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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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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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3
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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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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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5
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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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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7
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Kohailan M, Alanazi M, Rouabhia M, Al Amri A, Parine NR, Semlali A. Two SNPs in the promoter region of Toll-like receptor 4 gene are not associated with smoking in Saudi Arabia. Onco Targets Ther 2017; 10:745-752. [PMID: 28223830 PMCID: PMC5308598 DOI: 10.2147/ott.s111971] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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] [Indexed: 01/24/2023] Open
Abstract
Defects in the innate immune system, particularly in Toll-like receptors (TLRs), have been reported in several cigarette smoke-promoted diseases. The aim of this study was to examine the impact of tobacco smoke on allelic frequencies of TLR4 single-nucleotide polymorphisms (SNPs) and to compare the genotypic distribution of these SNPs in a Saudi Arabian population with that in previously studied populations. DNA was extracted from 303 saliva samples collected from smokers and nonsmokers. Two transitional SNPs in the promoter region of TLR4 were selected, rs2770150 (T/C) and rs10759931 (G/A). Genotype frequencies were determined using quantitative polymerase chain reaction. Our results showed a slight effect of smoking on the distribution of rs2770150 and rs10759931. However, the differences were not significant. Thus, we conclude that the SNPs selected for this study were independent of smoking and may not be related to smoking-induced diseases.
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Affiliation(s)
- Muhammad Kohailan
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mohammad Alanazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mahmoud Rouabhia
- Groupe de Recherche en Écologie Buccale, Département de Stomatologie, Faculté de Médecine Dentaire, Université Laval, Québec, QC, Canada
| | - Abdullah Al Amri
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Narasimha Reddy Parine
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdelhabib Semlali
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
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8
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Semlali A, Parine NR, Al Amri A, Azzi A, Arafah M, Kohailan M, Shaik JP, Almadi MA, Aljebreen AM, Alharbi O, Ali Azzam N, Rouabhia M, Alanazi MS. Association between TLR-9 polymorphisms and colon cancer susceptibility in Saudi Arabian female patients. Onco Targets Ther 2016; 10:1-11. [PMID: 28031717 PMCID: PMC5179201 DOI: 10.2147/ott.s106024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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] [Indexed: 01/19/2023] Open
Abstract
Objective The authors aimed to explore the relationship between the expression/polymorphisms of TLR-9 and susceptibility to colon cancer development in the Saudi Arabian population. Methods In total, blood samples from 115 patients with colon cancer and 102 participants without colon cancer were analyzed in this study. Three single-nucleotide polymorphisms (SNPs) were selected from the TLR-9 gene, including two sites within the TLR-9 gene’s promoter region (rs352144 and rs187084) and one site in a TLR-9 intron region (rs5743839). Odds ratios (ORs) and 95% confidence intervals (CIs) were computed from logistic regression models after adjusting for age, gender, and tumor localization. To investigate the differential expression of TLR-9 in colon cancer, TLR-9 expression was evaluated using quantitative real-time reverse transcription polymerase chain reaction on 40 matched normal and colon tissues. Results The authors found that TLR-9 expression was decreased in colon cancer tissues as compared with that in normal tissues. Moreover, significant associations between the TLR-9 rs187084 SNP and colon cancer risk were observed in female patients only. In rs187084, the T allele had a significantly lower frequency (2.8 times) in female cancer patients than in controls (0.27 vs 0.41). The TLR-9 rs352139 and rs352144 SNPs were significantly associated with colon cancer development when the tumor was located in the rectal area. Conclusion The findings support the hypothesis that TLR-9 has an anticancer role in colon cancer development. Furthermore, genetic variation may influence colon cancer development, and SNPs in TLR-9 could serve as biomarkers for decision making in the treatment of females with rectal cancer.
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Affiliation(s)
- Abdelhabib Semlali
- Genome Research, Department of Biochemistry, College of Sciences, King Saud University
| | | | - Abdullah Al Amri
- Genome Research, Department of Biochemistry, College of Sciences, King Saud University
| | - Arezki Azzi
- College of Medicine, Al Imam Muhammad Ibn Saud Islamic University
| | | | - Muhammad Kohailan
- Genome Research, Department of Biochemistry, College of Sciences, King Saud University
| | - Jilani P Shaik
- Genome Research, Department of Biochemistry, College of Sciences, King Saud University
| | - Majid Abdulrahman Almadi
- Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia; Division of Gastroenterology, McGill University Health Center, Montreal General Hospital, Montreal
| | - Abdulrahman M Aljebreen
- College of Medicine, King Saud University; Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Othman Alharbi
- College of Medicine, King Saud University; Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Nahla Ali Azzam
- College of Medicine, King Saud University; Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mahmoud Rouabhia
- Groupe de Recherche en Écologie Buccale, Département de Stomatologie, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, Canada
| | - Mohammad Saud Alanazi
- Genome Research, Department of Biochemistry, College of Sciences, King Saud University
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Kohailan M, Alanazi M, Rouabhia M, Alamri A, Parine NR, Alhadheq A, Basavarajappa S, Abdullah Al-Kheraif AA, Semlali A. Effect of smoking on the genetic makeup of toll-like receptors 2 and 6. Onco Targets Ther 2016; 9:7187-7198. [PMID: 27920557 PMCID: PMC5123654 DOI: 10.2147/ott.s109650] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Cigarette smoking is a major risk factor for lung cancer, asthma, and oral cancer, and is central to the altered innate immune responsiveness to infection. Many hypotheses have provided evidence that cigarette smoking induces more genetic changes in genes involved in the development of many cigarette-related diseases. This alteration may be from single-nucleotide polymorphisms (SNPs) in innate immunity genes, especially the toll-like receptors (TLRs). Objective In this study, the genotype frequencies of TLR2 and TLR6 in smoking and nonsmoking population were examined. Methods Saliva samples were collected from 177 smokers and 126 nonsmokers. The SNPs used were rs3804100 (1350 T/C, Ser450Ser) and rs3804099 (597 T/C, Asn199Asn) for TLR2 and rs3796508 (979 G/A, Val327Met) and rs5743810 (745 T/C, Ser249Pro) for TLR6. Results Results showed that TLR2 rs3804100 has a significant effect in short-term smokers (OR =2.63; P=0.04), and this effect is not observed in long-term smokers (>5 years of smoking). Therefore, this early mutation may be repaired by the DNA repair system. For TLR2 rs3804099, the variation in genotype frequencies between the smokers and control patients was due to a late mutation, and its protective role appears only in long-term smokers (OR =0.40, P=0.018). In TLR6 rs5743810, the TT genotype is significantly higher in smokers than in nonsmokers (OR =6.90). The effect of this SNP is observed in long-term smokers, regardless of the smoking regime per day. Conclusion TLR2 (rs3804100 and rs3804099) and TLR6 (rs5743810) can be used as a potential index in the diagnosis and prevention of more diseases caused by smoking.
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Affiliation(s)
- Muhammad Kohailan
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mohammad Alanazi
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mahmoud Rouabhia
- Département de Stomatologie, Faculté de Médecine Dentaire, Groupe de Recherche en Écologie Buccale, Université Laval, Québec City, QC, Canada
| | - Abdullah Alamri
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Narasimha Reddy Parine
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdullah Alhadheq
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Santhosh Basavarajappa
- Dental Biomaterial Research Chair, Department of Dental Health, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdul Aziz Abdullah Al-Kheraif
- Dental Biomaterial Research Chair, Department of Dental Health, College of Applied Medical Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdelhabib Semlali
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
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10
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Semlali A, Reddy Parine N, Arafah M, Mansour L, Azzi A, Al Shahrani O, Al Amri A, Shaik JP, Aljebreen AM, Alharbi O, Almadi MA, Azzam NA, Kohailan M, Rouabhia M, Alanazi MS. Expression and Polymorphism of Toll-Like Receptor 4 and Effect on NF-κB Mediated Inflammation in Colon Cancer Patients. PLoS One 2016; 11:e0146333. [PMID: 26771524 PMCID: PMC4714746 DOI: 10.1371/journal.pone.0146333] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/20/2015] [Indexed: 12/26/2022] Open
Abstract
Our aim was to evaluate the association between the expression and the polymorphism of TLR4/NF-κB pathways and colon cancer. TLR4 (rs4986790, rs10759932, rs10759931 and rs2770150) were genotyped in blood samples from Colorectal patients and healthy controls. TLR4 and cytokines inflammatory expression were evaluated by real time PCR on 40 matching normal and colon tissues and the protein level by Immunohistochemistry. The high level of TLR4 expression in colon cancer tissues is mainly due to infections by bacteria in the human colon and leads to induction of an acute secretion of inflammatory cytokines mediated by NF-κB. Also, we report here a clear evidence for an association between TLR4 rs10759931 polymorphism (OR = 0.086, CI: 0.04–0.18, P = <0.00001). This polymorphism affects the entire population without being specific to either gender or to any age group. In contrast, the rs2770150 is associated with colon cancer in women aged over 50 years and is closely linked with the decreased levels of female sex hormones during the post-menopausal period (OR = 0.188, CI: 0.074–0.48, P = <0.00084). rs10759932 and rs4986790 appear to have any association with colon cancer. Our data suggest that TLR4 SNPs could possibly serve as biomarkers for decision making in colon cancer treatment.
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Affiliation(s)
- Abdelhabib Semlali
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
- * E-mail: ;
| | - Narasimha Reddy Parine
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Maha Arafah
- College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Lamjed Mansour
- Department of Zoology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Arezki Azzi
- College of Medicine, Al Imam Muhammad Ibn Saud Islamic University (IMSIU), Riyadh, Kingdom of Saudi Arabia
| | - Omair Al Shahrani
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdullah Al Amri
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Jilani P. Shaik
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Abdulrahman M. Aljebreen
- College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Othman Alharbi
- College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Majid A. Almadi
- Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Division of Gastroenterology, The McGill University Health Center, Montreal General Hospital, McGill University, Montreal, Québec, Canada
| | - Nahla Ali Azzam
- College of Medicine, King Saud University, Riyadh, Kingdom of Saudi Arabia
- Division of Gastroenterology, King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Muhammad Kohailan
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Mahmoud Rouabhia
- Groupe de Recherche en Écologie Buccale, Département de stomatologie, Faculté de Médecine Dentaire, Université Laval, Québec, Québec, Canada
| | - Mohammad Saud Alanazi
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
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