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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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Gong R, Greenbaum J, Lin X, Du Y, Su KJ, Gong Y, Shen J, Deng HW. Identification of potential genetic causal variants for obesity-related traits using statistical fine mapping. Mol Genet Genomics 2023; 298:1309-1319. [PMID: 37498361 DOI: 10.1007/s00438-023-02055-9] [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: 05/08/2022] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
BACKGROUND Obesity is highly influenced by heritability and variant effects. While previous genome-wide association studies (GWASs) have successfully identified numerous genetic loci associated with obesity-related traits [body mass index (BMI) and waist-to-hip ratio (WHR)], most causal variants remain unidentified. The high degree of linkage disequilibrium (LD) throughout the genome makes it extremely difficult to distinguish the GWAS-associated SNPs that exert a true biological effect. OBJECTIVE This study was to identify the potential causal variants having a biological effect on obesity-related traits. METHODS We used Probabilistic Annotation INTegratOR, a Bayesian fine-mapping method, which incorporated genetic association data (GWAS summary statistics), LD structure, and functional annotations to calculate a posterior probability of causality for SNPs across all loci of interest. Moreover, we performed gene expression analysis using the available public transcriptomic data to validate the corresponding genes of the potential causal SNPs partially. RESULTS We identified 96 SNPs for BMI and 43 SNPs for WHR with a high posterior probability of causality (> 99%), including 49 BMI SNPs and 24 WHR SNPs which did not reach genome-wide significance in the original GWAS. Finally, we partially validated some genes corresponding to the potential causal SNPs. CONCLUSION Using a statistical fine-mapping approach, we identified a set of potential causal variants to be prioritized for future functional validation and also detected some novel trait-associated variants. These results provided novel insight into our understanding of the genetics of obesity and also demonstrated that fine mapping may improve upon the results identified by the original GWASs.
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Affiliation(s)
- Rui Gong
- Endocrinology Cadre Ward, Gansu Provincial Hospital, Lanzhou, 730000, Gansu, China
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
- The 3rd Affiliated Hospital of Southern Medical University, Guangdong, 510000, Guangzhou, China
| | - Jonathan Greenbaum
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Xu Lin
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, 528000, China
| | - Yan Du
- School of Nursing, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA
| | - Kuan-Jui Su
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Yun Gong
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA
| | - Jie Shen
- Shunde Hospital of Southern Medical University (The First People's Hospital of Shunde), Foshan, 528000, China
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA, 70112, USA.
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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Denham AN, Drake J, Gavrilov M, Taylor ZN, Bacanu SA, Vladimirov VI. Long Non-Coding RNAs: The New Frontier into Understanding the Etiology of Alcohol Use Disorder. Noncoding RNA 2022; 8:ncrna8040059. [PMID: 36005827 PMCID: PMC9415279 DOI: 10.3390/ncrna8040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, debilitating condition impacting millions worldwide. Genetic, environmental, and epigenetic factors are known to contribute to the development of AUD. Long non-coding RNAs (lncRNAs) are a class of regulatory RNAs, commonly referred to as the “dark matter” of the genome, with little to no protein-coding potential. LncRNAs have been implicated in numerous processes critical for cell survival, suggesting that they play important functional roles in regulating different cell processes. LncRNAs were also shown to display higher tissue specificity than protein-coding genes and have a higher abundance in the brain and central nervous system, demonstrating a possible role in the etiology of psychiatric disorders. Indeed, genetic (e.g., genome-wide association studies (GWAS)), molecular (e.g., expression quantitative trait loci (eQTL)) and epigenetic studies from postmortem brain tissues have identified a growing list of lncRNAs associated with neuropsychiatric and substance use disorders. Given that the expression patterns of lncRNAs have been associated with widespread changes in the transcriptome, including methylation, chromatin architecture, and activation or suppression of translational activity, the regulatory nature of lncRNAs may be ubiquitous and an innate component of gene regulation. In this review, we present a synopsis of the functional impact that lncRNAs may play in the etiology of AUD. We also discuss the classifications of lncRNAs, their known functional roles, and therapeutic advancements in the field of lncRNAs to further clarify the functional relationship between lncRNAs and AUD.
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Affiliation(s)
- Allie N. Denham
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Correspondence:
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- MSCI Program, Texas A&M University, Bryan, TX 77807, USA
| | - Matthew Gavrilov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
| | - Zachary N. Taylor
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
- Texas A&M Institute for Neuroscience, College Station, Texas A&M University, College Station, TX 77843, USA
- Genetics Interdisciplinary Program, College Station, Texas A&M University, College Station, TX 77843, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
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Sunita, Singh Y, Beamer G, Sun X, Shukla P. Recent developments in systems biology and genetic engineering toward design of vaccines for TB. Crit Rev Biotechnol 2022; 42:532-547. [PMID: 34641752 PMCID: PMC11208086 DOI: 10.1080/07388551.2021.1951649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
Abstract
Tuberculosis (TB) is one of the most prevalent diseases worldwide. The currently available Bacillus Calmette-Guérin vaccine is not sufficient in protecting against pulmonary TB. Although many vaccines have been evaluated in clinical trials, but none of them yet has proven to be more successful. Thus, new strategies are urgently needed to design more effective TB vaccines. The emergence of new technologies will undoubtedly accelerate the process of vaccine development. This review summarizes the potential and validated applications of emerging technologies, including: systems biology (genomics, proteomics, and transcriptomics), genetic engineering, and other computational tools to discover and develop novel vaccines against TB. It also discussed that the significant implementation of these approaches will play crucial roles in the development of novel vaccines to cure and control TB.
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Affiliation(s)
- Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Gillian Beamer
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, MA, USA
| | - Xingmin Sun
- Department of Molecular Medicine, College of Medicine (COM), University of South Florida, Tampa, FL, USA
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
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6
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Ding X, Guo Y, Ye J, Wu X, Lin S, Chen F, Zhu L, Huang L, Song X, Zhang Y, Dai L, Xi X, Huang J, Wang K, Fan B, Li D. Population differentiation and epidemic tracking of Bursaphelenchus xylophilus in China based on chromosome-level assembly and whole-genome sequencing data. PEST MANAGEMENT SCIENCE 2022; 78:1213-1226. [PMID: 34839581 PMCID: PMC9300093 DOI: 10.1002/ps.6738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/09/2021] [Accepted: 11/28/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Bursaphelenchus xylophilus, the pinewood nematode, kills millions of pine trees worldwide every year, and causes enormous economic and ecological losses. Despite extensive research on population variation, there is little understanding of the population-wide variation spectrum in China. RESULTS We sequenced an inbred B. xylophilus strain using Pacbio+Illumina+Bionano+Hi-C and generated a chromosome-level assembly (AH1) with six chromosomes of 77.1 Mb (chromosome N50: 12 Mb). The AH1 assembly shows very high continuity and completeness, and contains novel genes with potentially important functions compared with previous assemblies. Subsequently, we sequenced 181 strains from China and the USA and found ~7.8 million single nucleotide polymorphisms (SNPs). Analysis shows that the B. xylophilus population in China can be divided into geographically bounded subpopulations with severe cross-infection and potential migrations. In addition, distribution of B. xylophilus is dominated by temperature zones while geographically associated SNPs are mainly located on adaptation related GPCR gene families, suggesting the nematode has been evolving to adapt to different temperatures. A machine-learning based epidemic tracking method has been established to predict their geographical origins, which can be applied to any other species. CONCLUSION Our study provides the community with the first high-quality chromosome-level assembly which includes a comprehensive catalogue of genetic variations. It provides insights into population structure and effective tracking method for this invasive species, which facilitates future studies to address a variety of applied, genomic and evolutionary questions in B. xylophilus as well as related species.
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Affiliation(s)
- Xiaolei Ding
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
| | - Yunfei Guo
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Jianren Ye
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaoqin Wu
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Sixi Lin
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Fengmao Chen
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Lihua Zhu
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Lin Huang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaofeng Song
- Department of Biomedical EngineeringNanjing University of Aeronautics and AstronauticsNanjingChina
| | - Yi Zhang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Ling Dai
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Xiaotong Xi
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Jinsi Huang
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - Kai Wang
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesCAUSA
- Department of Preventive MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of PhiladelphiaPhiladelphiaPAUSA
- Department of Pathology and Laboratory MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Ben Fan
- Co‐Innovation Center for Sustainable Forestry in Southern China, College of ForestryNanjing Forestry UniversityNanjingChina
- Jiangsu Key Laboratory for Prevention and Management of Invasive SpeciesNanjingChina
| | - De‐Wei Li
- The Connecticut Agricultural Experiment Station Valley LaboratoryWindsorCTUSA
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ali F, Shen A, Islam W, Saleem MZ, Muthu R, Xie Q, Wu M, Cheng Y, Chu J, Lin W, Peng J. Role of MicroRNAs and their corresponding ACE2/Apelin signaling pathways in hypertension. Microb Pathog 2021; 162:105361. [PMID: 34919993 DOI: 10.1016/j.micpath.2021.105361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/12/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
Abstract
Hypertension is controlled via the alteration of microRNAs (miRNAs), their therapeutic targets angiotensin II type I receptor (AT1R) and cross talk of signaling pathways. The stimulation of the Ang II/AT1R pathway by deregulation of miRNAs, has also been linked to cardiac remodeling as well as the pathophysiology of high blood pressure. As miRNAs have been associated to ACE2/Apelin and Mitogen-activated protein kinases (MAPK) signaling, it has revealed an utmost protective impact over hypertension and cardiovascular system. The ACE2-coupled intermodulation between RAAS, Apelin system, MAPK signaling pathways, and miRNAs reveal the practicalities of high blood pressure. The research of miRNAs may ultimately lead to the expansion of an innovative treatment strategy for hypertension, which indicates the need to explore them further at the molecular level. Therefore, here we have focused on the mechanistic importance of miRNAs in hypertension, ACE2/Apelin signaling as well as their biological functions, with a focus on interplay and crosstalk between ACE2/Apelin signaling, miRNAs, and hypertension, and the progress in miRNA-based diagnostic techniques with the goal of facilitating the development of new hypertension-controlling therapeutics.
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Affiliation(s)
- Farman Ali
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Aling Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Ragunath Muthu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Qiurong Xie
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Meizhu Wu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Ying Cheng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Jiangfeng Chu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Wei Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Chen Keji Academic Thought Inheritance Studio, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China; Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, 350122, China.
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Pignataro G. Emerging Role of microRNAs in Stroke Protection Elicited by Remote Postconditioning. Front Neurol 2021; 12:748709. [PMID: 34744984 PMCID: PMC8567963 DOI: 10.3389/fneur.2021.748709] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 12/27/2022] Open
Abstract
Remote ischemic conditioning (RIC) represents an innovative and attractive neuroprotective approach in brain ischemia. The purpose of this intervention is to activate endogenous tolerance mechanisms by inflicting a subliminal ischemia injury to the limbs, or to another “remote” region, leading to a protective systemic response against ischemic brain injury. Among the multiple candidates that have been proposed as putative mediators of the protective effect generated by the subthreshold peripheral ischemic insult, it has been hypothesized that microRNAs may play a vital role in the infarct-sparing effect of RIC. The effect of miRNAs can be exploited at different levels: (1) as transducers of protective messages to the brain or (2) as effectors of brain protection. The purpose of the present review is to summarize the most recent evidence supporting the involvement of microRNAs in brain protection elicited by remote conditioning, highlighting potential and pitfalls in their exploitation as diagnostic and therapeutic tools. The understanding of these processes could help provide light on the molecular pathways involved in brain protection for the future development of miRNA-based theranostic agents in stroke.
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Affiliation(s)
- Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience, School of Medicine, "Federico II" University of Naples, Naples, Italy
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10
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Morrow A, Chan P, Tucker KM, Taylor N. The design, implementation, and effectiveness of intervention strategies aimed at improving genetic referral practices: a systematic review of the literature. Genet Med 2021; 23:2239-2249. [PMID: 34426665 PMCID: PMC8629749 DOI: 10.1038/s41436-021-01272-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 11/29/2022] Open
Abstract
Purpose Despite rapid advancements in genetics and genomics, referral practices remain suboptimal. This systematic review assesses the extent to which approaches from implementation science have been applied to address suboptimal genetic referral practices. Methods A search of MEDLINE, EMBASE, and PsycINFO generated 7,794 articles, of which 28 were included. Lay barriers were mapped to the Theoretical Domains Framework (TDF) and interventions mapped to behavior change techniques. Use of implementation and behavior change frameworks was assessed, and the Theory and Techniques Tool used to determine theoretical alignment. Results Knowledge was the most frequent retrospectively TDF-coded barrier, followed by environmental context and resources, and skills. Significant referral improvements occurred in 56% of studies. Among these, the most frequent interventions were clinical data review systems, family history collection and referral tools, and embedding genetics staff into nongenetic specialties. Few studies used implementation frameworks or reported implementation outcomes, though some deployed intuitive strategies that aligned with theory. Conclusion Genetic referral interventions are rarely informed by implementation and/or behavior change theories, limiting opportunities for learning across contexts. Retrospective coding has provided a suite of theoretically linked strategies, which may be useful for informing future efforts. Incorporating these strategies into clinical guidelines may facilitate operationalization within the system.
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Affiliation(s)
- April Morrow
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia. .,Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia.
| | - Priscilla Chan
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia
| | - Katherine M Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital and Community Health Services, Randwick, NSW, Australia.,UNSW Prince of Wales Clinical School, Randwick, NSW, Australia
| | - Natalie Taylor
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, NSW, Australia.,Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, Australia
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11
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The influence of X chromosome variants on trait neuroticism. Mol Psychiatry 2021; 26:483-491. [PMID: 30842574 PMCID: PMC7850965 DOI: 10.1038/s41380-019-0388-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/29/2019] [Accepted: 02/14/2019] [Indexed: 12/26/2022]
Abstract
Autosomal variants have successfully been associated with trait neuroticism in genome-wide analysis of adequately powered samples. But such studies have so far excluded the X chromosome from analysis. Here, we report genetic association analyses of X chromosome and XY pseudoautosomal single nucleotide polymorphisms (SNPs) and trait neuroticism using UK Biobank samples (N = 405,274). Significant association was found with neuroticism on the X chromosome for 204 markers found within three independent loci (a further 783 were suggestive). Most of the lead neuroticism-related X chromosome variants were located in intergenic regions (n = 397). Involvement of HS6ST2, which has been previously associated with sociability behaviour in the dog, was supported by single SNP and gene-based tests. We found that the amino acid and nucleotide sequences are highly conserved between dogs and humans. From the suggestive X chromosome variants, there were 19 nearby genes which could be linked to gene ontology information. Molecular function was primarily related to binding and catalytic activity; notable biological processes were cellular and metabolic, and nucleic acid binding and transcription factor protein classes were most commonly involved. X-variant heritability of neuroticism was estimated at 0.22% (SE = 0.05) from a full dosage compensation model. A polygenic X-variant score created in an independent sample (maximum N ≈ 7,300) did not predict significant variance in neuroticism, psychological distress, or depressive disorder. We conclude that the X chromosome harbours significant variants influencing neuroticism, and might prove important for other quantitative traits and complex disorders.
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12
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Pathomthongtaweechai N, Chutipongtanate S. AGE/RAGE signaling-mediated endoplasmic reticulum stress and future prospects in non-coding RNA therapeutics for diabetic nephropathy. Biomed Pharmacother 2020; 131:110655. [PMID: 32853909 DOI: 10.1016/j.biopha.2020.110655] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/01/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Disturbance of endoplasmic reticulum (ER) homeostasis triggered by the accumulation of unfolded proteins and advanced glycation end-products (AGEs) plays a major role in pathophysiology of diabetic nephropathy. Activation of receptor for AGEs (RAGE) stimulates NADPH oxidase-mediated reactive oxygen species (ROS) production, leading to ER stress, inflammation, glomerular hypertrophy, podocyte injury, and renal fibrosis. A growing body of evidence indicates that non-coding RNAs (ncRNAs) could rescue ER stress and renal inflammation by the epigenetic modification. This review summarizes ncRNA regulation in AGE/RAGE signaling-mediated ER stress, and discusses the opportunities and challenges of ncRNA-loaded extracellular vesicle therapy in diabetic nephropathy.
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Affiliation(s)
- Nutthapoom Pathomthongtaweechai
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan, 10540, Thailand.
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand; Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand.
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13
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Fatumo S, Ebenezer TE, Ekenna C, Isewon I, Ahmad U, Adetunji C, Oladipo EK, Adebiyi M, Adebiyi E, Nashiru O. The Nigerian Bioinformatics and Genomics Network (NBGN): a collaborative platform to advance bioinformatics and genomics in Nigeria. Glob Health Epidemiol Genom 2020; 5:e3. [PMID: 32742665 PMCID: PMC7372179 DOI: 10.1017/gheg.2020.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/24/2020] [Accepted: 04/20/2020] [Indexed: 12/29/2022] Open
Abstract
Africa plays a central importance role in the human origins, and disease susceptibility, agriculture and biodiversity conservation. Nigeria as the most populous and most diverse country in Africa, owing to its 250 ethnic groups and over 500 different native languages is imperative to any global genomic initiative. The newly inaugurated Nigerian Bioinformatics and Genomics Network (NBGN) becomes necessary to facilitate research collaborative activities and foster opportunities for skills' development amongst Nigerian bioinformatics and genomics investigators. NBGN aims to advance and sustain the fields of genomics and bioinformatics in Nigeria by serving as a vehicle to foster collaboration, provision of new opportunities for interactions between various interdisciplinary subfields of genomics, computational biology and bioinformatics as this will provide opportunities for early career researchers. To provide the foundation for sustainable collaborations, the network organises conferences, workshops, trainings and create opportunities for collaborative research studies and internships, recognise excellence, openly share information and create opportunities for more Nigerians to develop the necessary skills to exceed in genomics and bioinformatics. NBGN currently has attracted more than 650 members around the world. Research collaborations between Nigeria, Africa and the West will grow and all stakeholders, including funding partners, African scientists, researchers across the globe, physicians and patients will be the eventual winners. The exponential membership growth and diversity of research interests of NBGN just within weeks of its establishment and the unanticipated attendance of its activities suggest the significant importance of the network to bioinformatics and genomics research in Nigeria.
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Affiliation(s)
- Segun Fatumo
- London School of Hygiene and Tropical Medicine, London, UK
- Uganda Medical Informatics Centre, MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
| | - ThankGod E. Ebenezer
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park Innovation Centre, NorwichNR4 7UZ, UK
| | | | - Itunuoluwa Isewon
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Umar Ahmad
- Medical Genetics Laboratory, Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra, Selangor, Malaysia
- Department of Anatomy, Faculty of Medicine, Bauchi State University, Gadau, Nigeria
| | | | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
| | - Marion Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
- Department of Computer Science, Landmark University, Omu-Aran, Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Oyekanmi Nashiru
- H3 Africa Bioinformatics Network (H3 ABioNet) Node, CGRI/NABDA, Abuja, Nigeria
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14
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Liu L, Caselli RJ. Unbalanced Sample Size Introduces Spurious Correlations to Genome-Wide Heterozygosity Analyses. Hum Hered 2020; 84:197-202. [PMID: 32541150 DOI: 10.1159/000507576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/27/2020] [Indexed: 11/19/2022] Open
Abstract
Excess of heterozygosity (H) is a widely used measure of genetic diversity of a population. As high-throughput sequencing and genotyping data become readily available, it has been applied to investigating the associations of genome-wide genetic diversity with human diseases and traits. However, these studies often report contradictory results. In this paper, we present a meta-analysis of five whole-exome studies to examine the association of H scores with Alzheimer's disease. We show that the mean H score of a group is not associated with the disease status, but ot is associated with the sample size. Across all five studies, the group with more samples has a significantly lower H score than the group with fewer samples. To remove potential confounders in empirical data sets, we perform computer simulations to create artificial genomes controlled for the number of polymorphic loci, the sample size, and the allele frequency. Analyses of these simulated data confirm the negative correlation between the sample size and the H score. Furthermore, we find that genomes with a large number of rare variants also have inflated H scores. These biases altogether can lead to spurious associations between genetic diversity and the phenotype of interest. Based on these findings, we advocate that studies shall balance the sample sizes when using genome-wide H scores to assess genetic diversities of different populations, which helps improve the reproducibility of future research.
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Affiliation(s)
- Li Liu
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA, .,Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA, .,Department of Neurology, Mayo Clinic Arizona, Scottsdale, Arizona, USA,
| | - Richard J Caselli
- Department of Neurology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
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15
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Abstract
The kidney is subject to a wide range of abnormalities, many of which have a significant hereditable component. Next generation sequencing is increasingly bringing the genetic drivers of Mendelian disease into focus at the base pair level, whereas inexpensive genotyping arrays have surveyed hundreds of thousands of individuals to identify common variants that predispose to kidney dysfunction. In this first article in a CJASN series on kidney genomics, we review how both rare and common variants contribute to kidney disease, explore how evolution may influence the genetic variants that affect kidney function, consider how genetic information is and will be used in the clinic, and identify some of the most important future directions for kidney disease research. Forthcoming articles in the series will elaborate on many of these themes.
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Affiliation(s)
- Martin R Pollak
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - David J Friedman
- Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
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16
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Tavares V, Pinto R, Assis J, Pereira D, Medeiros R. Venous thromboembolism GWAS reported genetic makeup and the hallmarks of cancer: Linkage to ovarian tumour behaviour. Biochim Biophys Acta Rev Cancer 2020; 1873:188331. [DOI: 10.1016/j.bbcan.2019.188331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/01/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022]
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17
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Ewing AT, Kalu N, Cain G, Erby LH, Ricks-Santi LJ, Tetteyfio-Kidd Telemaque E, Scott DM. Factors associated with willingness to provide biospecimens for genetics research among African American cancer survivors. J Community Genet 2019; 10:471-480. [PMID: 30877487 PMCID: PMC6754482 DOI: 10.1007/s12687-019-00411-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/05/2019] [Indexed: 11/25/2022] Open
Abstract
This study evaluated factors associated with willingness to provide biospecimens for cancer genetic research among African American cancer survivors. A total of 200 African American adults diagnosed with breast, colon, and/or prostate cancers completed a self-administered survey. Family history information, beliefs about cancer research, cancer genetics and disparities knowledge, willingness to provide a biospecimen, and demographics were obtained. Chi-square, independent samples t tests, and logistic regression analyses were performed. Overall, 79% of this sample was willing to provide a biospecimen for cancer genetics research. Independent associations of willingness to provide a biospecimen existed among demographics (males (p = 0.041)), those who believed in the importance of genetic causes of cancer (p < 0.001), individuals who believe it is important to participate in genetics research (p < 0.001), and those who indicated they would participate in genetics research to help future generations (p = 0.026). Overall, 12.5-56% of participants demonstrated some level of genetics and cancer disparities. This study identified factors that may be incorporated into future research interventions to engage the African American cancer population in cancer genetics biobanking research.
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Affiliation(s)
| | - Nnenna Kalu
- College of Medicine Alcohol Research Center, Howard University, Washington, DC USA
| | - Gloria Cain
- College of Medicine Alcohol Research Center, Howard University, Washington, DC USA
| | - Lori H. Erby
- Genetic Counseling Training Program, Johns Hopkins University/National Human Genome Research Institute (JHU/NHGRI), 31 Center Dr B1B36, Bethesda, MD USA
| | - Luisel J. Ricks-Santi
- Department of Cancer Research Center, Hampton University Cancer Center, Hampton, VA USA
| | | | - Denise M. Scott
- College of Medicine Alcohol Research Center, Howard University, Washington, DC USA
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18
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Wang J, LaFramboise T. CytoConverter: a web-based tool to convert karyotypes to genomic coordinates. BMC Bioinformatics 2019; 20:467. [PMID: 31510921 PMCID: PMC6739950 DOI: 10.1186/s12859-019-3062-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/29/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cytogenetic nomenclature is used to describe chromosomal aberrations (or lack thereof) in a collection of cells, referred to as the cells' karyotype. The nomenclature identifies locations on chromosomes using a system of cytogenetic bands, each with a unique name and region on a chromosome. Each band is microscopically visible after staining, and encompasses a large portion of the chromosome. More modern analyses employ genomic coordinates, which precisely specify a chromosomal location according to its distance from the end of the chromosome. Currently, there is no tool to convert cytogenetic nomenclature into genomic coordinates. Since locations of genes and other genomic features are usually specified by genomic coordinates, a conversion tool will facilitate the identification of the features that are harbored in the regions of chromosomal gain and loss that are implied by a karyotype. RESULTS Our tool, termed CytoConverter, takes as input either a single karyotype or a file consisting of multiple karyotypes from several individuals. All net chromosomal gains and losses implied by the karyotype are returned in standard genomic coordinates, along with the numbers of cells harboring each aberration if included in the input. CytoConverter also returns graphical output detailing areas of gains and losses of chromosomes and chromosomal segments. CONCLUSIONS CytoConverter is available as a web-based application at https://jxw773.shinyapps.io/Cytogenetic__software/ and as an R script at https://sourceforge.net/projects/cytoconverter/ . Supplemental Material detailing the underlying algorithms is available.
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Affiliation(s)
- Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
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19
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Fattahi Z, Beheshtian M, Mohseni M, Poustchi H, Sellars E, Nezhadi SH, Amini A, Arzhangi S, Jalalvand K, Jamali P, Mohammadi Z, Davarnia B, Nikuei P, Oladnabi M, Mohammadzadeh A, Zohrehvand E, Nejatizadeh A, Shekari M, Bagherzadeh M, Shamsi-Gooshki E, Börno S, Timmermann B, Haghdoost A, Najafipour R, Khorram Khorshid HR, Kahrizi K, Malekzadeh R, Akbari MR, Najmabadi H. Iranome: A catalog of genomic variations in the Iranian population. Hum Mutat 2019; 40:1968-1984. [PMID: 31343797 DOI: 10.1002/humu.23880] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/16/2019] [Accepted: 07/22/2019] [Indexed: 11/12/2022]
Abstract
Considering the application of human genome variation databases in precision medicine, population-specific genome projects are continuously being developed. However, the Middle Eastern population is underrepresented in current databases. Accordingly, we established Iranome database (www.iranome.com) by performing whole exome sequencing on 800 individuals from eight major Iranian ethnic groups representing the second largest population of Middle East. We identified 1,575,702 variants of which 308,311 were novel (19.6%). Also, by presenting higher frequency for 37,384 novel or known rare variants, Iranome database can improve the power of molecular diagnosis. Moreover, attainable clinical information makes this database a good resource for classifying pathogenicity of rare variants. Principal components analysis indicated that, apart from Iranian-Baluchs, Iranian-Turkmen, and Iranian-Persian Gulf Islanders, who form their own clusters, rest of the population were genetically linked, forming a super-population. Furthermore, only 0.6% of novel variants showed counterparts in "Greater Middle East Variome Project", emphasizing the value of Iranome at national level by releasing a comprehensive catalog of Iranian genomic variations and also filling another gap in the catalog of human genome variations at international level. We introduce Iranome as a resource which may also be applicable in other countries located in neighboring regions historically called Greater Iran (Persia).
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Affiliation(s)
- Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - Hossein Poustchi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Erin Sellars
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | | | - Amir Amini
- Information Technology Office, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Peyman Jamali
- Shahrood Genetic Counseling Center, Welfare Office, Semnan, Iran
| | - Zahra Mohammadi
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behzad Davarnia
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Pooneh Nikuei
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Akbar Mohammadzadeh
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Elham Zohrehvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Azim Nejatizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mohammad Shekari
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Bagherzadeh
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Ehsan Shamsi-Gooshki
- Medical Ethics and History of Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Ethics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Stefan Börno
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Aliakbar Haghdoost
- Modeling in Health Research Center, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran.,Regional Knowledge Hub, and WHO Collaborating Centre for HIV Surveillance, Institute for Futures Studies in Health, Kerman University of Medical Sciences, Kerman, Iran
| | - Reza Najafipour
- Cellular and Molecular Research Centre, Qazvin University of Medical Sciences, Qazvin, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Diseases Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad R Akbari
- Women's College Research Institute, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.,Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
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20
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Field MA, Burgio G, Chuah A, Al Shekaili J, Hassan B, Al Sukaiti N, Foote SJ, Cook MC, Andrews TD. Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics 2019; 20:546. [PMID: 31307400 PMCID: PMC6631443 DOI: 10.1186/s12864-019-5863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation. Results We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2–300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3–5000 recurrent false positive variants per mouse – the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. Conclusion Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome – which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time. Electronic supplementary material The online version of this article (10.1186/s12864-019-5863-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Field
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jalila Al Shekaili
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Seeb, Oman
| | - Batool Hassan
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Department of Paediatrics, Allergy, and Clinical Immunology Unit, Royal Hospital, Muscat, Oman
| | - Simon J Foote
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
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21
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Poulet A, Li B, Dubos T, Rivera-Mulia JC, Gilbert DM, Qin ZS. RT States: systematic annotation of the human genome using cell type-specific replication timing programs. Bioinformatics 2019; 35:2167-2176. [PMID: 30475980 PMCID: PMC6681175 DOI: 10.1093/bioinformatics/bty957] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/05/2018] [Accepted: 11/21/2018] [Indexed: 12/20/2022] Open
Abstract
MOTIVATION The replication timing (RT) program has been linked to many key biological processes including cell fate commitment, 3D chromatin organization and transcription regulation. Significant technology progress now allows to characterize the RT program in the entire human genome in a high-throughput and high-resolution fashion. These experiments suggest that RT changes dynamically during development in coordination with gene activity. Since RT is such a fundamental biological process, we believe that an effective quantitative profile of the local RT program from a diverse set of cell types in various developmental stages and lineages can provide crucial biological insights for a genomic locus. RESULTS In this study, we explored recurrent and spatially coherent combinatorial profiles from 42 RT programs collected from multiple lineages at diverse differentiation states. We found that a Hidden Markov Model with 15 hidden states provide a good model to describe these genome-wide RT profiling data. Each of the hidden state represents a unique combination of RT profiles across different cell types which we refer to as 'RT states'. To understand the biological properties of these RT states, we inspected their relationship with chromatin states, gene expression, functional annotation and 3D chromosomal organization. We found that the newly defined RT states possess interesting genome-wide functional properties that add complementary information to the existing annotation of the human genome. AVAILABILITY AND IMPLEMENTATION R scripts for inferring HMM models and Perl scripts for further analysis are available https://github.com/PouletAxel/script_HMM_Replication_timing. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Axel Poulet
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Ben Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | | | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA
| | - David M Gilbert
- Department of Biological Science, Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA
| | - Zhaohui S Qin
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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22
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Goodarzi P, Alavi-Moghadam S, Payab M, Larijani B, Rahim F, Gilany K, Bana N, Tayanloo-Beik A, Foroughi Heravani N, Hadavandkhani M, Arjmand B. Metabolomics Analysis of Mesenchymal Stem Cells. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2019; 8:30-40. [PMID: 32351907 PMCID: PMC7175611 DOI: 10.22088/ijmcm.bums.8.2.30] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/20/2019] [Indexed: 12/12/2022]
Abstract
Various mesenchymal stem cells as easily accessible and multipotent cells can share different essential signaling pathways related to their stemness ability. Understanding the mechanism of stemness ability can be useful for controlling the stem cells for regenerative medicine targets. In this context, OMICs studies can analyze the mechanism of different stem cell properties or stemness ability via a broad range of current high-throughput techniques. This field is fundamentally directed toward the analysis of whole genome (genomics), mRNAs (transcriptomics), proteins (proteomics) and metabolites (metabolomics) in biological samples. According to several studies, metabolomics is more effective than other OMICs ّfor various system biology concerns. Metabolomics can elucidate the biological mechanisms of various mesenchymal stem cell function by measuring their metabolites such as their secretome components. Analyzing the metabolic alteration of mesenchymal stem cells can be useful to promote their regenerative medicine application.
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Affiliation(s)
- Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical sciences, Tehran, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathies Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Kambiz Gilany
- Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran .,Department of Biomedical Sciences, University of Antwerp, Belgium
| | - Nikoo Bana
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Akram Tayanloo-Beik
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Najmeh Foroughi Heravani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Hadavandkhani
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran .,Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular- Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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23
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Atturu G, Gooneratne T. Introduction to translational research in vascular surgery/medicine. INDIAN JOURNAL OF VASCULAR AND ENDOVASCULAR SURGERY 2019. [DOI: 10.4103/ijves.ijves_30_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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24
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Jackson M, Marks L, May GHW, Wilson JB. The genetic basis of disease. Essays Biochem 2018; 62:643-723. [PMID: 30509934 PMCID: PMC6279436 DOI: 10.1042/ebc20170053] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/02/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
Genetics plays a role, to a greater or lesser extent, in all diseases. Variations in our DNA and differences in how that DNA functions (alone or in combinations), alongside the environment (which encompasses lifestyle), contribute to disease processes. This review explores the genetic basis of human disease, including single gene disorders, chromosomal imbalances, epigenetics, cancer and complex disorders, and considers how our understanding and technological advances can be applied to provision of appropriate diagnosis, management and therapy for patients.
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Affiliation(s)
- Maria Jackson
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Leah Marks
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
| | - Gerhard H W May
- School of Medicine, Dentistry and Nursing, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Joanna B Wilson
- School of Life Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, U.K
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25
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [PMID: 30714022 PMCID: PMC6358002 DOI: 10.12688/aasopenres.12832.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Here, we describe how the Collaborative African Genomics Network ( CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - David Kateete
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Betty Nsangi Kintu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.,Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.,St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland
| | - Ed Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Masego Tsimako-Johnstone
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Maplanka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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26
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and anchor-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341.3 DOI: 10.12688/f1000research.14880.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/07/2019] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (anchor-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and anchor-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and anchor-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and anchor-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and anchor-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and anchor-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and anchor-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and anchor-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and anchor-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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27
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341 DOI: 10.12688/f1000research.14880.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2018] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in Jupyter Notebook, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J. Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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28
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341 DOI: 10.12688/f1000research.14880.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 12/02/2022] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in markdown language, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Ather SH, Awe OI, Butler TJ, Denka T, Semick SA, Tang W, Busby B. SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis. F1000Res 2018; 7:ISCB Comm J-628. [PMID: 33014338 PMCID: PMC7525341.2 DOI: 10.12688/f1000research.14880.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/28/2018] [Indexed: 03/30/2024] Open
Abstract
Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome and difficult for beginners to learn. To teach interested students and scientists how to analyze RNA-Seq and ChIP-Seq data, we present a start-to-finish tutorial for analyzing RNA-Seq and ChIP-Seq data: SeqAcademy ( source code: https://github.com/NCBI-Hackathons/seqacademy, webpage: http://www.seqacademy.org/). This user-friendly pipeline, fully written in Jupyter Notebook, emphasizes the use of publicly available RNA-Seq and ChIP-Seq data and strings together popular tools that bridge that gap between raw sequencing reads and biological insight. We demonstrate practical and conceptual considerations for various RNA-Seq and ChIP-Seq analysis steps with a biological use case - a previously published yeast experiment. This work complements existing sophisticated RNA-Seq and ChIP-Seq pipelines designed for advanced users by gently introducing the critical components of RNA-Seq and ChIP-Seq analysis to the novice bioinformatician. In conclusion, this well-documented pipeline will introduce state-of-the-art RNA-Seq and ChIP-Seq analysis tools to beginning bioinformaticians and help facilitate the analysis of the burgeoning amounts of public RNA-Seq and ChIP-Seq data.
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Affiliation(s)
- Syed Hussain Ather
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Olaitan Igbagbo Awe
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Thomas J Butler
- National Institute on Aging , National Institutes of Health, Baltimore , MD, 21224, USA
| | - Tamiru Denka
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | | | - Wanhu Tang
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ben Busby
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
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Bryzgalov LO, Korbolina EE, Brusentsov II, Leberfarb EY, Bondar NP, Merkulova TI. Novel functional variants at the GWAS-implicated loci might confer risk to major depressive disorder, bipolar affective disorder and schizophrenia. BMC Neurosci 2018; 19:22. [PMID: 29745862 PMCID: PMC5998904 DOI: 10.1186/s12868-018-0414-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND A challenge of understanding the mechanisms underlying cognition including neurodevelopmental and neuropsychiatric disorders is mainly given by the potential severity of cognitive disorders for the quality of life and their prevalence. However, the field has been focused predominantly on protein coding variation until recently. Given the importance of tightly controlled gene expression for normal brain function, the goal of the study was to assess the functional variation including non-coding variation in human genome that is likely to play an important role in cognitive functions. To this end, we organized and utilized available genome-wide datasets from genomic, transcriptomic and association studies into a comprehensive data corpus. We focused on genomic regions that are enriched in regulatory activity-overlapping transcriptional factor binding regions and repurpose our data collection especially for identification of the regulatory SNPs (rSNPs) that showed associations both with allele-specific binding and allele-specific expression. We matched these rSNPs to the nearby and distant targeted genes and then selected the variants that could implicate the etiology of cognitive disorders according to Genome-Wide Association Studies (GWAS). Next, we use DeSeq 2.0 package to test the differences in the expression of the certain targeted genes between the controls and the patients that were diagnosed bipolar affective disorder and schizophrenia. Finally, we assess the potential biological role for identified drivers of cognition using DAVID and GeneMANIA. RESULTS As a result, we selected fourteen regulatory SNPs locating within the loci, implicated from GWAS for cognitive disorders with six of the variants unreported previously. Grouping of the targeted genes according to biological functions revealed the involvement of processes such as 'posttranscriptional regulation of gene expression', 'neuron differentiation', 'neuron projection development', 'regulation of cell cycle process' and 'protein catabolic processes'. We identified four rSNP-targeted genes that showed differential expression between patient and control groups depending on brain region: NRAS-in schizophrenia cohort, CDC25B, DDX21 and NUCKS1-in bipolar disorder cohort. CONCLUSIONS Overall, our findings are likely to provide the keys for unraveling the mechanisms that underlie cognitive functions including major depressive disorder, bipolar disorder and schizophrenia etiopathogenesis.
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Affiliation(s)
- Leonid O. Bryzgalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena E. Korbolina
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Ilja I. Brusentsov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Elena Y. Leberfarb
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
| | - Tatiana I. Merkulova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Science, 10 Lavrentyeva Prospekt, Novosibirsk, Russian Federation 630090
- The Novosibirsk State University, 1 Pirogova st., Novosibirsk, Russian Federation 630090
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [DOI: 10.12688/aasopenres.12832.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. J Virol 2018; 92:JVI.01413-17. [PMID: 29142137 PMCID: PMC5774889 DOI: 10.1128/jvi.01413-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 11/06/2017] [Indexed: 12/11/2022] Open
Abstract
The human genome is structurally organized in three-dimensional space to facilitate functional partitioning of transcription. We learned that the latent episome of the human Epstein-Barr virus (EBV) preferentially associates with gene-poor chromosomes and avoids gene-rich chromosomes. Kaposi's sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not. Contacts on the EBV side localize to OriP, the latent origin of replication. This genetic element and the EBNA1 protein that binds there are sufficient to reconstitute chromosome association preferences of the entire episome. Contacts on the human side localize to gene-poor and AT-rich regions of chromatin distant from transcription start sites. Upon reactivation from latency, however, the episome moves away from repressive heterochromatin and toward active euchromatin. Our work adds three-dimensional relocalization to the molecular events that occur during reactivation. Involvement of myriad interchromosomal associations also suggests a role for this type of long-range association in gene regulation. IMPORTANCE The human genome is structurally organized in three-dimensional space, and this structure functionally affects transcriptional activity. We set out to investigate whether a double-stranded DNA virus, Epstein-Barr virus (EBV), uses mechanisms similar to those of the human genome to regulate transcription. We found that the EBV genome associates with repressive compartments of the nucleus during latency and with active compartments during reactivation. This study advances our knowledge of the EBV life cycle, adding three-dimensional relocalization as a novel component to the molecular events that occur during reactivation. Furthermore, the data add to our understanding of nuclear compartments, showing that disperse interchromosomal interactions may be important for regulating transcription.
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Abbott RD, Raskind WH, Matsushita M, Price ND, Richards T, Berninger VW. Patterns of biomarkers for three phenotype profiles of persisting specific learning disabilities during middle childhood and early adolescence: A preliminary study. BIOMARKERS AND GENES 2017; 1:103. [PMID: 30854516 PMCID: PMC6407889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Students without specific learning disabilities [SLDs] [n=18] and with one of three persisting SLDs in written language despite early and current specialized instruction-Dysgraphia [n=21], Dyslexia [n=40], or oral and written language learning disability OWL LD [n=14]- in grades 4 to 9 [N=56 boys, 38 girls] completed behavioral phenotyping assessment and gave a small blood or saliva sample. Molecular analyses informed by current cross-site research on gene candidates for learning disabilities identified associations between molecular genetic markers and the two defining behavioral phenotypes for each SLDs-WL; dysgraphia [impaired writing alphabet from memory for rs3743204 and sentence copying in best handwriting for rs79382 both in DYX1C1], dyslexia [impaired silent word reading/decoding rate for rs4535189 in DCDC2 and impaired spelling/encoding for rs374205 in DYX1C1], and OWL LD [impaired aural syntax comprehension for rs807701 and oral syntax construction for rs807701 both in DYX1C1]. Implications of these identified associations between molecular markers for alleles for different sites within two gene candidates [and mostly one] and hallmark phenotypes are discussed for translation science [application to practice] and neuroimaging that has identified contrasting brain bases for each of the three SLDs.
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Affiliation(s)
- Robert D. Abbott
- University of Washington, Quantitative Studies and Measurement, USA
| | - Wendy H. Raskind
- University of Washington, Medicine, USA,University of Washington, Psychiatry and Behavioral Sciences, USA
| | | | - Nathan D. Price
- Institute for Systems Biology, USA,University of Washington, Bioengineering, Computer Science & Engineering, Molecular & Cellular Biology, USA
| | - Todd Richards
- University of Washington, Integrated Brain Imaging Center and Radiology, USA
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Müllauer L. Next generation sequencing: clinical applications in solid tumours. MEMO 2017; 10:244-247. [PMID: 29250205 PMCID: PMC5725522 DOI: 10.1007/s12254-017-0361-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/17/2017] [Indexed: 12/25/2022]
Abstract
Next generation sequencing (NGS) has unravelled the genetic alterations that underlie the pathogenesis of cancer. It is now becoming integrated into routine clinical diagnostics of malignant tumours. NGS supports diagnosis, identifies therapeutic targets, reveals resistance mechanisms and facilitates disease monitoring. It takes a central function in the implementation of cancer therapies adapted to the molecular alterations of tumours.
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Affiliation(s)
- Leonhard Müllauer
- Department of Pathology, Medical University Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria
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Nkili-Meyong AA, Bigarré L, Labouba I, Vallaeys T, Avarre JC, Berthet N. Contribution of Next-Generation Sequencing to Aquatic and Fish Virology. Intervirology 2017; 59:285-300. [PMID: 28668959 DOI: 10.1159/000477808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/27/2017] [Indexed: 12/13/2022] Open
Abstract
The recent technological advances in nucleic acid sequencing, called next-generation sequencing (NGS), have revolutionized the field of genomics and have also influenced viral research. Aquatic viruses, and especially those infecting fish, have also greatly benefited from NGS technologies, which provide a huge amount of molecular information at a low cost in a relatively short period of time. Here, we review the use of the current high-throughput sequencing platforms with a special focus on the associated challenges (regarding sample preparation and bioinformatics) in their applications to the field of aquatic virology, especially for: (i) discovering novel viruses that may be associated with fish mortalities, (ii) elucidating the mechanisms of pathogenesis, and finally (iii) studying the molecular epidemiology of these pathogens.
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Affiliation(s)
- Andriniaina Andy Nkili-Meyong
- Département Zoonoses et Maladies Emergentes, Centre International de Recherches Médicales de Franceville (CIRMF), Franceville, Gabon
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Say YH. The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with obesity and its related traits and complications. J Physiol Anthropol 2017; 36:25. [PMID: 28615046 PMCID: PMC5471687 DOI: 10.1186/s40101-017-0142-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the fact that insertions/deletions (INDELs) are the second most common type of genetic variations and variable number tandem repeats (VNTRs) represent a large portion of the human genome, they have received far less attention than single nucleotide polymorphisms (SNPs) and larger forms of structural variation like copy number variations (CNVs), especially in genome-wide association studies (GWAS) of complex diseases like polygenic obesity. This is exemplified by the vast amount of review papers on the role of SNPs and CNVs in obesity, its related traits (like anthropometric measurements, biochemical variables, and eating behavior), and its related complications (like hypertension, hypertriglyceridemia, hypercholesterolemia, and insulin resistance-collectively known as metabolic syndrome). Hence, this paper reviews the types of INDELs and VNTRs that have been studied for association with obesity and its related traits and complications. These INDELs and VNTRs could be found in the obesity loci or genes from the earliest GWAS and candidate gene association studies, like FTO, genes in the leptin-proopiomelanocortin pathway, and UCP2/3. Given the important role of the brain serotonergic and dopaminergic reward system in obesity susceptibility, the association of INDELs and VNTRs in these neurotransmitters' metabolism and transport genes with obesity is also reviewed. Next, the role of INS VNTR in obesity and its related traits is questionable, since recent large-scale studies failed to replicate the earlier positive associations. As obesity results in chronic low-grade inflammation of the adipose tissue, the proinflammatory cytokine gene IL1RA and anti-inflammatory cytokine gene IL4 have VNTRs that are implicated in obesity. A systemic proinflammatory state in combination with activation of the renin-angiotensin system and decreased nitric oxide bioavailability as found in obesity leads to endothelial dysfunction. This explains why VNTR and INDEL in eNOS and ACE, respectively, could be predisposing factors of obesity. Finally, two novel genes, DOCK5 and PER3, which are involved in the regulation of the Akt/MAPK pathway and circadian rhythm, respectively, have VNTRs and INDEL that might be associated with obesity. SHORT CONCLUSION In conclusion, INDELs and VNTRs could have important functional consequences in the pathophysiology of obesity, and research on them should be continued to facilitate obesity prediction, prevention, and treatment.
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Affiliation(s)
- Yee-How Say
- Department of Biomedical Science, Faculty of Science, Universiti Tunku Abdul Rahman (UTAR) Kampar Campus, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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Ang HX, Chan SL, Sani LL, Quah CB, Brunham LR, Tan BOP, Winther MD. Pharmacogenomics in Asia: a systematic review on current trends and novel discoveries. Pharmacogenomics 2017; 18:891-910. [DOI: 10.2217/pgs-2017-0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
While early pharmacogenomic studies have primarily been carried out in Western populations, there has been a notable increase in the number of Asian studies over the past decade. We systematically reviewed all pharmacogenomic studies conducted in Asia published before 2016 to highlight trends and identify research gaps in Asia. We observed that pharmacogenomic research in Asia was dominated by larger developed countries, notably Japan and Korea, and mainly driven by local researchers. Studies were focused on drugs acting on the CNS, chemotherapeutics and anticoagulants. Significantly, several novel pharmacogenomic associations have emerged from Asian studies. These developments are highly encouraging for the strength of regional scientific and clinical community and propound the importance of discovery studies in different populations.
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Affiliation(s)
- Hazel Xiaohui Ang
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
| | - Sze Ling Chan
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology & Research, Singapore
| | - Levana L Sani
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
| | | | - Liam R Brunham
- Translational Laboratory in Genetic Medicine, Agency for Science, Technology & Research, Singapore
- Department of Medicine, Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Boon Ooi Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Cancer & Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
- Division of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore
| | - Michael D Winther
- Genome Institute of Singapore, Agency for Science, Technology & Research, Singapore
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Nakano K, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, Shinzato M, Minami M, Nakanishi T, Teruya K, Satou K, Hirano T. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell 2017; 30:149-161. [PMID: 28364362 PMCID: PMC5486853 DOI: 10.1007/s13577-017-0168-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.
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Affiliation(s)
- Kazuma Nakano
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan.
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Noriko Ashimine
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Shun Ohki
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Misuzu Shinzato
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Maiko Minami
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | | | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
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Abildinova G, Abdrakhmanova Z, Tuchinsky H, Nesher E, Pinhasov A, Raskin L. Fast detection of deletion breakpoints using quantitative PCR. Genet Mol Biol 2016; 39:365-9. [PMID: 27560363 PMCID: PMC5004823 DOI: 10.1590/1678-4685-gmb-2015-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/29/2015] [Indexed: 11/22/2022] Open
Abstract
The routine detection of large and medium copy number variants (CNVs) is well
established. Hemizygotic deletions or duplications in the large Duchenne muscular
dystrophy DMD gene responsible for Duchenne and Becker muscular
dystrophies are routinely identified using multiple ligation probe amplification and
array-based comparative genomic hybridization. These methods only map deleted or
duplicated exons, without providing the exact location of breakpoints. Commonly used
methods for the detection of CNV breakpoints include long-range PCR and primer
walking, their success being limited by the deletion size, GC content and presence of
DNA repeats. Here, we present a strategy for detecting the breakpoints of medium and
large CNVs regardless of their size. The hemizygous deletion of exons 45-50 in the
DMD gene and the large autosomal heterozygous
PARK2 deletion were used to demonstrate the workflow that relies
on real-time quantitative PCR to narrow down the deletion region and Sanger
sequencing for breakpoint confirmation. The strategy is fast, reliable and
cost-efficient, making it amenable to widespread use in genetic laboratories.
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Affiliation(s)
| | | | - Helena Tuchinsky
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Elimelech Nesher
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Albert Pinhasov
- Department of Molecular Biology, Ariel University, Ariel, Israel
| | - Leon Raskin
- Department of Medicine, Vanderbilt University, Nashville, TN, USA
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Raghow R. An 'Omics' Perspective on Cardiomyopathies and Heart Failure. Trends Mol Med 2016; 22:813-827. [PMID: 27499035 DOI: 10.1016/j.molmed.2016.07.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Pathological enlargement of the heart, represented by hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM), occurs in response to many genetic and non-genetic factors. The clinical course of cardiac hypertrophy is remarkably variable, ranging from lifelong absence of symptoms to rapidly declining heart function and sudden cardiac death (SCD). Unbiased omics studies have begun to provide a glimpse into the molecular framework underpinning altered mechanotransduction, mitochondrial energetics, oxidative stress, and extracellular matrix in the heart undergoing physiological and pathological hypertrophy. Omics analyses indicate that post-transcriptional regulation of gene expression plays an overriding role in the normal and diseased heart. Studies to date highlight a need for more effective bioinformatics to better integrate patient omics data with their comprehensive clinical histories.
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Affiliation(s)
- Rajendra Raghow
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center and the VA Medical Center, Memphis, TN 38104, USA.
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Lu Y, Liu Y, Niu X, Yang Q, Hu X, Zhang HY, Xia J. Systems Genetic Validation of the SNP-Metabolite Association in Rice Via Metabolite-Pathway-Based Phenome-Wide Association Scans. FRONTIERS IN PLANT SCIENCE 2015; 6:1027. [PMID: 26640468 PMCID: PMC4661230 DOI: 10.3389/fpls.2015.01027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/05/2015] [Indexed: 06/05/2023]
Abstract
In the post-GWAS (Genome-Wide Association Scan) era, the interpretation of GWAS results is crucial to screen for highly relevant phenotype-genotype association pairs. Based on the single genotype-phenotype association test and a pathway enrichment analysis, we propose a Metabolite-pathway-based Phenome-Wide Association Scan (M-PheWAS) to analyze the key metabolite-SNP pairs in rice and determine the regulatory relationship by assessing similarities in the changes of enzymes and downstream products in a pathway. Two SNPs, sf0315305925 and sf0315308337, were selected using this approach, and their molecular function and regulatory relationship with Enzyme EC:5.5.1.6 and with flavonoids, a significant downstream regulatory metabolite product, were demonstrated. Moreover, a total of 105 crucial SNPs were screened using M-PheWAS, which may be important for metabolite associations.
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Shelton CA, Whitcomb DC. Evolving Roles for Physicians and Genetic Counselors in Managing Complex Genetic Disorders. Clin Transl Gastroenterol 2015; 6:e124. [PMID: 26561988 PMCID: PMC4817528 DOI: 10.1038/ctg.2015.46] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/29/2015] [Indexed: 12/13/2022] Open
Abstract
Proponents of personalized medicine predict that genetic information will provide pivotal perspectives for the prevention and management of complex disorders. Personalized medicine differs from traditional Western medicine, in that it focuses on more complex disorders that require mechanistic disease modeling and outcome simulation by integrating genomic risk, environmental stressors, and biomarkers as indicators of disease state. This information could be useful to guide targeted therapy and prevent pathologic outcomes. However, gaps exist in the process of linking the pieces together; currently, genetic data are seldom used to assist physicians in clinical decision making. With rapid growth in genetic data and the requirements for new paradigms for complex disorders comes the need to train professionals to understand and manage the impact of genetic information on patients within these clinical settings. Here we describe the challenges, controversies, and opportunities for genetics and genetic counselors in managing complex disorders and discuss the rationale for modifications in genetic counselor training and function. We conclude that a major paradigm shift is underway and a compelling functional, ethical, and financial argument can be made for employing properly trained genetic counselors to be strategically positioned within the health-care industries that are responsible for managing complex disorders.
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Affiliation(s)
- Celeste A Shelton
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh, and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - David C Whitcomb
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh, and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh, and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
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Roman S, Panduro A. Genomic medicine in gastroenterology: A new approach or a new specialty? World J Gastroenterol 2015; 21:8227-37. [PMID: 26217074 PMCID: PMC4507092 DOI: 10.3748/wjg.v21.i27.8227] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/24/2015] [Accepted: 05/04/2015] [Indexed: 02/06/2023] Open
Abstract
Throughout history, many medical milestones have been achieved to prevent and treat human diseases. Man's early conception of illness was naturally holistic or integrative. However, scientific knowledge was atomized into quantitative and qualitative research. In the field of medicine, the main trade-off was the creation of many medical specialties that commonly treat patients in advanced stages of disease. However, now that we are immersed in the post-genomic era, how should we reevaluate medicine? Genomic medicine has evoked a medical paradigm shift based on the plausibility to predict the genetic susceptibility to disease. Additionally, the development of chronic diseases should be viewed as a continuum of interactions between the individual's genetic make-up and environmental factors such as diet, physical activity, and emotions. Thus, personalized medicine is aimed at preventing or reversing clinical symptoms, and providing a better quality of life by integrating the genetic, environmental and cultural factors of diseases. Whether using genomic medicine in the field of gastroenterology is a new approach or a new medical specialty remains an open question. To address this issue, it will require the mutual work of educational and governmental authorities with public health professionals, with the goal of translating genomic medicine into better health policies.
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Ioannou D, Kandukuri L, Simpson JL, Tempest HG. Chromosome territory repositioning induced by PHA-activation of lymphocytes: A 2D and 3D appraisal. Mol Cytogenet 2015; 8:47. [PMID: 26146516 PMCID: PMC4490598 DOI: 10.1186/s13039-015-0146-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/14/2015] [Indexed: 11/26/2022] Open
Abstract
Background Genomes and by extension chromosome territories (CTs) in a variety of organisms exhibit nonrandom organization within interphase nuclei. CTs are susceptible to movement upon induction by a variety of stimuli, including: cell differentiation, growth factors, genotoxic agents, proliferating status, and stimulants that induce novel transcription profiles. These findings suggest nuclear architecture can undergo reorganization, providing support for a functional significance of CT organization. The effect of the initiation of transcription on global scale chromatin architecture has been underexplored. This study investigates the organization of all 24 human chromosomes in lymphocytes from two individuals in resting and phytohaemagglutinin activated lymphocytes using 2D and 3D approaches. Results The radial organization of CTs in lymphocytes in both resting and activated lymphocytes follows a gene-density pattern. However, CT organization in activated nuclei appears less constrained exhibiting a more random organization. We report differences in the spatial relationship between homologous and heterologous CTs in activated nuclei. In addition, a reproducible radial hierarchy of CTs was identified and evidence of a CT repositioning was observed in activated nuclei using both 2D and 3D approaches. Conclusions Alterations between resting and activated lymphocytes could be adaptation of CTs to the new transcription profile and possibly the formation of new neighborhoods of interest or interaction of CTs with nuclear landmarks. The increased distances between homologous and heterologous CTs in activated lymphocytes could be a reflection of a defensive mechanism to reduce potential interaction to prevent any structural chromosome abnormalities (e.g. translocations) as a result of DNA damage that increases during lymphocyte activation.
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Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Lakshmi Kandukuri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Present address Centre for Cellular and Molecular Biology (CCMB), Council of Scientific and Industrial Research (CSIR) Uppal Road, Hyderabad, 500 007 India
| | - Joe Leigh Simpson
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA
| | - Helen Ghislaine Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199 USA ; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199 USA
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Lächelt U, Wagner E. Nucleic Acid Therapeutics Using Polyplexes: A Journey of 50 Years (and Beyond). Chem Rev 2015; 115:11043-78. [DOI: 10.1021/cr5006793] [Citation(s) in RCA: 418] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ulrich Lächelt
- Pharmaceutical
Biotechnology, Department of Pharmacy, Ludwig Maximilians Universität, 81377 Munich, Germany
- Nanosystems
Initiative
Munich (NIM), 80799 Munich, Germany
| | - Ernst Wagner
- Pharmaceutical
Biotechnology, Department of Pharmacy, Ludwig Maximilians Universität, 81377 Munich, Germany
- Nanosystems
Initiative
Munich (NIM), 80799 Munich, Germany
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Ioannou D, Kandukuri L, Quadri A, Becerra V, Simpson JL, Tempest HG. Spatial positioning of all 24 chromosomes in the lymphocytes of six subjects: evidence of reproducible positioning and spatial repositioning following DNA damage with hydrogen peroxide and ultraviolet B. PLoS One 2015; 10:e0118886. [PMID: 25756782 PMCID: PMC4355486 DOI: 10.1371/journal.pone.0118886] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/18/2015] [Indexed: 12/18/2022] Open
Abstract
The higher-order organization of chromatin is well-established, with chromosomes occupying distinct positions within the interphase nucleus. Chromatin is susceptible to, and constantly assaulted by both endogenous and exogenous threats. However, the effects of DNA damage on the spatial topology of chromosomes are hitherto, poorly understood. This study investigates the organization of all 24 human chromosomes in lymphocytes from six individuals prior to- and following in-vitro exposure to genotoxic agents: hydrogen peroxide and ultraviolet B. This study is the first to report reproducible distinct hierarchical radial organization of chromosomes with little inter-individual differences between subjects. Perturbed nuclear organization was observed following genotoxic exposure for both agents; however a greater effect was observed for hydrogen peroxide including: 1) More peripheral radial organization; 2) Alterations in the global distribution of chromosomes; and 3) More events of chromosome repositioning (18 events involving 10 chromosomes vs. 11 events involving 9 chromosomes for hydrogen peroxide and ultraviolet B respectively). Evidence is provided of chromosome repositioning and altered nuclear organization following in-vitro exposure to genotoxic agents, with notable differences observed between the two investigated agents. Repositioning of chromosomes following genotoxicity involved recurrent chromosomes and is most likely part of the genomes inherent response to DNA damage. The variances in nuclear organization observed between the two agents likely reflects differences in mobility and/or decondensation of chromatin as a result of differences in the type of DNA damage induced, chromatin regions targeted, and DNA repair mechanisms.
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Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Lakshmi Kandukuri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Ameer Quadri
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Victor Becerra
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
| | - Joe Leigh Simpson
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- March of Dimes Foundation, White Plains, New York, United States of America
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, Florida, United States of America
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- * E-mail:
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Apalasamy YD, Mohamed Z. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity. Hum Genet 2015; 134:361-74. [PMID: 25687726 DOI: 10.1007/s00439-015-1533-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023]
Abstract
Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.
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Affiliation(s)
- Yamunah Devi Apalasamy
- Department of Pharmacology, Pharmacogenomics Laboratory, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia,
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Talwar P, Silla Y, Grover S, Gupta M, Grewal GK, Kukreti R. Systems Pharmacology and Pharmacogenomics for Drug Discovery and Development. SYSTEMS AND SYNTHETIC BIOLOGY 2015. [DOI: 10.1007/978-94-017-9514-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Jeong SW, Chung M, Park SJ, Cho SB, Hong KW. Genome-wide association study of metabolic syndrome in koreans. Genomics Inform 2014; 12:187-94. [PMID: 25705157 PMCID: PMC4330253 DOI: 10.5808/gi.2014.12.4.187] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 09/16/2014] [Accepted: 09/29/2014] [Indexed: 12/17/2022] Open
Abstract
Metabolic syndrome (METS) is a disorder of energy utilization and storage and increases the risk of developing cardiovascular disease and diabetes. To identify the genetic risk factors of METS, we carried out a genome-wide association study (GWAS) for 2,657 cases and 5,917 controls in Korean populations. As a result, we could identify 2 single nucleotide polymorphisms (SNPs) with genome-wide significance level p-values (<5 × 10-8), 8 SNPs with genome-wide suggestive p-values (5 × 10-8 ≤ p < 1 × 10-5), and 2 SNPs of more functional variants with borderline p-values (5 × 10-5 ≤ p < 1 × 10-4). On the other hand, the multiple correction criteria of conventional GWASs exclude false-positive loci, but simultaneously, they discard many true-positive loci. To reconsider the discarded true-positive loci, we attempted to include the functional variants (nonsynonymous SNPs [nsSNPs] and expression quantitative trait loci [eQTL]) among the top 5,000 SNPs based on the proportion of phenotypic variance explained by genotypic variance. In total, 159 eQTLs and 18 nsSNPs were presented in the top 5,000 SNPs. Although they should be replicated in other independent populations, 6 eQTLs and 2 nsSNP loci were located in the molecular pathways of LPL, APOA5, and CHRM2, which were the significant or suggestive loci in the METS GWAS. Conclusively, our approach using the conventional GWAS, reconsidering functional variants and pathway-based interpretation, suggests a useful method to understand the GWAS results of complex traits and can be expanded in other genomewide association studies.
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Affiliation(s)
- Seok Won Jeong
- Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, KCDC, Cheongju 363-951, Korea
| | - Myungguen Chung
- Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, KCDC, Cheongju 363-951, Korea
| | - Soo-Jung Park
- Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, KCDC, Cheongju 363-951, Korea
| | - Seong Beom Cho
- Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, KCDC, Cheongju 363-951, Korea
| | - Kyung-Won Hong
- Division of Bio-Medical Informatics, Center for Genome Science, National Institute of Health, KCDC, Cheongju 363-951, Korea
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Delikurt T, Williamson GR, Anastasiadou V, Skirton H. A systematic review of factors that act as barriers to patient referral to genetic services. Eur J Hum Genet 2014; 23:739-45. [PMID: 25205405 DOI: 10.1038/ejhg.2014.180] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 07/23/2014] [Accepted: 08/07/2014] [Indexed: 11/09/2022] Open
Abstract
Patients who might benefit from genetic services may be denied access through failure to be referred. To investigate the evidence on barriers to referral to genetic services, we conducted a systematic review of empirical evidence on this topic. Nine studies were included in the review. Barriers related to non-genetic healthcare professionals were: lack of awareness of patient risk factors, failure to obtain adequate family history, lack of knowledge of genetics and genetic conditions, lack of awareness of genetic services, inadequate coordination of referral and lack of genetics workforce. Those related to individuals affected by or at risk of a genetic condition were: lack of awareness of personal risk, lack of knowledge and/or awareness of medical history of family members and lack of knowledge of genetic services. Research on access to genetic services is heterogeneous; stronger empirical evidence is needed on factors that are barriers, and further research is needed to develop 'targeted interventions' for equitable access to genetic services in a range of populations.
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Affiliation(s)
- Türem Delikurt
- 1] Faculty of Health and Human Sciences, Plymouth University, Plymouth, UK [2] Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Violetta Anastasiadou
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Heather Skirton
- Faculty of Health and Human Sciences, Plymouth University, Plymouth, UK
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