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Rossi N, Syed N, Visconti A, Aliyev E, Berry S, Bourbon M, Spector TD, Hysi PG, Fakhro KA, Falchi M. Rare variants at KCNJ2 are associated with LDL-cholesterol levels in a cross-population study. NPJ Genom Med 2024; 9:36. [PMID: 38942744 PMCID: PMC11213907 DOI: 10.1038/s41525-024-00417-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 05/03/2024] [Indexed: 06/30/2024] Open
Abstract
Leveraging whole genome sequencing data of 1751 individuals from the UK and 2587 Qatari subjects, we suggest here an association of rare variants mapping to the sour taste-associated gene KCNJ2 with reduced low-density lipoprotein cholesterol (LDL-C, P = 2.10 × 10-12) and with a 22% decreased dietary trans-fat intake. This study identifies a novel candidate rare locus for LDL-C, adding insights into the genetic architecture of a complex trait implicated in cardiovascular disease.
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Affiliation(s)
- Niccolò Rossi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Alessia Visconti
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
- Center for Biostatistics, Epidemiology and Public Health, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medical and Research Center, Doha, Qatar
| | - Sarah Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Mafalda Bourbon
- Cardiovascular Research Group, Department of Health Promotion and Prevention of non-Communicable Diseases, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisbon, Portugal
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Pirro G Hysi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medical and Research Center, Doha, Qatar
- Department of Genetic Medicine, Weill-Cornell Medical College, Doha, Qatar
| | - Mario Falchi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK.
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2
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Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, Syed N, Shaath R, Gandhi GD, Engchuan W, Howe J, Thiruvahindrapuram B, Geng M, Whitney J, Syed A, Lakshmi J, Hussein S, Albashir N, Hussein A, Poggiolini I, Elhag SF, Palaniswamy S, Kambouris M, de Fatima Janjua M, Tahir MOE, Nazeer A, Shahwar D, Azeem MW, Mokrab Y, Aati NA, Akil A, Scherer SW, Kamal M, Fakhro KA. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Genome Med 2023; 15:81. [PMID: 37805537 PMCID: PMC10560429 DOI: 10.1186/s13073-023-01228-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study-a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research. METHODS In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families. RESULTS Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts. CONCLUSIONS This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.
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Affiliation(s)
- Mona Abdi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Waleed Aamer
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Genomics Data Science Core, Sidra Medicine, Doha, Qatar
| | - Rulan Shaath
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melissa Geng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Amira Syed
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Sura Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Amal Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Saba F Elhag
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | | | - Marios Kambouris
- Pathology and Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | | | | | - Ahsan Nazeer
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Durre Shahwar
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Muhammad Waqar Azeem
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Younes Mokrab
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
- Qatar University, Doha, Qatar
| | | | - Ammira Akil
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Madeeha Kamal
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar.
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3
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Luo J, Ruan X, Ang CS, Nolvachai Y, Marriott PJ, Zhang P, Howell K. Variation of wine preference amongst consumers is influenced by the composition of salivary proteins. NPJ Sci Food 2023; 7:51. [PMID: 37717071 PMCID: PMC10505211 DOI: 10.1038/s41538-023-00222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 09/18/2023] Open
Abstract
The preferences of consumers for different flavours and aromas in wine are varied and may be explained by inherent factors such as cultural background, wine education and personal taste of the wine consumer. Wine flavour, as perceived in the mouth, includes aroma compounds released through the retronasal pathway, which are shaped by interactions with saliva. Saliva and wine interactions could provide an explanation as to why wine tasters express different preferences for wine. To test this hypothesis, 13 Western and 13 Chinese experienced wine tasters were recruited. Sensory evaluation was performed in formal surroundings to acquire free description-based and perceived sensory intensity data using the Pivot® Profile and continuous scale assessment, respectively. Participants' saliva samples were collected before the sensory evaluation and spiked into a wine sample to investigate the impact on the wine's volatile release using comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC-MS). Saliva samples were subjected to enzyme activity assays and protein composition profiling by Tandem Mass Tag (TMT) quantitative proteomics. The wine tasters showed differences in wine flavour perception, which was supported by the difference in wine volatile release resulting from the addition of saliva. The two groups of participants did not have significant differences in total salivary protein concentrations or the amounts of esterase and α-amylase. However, statistically significant variations in the concentrations of specific proteins (proline-rich proteins (PRPs) and lipocalin-1 (LCN-1); p < 0.01) were found between the two groups. Significant correlations between perceived intensities of wine attributes and concentrations of PRPs and LCN-1 were observed. These results indicate that the composition of proteins in saliva is a factor that influences wine perception and preference. Our results provide a biochemical basis for understanding preference for food based on interactions between aroma compounds and salivary proteins and could be used to suggest foods or beverages to particular cultural groups.
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Affiliation(s)
- Jiaqiang Luo
- School of Chemical Engineering, Faculty of Engineering, The University of New South Wales, Kensington, Australia
| | - Xinwei Ruan
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Yada Nolvachai
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Clayton, Australia
| | - Philip J Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Clayton, Australia
| | - Pangzhen Zhang
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia
| | - Kate Howell
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Australia.
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4
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Nayema Z, Sato T, Kannon T, Tsujiguchi H, Hosomichi K, Nakamura H, Tajima A. Genetic factors associated with serum amylase in a Japanese population: combined analysis of copy-number and single-nucleotide variants. J Hum Genet 2023; 68:313-319. [PMID: 36599956 PMCID: PMC10125868 DOI: 10.1038/s10038-022-01111-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023]
Abstract
Amylase activity and levels in humans are heritable quantitative traits. Although many studies exist on the effects of copy-number variants (CNVs) in amylase genes (AMY) on human phenotypes, such as body mass index (BMI), the genetic factors controlling interindividual variation in amylase levels remain poorly understood. Here, we conducted a genome-wide association study (GWAS) of serum amylase levels (SAL) in 814 Japanese individuals to identify associated single-nucleotide variants (SNVs), after adjusting for non-genetic factors. Diploid copy numbers (CN) of AMY (AMY1, AMY2A, and AMY2B) were measured using droplet digital PCR to examine the association between each diploid CN and SAL. We further assessed the relative contribution of the GWAS-lead SNV and AMY CNVs to SAL. GWAS identified 14 significant SNVs (p < 5 × 10-8) within a linkage disequilibrium block near the AMY cluster on chromosome 1. The association analyses of AMY CNVs and SAL showed a significant association between AMY1 diploid CN and SAL (p = 1.89 × 10-19), while no significant association with SAL was found for AMY2A CN (p = 0.54) or AMY2B CN (p = 0.15). In a joint association analysis with SAL using the GWAS-lead SNV and AMY1 diploid CN, AMY1 CN remained significant (p = 5.4 ×10-13), while the association of the lead SNV was marginal (p = 0.08). We also found no association between AMY1 diploid CN and BMI (p = 0.14). Our results indicate that AMY1 CNV is the major genetic factor for Japanese SAL, with no significant association with BMI.
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Affiliation(s)
- Zannatun Nayema
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
| | - Hiromasa Tsujiguchi
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.,Laboratory of Computational Genomics, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Hachioji, Japan
| | - Hiroyuki Nakamura
- Department of Hygiene and Public Health, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan.
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5
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Merico D, Pasternak Y, Zarrei M, Higginbotham EJ, Thiruvahindrapuram B, Scott O, Willett-Pachul J, Grunebaum E, Upton J, Atkinson A, Kim VHD, Aliyev E, Fakhro K, Scherer SW, Roifman CM. Homozygous duplication identified by whole genome sequencing causes LRBA deficiency. NPJ Genom Med 2021; 6:96. [PMID: 34795304 PMCID: PMC8602677 DOI: 10.1038/s41525-021-00263-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/21/2021] [Indexed: 12/17/2022] Open
Abstract
In more than one-third of primary immunodeficiency (PID) patients, extensive genetic analysis including whole-exome sequencing (WES) fails to identify the genetic defect. Whole-genome sequencing (WGS) is able to detect variants missed by other genomics platforms, enabling the molecular diagnosis of otherwise unresolved cases. Here, we report two siblings, offspring of consanguineous parents, who experienced similar severe events encompassing early onset of colitis, lymphoproliferation, and hypogammaglobulinemia, typical of lipopolysaccharide-responsive and beige-like anchor (LRBA) or cytotoxic T lymphocyte antigen 4 (CTLA4) deficiencies. Gene-panel sequencing, comparative genomic hybridization (CGH) array, and WES failed to reveal a genetic aberration in relevant genes. WGS of these patients detected a 12.3 kb homozygous tandem duplication that was absent in control cohorts and is predicted to disrupt the reading frame of the LRBA gene. The variant was validated by PCR and Sanger sequencing, demonstrating the presence of the junction between the reference and the tandem-duplicated sequence. Droplet digital PCR (ddPCR) further confirmed the copy number in the unaffected parents (CN = 3, heterozygous) and affected siblings (CN = 4, homozygous), confirming the expected segregation pattern. In cases of suspected inherited immunodeficiency, WGS may reveal a mutation when other methods such as microarray and WES analysis failed to detect an aberration.
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Affiliation(s)
- Daniele Merico
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada ,Deep Genomics Inc., Toronto, M5G 1M1 ON Canada
| | - Yehonatan Pasternak
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Mehdi Zarrei
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Edward J. Higginbotham
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Bhooma Thiruvahindrapuram
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada
| | - Ori Scott
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Jessica Willett-Pachul
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada
| | - Eyal Grunebaum
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Julia Upton
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Adelle Atkinson
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Vy H. D. Kim
- grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
| | - Elbay Aliyev
- grid.467063.00000 0004 0397 4222Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Khalid Fakhro
- grid.467063.00000 0004 0397 4222Department of Human Genetics, Sidra Medicine, Doha, Qatar ,grid.416973.e0000 0004 0582 4340Department of Genetic Medicine, Weill-Cornell Medical College, Doha, Qatar
| | - Stephen W. Scherer
- grid.42327.300000 0004 0473 9646The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, M5G 0A4 ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8 ON Canada ,grid.17063.330000 0001 2157 2938McLaughlin Centre, University of Toronto, Toronto, M5G 0A4 ON Canada
| | - Chaim M. Roifman
- Canadian Center for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, Toronto, M5G1X8 ON Canada ,grid.42327.300000 0004 0473 9646Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children, Toronto, M5G 1×8 ON Canada ,grid.17063.330000 0001 2157 2938University of Toronto, Toronto, M5S 1A8 ON Canada
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6
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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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7
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Ramos-Lopez O, Milton-Laskibar I, Martínez JA. Precision nutrition based on phenotypical traits and the (epi)genotype: nutrigenetic and nutrigenomic approaches for obesity care. Curr Opin Clin Nutr Metab Care 2021; 24:315-325. [PMID: 33859118 DOI: 10.1097/mco.0000000000000754] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW The purpose of this article is to rationally review and critically appraise the current knowledge in the most relevant nongenetic and genetic factors influencing obesity predisposition. This information may be translated into the implementation of personalized nutrition approaches involving precision nutrigenetic and nutrigenomic strategies for obesity monitoring and weight management. RECENT FINDINGS The importance and influence of several nongenetic contributors to obesity onset and individual responses to weight-loss interventions have been highlighted including the role of age, sex or perinatal feeding and others related to an individual's lifestyle and modifiable. Nutrigenetic studies have analysed potential interactions between polymorphisms influencing energy homeostasis/body composition and dietary factors in relation to adiposity phenotypes and therapy responsiveness. A second approach comprises the Nutrigenomic analysis of gene expression modifications in response to the consumption of specific nutrients or dietary bioactive compounds, which may involve epigenetic mechanisms including deoxyribonucleic acid methylation and micro-ribonucleic acid expression profiles. SUMMARY Taken together, these findings encompass the importance of taking into account up-to-date advances in Nutrigenetic and Nutrigenomic hallmarks, globally analysing the risk of weight gain and related outcomes after following nutrition counselling, this contributing to improve obesity care considering phenotypical traits and the genetic make-up for precision obesity care.
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Affiliation(s)
- Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Baja California, Mexico
| | - Iñaki Milton-Laskibar
- Precision Nutrition and Cardiometabolic Health, IMDEA- Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM + CSIC, Spanish National Research Council
- CIBERobn Physiopathology of Obesity and Nutrition, Institute of Health Carlos III (ISCIII), Madrid
| | - J Alfredo Martínez
- Precision Nutrition and Cardiometabolic Health, IMDEA- Food Institute (Madrid Institute for Advanced Studies), Campus of International Excellence (CEI) UAM + CSIC, Spanish National Research Council
- CIBERobn Physiopathology of Obesity and Nutrition, Institute of Health Carlos III (ISCIII), Madrid
- Navarra Institute for Health Research (IdiSNa), Pamplona, Spain
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