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Aamer W, Al-Maraghi A, Syed N, Gandhi GD, Aliyev E, Al-Kurbi AA, Al-Saei O, Kohailan M, Krishnamoorthy N, Palaniswamy S, Al-Malki K, Abbasi S, Agrebi N, Abbaszadeh F, Akil ASAS, Badii R, Ben-Omran T, Lo B, Mokrab Y, Fakhro KA. Burden of Mendelian disorders in a large Middle Eastern biobank. Genome Med 2024; 16:46. [PMID: 38584274 PMCID: PMC11000384 DOI: 10.1186/s13073-024-01307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUND Genome sequencing of large biobanks from under-represented ancestries provides a valuable resource for the interrogation of Mendelian disease burden at world population level, complementing small-scale familial studies. METHODS Here, we interrogate 6045 whole genomes from Qatar-a Middle Eastern population with high consanguinity and understudied mutational burden-enrolled at the national Biobank and phenotyped for 58 clinically-relevant quantitative traits. We examine a curated set of 2648 Mendelian genes from 20 panels, annotating known and novel pathogenic variants and assessing their penetrance and impact on the measured traits. RESULTS We find that 62.5% of participants are carriers of at least 1 known pathogenic variant relating to recessive conditions, with homozygosity observed in 1 in 150 subjects (0.6%) for which Peninsular Arabs are particularly enriched versus other ancestries (5.8-fold). On average, 52.3 loss-of-function variants were found per genome, 6.5 of which affect a known Mendelian gene. Several variants annotated in ClinVar/HGMD as pathogenic appeared at intermediate frequencies in this cohort (1-3%), highlighting Arab founder effect, while others have exceedingly high frequencies (> 5%) prompting reconsideration as benign. Furthermore, cumulative gene burden analysis revealed 56 genes having gene carrier frequency > 1/50, including 5 ACMG Tier 3 panel genes which would be candidates for adding to newborn screening in the country. Additionally, leveraging 58 biobank traits, we systematically assess the impact of novel/rare variants on phenotypes and discover 39 candidate large-effect variants associating with extreme quantitative traits. Furthermore, through rare variant burden testing, we discover 13 genes with high mutational load, including 5 with impact on traits relevant to disease conditions, including metabolic disorder and type 2 diabetes, consistent with the high prevalence of these conditions in the region. CONCLUSIONS This study on the first phase of the growing Qatar Genome Program cohort provides a comprehensive resource from a Middle Eastern population to understand the global mutational burden in Mendelian genes and their impact on traits in seemingly healthy individuals in high consanguinity settings.
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Affiliation(s)
- Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- Applied Bioinformatics Core, Sidra Medicine, Doha, Qatar
| | | | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Omayma Al-Saei
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | | | | | - Saleha Abbasi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Nourhen Agrebi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | | | - Ramin Badii
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of pediatrics, Hamad Medical Corporation, Doha, Qatar
- Department of Pediatric, Weill Cornell Medical College, Doha, Qatar
- Division of Genetic & Genomics Medicine, Sidra Medicine, Doha, Qatar
| | - Bernice Lo
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
- College of Health Sciences, Qatar University, Doha, Qatar.
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar.
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Al-Kurbi AA, Aliyev E, AlSa’afin S, Aamer W, Palaniswamy S, Al-Maraghi A, Kilani H, Akil AAS, Stotland MA, Fakhro KA. A Complex Intrachromosomal Rearrangement Disrupting IRF6 in a Family with Popliteal Pterygium and Van der Woude Syndromes. Genes (Basel) 2023; 14:genes14040849. [PMID: 37107607 PMCID: PMC10137688 DOI: 10.3390/genes14040849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Clefts of the lip and/or palate (CL/P) are considered the most common form of congenital anomalies occurring either in isolation or in association with other clinical features. Van der woude syndrome (VWS) is associated with about 2% of all CL/P cases and is further characterized by having lower lip pits. Popliteal pterygium syndrome (PPS) is a more severe form of VWS, normally characterized by orofacial clefts, lower lip pits, skin webbing, skeletal anomalies and syndactyly of toes and fingers. Both syndromes are inherited in an autosomal dominant manner, usually caused by heterozygous mutations in the Interferon Regulatory Factor 6 (IRF6) gene. Here we report the case of a two-generation family where the index presented with popliteal pterygium syndrome while both the father and sister had clinical features of van der woude syndrome, but without any point mutations detected by re-sequencing of known gene panels or microarray testing. Using whole genome sequencing (WGS) followed by local de novo assembly, we discover and validate a copy-neutral, 429 kb complex intra-chromosomal rearrangement in the long arm of chromosome 1, disrupting the IRF6 gene. This variant is copy-neutral, novel against publicly available databases, and segregates in the family in an autosomal dominant pattern. This finding suggests that missing heritability in rare diseases may be due to complex genomic rearrangements that can be resolved by WGS and de novo assembly, helping deliver answers to patients where no genetic etiology was identified by other means.
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Affiliation(s)
- Alya A. Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sana AlSa’afin
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | | | | | - Houda Kilani
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
| | | | - Mitchell A. Stotland
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, Doha 26999, Qatar
- Department of Surgery, Weill Cornell Medical College, Doha 24144, Qatar
| | - Khalid A. Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha 24144, Qatar
- Correspondence:
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Al-Kurbi AA, Da'as SI, Aamer W, Krishnamoorthy N, Poggiolini I, Abdelrahman D, Elbashir N, Al-Shabeeb Akil A, Glass GE, Fakhro KA. A recessive variant in SIM2 in a child with complex craniofacial anomalies and global developmental delay. Eur J Med Genet 2022; 65:104455. [PMID: 35182808 DOI: 10.1016/j.ejmg.2022.104455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 02/02/2022] [Accepted: 02/14/2022] [Indexed: 11/26/2022]
Abstract
Rare deletions and duplications on the long arm of Chromosome 21 have previously been reported in many patients with craniofacial and developmental phenotypes. However, this Down Syndrome Critical Region (DSCR) contains multiple genes, making identifying a single causative gene difficult. Here, we report a case of a boy with bicoronal craniosynostosis, facial dysmorphism, developmental delay, and intellectual impairment who was found by whole genome sequencing to have a homozygous missense mutation in the Single-Minded Homolog 2 (SIM2) gene (c.461 A > G, p.Tyr154Cys) within the DSCR. SIM2 encodes an essential bHLH and PAS domain transcription factor expressed during fetal brain development and acts as a master regulator of neurogenesis. This variant is globally very rare, segregates in the family, and is predicted to be highly deleterious by in silico analysis, 3D molecular modeling of protein structure, and functional analysis of zebrafish models. Zebrafish expressing the human SIM2p.Y154C variant displayed a progressed microcephaly-like phenotype and head shape abnormalities. When combined with careful phenotyping of the patient vis-à-vis previously reported cases harboring structural variants in this critical 21q22 region, the data support a pathogenic role of SIM2 in this complex syndrome and demonstrates the utility of next-generation sequencing in prioritizing genes in contiguous deletions/duplications syndromes and diagnosing microarray-negative patients in the craniofacial clinic.
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Affiliation(s)
- Alya A Al-Kurbi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Sahar Isa Da'as
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | | | - Doua Abdelrahman
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | - Najwa Elbashir
- Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar
| | | | - Graeme E Glass
- Division of Plastic and Craniofacial Surgery, Sidra Medicine, 26999, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, 34110, Qatar; Department of Human Genetics, Sidra Medicine, 26999, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College, Doha, 24144, Qatar.
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