UNAM) , Mexico City, Mexico
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Philips A, Pinelli M, de Bie C, Mustonen A, Määttä T, Arts H, Wu K, Roepman R, Moilanen J, Raza S, Varilo T, Scala G, Cocozza S, Gilissen C, van Gassen K, Järvelä I. Identification ofC12orf4as a gene for autosomal recessive intellectual disability. Clin Genet 2016; 91:100-105. [DOI: 10.1111/cge.12821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 02/02/2023]
Affiliation(s)
- A.K. Philips
- Department of Medical Genetics; University of Helsinki; Helsinki Finland
| | - M. Pinelli
- Department of Human Genetics, Donders Centre for Neuroscience; Radboud University Medical Centre; Nijmegen the Netherlands
- The Telethon Institute of Genetics and Medicine (TIGEM); Naples Italy
| | - C.I. de Bie
- Department of Genetics; University Medical Center Utrecht; Utrecht the Netherlands
| | - A. Mustonen
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu; Oulu University Hospital and University of Oulu; Oulu Finland
| | - T. Määttä
- Disability Services; Joint Authority for Kainuu; Kainuu Finland
| | - H.H. Arts
- Department of Human Genetics; Radboud University of Molecular Sciences, Radboud University Medical Centre; Nijmegen the Netherlands
- Department of Biochemistry; University of Western Ontario; London Ontario Canada
| | - K. Wu
- Department of Human Genetics; Radboud University of Molecular Sciences, Radboud University Medical Centre; Nijmegen the Netherlands
| | - R. Roepman
- Department of Human Genetics; Radboud University of Molecular Sciences, Radboud University Medical Centre; Nijmegen the Netherlands
| | - J.S. Moilanen
- Department of Clinical Genetics, PEDEGO Research Unit and Medical Research Center Oulu; Oulu University Hospital and University of Oulu; Oulu Finland
| | - S. Raza
- Department of Medical Genetics; University of Helsinki; Helsinki Finland
| | - T. Varilo
- Department of Medical Genetics; University of Helsinki; Helsinki Finland
| | - G. Scala
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche; Università Degli Studi di Napoli “Federico II”; Naples Italy
| | - S. Cocozza
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche; Università Degli Studi di Napoli “Federico II”; Naples Italy
| | - C. Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience; Radboud University Medical Centre; Nijmegen the Netherlands
| | - K.L.I. van Gassen
- Department of Genetics; University Medical Center Utrecht; Utrecht the Netherlands
| | - I. Järvelä
- Department of Medical Genetics; University of Helsinki; Helsinki Finland
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