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Ahmed Z, Renart EG, Zeeshan S. Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PeerJ 2021; 9:e11724. [PMID: 34395068 PMCID: PMC8320519 DOI: 10.7717/peerj.11724] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.
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Affiliation(s)
- Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Eduard Gibert Renart
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Salmaninejad A, Motaee J, Farjami M, Alimardani M, Esmaeilie A, Pasdar A. Next-generation sequencing and its application in diagnosis of retinitis pigmentosa. Ophthalmic Genet 2020; 40:393-402. [PMID: 31755340 DOI: 10.1080/13816810.2019.1675178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Retinitis Pigmentosa (RP) is a major cause of heritable human blindness with a high genetic heterogeneity. It is characterized by the initial degeneration of rod photoreceptors followed by cone photoreceptors. RP is also a prominent reason of visual impairment, by a global prevalence of 1:4000. RP is usually specified with nyctalopia in puberty, followed by concentric visual field loss, that reflects the main impairment of rod photoreceptors; later in the life, as disease progresses, because of cone dysfunction, central vision loss also occurs. A precise molecular diagnosis is crucial for disease characterization and clinical prognosis. DNA sequencing is a powerful tool for deciphering various causes of different human diseases. The arrival of next-generation sequencing (NGS) technologies has diminished sequencing cost and considerably augmented the throughput, making whole-genome sequencing (WGS) a conceivable way for obtaining comprehensive genomic data and a more precise clinical decision. Nevertheless, the advantages gained from NGS technologies are among a number of challenges that must be sufficiently addressed before this technique can be altered from an investigation tools to a helpful method in routine clinical practices. This article aims to provide an overview about NGS technology and its related platforms. The challenges in the analysis and choosing an appropriate NGS method likewise their potential applications in clinical diagnosis are also discussed. The merit of such technique has been reflected in some recent studies where it is shown that using NGS and molecular information could help with clinical diagnosis, providing potential treatment options or changes, up-to-date family counseling and management.
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Affiliation(s)
- Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshid Motaee
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahsa Farjami
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maliheh Alimardani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine,Medical School, University of Aberdeen, Foresterhill, Aberdeen, UK
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Esposito M, Lagorio I, Peroni D, Bonuccelli A, Orsini A, Striano P. Genomic sequencing in severe epilepsy: a step closer to precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1732203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Mariagrazia Esposito
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Ilaria Lagorio
- Department of Neurology, University of Siena, Siena, Italy
| | - Diego Peroni
- Pediatric Department, “A.O.U. Pisana”, University Hospital of Pisa, Pisa, Italy
| | - Alice Bonuccelli
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Alessandro Orsini
- Pediatric Neurology Unit, “A.O.U. Pisana” University Hospital of Pisa, Pisa, Italy
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS “G. Gaslini” Institute, Genova, Italy
- Department Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health University of Genoa, Genova, Italy
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Delanty N, White M, Benson K, McCormack M, Heavin S, Comerford E, Gangadharan N, Power K, Dunleavey B, El‐Naggar H, Doherty C, Greally M, Cavalleri G, Fitzsimons M. Development of a genomics module within an epilepsy‐specific electronic health record: Toward genomic medicine in epilepsy care. Epilepsia 2019; 60:1670-1677. [DOI: 10.1111/epi.16278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/11/2019] [Accepted: 06/13/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Norman Delanty
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
- Department of Neurology Beaumont Hospital Dublin Ireland
| | - Maire White
- Department of Neurology Beaumont Hospital Dublin Ireland
| | - Katherine Benson
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
| | - Mark McCormack
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | - Sinead Heavin
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | - Elizabeth Comerford
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | - Nisha Gangadharan
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | - Kevin Power
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | | | - Hany El‐Naggar
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
- Department of Neurology Beaumont Hospital Dublin Ireland
| | - Colin Doherty
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
- Department of Neurology St. James's Hospital Dublin Ireland
| | - Marie Greally
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
| | - Gianpiero Cavalleri
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
| | - Mary Fitzsimons
- Department of Molecular and Cellular Therapeutics The Royal College of Surgeons in Ireland Dublin Ireland
- FutureNeuro Research Centre The Royal College of Surgeons in Ireland Dublin Ireland
- Department of Neurology Beaumont Hospital Dublin Ireland
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Cavalleri GL, Petrovski S, Fitzsimons M, Delanty N. eHealth as a Facilitator of Precision Medicine in Epilepsy. Biomed Hub 2017; 2:137-145. [PMID: 31988944 PMCID: PMC6945901 DOI: 10.1159/000481793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 09/27/2017] [Indexed: 12/31/2022] Open
Abstract
Epilepsy is a chronic neurological condition that affects approximately 50 million people worldwide. Current treatments are inadequate and around a third of patients continue to experience uncontrolled seizures. The genetic architecture of many of the epilepsies makes them amenable to next-generation sequencing technologies, enabling a molecular diagnosis in an increasing proportion of patients. As a result, rare but remarkable examples of precision therapeutics in epilepsy are emerging. Coordinated research efforts are required to increase the diagnostic yield of sequencing and translate diagnosis to improved prognosis. This review explores the potential of eHealth technologies in facilitating and accelerating precision therapeutics in epilepsy. We describe the state of the art in precision diagnostics and therapeutics in epilepsy and identify opportunities for eHealth to accelerate the realisation of precision therapeutics via patient registries, research-enabled electronic health records, and connected health solutions.
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Affiliation(s)
- Gianpiero L Cavalleri
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.,The FutureNeuro Research Centre, Dublin, Ireland
| | - Slave Petrovski
- Department of Medicine, The University of Melbourne, Austin Health and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Mary Fitzsimons
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Neurology, Beaumont Hospital, Dublin, Ireland.,The FutureNeuro Research Centre, Dublin, Ireland
| | - Norman Delanty
- Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Neurology, Beaumont Hospital, Dublin, Ireland.,The FutureNeuro Research Centre, Dublin, Ireland
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Mei D, Parrini E, Marini C, Guerrini R. The Impact of Next-Generation Sequencing on the Diagnosis and Treatment of Epilepsy in Paediatric Patients. Mol Diagn Ther 2017; 21:357-373. [DOI: 10.1007/s40291-017-0257-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Preeprem T, Gibson G. SDS, a structural disruption score for assessment of missense variant deleteriousness. Front Genet 2014; 5:82. [PMID: 24795746 PMCID: PMC4001065 DOI: 10.3389/fgene.2014.00082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/26/2014] [Indexed: 11/17/2022] Open
Abstract
We have developed a novel structure-based evaluation for missense variants that explicitly models protein structure and amino acid properties to predict the likelihood that a variant disrupts protein function. A structural disruption score (SDS) is introduced as a measure to depict the likelihood that a case variant is functional. The score is constructed using characteristics that distinguish between causal and neutral variants within a group of proteins. The SDS score is correlated with standard sequence-based deleteriousness, but shows promise for improving discrimination between neutral and causal variants at less conserved sites. The prediction was performed on 3-dimentional structures of 57 gene products whose homozygous SNPs were identified as case-exclusive variants in an exome sequencing study of epilepsy disorders. We contrasted the candidate epilepsy variants with scores for likely benign variants found in the EVS database, and for positive control variants in the same genes that are suspected to promote a range of diseases. To derive a characteristic profile of damaging SNPs, we transformed continuous scores into categorical variables based on the score distribution of each measurement, collected from all possible SNPs in this protein set, where extreme measures were assumed to be deleterious. A second epilepsy dataset was used to replicate the findings. Causal variants tend to receive higher sequence-based deleterious scores, induce larger physico-chemical changes between amino acid pairs, locate in protein domains, buried sites or on conserved protein surface clusters, and cause protein destabilization, relative to negative controls. These measures were agglomerated for each variant. A list of nine high-priority putative functional variants for epilepsy was generated. Our newly developed SDS protocol facilitates SNP prioritization for experimental validation.
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Affiliation(s)
| | - Greg Gibson
- School of Biology, Georgia Institute of Technology Atlanta, GA, USA
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Abstract
Genomic tools have evolved with remarkable rapidity, but their clinical relevance and application have lagged behind. Now, consistent clinical applications have finally arrived and bring with them the promise of identifying the underlying causes of complex neurological disorders in a patient-specific manner.
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Affiliation(s)
- Norman Delanty
- Department of Neurology, Beaumont Hospital, Royal College of Surgeons, Dublin 9, Ireland.
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