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Mathur Y, Shafie A, Alharbi B, Ashour AA, Al-Soud WA, Alhassan HH, Alharethi SH, Anjum F. Genome-Wide Analysis of Kidney Renal Cell Carcinoma: Exploring Differentially Expressed Genes for Diagnostic and Therapeutic Targets. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:393-401. [PMID: 37624678 DOI: 10.1089/omi.2023.0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Kidney renal cell carcinoma (KIRC) is the most common type of renal cancer. Kidney malignancies have been ranked in the top 10 most frequently occurring cancers. KIRC is a prevalent malignancy with a poor prognosis. The disease has risen for the last 40 years, and robust biomarkers for KIRC are needed for precision/personalized medicine. In this bioinformatics study, we utilized genomic data of KIRC patients from The Cancer Genome Atlas for biomarker discovery. A total of 314 samples were used in this study. We identified many differentially expressed genes (DEGs) categorized as upregulated or downregulated. A protein-protein interaction network for the DEGs was then generated and analyzed using the Search Tool for the Retrieval of Interacting Genes plugin of Cytoscape. A set of 10 hub genes was selected based on the Maximum Clique Centrality score defined by the CytoHubba plugin. The elucidated set of genes, that is, CALCA, CRH, TH, CHAT, SLC18A3, FSHB, MYH6, CAV3, KCNA4, and GBX2, were then categorized as potential candidates to be explored as KIRC biomarkers. The survival analysis plots for each gene suggested that alterations in CHAT, CAV3, CRH, MYH6, SLC18A3, and FSHB resulted in decreased survival of KIRC patients. In all, the results suggest that genomic alterations in selected genes can be explored to inform biomarker discovery and for therapeutic predictions in KIRC.
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Affiliation(s)
- Yash Mathur
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, India
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Hail, Saudi Arabia
| | - Amal Adnan Ashour
- Department of Oral and Maxillofacial Surgery and Diagnostic Sciences, Faculty of Dentistry, Taif University, Taif, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Science, College of Applied Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Hassan H Alhassan
- Department of Clinical Laboratory Science, College of Applied Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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Saghi M, InanlooRahatloo K, Alavi A, Kahrizi K, Najmabadi H. Intellectual disability associated with craniofacial dysmorphism due to POLR3B mutation and defect in spliceosomal machinery. BMC Med Genomics 2022; 15:89. [PMID: 35436926 PMCID: PMC9014605 DOI: 10.1186/s12920-022-01237-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background Intellectual disability (ID) is a clinically important disease and a most prevalent neurodevelopmental disorder. The etiology and pathogenesis of ID are poorly recognized. Exome sequencing revealed a homozygous missense mutation in the POLR3B gene in a consanguineous family with three Intellectual disability with craniofacial anomalies patients. POLR3B gene encoding the second largest subunit of RNA polymerase III. Methods We performed RNA sequencing on blood samples to obtain insights into the biological pathways influenced by POLR3B mutation. We applied the results of our RNA-Seq analysis to several gene ontology programs such as ToppGene, Enrichr, KEGG. Results A significant decrease in expression of several spliceosomal RNAs, ribosomal proteins, and transcription factors was detected in the affected, compared to unaffected, family members. Conclusions We hypothesize that POLR3B mutation dysregulates the expression of some important transcription factors, ribosomal and spliceosomal genes, and impairments in protein synthesis and splicing mediated in part by transcription factors such as FOXC2 and GATA1 contribute to impaired neuronal function and concurrence of intellectual disability and craniofacial anomalies in our patients. Our study highlights the emerging role of the spliceosome and ribosomal proteins in intellectual disability. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01237-5.
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Affiliation(s)
- Mostafa Saghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Afagh Alavi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Wen J, Chai H, Grommisch B, DiAdamo A, Dykas D, Ma D, Popa A, Zhao C, Spencer-Manzon M, Jiang YH, McGrath J, Li P, Bale A, Zhang H. Detecting regions of homozygosity improves the diagnosis of pathogenic variants and uniparental disomy in pediatric patients. Am J Med Genet A 2022; 188:1728-1738. [PMID: 35199448 DOI: 10.1002/ajmg.a.62693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/12/2022] [Accepted: 01/28/2022] [Indexed: 11/10/2022]
Abstract
Chromosomal microarray analysis using single nucleotide polymorphism probes can detect regions of homozygosity (ROH). This confers a potential utility in revealing autosomal recessive (AR) diseases and uniparental disomy (UPD). Results of genetic testing among pediatric patients from 2015 to 2019 were evaluated. Diagnostic findings with detected ROH from large consecutive case series in the literature were reviewed. Of 2050 pediatric patients, 65 (3%) had one or more ROH and 31 (53%) had follow-up whole exome sequencing (WES) and methylation studies. Seven homozygous variants were detected and four of them from three patients (9.6%) were within the detected ROH and classified as pathogenic or likely pathogenic variants for AR diseases. One patient (3%) had segmental UPD15q for a diagnosis of Prader-Willi syndrome. Additive diagnostic yield from ROH reporting was at least 0.2% (4/2050) of pediatric patients. These results were consistent with findings from several large case series reported in the literature. Detecting ROH had an estimated baseline predictive value of 10% for AR diseases and 3% for UPD. Consanguinity revealed by multiple ROH was a strong predictor for AR diseases. These results provide evidence for genetic counseling and recommendation of follow-up WES and methylation studies for pediatric patients reported with ROH.
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Affiliation(s)
- Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Daniel Dykas
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deqiong Ma
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Andreea Popa
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chen Zhao
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - James McGrath
- Department of Comparative medicine, Yale University, New Haven, Connecticut, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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Al-Mubarak BR, Omar A, Baz B, Al-Abdulaziz B, Magrashi AI, Al-Yemni E, Jabaan A, Monies D, Abouelhoda M, Abebe D, Ghaziuddin M, Al-Tassan NA. Whole exome sequencing in ADHD trios from single and multi-incident families implicates new candidate genes and highlights polygenic transmission. Eur J Hum Genet 2020; 28:1098-1110. [PMID: 32238911 PMCID: PMC7382449 DOI: 10.1038/s41431-020-0619-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/26/2020] [Accepted: 03/10/2020] [Indexed: 12/18/2022] Open
Abstract
Several types of genetic alterations occurring at numerous loci have been described in attention deficit hyperactivity disorder (ADHD). However, the role of rare single nucleotide variants (SNVs) remains under investigated. Here, we sought to identify rare SNVs with predicted deleterious effect that may contribute to ADHD risk. We chose to study ADHD families (including multi-incident) from a population with a high rate of consanguinity in which genetic risk factors tend to accumulate and therefore increasing the chance of detecting risk alleles. We employed whole exome sequencing (WES) to interrogate the entire coding region of 16 trios with ADHD. We also performed enrichment analysis on our final list of genes to identify the overrepresented biological processes. A total of 32 rare variants with predicted damaging effect were identified in 31 genes. At least two variants were detected per proband, most of which were not exclusive to the affected individuals. In addition, the majority of our candidate genes have not been previously described in ADHD including five genes (NEK4, NLE1, PSRC1, PTP4A3, and TMEM183A) that were not previously described in any human condition. Moreover, enrichment analysis highlighted brain-relevant biological themes such as "Glutamatergic synapse", "Cytoskeleton organization", and "Ca2+ pathway". In conclusion, our findings are in keeping with prior studies demonstrating the highly challenging genetic architecture of ADHD involving low penetrance, variable expressivity and locus heterogeneity.
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Affiliation(s)
- Bashayer R Al-Mubarak
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
| | - Aisha Omar
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
| | - Batoul Baz
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Basma Al-Abdulaziz
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
- National center for genomics technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amna I Magrashi
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
| | - Eman Al-Yemni
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amjad Jabaan
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
| | - Mohamed Abouelhoda
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
- Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Dejene Abebe
- Psychiatry Department, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia
| | | | - Nada A Al-Tassan
- Behavioral Genetics unit, Department of Genetics, King Faisal Specialist Hospital and Research Center, P.O Box 3354, Riyadh, 11211, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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Kornilov SA, Tan M, Aljughaiman A, Naumova OY, Grigorenko EL. Genome-Wide Homozygosity Mapping Reveals Genes Associated With Cognitive Ability in Children From Saudi Arabia. Front Genet 2019; 10:888. [PMID: 31620175 PMCID: PMC6759945 DOI: 10.3389/fgene.2019.00888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 08/22/2019] [Indexed: 11/28/2022] Open
Abstract
Recent studies of the genetic foundations of cognitive ability rely on large samples (in extreme, hundreds of thousands) of individuals from relatively outbred populations of mostly European ancestry. Hypothesizing that the genetic foundation of cognitive ability depends on the broader population-specific genetic context, we performed a genome-wide association study and homozygosity mapping of cognitive ability estimates obtained through latent variable modeling in a sample of 354 children from a consanguineous population of Saudi Arabia. Approximately half of the sample demonstrated significantly elevated homozygosity levels indicative of inbreeding, and among those with elevated levels, homozygosity was negatively associated with cognitive ability. Further homozygosity mapping identified a specific run, inclusive of the GRIA4 gene, that survived corrections for multiple testing for association with cognitive ability. The results suggest that in a consanguineous population, a notable proportion of the variance in cognitive ability in the normal range in children might be regulated by population-specific mechanisms such as patterns of elevated homozygosity. This observation has implications for the field's understanding of the etiological bases of intelligence and its variability around the world.
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Affiliation(s)
- Sergey A. Kornilov
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
| | - Mei Tan
- Department of Psychology, University of Houston, Houston, TX, USA
| | | | - Oxana Yu Naumova
- Department of Psychology, University of Houston, Houston, TX, USA
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elena L. Grigorenko
- Baylor College of Medicine, Department of Molecular and Human Genetics, Houston, TX, United States
- Department of Psychology, University of Houston, Houston, TX, USA
- Child Study Center, Yale University, New Haven, CT, USA
- Moscow State University for Psychology and Education, Moscow, Russia
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School Dropout and Associated Factors Among Omani Children with Attention-Deficit Hyperactivity Disorder: A Cross-Sectional Study. J Dev Behav Pediatr 2019; 39:109-115. [PMID: 29084072 DOI: 10.1097/dbp.0000000000000522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Despite the rising incidence of attention-deficit hyperactivity disorder (ADHD), there is a dearth of studies examining the rate of school dropout and its correlates in non-Western populations. METHODS Medical records were scrutinized to identify Omani children diagnosed with ADHD from 2006 to 2014 in a tertiary care hospital in Oman. The persistence of ADHD symptoms, school performance and dropout, as well as sociodemographic characteristics were examined. RESULTS Three hundred sixty-seven children fulfilled the diagnosis of ADHD based on Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) (DSM-IV) criteria and 16.6% of them had dropped out of school. School dropout was associated with poor school performance, comorbid conduct disorder, and parental divorce. CONCLUSION This study from Oman concurs with existing literature that school dropout is common among children with ADHD. Concerted efforts are needed to mitigate this trend. Management strategies should incorporate the treatment of comorbid conduct disorder.
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Amer YS, Al-Joudi HF, Varnham JL, Bashiri FA, Hamad MH, Al Salehi SM, Daghash HF, Albatti TH. Appraisal of clinical practice guidelines for the management of attention deficit hyperactivity disorder (ADHD) using the AGREE II Instrument: A systematic review. PLoS One 2019; 14:e0219239. [PMID: 31276528 PMCID: PMC6611626 DOI: 10.1371/journal.pone.0219239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVE High quality evidence-based clinical practice guidelines (CPGs) have a major impact on the appropriate diagnosis and management and positive outcomes. The evidence-based healthcare for patients with attention deficit hyperactive disorder (ADHD) is challenging. The objective of this study was to appraise the quality of published CPGs for ADHD. METHODS A systematic review was conducted for ADHD CPGs using CPG databases, DynaMed, PubMed, and Google Scholar. The quality of each included CPG was appraised by three independent appraisers using the Appraisal of Guidelines for Research & Evaluation II (AGREE II) instrument. RESULTS Six CPGs were critically reviewed. The AGREE II standardized domain scores revealed variation between the quality of these CPGs with the National Institute of Health and Care Excellence (NICE), University of Michigan Health System, and American Academy of Pediatrics CPGs as the top three. Overall, the recommendations for management of ADHD were similar in these CPGs. CONCLUSIONS Reporting of CPG development is often poorly documented. Guideline development groups should aim to follow the AGREE II criteria to improve the standards and quality of CPGs. The NICE CPG showed the best quality. Embedding the AGREE II appraisal of CPGs in the training and education of healthcare providers is recommended. The protocol for this study was published in PROSPERO (International prospective register of systematic reviews). Link: http://www.crd.york.ac.uk/PROSPERO/display_record.php?ID=CRD42017078712 and is additionally available from protocols.io. Link: https://dx.doi.org/10.17504/protocols.io.q27dyhn.
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Affiliation(s)
- Yasser Sami Amer
- CPG Unit, Quality Management Department, King Saud University Medical City, Riyadh, Saudi Arabia
- Pediatrics Department, King Khalid University Hospital, King Saud University Medical City, Riyadh, Saudi Arabia
- Research Chair for Evidence-Based Health Care and Knowledge Translation, Deanship of Scientific Research, King Saud University, Riyadh, Saudi Arabia
- Alexandria Center for Evidence-Based Clinical Practice Guidelines, Alexandria University, Alexandria, Egypt
| | - Haya Faisal Al-Joudi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jeremy L. Varnham
- Saudi ADHD Society, Riyadh, Saudi Arabia
- School of Psychology, University of East London, London, United Kingdom
| | - Fahad A. Bashiri
- Division of Neurology, Department of Pediatrics, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Muddathir Hamad Hamad
- Division of Neurology, Department of Pediatrics, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Saleh M. Al Salehi
- Child Development Center, King Abdullah Bin Abdulaziz University Hospital, Princess Noura Bint AbdulRahman University, Riyadh, Saudi Arabia
| | - Hadeel Fakhri Daghash
- Ada’a Program, Assistant Deputyship for Hospital Services, Ministry of Health, Riyadh, Saudi Arabia
| | - Turki Homod Albatti
- Saudi ADHD Society, Riyadh, Saudi Arabia
- Department of Psychiatry, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
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