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Dong H, Sang T, Ma X, Song J, Chen Z, Zhang H, Jin Y, Li M, Dong D, Sun L, Zhu Z, Zhang Y, Yang Y. Clinical features and CPS1 variants in Chinese patients with carbamoyl phosphate synthetase 1 deficiency. BMC Pediatr 2024; 24:539. [PMID: 39174957 PMCID: PMC11340094 DOI: 10.1186/s12887-024-05005-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Carbamoyl phosphate synthetase 1 (CPS1) deficiency (OMIM 237300), an autosomal recessive rare and severe urea cycle disorder, is associated with hyperammonemia and high mortality. METHODS Herein we present 12 genetic variants identified in seven clinically well-characterized Chinese patients with CPS1 deficiency who were admitted to the Children's Medical Center of Peking University First Hospital from September 2014 to August 2023. RESULTS Seven patients (two male and five female patients including two sisters) experienced symptoms onset between 2 days and 13 years of age, and they were diagnosed with CPS1 deficiency between 2 months and 20 years. Peak blood ammonia levels ranged from 160 to 1,000 µmol/L. Three patients showed early-onset CPS1 deficiency, with only one surviving after treatment with sodium phenylbutyrate, N-carbamoyl-L-glutamate, and liver transplantation at 4 months, showing a favorable outcome. The remaining four patients had late-onset CPS1 deficiency, presenting with mental retardation, psychiatric symptoms, and self-selected low-protein diets. Among the 12 CPS1 variants identified in these patients, 10 were novel, with all patients exhibiting compound heterozygosity for CPS1 mutant alleles. Seven variants (c.149T > C, c.616 A > T, c.1145 C > T, c.1294G > A, c.3029 C > T, c.3503 A > T, and c.3793 C > T) resulted in single amino acid substitutions. Three frameshift variations (c.2493del, c.3067dup, and c.3241del) were identified, leading to enzyme truncation. One mutation (c.3506_3508del) caused an in-frame single amino acid deletion, while another (c.2895 + 2T > C) resulted in aberrant splicing. CONCLUSIONS Except for two known variants, all other variants were identified as novel. No hotspot variants were observed among the patients. Our data contribute to expanding the mutation spectrum of CPS1.
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Affiliation(s)
- Hui Dong
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Tian Sang
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Xue Ma
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Jinqing Song
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Zhehui Chen
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, 361003, China
| | - Huiting Zhang
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Ying Jin
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Mengqiu Li
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Dingding Dong
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China
| | - Liying Sun
- Department of General Surgery, Beijing Friendship Hospital of Capital Medical University, Beijing, 100050, China
| | - Zhijun Zhu
- Department of General Surgery, Beijing Friendship Hospital of Capital Medical University, Beijing, 100050, China
| | - Yao Zhang
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China.
| | - Yanling Yang
- Children's Medical Center, Peking University First Hospital, Beijing, 102600, China.
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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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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Ferreira JC, Alshamali F, Pereira L, Fernandes V. Characterization of Arabian Peninsula whole exomes: Contributing to the catalogue of human diversity. iScience 2022; 25:105336. [DOI: 10.1016/j.isci.2022.105336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/24/2022] Open
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4
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Mezzavilla M, Cocca M, Maisano Delser P, Badii R, Abbaszadeh F, Hadi KA, Giorgia G, Gasparini P. Ancestry-related distribution of Runs of homozygosity and functional variants in Qatari population. BMC Genom Data 2022; 23:73. [PMID: 36131251 PMCID: PMC9490902 DOI: 10.1186/s12863-022-01087-1] [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: 02/21/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Background Describing how genetic history shapes the pattern of medically relevant variants could improve the understanding of how specific loci interact with each other and affect diseases and traits prevalence. The Qatari population is characterized by a complex history of admixture and substructure, and the study of its population genomic features would provide valuable insights into the genetic landscape of functional variants. Here, we analyzed the genomic variation of 186 newly-genotyped healthy individuals from the Qatari peninsula. Results We discovered an intricate genetic structure using ancestry related analyses. In particular, the presence of three different clusters, Cluster 1, Cluster 2 and Cluster 3 (with Near Eastern, South Asian and African ancestry, respectively), was detected with an additional fourth one (Cluster 4) with East Asian ancestry. These subpopulations show differences in the distribution of runs of homozygosity (ROH) and admixture events in the past, ranging from 40 to 5 generations ago. This complex genetic history led to a peculiar pattern of functional markers under positive selection, differentiated in shared signals and private signals. Interestingly we found several signatures of shared selection on SNPs in the FADS2 gene, hinting at a possible common evolutionary link to dietary intake. Among the private signals, we found enrichment for markers associated with HDL and LDL for Cluster 1(Near Eastern ancestry) and Cluster 3 (South Asian ancestry) and height and blood traits for Cluster 2 (African ancestry). The differences in genetic history among these populations also resulted in the different frequency distribution of putative loss of function variants. For example, homozygous carriers for rs2884737, a variant linked to an anticoagulant drug (warfarin) response, are mainly represented by individuals with predominant Bedouin ancestry (risk allele frequency G at 0.48). Conclusions We provided a detailed catalogue of the different ancestral pattern in the Qatari population highlighting differences and similarities in the distribution of selected variants and putative loss of functions. Finally, these results would provide useful guidance for assessing genetic risk factors linked to consanguinity and genetic ancestry.
Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01087-1.
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5
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Elfatih A, Da’as SI, Abdelrahman D, Mbarek H, Mohammed I, Hasan W, Fakhro KA, Estivill X, Mifsud B. Analysis of incidental findings in Qatar genome participants reveals novel functional variants in LMNA and DSP. Hum Mol Genet 2022; 31:2796-2809. [PMID: 35348702 PMCID: PMC9402234 DOI: 10.1093/hmg/ddac073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 11/21/2022] Open
Abstract
In order to report clinically actionable incidental findings in genetic testing, the American College of Medical Genetics and Genomics (ACMG) recommended the evaluation of variants in 59 genes associated with highly penetrant mutations. However, there is a lack of epidemiological data on medically actionable rare variants in these genes in Arab populations. We used whole genome sequencing data from 6045 participants from the Qatar Genome Programme and integrated it with phenotypic data collected by the Qatar Biobank. We identified novel putative pathogenic variants in the 59 ACMG genes by filtering previously unrecorded variants based on computational prediction of pathogenicity, variant rarity and segregation evidence. We assessed the phenotypic associations of candidate variants in genes linked to cardiovascular diseases. Finally, we used a zebrafish knockdown and synthetic human mRNA co-injection assay to functionally characterize two of these novel variants. We assessed the zebrafish cardiac function in terms of heart rate, rhythm and hemodynamics, as well as the heart structure. We identified 52 492 novel variants, which have not been reported in global and disease-specific databases. A total of 74 novel variants were selected with potentially pathogenic effect. We prioritized two novel cardiovascular variants, DSP c.1841A > G (p.Asp614Gly) and LMNA c.326 T > G (p.Val109Gly) for functional characterization. Our results showed that both variants resulted in abnormal zebrafish heart rate, rhythm and structure. This study highlights medically actionable variants that are specific to the Middle Eastern Qatari population.
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Affiliation(s)
- Amal Elfatih
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Sahar I Da’as
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Programme, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Idris Mohammed
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Waseem Hasan
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Xavier Estivill
- Quantitative Genomics Laboratories (qGenomics), 08950 Barcelona, Spain
| | - Borbala Mifsud
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- William Harvey Research Institute, Queen Mary University London, EC1M 6BQ London, United Kingdom
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6
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Mbarek H, Devadoss Gandhi G, Selvaraj S, Al-Muftah W, Badji R, Al-Sarraj Y, Saad C, Darwish D, Alvi M, Fadl T, Yasin H, Alkuwari F, Razali R, Aamer W, Abbaszadeh F, Ahmed I, Mokrab Y, Suhre K, Albagha O, Fakhro K, Badii R, Ismail SI, Althani A. Qatar Genome: Insights on Genomics from the Middle East. Hum Mutat 2022; 43:499-510. [PMID: 35112413 DOI: 10.1002/humu.24336] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/16/2021] [Accepted: 01/29/2022] [Indexed: 11/09/2022]
Abstract
Despite recent biomedical breakthroughs and large genomic studies growing momentum, the Middle Eastern population, home to over 400 million people, is under-represented in the human genome variation databases. Here we describe insights from phase 1 of the Qatar Genome Program with whole genome sequenced 6,047 individuals from Qatar. We identified more than 88 million variants of which 24 million are novel and 23 million are singletons. Consistent with the high consanguinity and founder effects in the region, we found that several rare deleterious variants were more common in the Qatari population while others seem to provide protection against diseases and have shaped the genetic architecture of adaptive phenotypes. These results highlight the value of our data as a resource to advance genetic studies in the Arab and neighbouring Middle Eastern populations and will significantly boost the current efforts to improve our understanding of global patterns of human variations, human history and genetic contributions to health and diseases in diverse populations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Geethanjali Devadoss Gandhi
- Department of Biomedical Sciences, College of Health Sciences, Qatar University.,College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Senthil Selvaraj
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Wadha Al-Muftah
- Department of Genetic Medicine, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Radja Badji
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Yasser Al-Sarraj
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar.,Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Dima Darwish
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Muhammad Alvi
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Tasnim Fadl
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Heba Yasin
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Fatima Alkuwari
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Rozaimi Razali
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Waleed Aamer
- Human Genetics Department, Sidra Medicine, Doha, Qatar
| | | | - Ikhlak Ahmed
- Sidra Medicine, Biomedical Informatics - Research Branch, Doha, Qatar
| | - Younes Mokrab
- Human Genetics Department, Sidra Medicine, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Omar Albagha
- College of Health & Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar.,Center of Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Khalid Fakhro
- Department of Biomedical Sciences, College of Health Sciences, Qatar University
| | - Ramin Badii
- Molecular Genetics Laboratory, Hamad Medical Corporation, Doha, Qatar
| | | | - Asma Althani
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar
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7
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Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-Khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Cruzado JCM, Mezey JG, Shakaki AA, Malek JA, Greenblatt MB, Fakhro KA, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail SI, Althani A, Crystal RG. The QChip1 knowledgebase and microarray for precision medicine in Qatar. NPJ Genom Med 2022; 7:3. [PMID: 35046417 PMCID: PMC8770564 DOI: 10.1038/s41525-021-00270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Ramzi Temanni
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Monika Markovic
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Eiman Al-Khayat
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Fatima Qafoud
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Weill Cornell Medicine, Doha, Qatar
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
| | | | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Khalid A Fakhro
- Weill Cornell Medicine, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Ajayeb Al-Nabet
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Nahla Afifi
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Andrew Brooks
- RUCDR Infinite Biologics, Piscataway, NJ, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | | | - Asmaa Althani
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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8
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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] [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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9
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Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies. Genes (Basel) 2021; 12:genes12040593. [PMID: 33921607 PMCID: PMC8074154 DOI: 10.3390/genes12040593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Whole Exome Sequencing (WES) is a powerful approach for detecting sequence variations in the human genome. The aim of this study was to investigate the genetic defects in Jordanian patients with inherited retinal dystrophies (IRDs) using WES. WES was performed on proband patients' DNA samples from 55 Jordanian families. Sanger sequencing was used for validation and segregation analysis of the detected, potential disease-causing variants (DCVs). Thirty-five putatively causative variants (6 novel and 29 known) in 21 IRD-associated genes were identified in 71% of probands (39 of the 55 families). Three families showed phenotypes different from the typically reported clinical findings associated with the causative genes. To our knowledge, this is the largest genetic analysis of IRDs in the Jordanian population to date. Our study also confirms that WES is a powerful tool for the molecular diagnosis of IRDs in large patient cohorts.
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Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank. NPJ Genom Med 2021; 6:8. [PMID: 33563995 PMCID: PMC7873199 DOI: 10.1038/s41525-021-00170-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Studies assessing the impact of amylase genes copy number (CN) on adiposity report conflicting findings in different global populations, likely reflecting the impact of ancestral and ethnic-specific environment and lifestyle on selection at the amylase loci. Here, we leverage population size and detailed adiposity measures from a large population biobank to resolve confounding effects and determine the relationship between salivary (AMY1) and pancreatic (AMY2A) amylase genes CN and adiposity in 2935 Qatari individuals who underwent whole-genome sequencing (WGS) as part of the Qatar Genome Programme. We observe a negative association between AMY1 CNs and trunk fat percentage in the Qatari population (P = 7.50 × 10-3) and show that Qataris of Arab descent have significantly lower CN at AMY1 (P = 1.32 × 10-10) as well as less favorable adiposity and metabolic profiles (P < 1.34 × 10-8) than Qataris with Persian ancestry. Indeed, lower AMY1 CN was associated with increased total and trunk fat percentages in Arabs (P < 4.60 × 10-3) but not in Persians. Notably, overweight and obese Persians reported a significant trend towards dietary restraint following weight gain compared to Arabs (P = 4.29 × 10-5), with AMY1 CN showing negative association with dietary self-restraint (P = 3.22 × 10-3). This study reports an association between amylase gene CN and adiposity traits in a large Middle Eastern population. Importantly, we leverage rich biobank data to demonstrate that the strength of this association varies with ethnicity, and may be influenced by population-specific behaviors that also contribute to adiposity traits.
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11
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Al-Mulla F, Mohammad A, Al Madhoun A, Haddad D, Ali H, Eaaswarkhanth M, John SE, Nizam R, Channanath A, Abu-Farha M, Ahmad R, Abubaker J, Thanaraj TA. ACE2 and FURIN variants are potential predictors of SARS-CoV-2 outcome: A time to implement precision medicine against COVID-19. Heliyon 2021; 7:e06133. [PMID: 33532652 PMCID: PMC7843038 DOI: 10.1016/j.heliyon.2021.e06133] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/26/2021] [Indexed: 01/08/2023] Open
Abstract
The severity of the new COVID-19 pandemic caused by the SARS-CoV-2 virus is strikingly variable in different global populations. SARS-CoV-2 uses ACE2 as a cell receptor, TMPRSS2 protease, and FURIN peptidase to invade human cells. Here, we investigated 1,378 whole-exome sequences of individuals from the Middle Eastern populations (Kuwait, Qatar, and Iran) to explore natural variations in the ACE2, TMPRSS2, and FURIN genes. We identified two activating variants (K26R and N720D) in the ACE2 gene that are more common in Europeans than in the Middle Eastern, East Asian, and African populations. We postulate that K26R can activate ACE2 and facilitate binding to S-protein RBD while N720D enhances TMPRSS2 cutting and, ultimately, viral entry. We also detected deleterious variants in FURIN that are frequent in the Middle Eastern but not in the European populations. This study highlights specific genetic variations in the ACE2 and FURIN genes that may explain SARS-CoV-2 clinical disparity. We showed structural evidence of the functionality of these activating variants that increase the SARS-CoV-2 aggressiveness. Finally, our data illustrate a significant correlation between ACE2 variants identified in people from Middle Eastern origins that can be further explored to explain the variation in COVID-19 infection and mortality rates globally.
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Affiliation(s)
- Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Ashraf Al Madhoun
- Department of Animal and Imaging Core Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Dania Haddad
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Hamad Ali
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
- Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, Health Sciences Center (HSC), Kuwait University, Jabriya, Kuwait
| | | | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Arshad Channanath
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Mohamed Abu-Farha
- Department of Special Services Facilities, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Rasheed Ahmad
- Department of Immunology & Microbiology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute (DDI), Dasman, Kuwait
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Zaganas I, Mastorodemos V, Spilioti M, Mathioudakis L, Latsoudis H, Michaelidou K, Kotzamani D, Notas K, Dimitrakopoulos K, Skoula I, Ioannidis S, Klothaki E, Erimaki S, Stavropoulos G, Vassilikos V, Amoiridis G, Efthimiadis G, Evangeliou A, Mitsias P. Genetic cause of heterogeneous inherited myopathies in a cohort of Greek patients. Mol Genet Metab Rep 2020; 25:100682. [PMID: 33304817 PMCID: PMC7711282 DOI: 10.1016/j.ymgmr.2020.100682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Inherited muscle disorders are caused by pathogenic changes in numerous genes. Herein, we aimed to investigate the etiology of muscle disease in 24 consecutive Greek patients with myopathy suspected to be genetic in origin, based on clinical presentation and laboratory and electrophysiological findings and absence of known acquired causes of myopathy. Of these, 16 patients (8 females, median 24 years-old, range 7 to 67 years-old) were diagnosed by Whole Exome Sequencing as suffering from a specific type of inherited muscle disorder. Specifically, we have identified causative variants in 6 limb-girdle muscular dystrophy genes (6 patients; ANO5, CAPN3, DYSF, ISPD, LAMA2, SGCA), 3 metabolic myopathy genes (4 patients; CPT2, ETFDH, GAA), 1 congenital myotonia gene (1 patient; CLCN1), 1 mitochondrial myopathy gene (1 patient; MT-TE) and 3 other myopathy-associated genes (4 patients; CAV3, LMNA, MYOT). In 6 additional family members affected by myopathy, we reached genetic diagnosis following identification of a causative variant in an index patient. In our patients, genetic diagnosis ended a lengthy diagnostic process and, in the case of Multiple acyl-CoA dehydrogenase deficiency and Pompe's disease, it enabled specific treatment to be initiated. These results further expand the genotypic and phenotypic spectrum of inherited myopathies.
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Affiliation(s)
- Ioannis Zaganas
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
- Neurology Department, University Hospital of Crete, Heraklion, Crete, Greece
| | | | - Martha Spilioti
- AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lambros Mathioudakis
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Helen Latsoudis
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Kleita Michaelidou
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Dimitra Kotzamani
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Konstantinos Notas
- AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Irene Skoula
- Neurogenetics Laboratory, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Stefanos Ioannidis
- Neurology Department, University Hospital of Crete, Heraklion, Crete, Greece
| | - Eirini Klothaki
- Neurology Department, University Hospital of Crete, Heraklion, Crete, Greece
| | - Sophia Erimaki
- Neurophysiology Unit, University Hospital of Crete, Heraklion, Crete, Greece
| | - Georgios Stavropoulos
- Hippokratio General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vassilios Vassilikos
- Hippokratio General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Amoiridis
- Neurophysiology Unit, University Hospital of Crete, Heraklion, Crete, Greece
| | - Georgios Efthimiadis
- AHEPA General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasios Evangeliou
- Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panayiotis Mitsias
- Neurology Department, University Hospital of Crete, Heraklion, Crete, Greece
- Neurophysiology Unit, University Hospital of Crete, Heraklion, Crete, Greece
- Department of Neurology, Henry Ford Hospital/Wayne State University, Detroit, Michigan, USA
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13
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Dakroury Y, Butler AE, Dargham SR, Latif A, Robay A, Crystal RG, Atkin SL. Association of Differing Qatari Genotypes with Vitamin D Metabolites. Int J Endocrinol 2020; 2020:7831590. [PMID: 32351562 PMCID: PMC7174927 DOI: 10.1155/2020/7831590] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/05/2020] [Accepted: 03/13/2020] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE Genetic studies have identified four Qatari genotypes: Q1 Arab, Bedouin; Q2 Asian/Persian; Q3 African; and a fourth admixed group not fitting into the previous 3 groups. This study was undertaken to determine if there was an increased risk of deficiency of vitamin D and its metabolites associated with differing genotypes, perhaps due to genetic differences in skin pigmentation. METHODS 398 Qatari subjects (220 type 2 diabetes and 178 controls) had their genotype determined by Affymetrix 500 k SNP arrays. Total values of 1,25-dihydroxyvitamin D (1,25(OH)2D), 25-hydroxyvitamin D (25(OH)D), 24,25-dihydroxyvitamin D (24,25(OH)2D), and 25-hydroxy-3epi-vitamin D (3epi-25(OH)D) concentrations were measured by the LC-MS/MS analysis. RESULTS The distribution was as follows: 164 (41.2%) genotyped Q1, 149 (37.4%) genotyped Q2, 31 (7.8%) genotyped Q3, and 54 (13.6%) genotyped "admixed." Median levels of 25(OH)D and 3epi-25(OH)D did not differ across Q1, Q2, Q3, and "admixed" genotypes, respectively. 1,25(OH)2D levels were lower (p < 0.04) between Q2 and the admixed groups, and 24,25(OH)2D levels were lower (p < 0.05) between Q1 and the admixed groups. Vitamin D metabolite levels were lower in females for 25(OH)D, 1,25(OH)2D (p < 0.001), and 24,25(OH)2D (p < 0.006), but 3epi-25(OH)D did not differ (p < 0.26). Diabetes prevalence was not different between genotypes. Total 1,25(OH)2D (p < 0.001), total 24,25(OH)2D (p < 0.001), and total 3epi-25(OH)D (p < 0.005) were all significantly lower in diabetes patients compared to controls whilst the total 25(OH)D was higher in diabetes than controls (p < 0.001). CONCLUSION Whilst 25(OH)D levels did not differ between genotype groups, 1,25(OH)2D and 24,25(OH)2D were lower in the admixed group, suggesting that there are genetic differences in vitamin D metabolism that may be of importance in a population that may allow a more targeted approach to vitamin D replacement. This may be of specific importance in vitamin D replacement strategies with the Q2 genotype requiring less, and the other genotypes requiring more to increase 1,25(OH)2D. Whilst overall the group was vitamin D deficient, total 25(OH)D was higher in diabetes, but 1,25(OH)2D, 24,25(OH)2D, and 3epi-25(OH)D were lower in diabetes that did not affect the relationship to genotype.
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Affiliation(s)
| | - Alexandra E. Butler
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | | | | | - Amal Robay
- Weill Cornell Medicine-Qatar, P.O. Box 24144, Doha, Qatar
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA
| | - Stephen L. Atkin
- Weill Cornell Medicine-Qatar, P.O. Box 24144, Doha, Qatar
- Royal College of Surgeons Ireland, Busaiteen, Bahrain
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Dakroury Y, Atkin SL, Dargham SR, Robay A, Rodriguez-Flores J, Crystal RG, Butler AE. Qatari Genotype May Contribute to Complications in Type 2 Diabetes. J Diabetes Res 2020; 2020:6356973. [PMID: 32587868 PMCID: PMC7303741 DOI: 10.1155/2020/6356973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE There is increasing evidence of a strong genetic component in type 2 diabetes (T2DM) that may contribute to diabetes complications. Given the high prevalence of diabetes with its associated complications in the Middle East, we sought to determine if the genotype within a Middle East population may be contributory. Therefore, three genotype-based Qatari ancestral groups, Q1 Arab Bedouin, Q2 Asian/Persian, and Q3 sub-Saharan African, with a fourth admixed group were correlated with T2DM prevalence and its complications to determine if they differed between the 4 Qatari ancestries, particularly for the SLMAP allele-associated diabetic retinopathy. METHODS In this cross-sectional study, 398 Qatari subjects, 220 with and 178 without T2DM, were genotyped by Affymetrix 500k SNP arrays. Ancestry was correlated with diabetes complications. RESULTS 398 subjects were included, the mean age was 49.8 years, and 56.8% were male. The genotype-based ancestry and T2DM prevalence were as follows: 164 (41.2%) with ancestry Q1, 60.4% with T2DM; 149 (37.4%) with ancestry Q2, 49.7% with T2DM; 31 (7.8%) with ancestry Q3, 61.3% with T2DM; and 54 (13.6%) with "admixed" ancestry, 51.9% with T2DM. For patients with diabetes, hypertension (p < 0.035) and retinopathy (p < 0.016) were greater in the Q3 ancestry. CONCLUSION These data suggest that the genotype may contribute to complication risk, as exemplified by the increase in hypertension and retinopathy in the Q3 ancestry, though the SLMAP allele was not implicated; however, diabetes prevalence did not differ between the four Qatari ancestries.
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Affiliation(s)
| | | | | | - Amal Robay
- Weill Cornell Medicine-Qatar, PO Box 24144, Doha, Qatar
| | | | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, USA
| | - Alexandra E. Butler
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
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15
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Barbitoff YA, Skitchenko RK, Poleshchuk OI, Shikov AE, Serebryakova EA, Nasykhova YA, Polev DE, Shuvalova AR, Shcherbakova IV, Fedyakov MA, Glotov OS, Glotov AS, Predeus AV. Whole-exome sequencing provides insights into monogenic disease prevalence in Northwest Russia. Mol Genet Genomic Med 2019; 7:e964. [PMID: 31482689 PMCID: PMC6825859 DOI: 10.1002/mgg3.964] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/07/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Allele frequency data from large exome and genome aggregation projects such as the Genome Aggregation Database (gnomAD) are of ultimate importance to the interpretation of medical resequencing data. However, allele frequencies might significantly differ in poorly studied populations that are underrepresented in large-scale projects, such as the Russian population. METHODS In this work, we leveraged our access to a large dataset of 694 exome samples to analyze genetic variation in the Northwest Russia. We compared the spectrum of genetic variants to the dbSNP build 151, and made estimates of ClinVar-based autosomal recessive (AR) disease allele prevalence as compared to gnomAD r. 2.1. RESULTS An estimated 9.3% of discovered variants were not present in dbSNP. We report statistically significant overrepresentation of pathogenic variants for several Mendelian disorders, including phenylketonuria (PAH, rs5030858), Wilson's disease (ATP7B, rs76151636), factor VII deficiency (F7, rs36209567), kyphoscoliosis type of Ehlers-Danlos syndrome (FKBP14, rs542489955), and several other recessive pathologies. We also make primary estimates of monogenic disease incidence in the population, with retinal dystrophy, cystic fibrosis, and phenylketonuria being the most frequent AR pathologies. CONCLUSION Our observations demonstrate the utility of population-specific allele frequency data to the diagnosis of monogenic disorders using high-throughput technologies.
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Affiliation(s)
- Yury A. Barbitoff
- Bioinformatics InstituteSt. PetersburgRussia
- Department of Genetics and BiotechnologySt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Anton E. Shikov
- Bioinformatics InstituteSt. PetersburgRussia
- City Hospital No. 40St. PetersburgRussia
| | - Elena A. Serebryakova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Yulia A. Nasykhova
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | | | - Irina V. Shcherbakova
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
| | | | - Oleg S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
| | - Andrey S. Glotov
- City Hospital No. 40St. PetersburgRussia
- Department of Genomic MedicineD.O. Ott Research Institute of Obstetrics, Gynaecology and ReproductionSt. PetersburgRussia
- Laboratory of Biobanking and Genomic Medicine of Institute of Translation BiomedicineSt. Petersburg State UniversitySt. PetersburgRussia
- Institute of Living SystemsImmanuel Kant Baltic Federal UniversityKaliningradRussia
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16
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Al-Khawaga S, Mohammed I, Saraswathi S, Haris B, Hasnah R, Saeed A, Almabrazi H, Syed N, Jithesh P, El Awwa A, Khalifa A, AlKhalaf F, Petrovski G, Abdelalim EM, Hussain K. The clinical and genetic characteristics of permanent neonatal diabetes (PNDM) in the state of Qatar. Mol Genet Genomic Med 2019; 7:e00753. [PMID: 31441606 PMCID: PMC6785445 DOI: 10.1002/mgg3.753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 04/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Neonatal diabetes mellitus (NDM) is a rare condition that occurs within the first six months of life. Permanent NDM (PNDM) is caused by mutations in specific genes that are known for their expression at early and/or late stages of pancreatic beta‐ cell development, and are either involved in beta‐cell survival, insulin processing, regulation, and release. The native population in Qatar continues to practice consanguineous marriages that lead to a high level of homozygosity. To our knowledge, there is no previous report on the genomics of NDM among the Qatari population. The aims of the current study are to identify patients with NDM diagnosed between 2001 and 2016, and examine their clinical and genetic characteristics. Methods To calculate the incidence of PNDM, all patients with PNDM diagnosed between 2001 and 2016 were compared to the total number of live births over the 16‐year‐period. Whole Genome Sequencing (WGS) was used to investigate the genetic etiology in the PNDM cohort. Results PNDM was diagnosed in nine (n = 9) patients with an estimated incidence rate of 1:22,938 live births among the indigenous Qatari. Seven different mutations in six genes (PTF1A, GCK, SLC2A2, EIF2AK3, INS, and HNF1B) were identified. In the majority of cases, the genetic etiology was part of a previously identified autosomal recessive disorder. Two novel de novo mutations were identified in INS and HNF1B. Conclusion Qatar has the second highest reported incidence of PNDM worldwide. A majority of PNDM cases present as rare familial autosomal recessive disorders. Pancreas associated transcription factor 1a (PTF1A) enhancer deletions are the most common cause of PNDM in Qatar, with only a few previous cases reported in the literature.
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Affiliation(s)
- Sara Al-Khawaga
- College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.,Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar.,Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Idris Mohammed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.,Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Saras Saraswathi
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Basma Haris
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Reem Hasnah
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Amira Saeed
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | | | - Najeeb Syed
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Puthen Jithesh
- Biomedical Informatics Division, Sidra Medicine, Doha, Qatar
| | - Ahmed El Awwa
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar.,Faculty of medicine, Alexandria University, Alexandria, Egypt
| | - Amal Khalifa
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Fawziya AlKhalaf
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Goran Petrovski
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Essam M Abdelalim
- College of Health & Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.,Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
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17
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Exome-based search for recurrent disease-causing alleles in Russian population. Eur J Med Genet 2019; 62:103656. [DOI: 10.1016/j.ejmg.2019.04.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 04/12/2019] [Accepted: 04/21/2019] [Indexed: 11/18/2022]
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Dankar FK, Gergely M, Dankar SK. Informed Consent in Biomedical Research. Comput Struct Biotechnol J 2019; 17:463-474. [PMID: 31007872 PMCID: PMC6458444 DOI: 10.1016/j.csbj.2019.03.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/27/2022] Open
Abstract
Informed consent is the result of tumultuous events in both the clinical and research arenas over the last 100 years. Throughout this time, the notion of informed consent has shifted tremendously, both due to advances in medicine, as well as the type of data being gathered. As such, informed consent has misaligned with the goals of medical research. It is becoming more and more vital to address this chasm, and begin building new frameworks to link this disconnect. Thus, we address three goals in this paper. First, we discuss the history of informed consent and unify the varying definitions of the term. Second, we evaluate the current research on the topic, classify them into themes, and attend to the problems therein. Lastly, we employ these themes of informed consent research mentioned previously to provide guidance and insight for future research in the arena.
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Affiliation(s)
- Fida K. Dankar
- College of IT, UAEU, Al Ain, P.O.Box 15551, United Arab Emirates
| | - Marton Gergely
- College of IT, UAEU, Al Ain, P.O.Box 15551, United Arab Emirates
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19
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Clinical Exome Sequencing unravels new disease-causing mutations in the myeloproliferative neoplasms: A pilot study in patients from the state of Qatar. Gene 2018; 689:34-42. [PMID: 30553997 DOI: 10.1016/j.gene.2018.12.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/27/2018] [Accepted: 12/10/2018] [Indexed: 01/04/2023]
Abstract
Clinical Exome Sequencing (CES) has increasingly become a popular diagnostic tool in patients suffering from genetic disorders that are clinically and genetically complicated. Myeloproliferative Neoplasms (MPNs) is an example of a heterogeneous disorder. In Qatar, familial cases of MPNs are more frequently seen than described in the literature. In this study, we aimed to use CES to classify six Qatari subjects that were suspected of clinical diagnosis of MPNs, according to the WHO 2008 diagnostic criteria for hematologic malignancies, and identify variants that can potentially explain the phenotypic diversity of MPNs. We sequenced six Qatari subjects using CES, of whom, three probands were unrelated families and three members were from the same family, all probands come from consanguineous families, and had a positive family history of MPNs. CES identified 61 variants in 50 genes; of which, 13 were recurrently mutated in our patients. Ten novel variants were identified in ten known genes related to MPNs and seven variants were identified in seven novel candidate genes. The genotype of the six subjects was due to a combination of different variants in different genes. This study serves as a pilot study to investigate the complexity of the genotype of patients with MPNS in Qatar, and serves as a guide for further well-controlled genetic epidemiological studies for patients with MPNs. CES is a powerful tool to be used in the genetic clinics for differential and definitive diagnosis of patients with MPNs.
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20
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Sivadas A, Scaria V. Population-scale genomics-Enabling precision public health. ADVANCES IN GENETICS 2018; 103:119-161. [PMID: 30904093 DOI: 10.1016/bs.adgen.2018.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The current excitement for affordable genomics technologies and national precision medicine initiatives marks a turning point in worldwide healthcare practices. The last decade of global population sequencing efforts has defined the enormous extent of genetic variation in the human population resulting in insights into differential disease burden and response to therapy within and between populations. Population-scale pharmacogenomics helps to provide insights into the choice of optimal therapies and an opportunity to estimate, predict and minimize adverse events. Such an approach can potentially empower countries to formulate national selection and dosing policies for therapeutic agents thereby promoting public health with precision. We review the breadth and depth of worldwide population-scale sequencing efforts and its implications for the implementation of clinical pharmacogenetics toward making precision medicine a reality.
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Affiliation(s)
- Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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21
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Assessment of coding region variants in Kuwaiti population: implications for medical genetics and population genomics. Sci Rep 2018; 8:16583. [PMID: 30409984 PMCID: PMC6224454 DOI: 10.1038/s41598-018-34815-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
Consanguineous populations of the Arabian Peninsula have been underrepresented in global efforts that catalogue human exome variability. We sequenced 291 whole exomes of unrelated, healthy native Arab individuals from Kuwait to a median coverage of 45X and characterised 170,508 single-nucleotide variants (SNVs), of which 21.7% were ‘personal’. Up to 12% of the SNVs were novel and 36% were population-specific. Half of the SNVs were rare and 54% were missense variants. The study complemented the Greater Middle East Variome by way of reporting many additional Arabian exome variants. The study corroborated Kuwaiti population genetic substructures previously derived using genome-wide genotype data and illustrated the genetic relatedness among Kuwaiti population subgroups, Middle Eastern, European and Ashkenazi Jewish populations. The study mapped 112 rare and frequent functional variants relating to pharmacogenomics and disorders (recessive and common) to the phenotypic characteristics of Arab population. Comparative allele frequency data and carrier distributions of known Arab mutations for 23 disorders seen among Arabs, of putative OMIM-listed causal mutations for 12 disorders observed among Arabs but not yet characterized for genetic basis in Arabs, and of 17 additional putative mutations for disorders characterized for genetic basis in Arab populations are presented for testing in future Arab studies.
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Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling. Genet Med 2017; 20:360-364. [DOI: 10.1038/gim.2017.168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 08/18/2017] [Indexed: 12/21/2022] Open
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Koshy R, Sivadas A, Scaria V. Genetic epidemiology of familial Mediterranean fever through integrative analysis of whole genome and exome sequences from Middle East and North Africa. Clin Genet 2017; 93:92-102. [PMID: 28597968 DOI: 10.1111/cge.13070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/27/2017] [Accepted: 06/06/2017] [Indexed: 02/02/2023]
Abstract
Familial Mediterranean fever (FMF), an autosomal recessive and rare autoinflammatory disease is caused by genetic mutations in the MEFV gene and is highly prevalent in the Mediterranean basin. Although the carrier frequency of specific disease variants in the MEFV gene has been reported from isolated studies, a comprehensive view of variants in the Mediterranean region has not been possible due to paucity of data. The recent availability of whole-genome and whole-exome datasets prompted us to study the genetic epidemiology of MEFV variants in the region. We assembled data from 5 datasets encompassing whole-genome and whole-exome datasets for 2115 individuals from multiple subpopulations in the region and also created a compendium for MEFV genetic variants, which were further systematically annotated as per the American College of Medical Genetics and Genomics (ACMG) guidelines. Our analysis points to significant differences in allele frequencies in the subpopulations, and the carrier frequency for MEFV genetic variants in the population to be about 8%. The MEFV gene appears to be under natural selection from our analysis. To the best of our knowledge, this is the most comprehensive study and analysis of population epidemiology of MEFV gene variants in the Middle East and North African populations.
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Affiliation(s)
- R Koshy
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - A Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, CSIR IGIB South Campus, Delhi, India
| | - V Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, CSIR IGIB South Campus, Delhi, India
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Jithesh PV, Scaria V. From genomes to genomic medicine: enabling personalized and precision medicine in the Middle East. Per Med 2017; 14:377-382. [DOI: 10.2217/pme-2017-0048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Puthen Veettil Jithesh
- Division of Biomedical Informatics Research, Sidra Medical & Research Center, OPC Building, PO Box 26999, Doha, Qatar
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics & Integrative Biology, Mathura Road, Delhi 110 025, India
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Kilshaw S. Qatari intersections with global genetics research and discourse. Anthropol Med 2017; 25:50-67. [PMID: 28728425 DOI: 10.1080/13648470.2017.1285003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Genetic discourses have taken a predominant role in approaches to combating a number of conditions that affect Qataris. This paper is derived from an exploration of Qatari encounters with globalizing discourses of genetics, particularly as they relate to notions of risk. It explores Qataris negotiations of global interactions and influences, including the discourses around genetic risk and cousin marriage. It suggests that family marriage can be seen as one of the main platforms of resistance and a means for modern, cosmopolitan and tradition to be negotiated.
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Affiliation(s)
- Susie Kilshaw
- a Department of Anthropology , University College London , London , UK
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Koshy R, Ranawat A, Scaria V. al mena: a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations. J Hum Genet 2017. [PMID: 28638141 DOI: 10.1038/jhg.2017.67] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Middle East and North Africa (MENA) encompass very unique populations, with a rich history and encompasses characteristic ethnic, linguistic and genetic diversity. The genetic diversity of MENA region has been largely unknown. The recent availability of whole-exome and whole-genome sequences from the region has made it possible to collect population-specific allele frequencies. The integration of data sets from this region would provide insights into the landscape of genetic variants in this region. We integrated genetic variants from multiple data sets systematically, available from this region to create a compendium of over 26 million genetic variations. The variants were systematically annotated and their allele frequencies in the data sets were computed and available as a web interface which enables quick query. As a proof of principle for application of the compendium for genetic epidemiology, we analyzed the allele frequencies for variants in transglutaminase 1 (TGM1) gene, associated with autosomal recessive lamellar ichthyosis. Our analysis revealed that the carrier frequency of selected variants differed widely with significant interethnic differences. To the best of our knowledge, al mena is the first and most comprehensive repertoire of genetic variations from the Arab, Middle Eastern and North African region. We hope al mena would accelerate Precision Medicine in the region.
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Affiliation(s)
- Remya Koshy
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Anop Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,The Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Genomics and Integrative Biology, Delhi, India
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27
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Sandhya P, Vellarikkal SK, Nair A, Ravi R, Mathew J, Jayarajan R, Kumar A, Verma A, Sivadas A, Danda D, Sivasubbu S, Scaria V. Egyptian tale from India: application of whole-exome sequencing in diagnosis of atypical familial Mediterranean fever. Int J Rheum Dis 2017; 20:1770-1775. [DOI: 10.1111/1756-185x.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pulukool Sandhya
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
| | - Aswin Nair
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Rowmika Ravi
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - John Mathew
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Anoop Kumar
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Ankit Verma
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Ambily Sivadas
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
- GN Ramachandran Knowledge Center for Genome Informatics; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
| | - Debashish Danda
- Department of Rheumatology; Christian Medical College and Hospital; Vellore India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
| | - Vinod Scaria
- Academy of Scientific and Innovative Research (AcSIR); Delhi India
- GN Ramachandran Knowledge Center for Genome Informatics; CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB); Delhi India
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Sivadas A, Sharma P, Scaria V. Landscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasets. Pharmacogenomics 2016; 17:1891-1901. [PMID: 27767380 DOI: 10.2217/pgs-2016-0130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
AIM Pharmacogenetic landscapes of commonly used antiplatelet drugs, warfarin and clopidogrel have been studied in-depth in many countries. However, there is a paucity of data to understand their patterns in the Arab populations. MATERIALS & METHODS We analyzed the whole exome sequencing datasets of 100 Qatar individuals available in public domain with this perspective. RESULTS We characterized the allelic distribution of variants routinely tested for warfarin and clopidogrel. We additionally evaluated the population stratification and its effect on allele frequency distribution. Our analysis points to ethnic differences in the frequency distribution even for the small population studied. CONCLUSION This is one of the first and most comprehensive pharmacogenetic maps of variants associated with warfarin and clopidogrel for an Arab population, which can help tailor the drug dosage to the population.
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Affiliation(s)
- Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India
| | - Parul Sharma
- Center for Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Industrial Estate, Phase III, New Delhi 110020, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi 110025, India.,Academy of Scientific & Innovative Research (AcSIR), New Delhi 110025, India.,Center for Computational Biology, Indraprastha Institute of Information Technology Delhi (IIIT-Delhi), Okhla Industrial Estate, Phase III, New Delhi 110020, India
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Al-Shamsi A, Hertecant JL, Souid AK, Al-Jasmi FA. Whole exome sequencing diagnosis of inborn errors of metabolism and other disorders in United Arab Emirates. Orphanet J Rare Dis 2016; 11:94. [PMID: 27391121 PMCID: PMC4939014 DOI: 10.1186/s13023-016-0474-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/22/2016] [Indexed: 12/16/2022] Open
Abstract
Background This study reports on the use of whole exome sequencing (WES) to diagnose children with inborn errors of metabolism and other disorders in United Arab Emirates. Methods From January 2012 to December 2014, 85 patients (46 % females) were seen in the metabolic center at Tawam Hospital (Abu Dhabi) and WES testing was requested because definitive diagnoses were not reached by conventional methods. Results Eighty (93 %) patients were <18 years old and 44 (52 %) were <5 years. Sixty-eight (80 %) patients had neurologic abnormalities. WES facilitated rapid diagnosis in 50 % of the patients, especially those with mitochondrial disorders. Yet, in most cases extensive investigation was required after the results were available. Most patients with confirmed molecular diagnoses had autosomal recessive disorders and were homozygous for the rare alleles. Most patients with autosomal dominant disorders and all patients with X-linked disorders had de novo mutations. WES results were negative (no pathogenic variants related to patient phenotype were identified) in six patients and incorrect in two patients. One patient had a reported “deleterious” hemizygous mutation in SLC35A2, c.617_620del (p.Q206fs), suggesting ‘congenital disorder of glycosylation, TYPE IIm’, but glycosylation studies were normal and healthy brothers had the same mutation. Another patient had “pathogenic” mutation in MCCC2, c.1015G > A (p.V339M), but urine organic acids was normal. WES confirmed inborn errors of metabolism (five mitochondrial diseases, three lysosomal storage diseases, and six other disorders) in 14 patients and genetic disorders (14 neurological diseases and three non-neurological diseases) in 17 patients. Variants of unknown significance were identified in 48 patients; 12 had “confirmed pathologic variants”and 12 had “likely pathologic variants”, based on consistent phenotypes, biochemical/ segregation studies, or reported pathogenicity. In 24 patients, the variants were inconsistent with phenotypes or biochemical/ familial studies. Conclusions Although WES provided molecular diagnoses, the results required careful interpretations and many patients required additional investigations. This tool is useful when conventional diagnostic methods fail. Staff competence in obtaining consent/ permission, interpreting the findings, and providing the proper counseling are essential before incorporating this technology into routine clinical practices.
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Affiliation(s)
| | | | - Abdul-Kader Souid
- Department of Pediatrics, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE
| | - Fatma A Al-Jasmi
- Department of Pediatrics, United Arab Emirates University, P.O. Box 17666, Al-Ain, UAE.
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The Qatar genome: a population-specific tool for precision medicine in the Middle East. Hum Genome Var 2016; 3:16016. [PMID: 27408750 PMCID: PMC4927697 DOI: 10.1038/hgv.2016.16] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 03/09/2016] [Accepted: 04/11/2016] [Indexed: 12/30/2022] Open
Abstract
Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%) and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis.
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Szego MJ, Zawati MH. Whole Genome Sequencing as a Genetic Test for Autism Spectrum Disorder: From Bench to Bedside and then Back Again. JOURNAL OF THE CANADIAN ACADEMY OF CHILD AND ADOLESCENT PSYCHIATRY = JOURNAL DE L'ACADEMIE CANADIENNE DE PSYCHIATRIE DE L'ENFANT ET DE L'ADOLESCENT 2016; 25:116-121. [PMID: 27274747 PMCID: PMC4879951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 03/26/2016] [Indexed: 06/06/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by repetitive patterns of behaviour and impairments in social interactions and communication abilities. Although ASD is a heterogeneous disorder, it is a highly genetic condition for which genetic testing is routinely performed. Microarray analysis is currently the standard of care genetic test for ASD, however whole genome sequencing offers several key advantages and will likely replace microarrays as a frontline genetic test in the near future. The 2nd Consultation on Translation of Genomic Advances into Health Applications took place in the spring of 2014 to broadly explore the current and potential impacts of genomic advances in supporting personalized and family-centered care for autism and related developmental conditions. In anticipation of WGS becoming a standard of care test, we examine the policy landscape and highlight the lack of consistency among guidelines regarding what genomic information should be returned to patients and their families. We also discuss the need to create the infrastructure to share clinical WGS data with researchers in a systematic and ethically defensible manner.
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Affiliation(s)
- Michael J. Szego
- Centre for Clinical Ethics, St. Joseph’s Health Centre, Toronto, Ontario
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario
- Department of Family and Community Medicine, The Dalla Lana School of Public Health, and The Joint Centre for Bioethics, University of Toronto, Toronto, Ontario
| | - Ma’n H. Zawati
- Centre of Genomics and Policy, McGill University, Montreal, Quebec
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Variation analysis to construct Korean-specific exome variation database of pilot scale. BIOCHIP JOURNAL 2016. [DOI: 10.1007/s13206-016-0207-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Rodriguez-Flores JL, Fakhro K, Agosto-Perez F, Ramstetter MD, Arbiza L, Vincent TL, Robay A, Malek JA, Suhre K, Chouchane L, Badii R, Al-Nabet Al-Marri A, Abi Khalil C, Zirie M, Jayyousi A, Salit J, Keinan A, Clark AG, Crystal RG, Mezey JG. Indigenous Arabs are descendants of the earliest split from ancient Eurasian populations. Genome Res 2016; 26:151-62. [PMID: 26728717 PMCID: PMC4728368 DOI: 10.1101/gr.191478.115] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/15/2015] [Indexed: 12/26/2022]
Abstract
An open question in the history of human migration is the identity of the earliest Eurasian populations that have left contemporary descendants. The Arabian Peninsula was the initial site of the out-of-Africa migrations that occurred between 125,000 and 60,000 yr ago, leading to the hypothesis that the first Eurasian populations were established on the Peninsula and that contemporary indigenous Arabs are direct descendants of these ancient peoples. To assess this hypothesis, we sequenced the entire genomes of 104 unrelated natives of the Arabian Peninsula at high coverage, including 56 of indigenous Arab ancestry. The indigenous Arab genomes defined a cluster distinct from other ancestral groups, and these genomes showed clear hallmarks of an ancient out-of-Africa bottleneck. Similar to other Middle Eastern populations, the indigenous Arabs had higher levels of Neanderthal admixture compared to Africans but had lower levels than Europeans and Asians. These levels of Neanderthal admixture are consistent with an early divergence of Arab ancestors after the out-of-Africa bottleneck but before the major Neanderthal admixture events in Europe and other regions of Eurasia. When compared to worldwide populations sampled in the 1000 Genomes Project, although the indigenous Arabs had a signal of admixture with Europeans, they clustered in a basal, outgroup position to all 1000 Genomes non-Africans when considering pairwise similarity across the entire genome. These results place indigenous Arabs as the most distant relatives of all other contemporary non-Africans and identify these people as direct descendants of the first Eurasian populations established by the out-of-Africa migrations.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Khalid Fakhro
- Sidra Medical and Research Center, Doha, Qatar; Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Francisco Agosto-Perez
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Monica D Ramstetter
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Leonardo Arbiza
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Thomas L Vincent
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Ramin Badii
- Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | | | - Charbel Abi Khalil
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Alon Keinan
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Andrew G Clark
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York 10065, USA; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
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Fakhro KA, Yousri NA, Rodriguez-Flores JL, Robay A, Staudt MR, Agosto-Perez F, Salit J, Malek JA, Suhre K, Jayyousi A, Zirie M, Stadler D, Mezey JG, Crystal RG. Copy number variations in the genome of the Qatari population. BMC Genomics 2015; 16:834. [PMID: 26490036 PMCID: PMC4618522 DOI: 10.1186/s12864-015-1991-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/06/2015] [Indexed: 12/25/2022] Open
Abstract
Background The populations of the Arabian Peninsula remain the least represented in public genetic databases, both in terms of single nucleotide variants and of larger genomic mutations. We present the first high-resolution copy number variation (CNV) map for a Gulf Arab population, using a hybrid approach that integrates array genotyping intensity data and next-generation sequencing reads to call CNVs in the Qatari population. Methods CNVs were detected in 97 unrelated Qatari individuals by running two calling algorithms on each of two primary datasets: high-resolution genotyping (Illumina Omni 2.5M) and high depth whole-genome sequencing (Illumina PE 100bp). The four call-sets were integrated to identify high confidence CNV regions, which were subsequently annotated for putative functional effect and compared to public databases of CNVs in other populations. The availability of genome sequence was leveraged to identify tagging SNPs in high LD with common deletions in this population, enabling their imputation from genotyping experiments in the future. Results Genotyping intensities and genome sequencing data from 97 Qataris were analyzed with four different algorithms and integrated to discover 16,660 high confidence CNV regions (CNVRs) in the total population, affecting ~28 Mb in the median Qatari genome. Up to 40 % of all CNVs affected genes, including novel CNVs affecting Mendelian disease genes, segregating at different frequencies in the 3 major Qatari subpopulations, including those with Bedouin, Persian/South Asian, and African ancestry. Consistent with high consanguinity levels in the Bedouin subpopulation, we found an increased burden for homozygous deletions in this group. In comparison to known CNVs in the comprehensive Database of Genomic Variants, we found that 5 % of all CNVRs in Qataris were completely novel, with an enrichment of CNVs affecting several known chromosomal disorder loci and genes known to regulate sugar metabolism and type 2 diabetes in the Qatari cohort. Finally, we leveraged the availability of genome sequence to find suitable tagging SNPs for common deletions in this population. Conclusion We combine four independently generated datasets from 97 individuals to study CNVs for the first time at high-resolution in a Gulf Arab population. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1991-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Khalid A Fakhro
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Division of Translational Medicine, Sidra Medical Research Centre, Doha, Qatar.
| | - Noha A Yousri
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Computer and Systems Engineering, Alexandria University, Alexandria, Egypt.
| | - Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Amal Robay
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Michelle R Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Francisco Agosto-Perez
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
| | - Joel A Malek
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Amin Jayyousi
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Mahmoud Zirie
- Department of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Dora Stadler
- Department of Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar.
| | - Jason G Mezey
- Computer and Systems Engineering, Alexandria University, Alexandria, Egypt. .,Department Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA.
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar. .,Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
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Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry. BMC Genomics 2015; 16:92. [PMID: 25765185 PMCID: PMC4336699 DOI: 10.1186/s12864-015-1233-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/12/2015] [Indexed: 12/30/2022] Open
Abstract
Background The 1000 Genome project paved the way for sequencing diverse human populations. New genome projects are being established to sequence underrepresented populations helping in understanding human genetic diversity. The Kuwait Genome Project an initiative to sequence individual genomes from the three subgroups of Kuwaiti population namely, Saudi Arabian tribe; “tent-dwelling” Bedouin; and Persian, attributing their ancestry to different regions in Arabian Peninsula and to modern-day Iran (West Asia). These subgroups were in line with settlement history and are confirmed by genetic studies. In this work, we report whole genome sequence of a Kuwaiti native from Persian subgroup at >37X coverage. Results We document 3,573,824 SNPs, 404,090 insertions/deletions, and 11,138 structural variations. Out of the reported SNPs and indels, 85,939 are novel. We identify 295 ‘loss-of-function’ and 2,314 ’deleterious’ coding variants, some of which carry homozygous genotypes in the sequenced genome; the associated phenotypes include pharmacogenomic traits such as greater triglyceride lowering ability with fenofibrate treatment, and requirement of high warfarin dosage to elicit anticoagulation response. 6,328 non-coding SNPs associate with 811 phenotype traits: in congruence with medical history of the participant for Type 2 diabetes and β-Thalassemia, and of participant’s family for migraine, 72 (of 159 known) Type 2 diabetes, 3 (of 4) β-Thalassemia, and 76 (of 169) migraine variants are seen in the genome. Intergenome comparisons based on shared disease-causing variants, positions the sequenced genome between Asian and European genomes in congruence with geographical location of the region. On comparison, bead arrays perform better than sequencing platforms in correctly calling genotypes in low-coverage sequenced genome regions however in the event of novel SNP or indel near genotype calling position can lead to false calls using bead arrays. Conclusions We report, for the first time, reference genome resource for the population of Persian ancestry. The resource provides a starting point for designing large-scale genetic studies in Peninsula including Kuwait, and Persian population. Such efforts on populations under-represented in global genome variation surveys help augment current knowledge on human genome diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1233-x) contains supplementary material, which is available to authorized users.
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Upadhyay R, Robay A, Fakhro K, Abi Khalil C, Zirie M, Jayyousi A, El-Shafei M, Kiss S, D'Amico DJ, Salit J, Staudt MR, O'Beirne SL, Chen X, Tuana B, Crystal RG, Ding H. Role of SLMAP genetic variants in susceptibility of diabetes and diabetic retinopathy in Qatari population. J Transl Med 2015; 13:61. [PMID: 25880194 PMCID: PMC4335364 DOI: 10.1186/s12967-015-0411-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 01/19/2015] [Indexed: 11/18/2022] Open
Abstract
Background Overexpression of SLMAP gene has been associated with diabetes and endothelial dysfunction of macro- and micro-blood vessels. In this study our primary objective is to explore the role of SLMAP gene polymorphisms in the susceptibility of type 2 diabetes (T2DM) with or without diabetic retinopathy (DR) in the Qatari population. Methods A total of 342 Qatari subjects (non-diabetic controls and T2DM patients with or without DR) were genotyped for SLMAP gene polymorphisms (rs17058639 C > T; rs1043045 C > T and rs1057719 A > G) using Taqman SNP genotyping assay. Results SLMAP rs17058639 C > T polymorphism was associated with the presence of DR among Qataris with T2DM. One-way ANOVA and multiple logistic regression analysis showed SLMAP SNP rs17058639 C > T as an independent risk factor for DR development. SLMAP rs17058639 C > T polymorphism also had a predictive role for the severity of DR. Haplotype Crs17058639Trs1043045Ars1057719 was associated with the increased risk for DR among Qataris with T2DM. Conclusions The data suggests the potential role of SLMAP SNPs as a risk factor for the susceptibility of DR among T2DM patients in the Qatari population. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0411-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rohit Upadhyay
- Departments of Pharmacology, Weill Cornell Medical College-Qatar, Doha, Qatar.
| | - Amal Robay
- Departments of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar.
| | - Khalid Fakhro
- Departments of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar.
| | - Charbel Abi Khalil
- Departments of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar.
| | - Mahmoud Zirie
- Departments of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Amin Jayyousi
- Departments of Medicine, Hamad Medical Corporation, Doha, Qatar.
| | - Maha El-Shafei
- Departments of Ophthalmology, Hamad Medical Corporation, Doha, Qatar.
| | - Szilard Kiss
- Departments of Ophthalmology, Weill Cornell Medical College, New York, NY, USA.
| | - Donald J D'Amico
- Departments of Ophthalmology, Weill Cornell Medical College, New York, NY, USA.
| | - Jacqueline Salit
- Departments of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Michelle R Staudt
- Departments of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Sarah L O'Beirne
- Departments of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Xiaoliang Chen
- Department of Cadre & Cardiology, The affiliated hospital of Hangzhou Normal University, Hangzhou, China.
| | - Balwant Tuana
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
| | - Ronald G Crystal
- Departments of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Hong Ding
- Departments of Pharmacology, Weill Cornell Medical College-Qatar, Doha, Qatar.
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Davey S. Next generation sequencing: considering the ethics. Int J Immunogenet 2014; 41:457-62. [DOI: 10.1111/iji.12155] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/17/2014] [Accepted: 09/25/2014] [Indexed: 12/01/2022]
Affiliation(s)
- S. Davey
- H&I Department; NHS Blood and Transplant; London UK
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Jiang YH, Wang Y, Xiu X, Choy KW, Pursley AN, Cheung SW. Genetic diagnosis of autism spectrum disorders: the opportunity and challenge in the genomics era. Crit Rev Clin Lab Sci 2014; 51:249-62. [PMID: 24878448 PMCID: PMC5937018 DOI: 10.3109/10408363.2014.910747] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genetic etiology for autism spectrum disorders (ASDs) was first suggested from twin studies reported in the 1970s. The identification of gene mutations in syndromic ASDs provided evidence to support a genetic cause of ASDs. More recently, genome-wide copy number variant and sequence analyses have uncovered a list of rare and highly penetrant copy number variants (CNVs) or single nucleotide variants (SNVs) associated with ASDs, which has strengthened the claim of a genetic etiology for ASDs. Findings from research studies in the genetics of ASD now support an important role for molecular diagnostics in the clinical genetics evaluation of ASDs. Various molecular diagnostic assays including single gene tests, targeted multiple gene panels and copy number analysis should all be considered in the clinical genetics evaluation of ASDs. Whole exome sequencing could also be considered in selected clinical cases. However, the challenge that remains is to determine the causal role of genetic variants identified through molecular testing. Variable expressivity, pleiotropic effects and incomplete penetrance associated with CNVs and SNVs also present significant challenges for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Yi Wang
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Xu Xiu
- Division of Child Development and Health, The Children’s Hospital of Fudan University Shanghai, People’s Republic of China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, and Joint Centre with Utrecht University Genetic core, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China
| | - Amber Nolen Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Alsmadi O, John SE, Thareja G, Hebbar P, Antony D, Behbehani K, Thanaraj TA. Genome at juncture of early human migration: a systematic analysis of two whole genomes and thirteen exomes from Kuwaiti population subgroup of inferred Saudi Arabian tribe ancestry. PLoS One 2014; 9:e99069. [PMID: 24896259 PMCID: PMC4045902 DOI: 10.1371/journal.pone.0099069] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 05/10/2014] [Indexed: 01/19/2023] Open
Abstract
Population of the State of Kuwait is composed of three genetic subgroups of inferred Persian, Saudi Arabian tribe and Bedouin ancestry. The Saudi Arabian tribe subgroup traces its origin to the Najd region of Saudi Arabia. By sequencing two whole genomes and thirteen exomes from this subgroup at high coverage (>40X), we identify 4,950,724 Single Nucleotide Polymorphisms (SNPs), 515,802 indels and 39,762 structural variations. Of the identified variants, 10,098 (8.3%) exomic SNPs, 139,923 (2.9%) non-exomic SNPs, 5,256 (54.3%) exomic indels, and 374,959 (74.08%) non-exomic indels are 'novel'. Up to 8,070 (79.9%) of the reported novel biallelic exomic SNPs are seen in low frequency (minor allele frequency <5%). We observe 5,462 known and 1,004 novel potentially deleterious nonsynonymous SNPs. Allele frequencies of common SNPs from the 15 exomes is significantly correlated with those from genotype data of a larger cohort of 48 individuals (Pearson correlation coefficient, 0.91; p <2.2×10-16). A set of 2,485 SNPs show significantly different allele frequencies when compared to populations from other continents. Two notable variants having risk alleles in high frequencies in this subgroup are: a nonsynonymous deleterious SNP (rs2108622 [19:g.15990431C>T] from CYP4F2 gene [MIM:*604426]) associated with warfarin dosage levels [MIM:#122700] required to elicit normal anticoagulant response; and a 3' UTR SNP (rs6151429 [22:g.51063477T>C]) from ARSA gene [MIM:*607574]) associated with Metachromatic Leukodystrophy [MIM:#250100]. Hemoglobin Riyadh variant (identified for the first time in a Saudi Arabian woman) is observed in the exome data. The mitochondrial haplogroup profiles of the 15 individuals are consistent with the haplogroup diversity seen in Saudi Arabian natives, who are believed to have received substantial gene flow from Africa and eastern provenance. We present the first genome resource imperative for designing future genetic studies in Saudi Arabian tribe subgroup. The full-length genome sequences and the identified variants are available at ftp://dgr.dasmaninstitute.org and http://dgr.dasmaninstitute.org/DGR/gb.html.
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Affiliation(s)
- Osama Alsmadi
- Dasman Diabetes Institute, Dasman, Kuwait
- * E-mail: (TAT); (OA)
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