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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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Da'as SI, Ahmed I, Hasan WH, Abdelrahman DA, Aliyev E, Nisar S, Bhat AA, Joglekar MV, Hardikar AA, Fakhro KA, Akil ASAS. The link between glycemic control measures and eye microvascular complications in a clinical cohort of type 2 diabetes with microRNA-223-3p signature. J Transl Med 2023; 21:171. [PMID: 36869348 PMCID: PMC9985290 DOI: 10.1186/s12967-023-03893-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/16/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) is a critical healthcare challenge and priority in Qatar which is listed amongst the top 10 countries in the world, with its prevalence presently at 17% double the global average. MicroRNAs (miRNAs) are implicated in the pathogenesis of (T2D) and long-term microvascular complications including diabetic retinopathy (DR). METHODS In this study, a T2D cohort that accurately matches the characteristics of the general population was employed to find microRNA (miRNA) signatures that are correlated with glycemic and β cell function measurements. Targeted miRNA profiling was performed in (471) T2D individuals with or without DR and (491) (non-diabetic) healthy controls from the Qatar Biobank. Discovery analysis identified 20 differentially expressed miRNAs in T2D compared to controls, of which miR-223-3p was significantly upregulated (fold change:5.16, p = 3.6e-02) and positively correlated with glucose and hemoglobin A1c (HbA1c) levels (p-value = 9.88e-04 and 1.64e-05, respectively), but did not show any significant associations with insulin or C-peptide. Accordingly, we performed functional validation using a miR-223-3p mimic (overexpression) under control and hyperglycemia-induced conditions in a zebrafish model. RESULTS Over-expression of miR-223-3p alone was associated with significantly higher glucose (42.7 mg/dL, n = 75 vs 38.7 mg/dL, n = 75, p = 0.02) and degenerated retinal vasculature, and altered retinal morphology involving changes in the ganglion cell layer and inner and outer nuclear layers. Assessment of retinal angiogenesis revealed significant upregulation in the expression of vascular endothelial growth factor and its receptors, including kinase insert domain receptor. Further, the pancreatic markers, pancreatic and duodenal homeobox 1, and the insulin gene expressions were upregulated in the miR-223-3p group. CONCLUSION Our zebrafish model validates a novel correlation between miR-223-3p and DR development. Targeting miR-223-3p in T2D patients may serve as a promising therapeutic strategy to control DR in at-risk individuals.
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Affiliation(s)
- Sahar I Da'as
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Ikhlak Ahmed
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Waseem H Hasan
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Doua A Abdelrahman
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Elbay Aliyev
- Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Sabah Nisar
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ajaz Ahmad Bhat
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW, 2560, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Narellan Road & Gilchrist Drive, Campbelltown, NSW, 2560, Australia.,Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
| | - Khalid A Fakhro
- Laboratory of Genomic Medicine-Precision Medicine Program, 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
| | - Ammira S Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes, Obesity and Cancer Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
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6
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Ahmed I, Ziab M, Da’as S, Hasan W, Jeya SP, Aliyev E, Nisar S, Bhat AA, Fakhro KA, Alshabeeb Akil AS. Network-based identification and prioritization of key transcriptional factors of diabetic kidney disease. Comput Struct Biotechnol J 2023; 21:716-730. [PMID: 36659918 PMCID: PMC9827363 DOI: 10.1016/j.csbj.2022.12.054] [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: 08/28/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 01/04/2023] Open
Abstract
Diabetic nephropathy (DN) is one of the most established microvascular complications of diabetes and a key cause of end-stage renal disease. It is well established that gene susceptibility to DN plays a critical role in disease pathophysiology. Therefore, many genetic studies have been performed to categorize candidate genes in prominent diabetic cohorts, aiming to investigate DN pathogenesis and etiology. In this study, we performed a meta-analysis on the expression profiles of GSE1009, GSE30122, GSE96804, GSE99340, GSE104948, GSE104954, and GSE111154 to identify critical transcriptional factors associated with DN progression. The analysis was conducted for all individual datasets for each kidney tissue (glomerulus, tubules, and kidney cortex). We identified distinct clusters of susceptibility genes that were dysregulated in a renal compartment-specific pattern. Further, we recognized a small but a closely connected set of these susceptibility genes enriched for podocyte differentiation, several of which were characterized as genes encoding critical transcriptional factors (TFs) involved in DN development and podocyte function. To validate the role of identified TFs in DN progression, we functionally validated the three main TFs (DACH1, LMX1B, and WT1) identified through differential gene expression and network analysis using the hyperglycemic zebrafish model. We report that hyperglycemia-induced altered gene expression of the key TF genes leads to morphological abnormalities in zebrafish glomeruli, pronephric tubules, proximal and distal ducts. This study demonstrated that altered expression of these TF genes could be associated with hyperglycemia-induced nephropathy and, thus, aids in understanding the molecular drivers, essential genes, and pathways that trigger DN initiation and development.
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Affiliation(s)
- Ikhlak Ahmed
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Mubarak Ziab
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Sahar Da’as
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, 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 Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Waseem Hasan
- Zebrafish Functional Genomics, Integrated Genomic Services Core Facility, Research Branch, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Sujitha P. Jeya
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Elbay Aliyev
- Human Genetics Department, Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Sabah Nisar
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Ajaz A. Bhat
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Khalid Adnan Fakhro
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, 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,Human Genetics Department, Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar
| | - Ammira S. Alshabeeb Akil
- Department of Human Genetics-Precision Medicine in Diabetes Prevention, Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Human Genetics Department, Laboratory of Genomic Medicine-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar,Department of Physiology and Biophysics, Weill Cornell Medical College, P.O. Box 24144, Doha, Qatar,Correspondence to: Precision Medicine of Diabetes, Obesity and Cancer Research Program, Human Genetics Department, Sidra Medicine, PO Box 26999, Doha, Qatar.
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7
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Trost B, Thiruvahindrapuram B, Chan AJS, Engchuan W, Higginbotham EJ, Howe JL, Loureiro LO, Reuter MS, Roshandel D, Whitney J, Zarrei M, Bookman M, Somerville C, Shaath R, Abdi M, Aliyev E, Patel RV, Nalpathamkalam T, Pellecchia G, Hamdan O, Kaur G, Wang Z, MacDonald JR, Wei J, Sung WWL, Lamoureux S, Hoang N, Selvanayagam T, Deflaux N, Geng M, Ghaffari S, Bates J, Young EJ, Ding Q, Shum C, D'Abate L, Bradley CA, Rutherford A, Aguda V, Apresto B, Chen N, Desai S, Du X, Fong MLY, Pullenayegum S, Samler K, Wang T, Ho K, Paton T, Pereira SL, Herbrick JA, Wintle RF, Fuerth J, Noppornpitak J, Ward H, Magee P, Al Baz A, Kajendirarajah U, Kapadia S, Vlasblom J, Valluri M, Green J, Seifer V, Quirbach M, Rennie O, Kelley E, Masjedi N, Lord C, Szego MJ, Zawati MH, Lang M, Strug LJ, Marshall CR, Costain G, Calli K, Iaboni A, Yusuf A, Ambrozewicz P, Gallagher L, Amaral DG, Brian J, Elsabbagh M, Georgiades S, Messinger DS, Ozonoff S, Sebat J, Sjaarda C, Smith IM, Szatmari P, Zwaigenbaum L, Kushki A, Frazier TW, Vorstman JAS, Fakhro KA, Fernandez BA, Lewis MES, Weksberg R, Fiume M, Yuen RKC, Anagnostou E, Sondheimer N, Glazer D, Hartley DM, Scherer SW. Genomic architecture of autism from comprehensive whole-genome sequence annotation. Cell 2022; 185:4409-4427.e18. [PMID: 36368308 PMCID: PMC10726699 DOI: 10.1016/j.cell.2022.10.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [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: 05/05/2022] [Revised: 08/30/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Fully understanding autism spectrum disorder (ASD) genetics requires whole-genome sequencing (WGS). We present the latest release of the Autism Speaks MSSNG resource, which includes WGS data from 5,100 individuals with ASD and 6,212 non-ASD parents and siblings (total n = 11,312). Examining a wide variety of genetic variants in MSSNG and the Simons Simplex Collection (SSC; n = 9,205), we identified ASD-associated rare variants in 718/5,100 individuals with ASD from MSSNG (14.1%) and 350/2,419 from SSC (14.5%). Considering genomic architecture, 52% were nuclear sequence-level variants, 46% were nuclear structural variants (including copy-number variants, inversions, large insertions, uniparental isodisomies, and tandem repeat expansions), and 2% were mitochondrial variants. Our study provides a guidebook for exploring genotype-phenotype correlations in families who carry ASD-associated rare variants and serves as an entry point to the expanded studies required to dissect the etiology in the ∼85% of the ASD population that remain idiopathic.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Ada J S Chan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Livia O Loureiro
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; CGEn, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | - Cherith Somerville
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Rulan Shaath
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Mona Abdi
- Department of Human Genetics, Sidra Medicine, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Rohan V Patel
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Giovanna Pellecchia
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Omar Hamdan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Wei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sylvia Lamoureux
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ny Hoang
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Thanuja Selvanayagam
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Genetic Counselling, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Nicole Deflaux
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Melissa Geng
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Siavash Ghaffari
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John Bates
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | - Edwin J Young
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Qiliang Ding
- Ted Rogers Centre for Heart Research, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Carole Shum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Clarrisa A Bradley
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Annabel Rutherford
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vernie Aguda
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Beverly Apresto
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Nan Chen
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sachin Desai
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Xiaoyan Du
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Matthew L Y Fong
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sanjeev Pullenayegum
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Kozue Samler
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ting Wang
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Karen Ho
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Tara Paton
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olivia Rennie
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elizabeth Kelley
- Department of Psychology, Queen's University, Kingston, ON K7L 3N6, Canada; Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada
| | - Nina Masjedi
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Catherine Lord
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90024, USA
| | - Michael J Szego
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Family and Community Medicine, University of Toronto, Toronto, ON M5G 1V7, Canada; Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Ma'n H Zawati
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Michael Lang
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Lisa J Strug
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Statistical Sciences, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Christian R Marshall
- Genome Diagnostics, Department of Paediatric Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gregory Costain
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Kristina Calli
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Alana Iaboni
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Afiqah Yusuf
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Patricia Ambrozewicz
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Louise Gallagher
- Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin 2, Ireland; Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Child, Youth and Family Services, The Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - David G Amaral
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jessica Brian
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Mayada Elsabbagh
- Montreal Neurological Institute, McGill University, Montreal, QC H3A 2B4, Canada
| | - Stelios Georgiades
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON L8N 3K7, Canada
| | | | - Sally Ozonoff
- MIND Institute, University of California, Davis, Sacramento, CA 95817, USA; Department of Psychiatry and Behavioral Sciences, University of California, Davis, Sacramento, CA 95817, USA
| | - Jonathan Sebat
- Department of Psychiatry and Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Calvin Sjaarda
- Department of Psychiatry, Queen's University, Kingston, ON K7L 7X3, Canada; Queen's Genomics Lab at Ongwanada, Queen's University, Kingston, ON K7M 8A6, Canada
| | - Isabel M Smith
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H 4R2, Canada; IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Peter Szatmari
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada; Centre for Addiction and Mental Health, Toronto, ON M6J 1H4, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Azadeh Kushki
- Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada; Institute of Biomedical Engineering, University of Toronto, Toronto, ON M5S 3G9, Canada
| | - Thomas W Frazier
- Autism Speaks, Princeton, NJ 08540, USA; Department of Psychology, John Carroll University, Cleveland, OH 44118, USA
| | - Jacob A S Vorstman
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - 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 Medical College in Qatar, Doha, Qatar
| | - Bridget A Fernandez
- Department of Pediatrics, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA; Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90033, USA
| | - M E Suzanne Lewis
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; BC Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | | | - Ryan K C Yuen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Evdokia Anagnostou
- Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Holland Bloorview Kids Rehabilitation Hospital, Toronto, ON M4G 1R8, Canada
| | - Neal Sondheimer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Pediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA 94080, USA
| | | | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; McLaughlin Centre, Toronto, ON M5G 0A4, Canada.
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8
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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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9
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Walker K, Kalra D, Lowdon R, Chen G, Molik D, Soto DC, Dabbaghie F, Khleifat AA, Mahmoud M, Paulin LF, Raza MS, Pfeifer SP, Agustinho DP, Aliyev E, Avdeyev P, Barrozo ER, Behera S, Billingsley K, Chong LC, Choubey D, De Coster W, Fu Y, Gener AR, Hefferon T, Henke DM, Höps W, Illarionova A, Jochum MD, Jose M, Kesharwani RK, Kolora SRR, Kubica J, Lakra P, Lattimer D, Liew CS, Lo BW, Lo C, Lötter A, Majidian S, Mendem SK, Mondal R, Ohmiya H, Parvin N, Peralta C, Poon CL, Prabhakaran R, Saitou M, Sammi A, Sanio P, Sapoval N, Syed N, Treangen T, Wang G, Xu T, Yang J, Zhang S, Zhou W, Sedlazeck FJ, Busby B. The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms. F1000Res 2022; 11:530. [PMID: 36262335 PMCID: PMC9557141 DOI: 10.12688/f1000research.110194.1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 01/25/2023] Open
Abstract
In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
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Affiliation(s)
- Kimberly Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | - Divya Kalra
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
| | | | - Guangyi Chen
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Center for Bioinformatics, Saarland University, Saarbrücken, Germany,
| | - David Molik
- Tropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Daniela C. Soto
- Biochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA
| | - Fawaz Dabbaghie
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany,Institute for Medical Biometry and Bioinformatics, University hospital Düsseldorf, Düsseldorf, Germany
| | - Ahmad Al Khleifat
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China
| | - Susanne P. Pfeifer
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Daniel Paiva Agustinho
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Elbay Aliyev
- Research Department, Sidra Medicine, Doha, Qatar
| | - Pavel Avdeyev
- Computational Biology Institute, The George Washington University, Washington, DC, 20052, USA
| | - Enrico R. Barrozo
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey
| | - Deepak Choubey
- Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Alejandro R. Gener
- Association of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA
| | - Timothy Hefferon
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David Morgan Henke
- Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wolfram Höps
- EMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany
| | | | - Michael D. Jochum
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Jose
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
| | - Rupesh K. Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | | - Priya Lakra
- Department of Zoology, University of Delhi, Delhi, India
| | - Damaris Lattimer
- University of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria
| | - Chia-Sin Liew
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
| | - Bai-Wei Lo
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Chunhsuan Lo
- Human Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan
| | - Anneri Lötter
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Rajarshi Mondal
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | - Hiroko Ohmiya
- Genetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan
| | - Nasrin Parvin
- Department of Biotechnology, The University of Burdwan, West Bengal, India
| | | | | | | | - Marie Saitou
- Center of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway
| | - Aditi Sammi
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
| | - Philippe Sanio
- University of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria
| | - Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Najeeb Syed
- Research Department, Sidra Medicine, Doha, Qatar
| | - Todd Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | - Tiancheng Xu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Jianzhi Yang
- Department of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA
| | - Shangzhe Zhang
- School of Biology, University of St Andrews, St Andrews, UK
| | - Weiyu Zhou
- Department of Statistical Science, George Mason University, Fairfax, Virginia, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA,
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10
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Merico D, Pasternak Y, Zarrei M, Higginbotham EJ, Thiruvahindrapuram B, Scott O, Willett-Pachul J, Grunebaum E, Upton J, Atkinson A, Kim VHD, Aliyev E, Fakhro K, Scherer SW, Roifman CM. Homozygous duplication identified by whole genome sequencing causes LRBA deficiency. NPJ Genom Med 2021; 6:96. [PMID: 34795304 PMCID: PMC8602677 DOI: 10.1038/s41525-021-00263-z] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
In more than one-third of primary immunodeficiency (PID) patients, extensive genetic analysis including whole-exome sequencing (WES) fails to identify the genetic defect. Whole-genome sequencing (WGS) is able to detect variants missed by other genomics platforms, enabling the molecular diagnosis of otherwise unresolved cases. Here, we report two siblings, offspring of consanguineous parents, who experienced similar severe events encompassing early onset of colitis, lymphoproliferation, and hypogammaglobulinemia, typical of lipopolysaccharide-responsive and beige-like anchor (LRBA) or cytotoxic T lymphocyte antigen 4 (CTLA4) deficiencies. Gene-panel sequencing, comparative genomic hybridization (CGH) array, and WES failed to reveal a genetic aberration in relevant genes. WGS of these patients detected a 12.3 kb homozygous tandem duplication that was absent in control cohorts and is predicted to disrupt the reading frame of the LRBA gene. The variant was validated by PCR and Sanger sequencing, demonstrating the presence of the junction between the reference and the tandem-duplicated sequence. Droplet digital PCR (ddPCR) further confirmed the copy number in the unaffected parents (CN = 3, heterozygous) and affected siblings (CN = 4, homozygous), confirming the expected segregation pattern. In cases of suspected inherited immunodeficiency, WGS may reveal a mutation when other methods such as microarray and WES analysis failed to detect an aberration.
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Affiliation(s)
- Daniele Merico
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada ,Deep Genomics Inc., Toronto, M5G 1M1 ON Canada
| | - Yehonatan Pasternak
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Mehdi Zarrei
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Edward J. Higginbotham
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Bhooma Thiruvahindrapuram
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Ori Scott
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Jessica Willett-Pachul
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada
| | - Eyal Grunebaum
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Julia Upton
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Adelle Atkinson
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Vy H. D. Kim
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Elbay Aliyev
- grid.467063.00000 0004 0397 4222Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Khalid Fakhro
- grid.467063.00000 0004 0397 4222Department of Human Genetics, Sidra Medicine, Doha, Qatar ,grid.416973.e0000 0004 0582 4340Department of Genetic Medicine, Weill-Cornell Medical College, Doha, Qatar
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8 ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre, University of Toronto, Toronto, M5G 0A4 ON Canada
| | - Chaim M. Roifman
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
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11
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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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12
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Akil AAS, Yassin E, Al-Maraghi A, Aliyev E, Al-Malki K, Fakhro KA. Diagnosis and treatment of type 1 diabetes at the dawn of the personalized medicine era. J Transl Med 2021; 19:137. [PMID: 33794915 PMCID: PMC8017850 DOI: 10.1186/s12967-021-02778-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [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: 12/18/2020] [Accepted: 03/08/2021] [Indexed: 12/21/2022] Open
Abstract
Type 1 diabetes affects millions of people globally and requires careful management to avoid serious long-term complications, including heart and kidney disease, stroke, and loss of sight. The type 1 diabetes patient cohort is highly heterogeneous, with individuals presenting with disease at different stages and severities, arising from distinct etiologies, and overlaying varied genetic backgrounds. At present, the “one-size-fits-all” treatment for type 1 diabetes is exogenic insulin substitution therapy, but this approach fails to achieve optimal blood glucose control in many individuals. With advances in our understanding of early-stage diabetes development, diabetes stratification, and the role of genetics, type 1 diabetes is a promising candidate for a personalized medicine approach, which aims to apply “the right therapy at the right time, to the right patient”. In the case of type 1 diabetes, great efforts are now being focused on risk stratification for diabetes development to enable pre-clinical detection, and the application of treatments such as gene therapy, to prevent pancreatic destruction in a sub-set of patients. Alongside this, breakthroughs in stem cell therapies hold great promise for the regeneration of pancreatic tissues in some individuals. Here we review the recent initiatives in the field of personalized medicine for type 1 diabetes, including the latest discoveries in stem cell and gene therapy for the disease, and current obstacles that must be overcome before the dream of personalized medicine for all type 1 diabetes patients can be realized.
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Affiliation(s)
- Ammira Al-Shabeeb Akil
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.
| | - Esraa Yassin
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Aljazi Al-Maraghi
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Khulod Al-Malki
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Khalid A Fakhro
- Department of Human Genetics-Precision Medicine Program, Sidra Medicine, P.O. Box 26999, Doha, Qatar.,Department of Genetic Medicine, Weill Cornell Medicine, P.O. Box 24144, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
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13
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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14
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Mc Cartney AM, Mahmoud M, Jochum M, Agustinho DP, Zorman B, Al Khleifat A, Dabbaghie F, K Kesharwani R, Smolka M, Dawood M, Albin D, Aliyev E, Almabrazi H, Arslan A, Balaji A, Behera S, Billingsley K, L Cameron D, Daw J, T. Dawson E, De Coster W, Du H, Dunn C, Esteban R, Jolly A, Kalra D, Liao C, Liu Y, Lu TY, M Havrilla J, M Khayat M, Marin M, Monlong J, Price S, Rafael Gener A, Ren J, Sagayaradj S, Sapoval N, Sinner C, C. Soto D, Soylev A, Subramaniyan A, Syed N, Tadimeti N, Tater P, Vats P, Vaughn J, Walker K, Wang G, Zeng Q, Zhang S, Zhao T, Kille B, Biederstedt E, Chaisson M, English A, Kronenberg Z, J. Treangen T, Hefferon T, Chin CS, Busby B, J Sedlazeck F. An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates. F1000Res 2021; 10:246. [PMID: 34621504 PMCID: PMC8479851 DOI: 10.12688/f1000research.51477.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/04/2021] [Indexed: 11/08/2023] Open
Abstract
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related research. The overarching focus was to assess the current status of the field and identify the remaining challenges. Furthermore, how to combine the strengths of the different interests to drive research and method development forward. Over the four days, eight groups each designed and developed new open-source methods to improve the identification and analysis of variations among species, including humans and SARS-CoV-2. These included improvements in SV calling, genotyping, annotations and filtering. Together with advancements in benchmarking existing methods. Furthermore, groups focused on the diversity of SARS-CoV-2. Daily discussion summary and methods are available publicly at https://github.com/collaborativebioinformatics provides valuable insights for both participants and the research community.
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Affiliation(s)
| | | | | | | | | | | | - Fawaz Dabbaghie
- Institute for Medical Biometry and Bioinformatics, Düsseldorf, Germany
| | | | | | | | | | | | | | - Ahmed Arslan
- Stanford University School of Medicine, California, USA
| | | | | | | | - Daniel L Cameron
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Joyjit Daw
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | - Haowei Du
- Baylor College of Medicine, Houston, USA
| | | | | | | | | | | | | | | | | | | | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, USA
| | | | | | | | | | | | | | | | - Arda Soylev
- Konya Food and Agriculture University, Konya, Turkey
| | | | | | | | | | - Pankaj Vats
- NVIDIA Corporation, Santa Clara, California, USA
| | | | | | | | - Qiandong Zeng
- Laboratory Corporation of America Holdings, Westborough, USA
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15
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Umar M, Megarbane A, Shan J, Syed N, Chouery E, Aliyev E, Jithesh P, Temanni R, Mansour I, Chouchane L, Ismail Chouchane A. Genome sequencing unveils mutational landscape of the familial Mediterranean fever: Potential implications of IL33/ST2 signalling. J Cell Mol Med 2020; 24:11294-11306. [PMID: 32853466 PMCID: PMC7576248 DOI: 10.1111/jcmm.15701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 03/20/2020] [Revised: 07/09/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
Familial Mediterranean fever (FMF) is the most common auto-inflammatory disease. It is transmitted as autosomal recessive trait with mutations in MEditerranean FeVer (MEFV) gene. Despite a typical clinical expression, many patients have either a single or no mutation in MEFV. The current work is aimed to revisit the genetic landscape of FMF disease using high-coverage whole genome sequencing. In atypical patients (carrying a single or no mutation in MEFV), we revealed many rare variants in genes associated with auto-inflammatory disorders, and more interestingly, we discovered a novel variant ( a 2.1-Kb deletion) in exon 11 of IL1RL1 gene, present only in patients. To validate and screen this patient-specific variant, a tandem of allele-specific PCR and quantitative real-time PCR was performed in 184 FMF patients and 218 healthy controls and we demonstrated that the novel deletion was absent in controls and was present in more than 19% of patients. This study sheds more light on the mutational landscape of FMF. Our discovery of a disease-specific variant in IL1RL1 gene may constitute a novel genetic marker for FMF. This finding suggesting a potential role of the IL33/ST2 signalling in the disease pathogenicity highlights a new paradigm in FMF pathophysiology.
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Affiliation(s)
- Meenakshi Umar
- Laboratory of Inflammation Research, Immunology Department, Sidra Medicine, Doha, Qatar
| | - Andre Megarbane
- Institut Jérôme Lejeune, Paris, France.,Centre Medical et Psychopedagogique, Beirut, Lebanon
| | - Jingxuan Shan
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Qatar.,Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Najeeb Syed
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Eliane Chouery
- Medical School, Lebanese American University, Beirut, Lebanon
| | - Elbay Aliyev
- Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Puthen Jithesh
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Ramzi Temanni
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Issam Mansour
- American University of Science and Technology (AUST), Beirut, Lebanon
| | - Lotfi Chouchane
- Laboratory of Genetic Medicine and Immunology, Weill Cornell Medicine-Qatar, Qatar.,Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.,Department of Microbiology & Immunology, Weill Cornell Medicine, New York, NY, USA
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16
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Uysal HK, Akgul O, Aliyev E, Tunc M, Oner Y. A rare case of urinary schistosomiasis in Turkey. Travel Med Infect Dis 2014; 12:283-5. [DOI: 10.1016/j.tmaid.2013.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/12/2013] [Accepted: 11/07/2013] [Indexed: 01/15/2023]
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17
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Engler O, Klingström J, Aliyev E, Niederhauser C, Fontana S, Strasser M, Portmann J, Signer J, Bankoul S, Frey F, Hatz C, Stutz A, Tschaggelar A, Mütsch M. Seroprevalence of hantavirus infections in Switzerland in 2009: difficulties in determining prevalence in a country with low endemicity. Euro Surveill 2013; 18:20660. [DOI: 10.2807/1560-7917.es2013.18.50.20660] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- O Engler
- SPIEZ LABORATORY, Federal Office for Civil Protection, Spiez, Switzerland
| | - J Klingström
- Swedish Institute for Communicable Disease Control, Solna, Sweden
- Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - E Aliyev
- Institute of Social and Preventive Medicine (ISPM), Division of Communicable Diseases, World Health Organization (WHO) Collaborating Centre for Travellers’ Health, University of Zurich, Zurich, Switzerland
| | - C Niederhauser
- Blood Transfusion Service, Swiss Red Cross Berne, Berne, Switzerland
| | - S Fontana
- Blood Transfusion Service, Swiss Red Cross Berne, Berne, Switzerland
| | - M Strasser
- SPIEZ LABORATORY, Federal Office for Civil Protection, Spiez, Switzerland
| | - J Portmann
- SPIEZ LABORATORY, Federal Office for Civil Protection, Spiez, Switzerland
| | - J Signer
- SPIEZ LABORATORY, Federal Office for Civil Protection, Spiez, Switzerland
| | - S Bankoul
- CBRN Defence of the Swiss Armed Forces, Medical Services Directorate, Ittigen, Switzerland
| | - F Frey
- Military Medical Service, Swiss Armed Forces, Ittigen, Switzerland
| | - C Hatz
- Institute of Social and Preventive Medicine (ISPM), Division of Communicable Diseases, World Health Organization (WHO) Collaborating Centre for Travellers’ Health, University of Zurich, Zurich, Switzerland
| | - A Stutz
- Institute of Social and Preventive Medicine (ISPM), Division of Communicable Diseases, World Health Organization (WHO) Collaborating Centre for Travellers’ Health, University of Zurich, Zurich, Switzerland
| | - A Tschaggelar
- Blood Transfusion Service, Swiss Red Cross Berne, Berne, Switzerland
| | - M Mütsch
- Institute of Social and Preventive Medicine (ISPM), Division of Communicable Diseases, World Health Organization (WHO) Collaborating Centre for Travellers’ Health, University of Zurich, Zurich, Switzerland
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Sakallioğlu EE, Lütfioğlu M, Ozkaya O, Aliyev E, Açikgöz G, Firatli E. Fluid dynamics of gingiva and gingival health in children with end stage renal failure. Arch Oral Biol 2007; 52:1194-9. [PMID: 17719557 DOI: 10.1016/j.archoralbio.2007.05.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 03/29/2007] [Revised: 05/15/2007] [Accepted: 05/21/2007] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Impaired homeostasis and fluid balance are important physiopathological alterations in patients with chronic renal failure which may adversely affect the fluid dynamics and health status of tissues and organs. There are insufficient data about this phenomenon in periodontal tissues. The aim of this study was to evaluate the fluid dynamics of gingiva in children with end stage renal failure (ESRF), correlating this entity with gingival health in the same patient group. DESIGN Fifteen paediatric ESRF patients undergoing peritoneal dialysis (test group) and 15 systemically healthy children (control group) who were without periodontitis participated in the study. Fluid dynamics of gingiva were assessed via the gingival crevicular fluid (GCF) volume and tissue osmotic pressure (GOP) levels in the groups. GCF volume was measured using a Periotron 8000, whereas GOP was measured using a digital osmometer. Silness and Löe Plaque index (PI) and, Löe and Silness gingival index (GI) scores were utilized to determine the gingival health status in the study population. RESULTS There were increases in the GCF volume and GOP of the test group compared to those of the control group (p<0.01). The PI and GI scores were higher in the test group than in the control group (p<0.01). Strong and positive correlations were found between GI and GCF volume, GI and GOP and, GCF volume and GOP in both groups (p<0.01). CONCLUSIONS Our findings suggest that the fluid dynamics of gingiva may alter in children with ESRF, and this phenomenon may consequently affect the gingival health of these patients.
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Affiliation(s)
- E E Sakallioğlu
- Department of Periodontology, Ondokuz Mayis University Dental Faculty, 55139 Kurupelit, Samsun, Turkey.
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