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Al-Maraghi A, Aamer W, Ziab M, Aliyev E, Elbashir N, Hussein S, Palaniswamy S, Anand D, Love DR, Charles A, A S Akil A, Fakhro KA. A loss-of-function AGTR1 variant in a critically-ill infant with renal tubular dysgenesis: case presentation and literature review. BMC Nephrol 2024; 25:139. [PMID: 38649831 PMCID: PMC11034062 DOI: 10.1186/s12882-024-03569-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Renal tubular dysgenesis (RTD) is a severe disorder with poor prognosis significantly impacting the proximal tubules of the kidney while maintaining an anatomically normal gross structure. The genetic origin of RTD, involving variants in the ACE, REN, AGT, and AGTR1 genes, affects various enzymes or receptors within the Renin angiotensin system (RAS). This condition manifests prenatally with oligohydramninos and postnatally with persistent anuria, severe refractory hypotension, and defects in skull ossification. CASE PRESENTATION In this report, we describe a case of a female patient who, despite receiving multi vasopressor treatment, experienced persistent hypotension, ultimately resulting in early death at five days of age. While there was a history of parental consanguinity, no reported family history of renal disease existed. Blood samples from the parents and the remaining DNA sample of the patient underwent Whole Genome Sequencing (WGS). The genetic analysis revealed a rare homozygous loss of function variant (NM_000685.5; c.415C > T; p.Arg139*) in the Angiotensin II Receptor Type 1 (AGTR1) gene. CONCLUSION This case highlights the consequence of loss-of-function variants in AGTR1 gene leading to RTD, which is characterized by high mortality rate at birth or during the neonatal period. Furthermore, we provide a comprehensive review of previously reported variants in the AGTR1 gene, which is the least encountered genetic cause of RTD, along with their associated clinical features.
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Affiliation(s)
- Aljazi Al-Maraghi
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Waleed Aamer
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Mubarak Ziab
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Elbay Aliyev
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Najwa Elbashir
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sura Hussein
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | | | - Dhullipala Anand
- Neonatology Division, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Donald R Love
- Genetic Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Adrian Charles
- Anatomical Pathology, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ammira A S Akil
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Khalid A Fakhro
- Laboratory of Genomic Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar.
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2
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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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3
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Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, Syed N, Shaath R, Gandhi GD, Engchuan W, Howe J, Thiruvahindrapuram B, Geng M, Whitney J, Syed A, Lakshmi J, Hussein S, Albashir N, Hussein A, Poggiolini I, Elhag SF, Palaniswamy S, Kambouris M, de Fatima Janjua M, Tahir MOE, Nazeer A, Shahwar D, Azeem MW, Mokrab Y, Aati NA, Akil A, Scherer SW, Kamal M, Fakhro KA. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Genome Med 2023; 15:81. [PMID: 37805537 PMCID: PMC10560429 DOI: 10.1186/s13073-023-01228-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study-a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research. METHODS In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families. RESULTS Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts. CONCLUSIONS This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.
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Affiliation(s)
- Mona Abdi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Waleed Aamer
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Genomics Data Science Core, Sidra Medicine, Doha, Qatar
| | - Rulan Shaath
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melissa Geng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Amira Syed
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Sura Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Amal Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Saba F Elhag
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | | | - Marios Kambouris
- Pathology and Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | | | | | - Ahsan Nazeer
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Durre Shahwar
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Muhammad Waqar Azeem
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Younes Mokrab
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
- Qatar University, Doha, Qatar
| | | | - Ammira Akil
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Madeeha Kamal
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar.
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4
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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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5
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Gandhi GD, Aamer W, Krishnamoorthy N, Syed N, Aliyev E, Al-Maraghi A, Kohailan M, Alenbawi J, Elanbari M, Mifsud B, Mokrab Y, Khalil CA, Fakhro KA. Assessing the genetic burden of familial hypercholesterolemia in a large middle eastern biobank. J Transl Med 2022; 20:502. [PMID: 36329474 PMCID: PMC9635206 DOI: 10.1186/s12967-022-03697-w] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The genetic architecture underlying Familial Hypercholesterolemia (FH) in Middle Eastern Arabs is yet to be fully described, and approaches to assess this from population-wide biobanks are important for public health planning and personalized medicine. METHODS We evaluate the pilot phase cohort (n = 6,140 adults) of the Qatar Biobank (QBB) for FH using the Dutch Lipid Clinic Network (DLCN) criteria, followed by an in-depth characterization of all genetic alleles in known dominant (LDLR, APOB, and PCSK9) and recessive (LDLRAP1, ABCG5, ABCG8, and LIPA) FH-causing genes derived from whole-genome sequencing (WGS). We also investigate the utility of a globally established 12-SNP polygenic risk score to predict FH individuals in this cohort with Arab ancestry. RESULTS Using DLCN criteria, we identify eight (0.1%) 'definite', 41 (0.7%) 'probable' and 334 (5.4%) 'possible' FH individuals, estimating a prevalence of 'definite or probable' FH in the Qatari cohort of ~ 1:125. We identify ten previously known pathogenic single-nucleotide variants (SNVs) and 14 putatively novel SNVs, as well as one novel copy number variant in PCSK9. Further, despite the modest sample size, we identify one homozygote for a known pathogenic variant (ABCG8, p. Gly574Arg, global MAF = 4.49E-05) associated with Sitosterolemia 2. Finally, calculation of polygenic risk scores found that individuals with 'definite or probable' FH have a significantly higher LDL-C SNP score than 'unlikely' individuals (p = 0.0003), demonstrating its utility in Arab populations. CONCLUSION We design and implement a standardized approach to phenotyping a population biobank for FH risk followed by systematically identifying known variants and assessing putative novel variants contributing to FH burden in Qatar. Our results motivate similar studies in population-level biobanks - especially those with globally under-represented ancestries - and highlight the importance of genetic screening programs for early detection and management of individuals with high FH risk in health systems.
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Affiliation(s)
- Geethanjali Devadoss Gandhi
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar ,grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Waleed Aamer
- grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- grid.467063.00000 0004 0397 4222Bioinformatics, Genomic Data Science Core, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Aljazi Al-Maraghi
- grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Muhammad Kohailan
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar ,grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Jamil Alenbawi
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Mohammed Elanbari
- grid.467063.00000 0004 0397 4222Clinical Research Centre, Sidra Medicine, Doha, Qatar
| | | | - Borbala Mifsud
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Younes Mokrab
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar ,grid.467063.00000 0004 0397 4222Laboratory of Medical and Population Genomics, Sidra Medicine, Doha, Qatar ,grid.416973.e0000 0004 0582 4340Department of Genetic Medicine, Weill Cornell Medicine, Education City, Qatar
| | - Charbel Abi Khalil
- grid.416973.e0000 0004 0582 4340Department of Genetic Medicine, Weill Cornell Medicine, Education City, Qatar ,grid.5386.8000000041936877XJoan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, US
| | - Khalid A. Fakhro
- grid.452146.00000 0004 1789 3191College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Doha, Qatar ,grid.467063.00000 0004 0397 4222Human Genetics Department, Sidra Medicine, Doha, Qatar ,grid.416973.e0000 0004 0582 4340Department of Genetic Medicine, Weill Cornell Medicine, Education City, Qatar
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6
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Kohailan M, Aamer W, Syed N, Padmajeya S, Hussein S, Sayed A, Janardhanan J, Palaniswamy S, El Hajj N, Al-Shabeeb Akil A, Fakhro KA. Patterns and distribution of de novo mutations in multiplex Middle Eastern families. J Hum Genet 2022; 67:579-588. [PMID: 35718832 PMCID: PMC9510050 DOI: 10.1038/s10038-022-01054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
While de novo mutations (DNMs) are key to genetic diversity, they are also responsible for a high number of rare disorders. To date, no study has systematically examined the rate and distribution of DNMs in multiplex families in highly consanguineous populations. Leveraging WGS profiles of 645 individuals in 146 families, we implemented a combinatorial approach using 3 complementary tools for DNM discovery in 353 unique trio combinations. We found a total of 27,168 DNMs (median: 70 single-nucleotide and 6 insertion-deletions per individual). Phasing revealed around 80% of DNMs were paternal in origin. Notably, using whole-genome methylation data of spermatogonial stem cells, these DNMs were significantly more likely to occur at highly methylated CpGs (OR: 2.03; p value = 6.62 × 10−11). We then examined the effects of consanguinity and ethnicity on DNMs, and found that consanguinity does not seem to correlate with DNM rate, and special attention has to be considered while measuring such a correlation. Additionally, we found that Middle-Eastern families with Arab ancestry had fewer DNMs than African families, although not significant (p value = 0.16). Finally, for families with diseased probands, we examined the difference in DNM counts and putative impact across affected and unaffected siblings, but did not find significant differences between disease groups, likely owing to the enrichment for recessive disorders in this part of the world, or the small sample size per clinical condition. This study serves as a reference for DNM discovery in multiplex families from the globally under-represented populations of the Middle-East.
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Affiliation(s)
- Muhammad Kohailan
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Najeeb Syed
- Biomedical Informatics Division, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sujitha Padmajeya
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sura Hussein
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Amira Sayed
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Jyothi Janardhanan
- Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | | | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | | | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar. .,Department of Human Genetics, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Department of Genetic Medicine, Weill-Cornell Medical College, P.O. Box 24144, Doha, Qatar.
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7
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Kohailan M, Al-Saei O, Padmajeya S, Aamer W, Elbashir N, Al-Shabeeb Akil A, Kamboh AR, Fakhro K. A de novo start-loss in EFTUD2 associated with mandibulofacial dysostosis with microcephaly: case report. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006206. [PMID: 35732499 PMCID: PMC9235844 DOI: 10.1101/mcs.a006206] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Mandibulofacial dysostosis with microcephaly (MFDM) is a rare genetic disorder inherited in an autosomal dominant pattern. Major characteristics include developmental delay, craniofacial malformations such as malar and mandibular hypoplasia, and ear anomalies. Here, we report a 4.5-yr-old female patient with symptoms fitting MFDM. Using whole-genome sequencing, we identified a de novo start-codon loss (c.3G > T) in the EFTUD2. We examined EFTUD2 expression in the patient by RNA sequencing and observed a notable functional consequence of the variant on gene expression in the patient. We identified a novel variant for the development of MFDM in humans. To the best of our knowledge, this is the first report of a start-codon loss in EFTUD2 associated with MFDM.
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Affiliation(s)
- Muhammad Kohailan
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Omayma Al-Saei
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | | | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Najwa Elbashir
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
| | | | - Abdul-Rauf Kamboh
- Department of Pediatric Ophthalmology, Sidra Medicine, Doha 26999, Qatar
| | - Khalid 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
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8
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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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9
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Mbarek H, Devadoss Gandhi G, Selvaraj S, Al-Muftah W, Badji R, Al-Sarraj Y, Saad C, Darwish D, Alvi M, Fadl T, Yasin H, Alkuwari F, Razali R, Aamer W, Abbaszadeh F, Ahmed I, Mokrab Y, Suhre K, Albagha O, Fakhro K, Badii R, Ismail SI, Althani A. Qatar Genome: Insights on Genomics from the Middle East. Hum Mutat 2022; 43:499-510. [PMID: 35112413 DOI: 10.1002/humu.24336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 09/10/2021] [Revised: 12/16/2021] [Accepted: 01/29/2022] [Indexed: 11/09/2022]
Abstract
Despite recent biomedical breakthroughs and large genomic studies growing momentum, the Middle Eastern population, home to over 400 million people, is under-represented in the human genome variation databases. Here we describe insights from phase 1 of the Qatar Genome Program with whole genome sequenced 6,047 individuals from Qatar. We identified more than 88 million variants of which 24 million are novel and 23 million are singletons. Consistent with the high consanguinity and founder effects in the region, we found that several rare deleterious variants were more common in the Qatari population while others seem to provide protection against diseases and have shaped the genetic architecture of adaptive phenotypes. These results highlight the value of our data as a resource to advance genetic studies in the Arab and neighbouring Middle Eastern populations and will significantly boost the current efforts to improve our understanding of global patterns of human variations, human history and genetic contributions to health and diseases in diverse populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Geethanjali Devadoss Gandhi
- Department of Biomedical Sciences, College of Health Sciences, Qatar University.,College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Senthil Selvaraj
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Wadha Al-Muftah
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Radja Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Yasser Al-Sarraj
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar.,Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Dima Darwish
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Muhammad Alvi
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Tasnim Fadl
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Heba Yasin
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Fatima Alkuwari
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Rozaimi Razali
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Waleed Aamer
- Human Genetics Department, Sidra Medicine, Doha, Qatar
| | | | - Ikhlak Ahmed
- Sidra Medicine, Biomedical Informatics - Research Branch, Doha, Qatar
| | - Younes Mokrab
- Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Omar Albagha
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar.,Center of Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Khalid Fakhro
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Ramin Badii
- Molecular Genetics Laboratory, Hamad Medical Corporation, Doha, Qatar
| | | | - Asma Althani
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar
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10
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Razali RM, Rodriguez-Flores J, Ghorbani M, Naeem H, Aamer W, Aliyev E, Jubran A, Clark AG, Fakhro KA, Mokrab Y. Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. Nat Commun 2021; 12:5929. [PMID: 34642339 PMCID: PMC8511259 DOI: 10.1038/s41467-021-25287-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East. Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.
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Affiliation(s)
| | | | | | - Haroon Naeem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Ali Jubran
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, New York, NY, USA
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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11
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Guennoun A, Bougarn S, Khan T, Mackeh R, Rahman M, Al-Ali F, Ata M, Aamer W, Prosser D, Habib T, Chin-Smith E, Al-Darwish K, Zhang Q, Al-Shakaki A, Robay A, Crystal RG, Fakhro K, Al-Naimi A, Al Maslamani E, Tuffaha A, Janahi I, Janahi M, Love DR, Karim MY, Lo B, Hassan A, Adeli M, Marr N. A Novel STK4 Mutation Impairs T Cell Immunity Through Dysregulation of Cytokine-Induced Adhesion and Chemotaxis Genes. J Clin Immunol 2021; 41:1839-1852. [PMID: 34427831 PMCID: PMC8604862 DOI: 10.1007/s10875-021-01115-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 08/01/2021] [Indexed: 11/06/2022]
Abstract
Purpose Human serine/threonine kinase 4 (STK4) deficiency is a rare, autosomal recessive genetic disorder leading to combined immunodeficiency; however, the extent to which immune signaling and host defense are impaired is unclear. We assessed the functional consequences of a novel, homozygous nonsense STK4 mutation (NM_006282.2:c.871C > T, p.Arg291*) identified in a pediatric patient by comparing his innate and adaptive cell-mediated and humoral immune responses with those of three heterozygous relatives and unrelated controls. Methods The genetic etiology was verified by whole genome and Sanger sequencing. STK4 gene and protein expression was measured by quantitative RT-PCR and immunoblotting, respectively. Cellular abnormalities were assessed by high-throughput RT-RCR, RNA-Seq, ELISA, and flow cytometry. Antibody responses were assessed by ELISA and phage immunoprecipitation-sequencing. Results The patient exhibited partial loss of STK4 expression and complete loss of STK4 function combined with recurrent viral and bacterial infections, notably persistent Epstein–Barr virus viremia and pulmonary tuberculosis. Cellular and molecular analyses revealed abnormal fractions of T cell subsets, plasmacytoid dendritic cells, and NK cells. The transcriptional responses of the patient’s whole blood and PBMC samples indicated dysregulated interferon signaling, impaired T cell immunity, and increased T cell apoptosis as well as impaired regulation of cytokine-induced adhesion and leukocyte chemotaxis genes. Nonetheless, the patient had detectable vaccine-specific antibodies and IgG responses to various pathogens, consistent with a normal CD19 + B cell fraction, albeit with a distinctive antibody repertoire, largely driven by herpes virus antigens. Conclusion Patients with STK4 deficiency can exhibit broad impairment of immune function extending beyond lymphoid cells. Supplementary Information The online version contains supplementary material available at 10.1007/s10875-021-01115-2.
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Affiliation(s)
| | - Salim Bougarn
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Taushif Khan
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Rafah Mackeh
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Mahbuba Rahman
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar.,Translational Cancer and Immunity Center, Qatar Biomedical Research Institute, Doha, Qatar
| | - Fatima Al-Ali
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Manar Ata
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Waleed Aamer
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Debra Prosser
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Tanwir Habib
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar.,Bioinformatics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | | | | | - Qian Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | | | - Amal Robay
- Weill Cornell Medicine-Qatar, Doha, Qatar
| | | | - Khalid Fakhro
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar.,Weill Cornell Medicine-Qatar, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Amal Al-Naimi
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | | | - Amjad Tuffaha
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | | | | | - Donald R Love
- Department of Pathology, Sidra Medicine, Doha, Qatar
| | | | - Bernice Lo
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Amel Hassan
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Mehdi Adeli
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Nico Marr
- Research Branch, Sidra Medicine, PO BOX 26999, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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