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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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2
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Bai W, Ren JS, Li KR, Jiang Q. An integrated analysis revealing the angiogenic function of TP53I11 in tumor microenvironment. Heliyon 2024; 10:e29504. [PMID: 38655349 PMCID: PMC11036061 DOI: 10.1016/j.heliyon.2024.e29504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Despite growing evidence suggesting an important contribution of Tumor Protein P53 Inducible Protein 11 (TP53I11) in cancer progression, the role of TP53I11 remains unclear. Our first pan-cancer analysis of TP53I11 showed some tumor tissues displayed reduced TP53I11 expression compared to normal tissues, while others exhibited high TP53I11 expression. Meanwhile, TP53I11 expression carries a particular pan-cancer risk, as high TP53I11 expression levels are detrimental to survival for BRCA, KIRP, MESO, and UVM, but to beneficial survival for KIRC. We demonstrated that TP53I11 expression negatively correlates with DNA methylation in most cancers, and the S14 residue of TP53I11 is phosphorylated in several cancer types. Additionally, TP53I11 was found to be associated with endothelial cells in pan-cancer, and functional enrichment analysis provided strong evidence for its role in tumor angiogenesis. In vitro angiogenesis assays confirmed that TP53I11 can promote angiogenic function of human umbilical vein endothelial cells (HUVECs) in vitro. Mechanistic investigations reveal that TP53I11 is transcriptionally up-regulated by HIF2A under hypoxia.
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Affiliation(s)
- Wen Bai
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Jun-Song Ren
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Ke-ran Li
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Qin Jiang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, China
- The Fourth School of Clinical Medicine, Nanjing Medical University, Nanjing, China
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3
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Jayasinghe K, Chamika WAS, Jayaweera K, Abhayasinghe K, Dissanayake L, Sumathipala A, Ives J. All you Need is Trust? Public Perspectives on Consenting to Participate in Genomic Research in the Sri Lankan District of Colombo. Asian Bioeth Rev 2024; 16:281-302. [PMID: 38586568 PMCID: PMC10994890 DOI: 10.1007/s41649-023-00269-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 04/09/2024] Open
Abstract
Engagement with genomic medicine and research has increased globally during the past few decades, including rapid developments in Sri Lanka. Genomic research is carried out in Sri Lanka on a variety of scales and with different aims and perspectives. However, there are concerns about participants' understanding of genomic research, including the validity of informed consent. This article reports a qualitative study aiming to explore the understanding, knowledge, and attitudes of the Sri Lankan public towards genomic medicine and to inform the development of an effective and appropriate process for informed consent in that setting. Purposive sampling was employed. Participants were recruited from a sub-group of the public in Colombo, Sri Lanka who had either consented or refused to donate genetic material for a biobank. Data were collected using face-to-face semi-structured interviews. Interview data were transcribed verbatim and translated into English. Conventional content analysis was used. The analysis developed three key themes: a) 'Scientific literacy' describes an apparent lack of scientific knowledge that seems to affect a participant's ability to understand the research, b) 'Motivation' describes narratives about why participants chose (not) to take part in the research, despite not understanding it, and c) 'Trust' describes how trust served to mitigate the apparent ethical deficit created by not being fully informed. In this article, we argue that informed trust is likely an acceptable basis for consent, particularly in settings where scientific literacy might be low. However, researchers must work to be worthy of that trust and ensure that misconceptions are actively addressed.
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Affiliation(s)
- Krishani Jayasinghe
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - W. A. S. Chamika
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Kaushalya Jayaweera
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Kalpani Abhayasinghe
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Lasith Dissanayake
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Athula Sumathipala
- Institute for Research and Development in Health & Social Care, Battaramulla, Sri Lanka
| | - Jonathan Ives
- Centre for Ethics in Medicine, Bristol Medical School, University of Bristol, Bristol, UK
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Seo SH, Kim N, Yoo J, Kim DH, Kim J, Huh J, Kong SY, Seo EJ. Issues, challenges, and future perspectives of genetic counseling in Republic of Korea: Perspectives of laboratory physicians based on a 2022 survey. J Genet Couns 2024. [PMID: 38225817 DOI: 10.1002/jgc4.1863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 01/17/2024]
Abstract
The field of genetic counseling (GC) in the Republic of Korea has evolved from a single medical doctor's clinic to a multidisciplinary service with medical geneticists and non-medical professionals working as a team. Here, we assessed the current status of GC in the Republic of Korea based on professional surveys from the perspective of laboratory physicians. An electronic survey was designed and conducted, with the respondents being 50 certified laboratory physicians who were members of the Korean Society for Genetic Diagnostics. Among the 50 respondents, 12 (24%) operated GC clinics. The number of sessions and cases of GC have been on the rise over the last few years, and counseling for cancer genetics was the most common request. Most respondents considered a good understanding of the genetic test and the ability to interpret the test results as strengths of laboratory physicians as medical geneticists, while the lack of clinical experience was a weakness. Education programs regarding laboratory physicians' needs should be provided for high-quality counseling. Lastly, improving the efficiency of GC by strengthening the workforce through a multidisciplinary team is necessary.
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Affiliation(s)
- Soo Hyun Seo
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, South Korea
| | - Namhee Kim
- Department of Laboratory Medicine, Dong-A University Medical Center, Dong-A University College of Medicine, Busan, South Korea
| | - Jongha Yoo
- Department of Laboratory Medicine, National Health Insurance Service, Ilsan Hospital, Goyang, South Korea
| | - Do-Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, South Korea
| | - Jieun Kim
- Department of Laboratory Medicine, Soonchunhyang University Seoul Hospital, Soonchunhyang University College of Medicine, Seoul, South Korea
| | - Jungwon Huh
- Department of Laboratory Medicine, Ewha Womans University College of Medicine, Seoul, South Korea
| | - Sun-Young Kong
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, South Korea
- Department of Laboratory Medicine, National Cancer Center, Goyang, South Korea
| | - Eul Joo Seo
- Department of Laboratory Medicine, Asan Medical Centre, University of Ulsan College of Medicine, Seoul, South Korea
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Actis S, D'Alonzo M, Pace L, Mucciacito S, Bounous VE, Sgrò LG, Mancarella M, Ferrero A, Biglia N. Factors associated with adherence to BRCA1/2 mutation testing after oncogenetic counseling in long-surviving patients with a previous diagnosis of breast or ovarian cancer. J Community Genet 2023; 14:649-656. [PMID: 37723374 PMCID: PMC10725406 DOI: 10.1007/s12687-023-00671-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023] Open
Abstract
BRCA1/2 mutations account for 5 to 10% of breast and 15% of ovarian cancers. Various guidelines on BRCA1/2 genetic counseling and testing have been issued, and the criteria have evolved over the years. Oncogenetic counseling aims to inform patients about the possibility and implications of undergoing predictive testing and risk management programs. We analyzed a cohort of 50 subjects with a previous personal history of breast or ovarian cancer who had not been tested for BRCA1/2 mutations at the time of diagnosis but were found eligible according to the most recent guidelines. All patients were offered pre-test oncogenetic counseling and BRCA1/2 genetic testing. The mean time from cancer diagnosis to genetic counseling was over 10 years. We analyzed socio-demographic and psychological parameters associated with the decision to undergo BRCA1/2 genetic testing or the reasons behind the withdrawal. Thirty-nine patients underwent BRCA1/2 genetic testing. Patients who accept the genetic test communicate more easily with family members than those who refuse. Factors associated with test refusal are having a long-term partner and having a negative perception of life. There is a trend, although not statistically significant, toward younger age at cancer diagnosis, more likely to participate in cancer screening programs (71.8% vs. 45.5%), and more likely to have daughters (63.3% vs. 37.5%) in the group that accepted the test. The offer of BRCA testing was well accepted by our study population, despite the many years since the cancer diagnosis. With the perspective of further broadening the access criteria to genetic testing, it is important to understand how to best approach pre-test counseling in long-surviving patients with a previous diagnosis of cancer.
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Affiliation(s)
- Silvia Actis
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy.
| | - Marta D'Alonzo
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
| | - Luca Pace
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
| | - Serena Mucciacito
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
| | - Valentina Elisabetta Bounous
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
| | - Luca Giuseppe Sgrò
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, 10128, Turin, Italy
| | - Matteo Mancarella
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, 10128, Turin, Italy
| | - Annamaria Ferrero
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
| | - Nicoletta Biglia
- Gynecology and Obstetrics Unit, Mauriziano Umberto I Hospital, Department of Surgical Sciences, University of Turin, Largo Filippo Turati, 62, 10128, Turin, Italy
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Lee B, Gries K, Valimukhametova AR, McKinney RL, Gonzalez-Rodriguez R, Topkiran UC, Coffer J, Akkaraju GR, Naumov AV. In Vitro Prostate Cancer Treatment via CRISPR-Cas9 Gene Editing Facilitated by Polyethyleneimine-Derived Graphene Quantum Dots. ADVANCED FUNCTIONAL MATERIALS 2023; 33:2305506. [PMID: 38144446 PMCID: PMC10746168 DOI: 10.1002/adfm.202305506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 12/26/2023]
Abstract
CRISPR-Cas9 is a programmable gene editing tool with a promising potential for cancer gene therapy. This therapeutic function is enabled in the present work via the non-covalent delivery of CRISPR ribonucleic protein (RNP) by cationic glucosamine/PEI-derived graphene quantum dots (PEI-GQD) that aid in overcoming physiological barriers and tracking genes of interest. PEI-GQD/RNP complex targeting the TP53 mutation overexpressed in ~50% of cancers successfully produces its double-stranded breaks in solution and in PC3 prostate cancer cells. Restoring this cancer "suicide" gene can promote cellular repair pathways and lead to cancer cell apoptosis. Its repair to the healthy form performed by simultaneous PEI-GQD delivery of CRISPR RNP and a gene repair template leads to a successful therapeutic outcome: 40% apoptotic cancer cell death, while having no effect on non-cancerous HeK293 cells. The translocation of PEI-GQD/RNP complex into PC3 cell cytoplasm is tracked via GQD intrinsic fluorescence, while EGFP-tagged RNP is detected in the cell nucleus, showing the successful detachment of the gene editing tool upon internalization. Using GQDs as non-viral delivery and imaging agents for CRISPR-Cas9 RNP sets the stage for image-guided cancer-specific gene therapy.
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Affiliation(s)
- Bong Lee
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX
| | - Klara Gries
- Department of Chemistry and Biochemistry, Heidelberg University, Heidelberg, Germany
| | | | - Ryan L. McKinney
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX
| | | | - Ugur C. Topkiran
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX
| | - Jeffery Coffer
- Department of Chemistry and Biochemistry, Texas Christian University, Fort Worth, TX
| | | | - Anton V. Naumov
- Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX
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7
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Kösoglu-Kind B, Loredo R, Grossi M, Bernecker C, Burks JM, Buchkremer R. A biological sequence comparison algorithm using quantum computers. Sci Rep 2023; 13:14552. [PMID: 37666875 PMCID: PMC10477269 DOI: 10.1038/s41598-023-41086-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023] Open
Abstract
Genetic information is encoded as linear sequences of nucleotides, represented by letters ranging from thousands to billions. Differences between sequences are identified through comparative approaches like sequence analysis, where variations can occur at the individual nucleotide level or collectively due to various phenomena such as recombination or deletion. Detecting these sequence differences is vital for understanding biology and medicine, but the complexity and size of genomic data require substantial classical computing power. Inspired by human visual perception and pixel representation on quantum computers, we leverage these techniques to implement pairwise sequence analysis. Our method utilizes the Flexible Representation of Quantum Images (FRQI) framework, enabling comparisons at a fine granularity to single letters or amino acids within gene sequences. This novel approach enhances accuracy and resolution, surpassing traditional methods by capturing subtle genetic variations with precision. In summary, our approach offers algorithmic advantages, including reduced time complexity, improved space efficiency, and accurate sequence comparisons. The novelty lies in applying the FRQI algorithm to compare quantum images in genome sequencing, allowing for examination at the individual letter or amino acid level. This breakthrough holds promise for advancing biological data analysis and enables a more comprehensive understanding of genetic information.
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Affiliation(s)
- Büsra Kösoglu-Kind
- Institute of IT Management and Digitization Research (IFID), FOM University of Applied Sciences in Economics and Management, 40476, Dusseldorf, Germany
| | - Robert Loredo
- International Business Machines Corporation (IBM), Armonk, NY, 10504, USA
- IBM Quantum, IBM Thomas J. Watson Research Center, 1101 Kitchawan Rd, NY, 10598, Yorktown Heights, USA
| | - Michele Grossi
- European Organization for Nuclear Research (CERN), 1211, Geneva, Switzerland
| | | | - Jody M Burks
- International Business Machines Corporation (IBM), Armonk, NY, 10504, USA
| | - Rüdiger Buchkremer
- Institute of IT Management and Digitization Research (IFID), FOM University of Applied Sciences in Economics and Management, 40476, Dusseldorf, Germany.
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Glotov OS, Chernov AN, Glotov AS. Human Exome Sequencing and Prospects for Predictive Medicine: Analysis of International Data and Own Experience. J Pers Med 2023; 13:1236. [PMID: 37623486 PMCID: PMC10455459 DOI: 10.3390/jpm13081236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Today, whole-exome sequencing (WES) is used to conduct the massive screening of structural and regulatory genes in order to identify the allele frequencies of disease-associated polymorphisms in various populations and thus detect pathogenic genetic changes (mutations or polymorphisms) conducive to malfunctional protein sequences. With its extensive capabilities, exome sequencing today allows both the diagnosis of monogenic diseases (MDs) and the examination of seemingly healthy populations to reveal a wide range of potential risks prior to disease manifestation (in the future, exome sequencing may outpace costly and less informative genome sequencing to become the first-line examination technique). This review establishes the human genetic passport as a new WES-based clinical concept for the identification of new candidate genes, gene variants, and molecular mechanisms in the diagnosis, prediction, and treatment of monogenic, oligogenic, and multifactorial diseases. Various diseases are addressed to demonstrate the extensive potential of WES and consider its advantages as well as disadvantages. Thus, WES can become a general test with a broad spectrum pf applications, including opportunistic screening.
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Affiliation(s)
- Oleg S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of Experimental Medical Virology, Molecular Genetics and Biobanking of Pediatric Research and Clinical Center for Infectious Diseases, 197022 St. Petersburg, Russia
| | - Alexander N. Chernov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Andrey S. Glotov
- Department of Genomic Medicine, D. O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 St. Petersburg, Russia;
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Fahim SM, Alexander CSW, Qian J, Ngorsuraches S, Hohmann NS, Lloyd KB, Reagan A, Hart L, McCormick N, Westrick SC. Current published evidence on barriers and proposed strategies for genetic testing implementation in health care settings: A scoping review. J Am Pharm Assoc (2003) 2023; 63:998-1016. [PMID: 37119989 DOI: 10.1016/j.japh.2023.04.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/20/2023] [Accepted: 04/22/2023] [Indexed: 05/01/2023]
Abstract
BACKGROUND The slow uptake of genetic testing in routine clinical practice warrants the attention of researchers and practitioners to find effective strategies to facilitate implementation. OBJECTIVES This study aimed to identify the barriers to and strategies for pharmacogenetic testing implementation in a health care setting from published literature. METHODS A scoping review was conducted in August 2021 with an expanded literature search using Ovid MEDLINE, Web of Science, International Pharmaceutical Abstract, and Google Scholar to identify studies reporting implementation of pharmacogenetic testing in a health care setting, from a health care system's perspective. Articles were screened using DistillerSR and findings were organized using the 5 major domains of Consolidated Framework for Implementation Research (CFIR). RESULTS A total of 3536 unique articles were retrieved from the above sources, with only 253 articles retained after title and abstract screening. Upon screening the full texts, 57 articles (representing 46 unique practice sites) were found matching the inclusion criteria. We found that most reported barriers and their associated strategies to the implementation of pharmacogenetic testing surrounded 2 CFIR domains: intervention characteristics and inner settings. Factors relating to cost and reimbursement were described as major barriers in the intervention characteristics. In the same domain, another major barrier was the lack of utility studies to provide evidence for genetic testing uptake. Technical hurdles, such as integrating genetic information to medical records, were identified as an inner settings barrier. Collaborations and lessons from early implementers could be useful strategies to overcome majority of the barriers across different health care settings. Strategies proposed by the included implementation studies to overcome these barriers are summarized and can be used as guidance in future. CONCLUSION Barriers and strategies identified in this scoping review can provide implementation guidance for practice sites that are interested in implementing genetic testing.
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Rothman DL, Moore PB, Shulman RG. The impact of metabolism on the adaptation of organisms to environmental change. Front Cell Dev Biol 2023; 11:1197226. [PMID: 37377740 PMCID: PMC10291235 DOI: 10.3389/fcell.2023.1197226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Since Jacob and Monod's discovery of the lac operon ∼1960, the explanations offered for most metabolic adaptations have been genetic. The focus has been on the adaptive changes in gene expression that occur, which are often referred to as "metabolic reprogramming." The contributions metabolism makes to adaptation have been largely ignored. Here we point out that metabolic adaptations, including the associated changes in gene expression, are highly dependent on the metabolic state of an organism prior to the environmental change to which it is adapting, and on the plasticity of that state. In support of this hypothesis, we examine the paradigmatic example of a genetically driven adaptation, the adaptation of E. coli to growth on lactose, and the paradigmatic example of a metabolic driven adaptation, the Crabtree effect in yeast. Using a framework based on metabolic control analysis, we have reevaluated what is known about both adaptations, and conclude that knowledge of the metabolic properties of these organisms prior to environmental change is critical for understanding not only how they survive long enough to adapt, but also how the ensuing changes in gene expression occur, and their phenotypes post-adaptation. It would be useful if future explanations for metabolic adaptations acknowledged the contributions made to them by metabolism, and described the complex interplay between metabolic systems and genetic systems that make these adaptations possible.
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Affiliation(s)
- Douglas L. Rothman
- Departments of Radiology, Yale University, New Haven, CT, United States
- Biomedical Engineering, Yale University, New Haven, CT, United States
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
| | - Peter B. Moore
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Robert G. Shulman
- Yale Magnetic Resonance Research Center, Yale University School of Medicine, New Haven, CT, United States
- Department of Molecular Biology and Biophysics, Yale University, New Haven, CT, United States
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11
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Deriu C, Thakur S, Tammaro O, Fabris L. Challenges and opportunities for SERS in the infrared: materials and methods. NANOSCALE ADVANCES 2023; 5:2132-2166. [PMID: 37056617 PMCID: PMC10089128 DOI: 10.1039/d2na00930g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
In the wake of a global, heightened interest towards biomarker and disease detection prompted by the SARS-CoV-2 pandemic, surface enhanced Raman spectroscopy (SERS) positions itself again at the forefront of biosensing innovation. But is it ready to move from the laboratory to the clinic? This review presents the challenges associated with the application of SERS to the biomedical field, and thus, to the use of excitation sources in the near infrared, where biological windows allow for cell and through-tissue measurements. Two main tackling strategies will be discussed: (1) acting on the design of the enhancing substrate, which includes manipulation of nanoparticle shape, material, and supramolecular architecture, and (2) acting on the spectral collection set-up. A final perspective highlights the upcoming scientific and technological bets that need to be won in order for SERS to stably transition from benchtop to bedside.
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Affiliation(s)
- Chiara Deriu
- Department of Applied Science and Technology, Politecnico di Torino 10129 Turin Italy
| | - Shaila Thakur
- Department of Applied Science and Technology, Politecnico di Torino 10129 Turin Italy
| | - Olimpia Tammaro
- Department of Applied Science and Technology, Politecnico di Torino 10129 Turin Italy
| | - Laura Fabris
- Department of Applied Science and Technology, Politecnico di Torino 10129 Turin Italy
- Department of Materials Science and Engineering, Rutgers University Piscataway NJ 08854 USA
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Toyokuni S, Zheng H, Kong Y, Sato K, Nakamura K, Tanaka H, Okazaki Y. Low-temperature plasma as magic wand to differentiate between the good and the evil. Free Radic Res 2023; 57:38-46. [PMID: 36919449 DOI: 10.1080/10715762.2023.2190860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plasma is the fourth physical state of matter, characterized by an ionized gaseous mixture, after solid, liquid, and gas phases, and contains a wide array of components such as ions, electrons, radicals, and ultraviolet ray. Whereas the sun and thunder are typical natural plasma, recent progress in the electronics enabled the generation of body-temperature plasma, designated as low-temperature plasma (LTP) or non-thermal plasma since the 1990s. LTP has attracted the attention of researchers for possible biological and medical applications. All the living species on earth utilize water as essential media for solvents and molecular transport. Thus, biological application of LTP naturally intervenes water whether LTP is exposed directly or indirectly, where plasma-activated lactate (PAL) is a standard, containing H2O2, NO2- and other identified molecules. Electron spin resonance and immunohistochemical studies demonstrated that LTP exposure is a handy method to load local oxidative stress. Cancer cells are characterized by persistent self-replication and high cytosolic catalytic Fe(II). Therefore, both direct exposure of LTP and PAL can provide higher damage to cancer cells in comparison to non-tumorous cells, which has been demonstrated in a variety of cancer types. The cell death mode is either apoptosis or ferroptosis, depending on the cancer-type. Thus, LTP and PAL are expected to work as an additional cancer therapy to the established guideline protocols, especially for use in somatic cavities or surgical margins.
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Affiliation(s)
- Shinya Toyokuni
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Hao Zheng
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yingyi Kong
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kotaro Sato
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Oral and Maxillofacial Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kae Nakamura
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Hiromasa Tanaka
- Center for Low-temperature Plasma Sciences, Nagoya University, Nagoya, Japan
| | - Yasumasa Okazaki
- Department of Pathology and Biological Response, Nagoya University Graduate School of Medicine, Nagoya, Japan
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13
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Wang S, Wang S, Wang Z. A survey on multi-omics-based cancer diagnosis using machine learning with the potential application in gastrointestinal cancer. Front Med (Lausanne) 2023; 9:1109365. [PMID: 36703893 PMCID: PMC9871466 DOI: 10.3389/fmed.2022.1109365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Gastrointestinal cancer is becoming increasingly common, which leads to over 3 million deaths every year. No typical symptoms appear in the early stage of gastrointestinal cancer, posing a significant challenge in the diagnosis and treatment of patients with gastrointestinal cancer. Many patients are in the middle and late stages of gastrointestinal cancer when they feel uncomfortable, unfortunately, most of them will die of gastrointestinal cancer. Recently, various artificial intelligence techniques like machine learning based on multi-omics have been presented for cancer diagnosis and treatment in the era of precision medicine. This paper provides a survey on multi-omics-based cancer diagnosis using machine learning with potential application in gastrointestinal cancer. Particularly, we make a comprehensive summary and analysis from the perspective of multi-omics datasets, task types, and multi-omics-based integration methods. Furthermore, this paper points out the remaining challenges of multi-omics-based cancer diagnosis using machine learning and discusses future topics.
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Affiliation(s)
- Suixue Wang
- School of Information and Communication Engineering, Hainan University, Haikou, China
| | - Shuling Wang
- Department of Neurology, Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou, China
| | - Zhengxia Wang
- School of Computer Science and Technology, Hainan University, Haikou, China
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14
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Catapano F, El Hachmi M, Ketterer-Heng N, Renieri A, Mari F, Morris M, Cordier C. The role of the Genetic Counsellor in the multidisciplinary team: the perception of geneticists in Europe. Eur J Hum Genet 2022; 30:1432-1438. [PMID: 36198805 PMCID: PMC9712381 DOI: 10.1038/s41431-022-01189-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/24/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
Genetics has begun to be considered a key medical discipline which can have an impact on everyday clinical practice. Therefore, it is necessary to understand what the most effective way is of caring for people affected by or at risk of genetic disorders. In this context, the team dealing with such patients has evolved with the emergence of the Genetic Counsellor figure. The profession of Genetic Counsellor appeared in Europe in 1980, but it is still a much-debated profession and not yet recognized in all European countries. The aim of this research is to investigate both how a team should be composed in the care of patients affected by or at risk of genetic disorders and what the role of the Genetic Counsellor should be-the field of action and the competences. The research has been carried out at the European level, submitting an online questionnaire to geneticists who, having the ultimate responsibility for the diagnosis and being in the field for the longest time, expressing their opinion, can identify strengths and potential areas for improvement in genetic care. 200 responses were collected from all over Europe. This led to awareness of the importance of the role of the counsellor within the medical genetics multidisciplinary team, and, above all, what the counsellor's skills and qualifications should be-for geneticists. Although this new profession has difficulties in being recognized in some countries, it seems clear that these highly competent professionals are essential for in-patient care and in the multidisciplinary team.
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Affiliation(s)
- Francesca Catapano
- Medical Genetics, University of Siena, Siena, Italy.
- Department of Genetics, SYNLAB Suisse SA, Lausanne, Switzerland.
| | - Mohamed El Hachmi
- Medical Genetics, University of Siena, Siena, Italy
- Department of Genetics, SYNLAB Suisse SA, Lausanne, Switzerland
| | | | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy
- Medical Genetics, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Michael Morris
- Department of Genetics, SYNLAB Suisse SA, Lausanne, Switzerland
| | - Christophe Cordier
- Medical Genetics, University of Siena, Siena, Italy
- Department of Genetics, SYNLAB Suisse SA, Lausanne, Switzerland
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15
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A Theory-Informed Systematic Review of Barriers and Enablers to Implementing Multi-Drug Pharmacogenomic Testing. J Pers Med 2022; 12:jpm12111821. [PMID: 36579514 PMCID: PMC9696651 DOI: 10.3390/jpm12111821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
Abstract
PGx testing requires a complex set of activities undertaken by practitioners and patients, resulting in varying implementation success. This systematic review aimed (PROSPERO: CRD42019150940) to identify barriers and enablers to practitioners and patients implementing pharmacogenomic testing. We followed PRISMA guidelines to conduct and report this review. Medline, EMBASE, CINAHL, PsycINFO, and PubMed Central were systematically searched from inception to June 2022. The theoretical domain framework (TDF) guided the organisation and reporting of barriers or enablers relating to pharmacogenomic testing activities. From the twenty-five eligible reports, eleven activities were described relating to four implementation stages: ordering, facilitating, interpreting, and applying pharmacogenomic testing. Four themes were identified across the implementation stages: IT infrastructure, effort, rewards, and unknown territory. Barriers were most consistently mapped to TDF domains: memory, attention and decision-making processes, environmental context and resources, and belief about consequences.
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16
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Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. J Transl Med 2022; 102:1170-1181. [PMID: 36775443 PMCID: PMC9362039 DOI: 10.1038/s41374-022-00830-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/15/2022] Open
Abstract
Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other 'omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.
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Affiliation(s)
- Miao Cui
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Mount Sinai West, New York, NY, USA
| | - Chao Cheng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA. .,Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
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17
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Primiero CA, Baker AM, Wallingford CK, Maas EJ, Yanes T, Fowles L, Janda M, Young MA, Nisselle A, Terrill B, Lodge JM, Tiller JM, Lacaze P, Andersen H, McErlean G, Turbitt E, Soyer HP, McInerney-Leo AM. Attitudes of Australian dermatologists on the use of genetic testing: A cross-sectional survey with a focus on melanoma. Front Genet 2022; 13:919134. [PMID: 36353112 PMCID: PMC9638172 DOI: 10.3389/fgene.2022.919134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 10/10/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Melanoma genetic testing reportedly increases preventative behaviour without causing psychological harm. Genetic testing for familial melanoma risk is now available, yet little is known about dermatologists’ perceptions regarding the utility of testing and genetic testing ordering behaviours. Objectives: To survey Australasian Dermatologists on the perceived utility of genetic testing, current use in practice, as well as their confidence and preferences for the delivery of genomics education. Methods: A 37-item survey, based on previously validated instruments, was sent to accredited members of the Australasian College of Dermatologists in March 2021. Quantitative items were analysed statistically, with one open-ended question analysed qualitatively. Results: The response rate was 56% (256/461), with 60% (153/253) of respondents between 11 and 30 years post-graduation. While 44% (112/252) of respondents agreed, or strongly agreed, that genetic testing was relevant to their practice today, relevance to future practice was reported significantly higher at 84% (212/251) (t = -9.82, p < 0.001). Ninety three percent (235/254) of respondents reported rarely or never ordering genetic testing. Dermatologists who viewed genetic testing as relevant to current practice were more likely to have discussed (p < 0.001) and/or offered testing (p < 0.001). Respondents indicated high confidence in discussing family history of melanoma, but lower confidence in ordering genetic tests and interpreting results. Eighty four percent (207/247) believed that genetic testing could negatively impact life insurance, while only 26% (63/244) were aware of the moratorium on using genetic test results in underwriting in Australia. A minority (22%, 55/254) reported prior continuing education in genetics. Face-to-face courses were the preferred learning modality for upskilling. Conclusion: Australian Dermatologists widely recognise the relevance of genetic testing to future practice, yet few currently order genetic tests. Future educational interventions could focus on how to order appropriate genetic tests and interpret results, as well as potential implications on insurance.
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Affiliation(s)
- Clare A. Primiero
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Amy M. Baker
- Discipline of Genetic Counselling, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Courtney K. Wallingford
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Ellie J. Maas
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Tatiane Yanes
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Lindsay Fowles
- Genetic Health Queensland, Royal Brisbane and Women’s Hospital, Brisbane, QLD, Australia
| | - Monika Janda
- Centre for Health Services Research, The University of Queensland, Brisbane, QLD, Australia
| | - Mary-Anne Young
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Amy Nisselle
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Murdoch Children’s Research Institute, Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Bronwyn Terrill
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Jason M. Lodge
- School of Education, The University of Queensland, Brisbane, QLD, Australia
| | - Jane M. Tiller
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Paul Lacaze
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Hayley Andersen
- Melanoma and Skin Cancer Advocacy Network, Carlton, VIC, Australia
| | - Gemma McErlean
- SWS Nursing and Midwifery Research Alliance, Ingham Institute for Applied Medical Research, Liverpool, NSW, Australia
- School of Nursing, University of Wollongong, Wollongong, NSW, Australia
| | - Erin Turbitt
- Discipline of Genetic Counselling, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - H. Peter Soyer
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
- Department of Dermatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Aideen M. McInerney-Leo
- The University of Queensland Diamantina Institute, Dermatology Research Centre, The University of Queensland, Brisbane, QLD, Australia
- *Correspondence: Aideen M. McInerney-Leo,
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18
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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19
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Pitini E, Migliara G, Baccolini V, Isonne C, Mazzalai E, Turatto F, Salerno C, Pagano F, Menzano MT, De Vito C, Marzuillo C, Villari P. Managing the introduction of genomic applications into the National Health Service: A special challenge for health technology assessment in Italy. Front Public Health 2022; 10:932093. [PMID: 36033790 PMCID: PMC9399489 DOI: 10.3389/fpubh.2022.932093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 01/25/2023] Open
Abstract
In recent years, the rapid proliferation of genomic tests for use in clinical practice has prompted healthcare systems to use a health technology assessment (HTA) approach to distinguish valuable from unwarranted applications. In this study, we narratively review the Italian HTA mechanisms for medical devices (MDs), both at the national and regional levels, and discuss the opportunity and benefits of extending them to genomic technologies, for which a dedicated assessment path was advocated by the National Plan for Public Health Genomics in 2017. We found that the National Health Technology Assessment Program for MDs, completed in 2019, had developed a structured pathway for the HTA of MDs; it established a hub-and-spoke structure, run by a governmental institution, and put in place transparent methodological procedures to cover all four HTA phases (i.e., proposal and prioritization, assessment, appraisal, and dissemination). However, several factors have hindered its adoption, and the regions are at different stages of its implementation. For these reasons, efforts should be made to ensure its effective deployment, both at national and regional levels. In addition, we argue that to harmonize the institutional roles and methodological procedures adopted, the time has come to concentrate resources on a single pathway for the assessment of all technologies that include both MDs and genomic applications.
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Affiliation(s)
- Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy,*Correspondence: Erica Pitini
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Valentina Baccolini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Claudia Isonne
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Elena Mazzalai
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Turatto
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carla Salerno
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Pagano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Teresa Menzano
- Italian Ministry of Health, General Directorate for Health Prevention, Rome, Italy
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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20
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Genie Out of the Bottle: Is There a Role for Gene-Gene Interactions in Early Detection of Lung Cancer? J Thorac Oncol 2022; 17:946-948. [PMID: 35931422 DOI: 10.1016/j.jtho.2022.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022]
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21
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Fernández-Santiago R, Sharma M. What have we learned from genome-wide association studies (GWAS) in Parkinson's disease? Ageing Res Rev 2022; 79:101648. [PMID: 35595184 DOI: 10.1016/j.arr.2022.101648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/11/2022] [Accepted: 05/11/2022] [Indexed: 11/01/2022]
Abstract
After fifteen years of genome-wide association studies (GWAS) in Parkinson's disease (PD), what have we learned? Addressing this question will help catalogue the progress made towards elucidating disease mechanisms, improving the clinical utility of the identified loci, and envisioning how we can harness the strides to develop translational GWAS strategies. Here we review the advances of PD GWAS made to date while critically addressing the challenges and opportunities for next-generation GWAS. Thus, deciphering the missing heritability in underrepresented populations is currently at the reach of hand for a truly comprehensive understanding of the genetics of PD across the different ethnicities. Moreover, state-of-the-art GWAS designs hold a true potential for enhancing the clinical applicability of genetic findings, for instance, by improving disease prediction (PD risk and progression). Lastly, advanced PD GWAS findings, alone or in combination with clinical and environmental parameters, are expected to have the capacity for defining patient enriched cohorts stratified by genetic risk profiles and readily available for neuroprotective clinical trials. Overall, envisioning future strategies for advanced GWAS is currently timely and can be instrumental in providing novel genetic readouts essential for a true clinical translatability of PD genetic findings.
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Abstract
Behavior genetics is a controversial science. For decades, scholars have sought to understand the role of heredity in human behavior and life-course outcomes. Recently, technological advances and the rapid expansion of genomic databases have facilitated the discovery of genes associated with human phenotypes such as educational attainment and substance use disorders. To maximize the potential of this flourishing science, and to minimize potential harms, careful analysis of what it would mean for genes to be causes of human behavior is needed. In this paper, we advance a framework for identifying instances of genetic causes, interpreting those causal relationships, and applying them to advance causal knowledge more generally in the social sciences. Central to thinking about genes as causes is counterfactual reasoning, the cornerstone of causal thinking in statistics, medicine, and philosophy. We argue that within-family genetic effects represent the product of a counterfactual comparison in the same way as average treatment effects (ATEs) from randomized controlled trials (RCTs). Both ATEs from RCTs and within-family genetic effects are shallow causes: They operate within intricate causal systems (non-unitary), produce heterogeneous effects across individuals (non-uniform), and are not mechanistically informative (non-explanatory). Despite these limitations, shallow causal knowledge can be used to improve understanding of the etiology of human behavior and to explore sources of heterogeneity and fade-out in treatment effects.
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Affiliation(s)
- James W Madole
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- VA Puget Sound Health Care System, Seattle, WA, USA
| | - K Paige Harden
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
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23
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Bozdag M, Cravey L, Combs J, Kota A, Mckenna R, Angeli A, Selleri S, Carta F, Supuran CT. Small Molecule Alkoxy Oriented Selectiveness on Human Carbonic Anhydrase II and IX Inhibition. ChemMedChem 2022; 17:e202200148. [PMID: 35388618 DOI: 10.1002/cmdc.202200148] [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: 03/22/2022] [Revised: 04/06/2022] [Indexed: 11/07/2022]
Abstract
We report aryl sulfonamide inhibitors of human Carbonic Anhydrase (hCA; EC 4.2.1.1) enzymes containing short ureido alkoxy tails. The inhibition potency of such compounds was investigated in vitro on the major hCA isoforms (i.e. I, II, IX and XII). A selection of the most potent inhibitory derivatives against the hCA IX isoform (i.e. 5a, 5c and 6c) was studied and their binding modes on either hCA II and IX-mimic isoform were assessed by X-ray crystallography on the corresponding ligand/protein adducts. This study adds to the field of developing hCA inhibitors at molecular level the critical interactions governing ligand selectivity.
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Affiliation(s)
- Murat Bozdag
- University of Florence: Universita degli Studi di Firenze, Neurofarba dept, ITALY
| | - Lochlin Cravey
- University of Florida, Department of Biochemistry and Molecular Biology, UNITED STATES
| | - Jacob Combs
- University of Florida, Department of Biochemistry and Molecular Biology, UNITED STATES
| | - Anusha Kota
- University of Florida, Department of Biochemistry and Molecular Biology, UNITED STATES
| | - Robert Mckenna
- University of Florida, Department of Biochemistry and Molecular Biology, UNITED STATES
| | - Andrea Angeli
- University of Florence: Universita degli Studi di Firenze, Neurofarba dept, ITALY
| | - Silvia Selleri
- University of Florence: Universita degli Studi di Firenze, Neurofarba dept, ITALY
| | - Fabrizio Carta
- University of Florence: Universita degli Studi di Firenze, NEUROFARBA, Sez. Chimica Farmaceutica e Nutraceutica, via U. Schiff 6, 50019, Sesto Fiorentino, ITALY
| | - Claudiu T Supuran
- University of Florence: Universita degli Studi di Firenze, Neurofarba dept, ITALY
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24
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Harnish SM, Diedrichs VA, Bartlett CW. EARLY CONSIDERATIONS OF GENETICS IN APHASIA REHABILITATION: A NARRATIVE REVIEW. APHASIOLOGY 2022; 37:835-853. [PMID: 37346093 PMCID: PMC10281715 DOI: 10.1080/02687038.2022.2043234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/14/2022] [Indexed: 06/23/2023]
Abstract
Background Early investigations linking language and genetics were focused on the evolution of human communication in populations with developmental speech and language disorders. Recently, studies suggest that genes may also modulate recovery from post-stroke aphasia. Aims Our goal is to review current literature related to the influence of genetics on post-stroke recovery, and the implications for aphasia rehabilitation. We describe candidate genes implicated by empirical findings and address additional clinical considerations. Main Contribution We describe existing evidence and mechanisms supporting future investigations into how genetic factors may modulate aphasia recovery and propose that two candidate genes, brain derived neurotrophic factor (BDNF) and apolipoprotein E (APOE), may be important considerations for future research assessing response to aphasia treatment. Evidence suggests that BDNF is important for learning, memory, and neuroplasticity. APOE influences cognitive functioning and memory in older individuals and has also been implicated in neural repair. Moreover, recent data suggest an interaction between specific alleles of the BDNF and APOE genes in influencing episodic memory. Conclusions Genetic influences on recovery from aphasia have been largely unexplored in the literature despite evidence that genetic factors influence behaviour and recovery from brain injury. As researchers continue to explore prognostic factors that may influence response to aphasia treatment, it is time for genetic factors to be considered as a source of variability. As the field moves in the direction of personalized medicine, eventually allied health professionals may utilize genetic profiles to inform treatment decisions and education for patients and care partners.
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Affiliation(s)
- Stacy M Harnish
- Department of Speech and Hearing Science, The Ohio State University
| | | | - Christopher W Bartlett
- Battelle Center for Mathematical Medicine, Abigail Wexner Research Institute at Nationwide Children's Hospital and Department of Pediatrics, College of Medicine, The Ohio State University
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Liscum M, Garcia ML. You can't keep a bad idea down: Dark history, death, and potential rebirth of eugenics. Anat Rec (Hoboken) 2021; 305:902-937. [PMID: 34919789 DOI: 10.1002/ar.24849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
Abstract
"Be careful what you wish for": This adage guides both how this project came to life, and how the topic covered in this review continues to unfold. What began as talks between two friends on shared interests in military history led to a 4-year discussion about how our science curriculum does little to introduce our students to societal and ethical impacts of the science they are taught. What emerged was a curricular idea centered on how "good intentions" of some were developed and twisted by others to result in disastrous consequences of state-sanctioned eugenics. In this article, we take the reader (as we did our students) through the long and soiled history of eugenic thought, from its genesis to the present. Though our focus is on European and American eugenics, we will show how the interfaces and interactions between science and society have evolved over time but have remained ever constant. Four critical 'case studies' will also be employed here for deep, thoughtful exploration on a particular eugenic issue. The goal of the review, as it is with our course, is not to paint humanity with a single evil brush. Instead, our ambition is to introduce our students/readers to the potential for harm through the misapplication and misappropriation of science and scientific technology, and to provide them with the tools to ask the appropriate questions of their scientists, physicians, and politicians.
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Affiliation(s)
- Mannie Liscum
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
| | - Michael L Garcia
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, USA
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Shu T, Hunter H, Zhou Z, Sun Y, Cheng X, Ma J, Su L, Zhang X, Serpe MJ. Portable point-of-care diagnostic devices: an updated review. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5418-5435. [PMID: 34787609 DOI: 10.1039/d1ay01643a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The global pandemic caused by the SARS-CoV-2 (COVID) virus indiscriminately impacted people worldwide with unquantifiable and severe impacts on all aspects of our lives, regardless of socioeconomic status. The pandemic brought to light the very real possibility of pathogens changing and shaping the way we live, and our lack of preparedness to deal with viral/bacterial outbreaks. Importantly, the quick detection of pathogens can help prevent and control the spread of disease, making the importance of diagnostic techniques undeniable. Point-of-care diagnostics started as a supplement to standard lab-based diagnostics, and are gradually becoming mainstream. Because of this, and their importance in detecting pathogens (especially in the developing world), their development has accelerated at an unprecedented rate. In this review, we highlight some important and recent examples of point-of-care diagnostics for detecting nucleic acids, proteins, bacteria, and other biomarkers, with the intent of making apparent their positive impact on society and human health.
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Affiliation(s)
- Tong Shu
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Haley Hunter
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2.
| | - Ziping Zhou
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Yanping Sun
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Xiaojun Cheng
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Jianxin Ma
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
- Beijing Key Laboratory for Bioengineering and Sensing Technology, Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, P. R. China
| | - Lei Su
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Xueji Zhang
- Research Center for Biosensor and Nanotheranostic, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen 518060, P. R. China
| | - Michael J Serpe
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada, T6G 2G2.
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Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2021; 2021:8008731. [PMID: 34812271 PMCID: PMC8605909 DOI: 10.1155/2021/8008731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/24/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022]
Abstract
The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.
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Russell A, Wang W. The Rapidly Expanding Nexus of Immunoglobulin G N-Glycomics, Suboptimal Health Status, and Precision Medicine. EXPERIENTIA. SUPPLEMENTUM 2021; 112:545-564. [PMID: 34687022 DOI: 10.1007/978-3-030-76912-3_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Immunoglobulin G is a prevalent glycoprotein, whose downstream immune responses are partially mediated by the N-glycans within the fragment crystallisable domain. Collectively termed the N-glycome, it is considered a complex intermediate phenotype: an amalgamation of genetic predisposition, environmental exposure, and health behaviours over the life-course. Thus, the immunoglobulin G N-glycome may provide an indication of health status on the spectrum from health to disease and infirmary. Although variability exists within and between populations, composition of the immunoglobulin G N-glycome remains stable over short periods of time. This underscores the potential of harnessing the immunoglobulin G N-glycome as an ideal tool for preclinical disease risk prediction, stratification, and prognosis through the development of precise dynamic biomarkers.
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Affiliation(s)
- Alyce Russell
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Wei Wang
- Centre for Precision Health, Edith Cowan University, Joondalup, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.
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Review of the genomic landscape of common pediatric CNS tumors and how data sharing will continue to shape this landscape in the future. Mol Biol Rep 2021; 48:7537-7544. [PMID: 34643931 DOI: 10.1007/s11033-021-06811-1] [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: 07/20/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Over the past decade we have witnessed a rapid increase in our understanding of the molecular characteristics of pediatric central nervous system (CNS) tumors. Studies that utilize genomic sequencing have revealed a heterogeneous group of genetic drivers in pediatric CNS tumors including point mutations, gene fusions, and copy number alterations. This manuscript provides an overview of somatic genomic alterations in the most common pediatric CNS tumors including low grade gliomas, high grade gliomas, medulloblastomas, and ependymomas. Additionally, we will discuss the need and opportunity for genomic and clinical data sharing through the children's brain tumor network and other international initiatives.
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Liang C, Qiao S, Olatosi B, Lyu T, Li X. Emergence and evolution of big data science in HIV research: Bibliometric analysis of federally sponsored studies 2000-2019. Int J Med Inform 2021; 154:104558. [PMID: 34481301 DOI: 10.1016/j.ijmedinf.2021.104558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/14/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The rapid growth of inherently complex and heterogeneous data in HIV/AIDS research underscores the importance of Big Data Science. Recently, there have been increasing uptakes of Big Data techniques in basic, clinical, and public health fields of HIV/AIDS research. However, no studies have systematically elaborated on the evolving applications of Big Data in HIV/AIDS research. We sought to explore the emergence and evolution of Big Data Science in HIV/AIDS-related publications that were funded by the US federal agencies. METHODS We identified HIV/AIDS and Big Data related publications that were funded by seven federal agencies from 2000 to 2019 by integrating data from National Institutes of Health (NIH) ExPORTER, MEDLINE, and MeSH. Building on bibliometrics and Natural Language Processing (NLP) methods, we constructed co-occurrence networks using bibliographic metadata (e.g., countries, institutes, MeSH terms, and keywords) of the retrieved publications. We then detected clusters among the networks as well as the temporal dynamics of clusters, followed by expert evaluation and clinical implications. RESULTS We harnessed nearly 600 thousand publications related to HIV/AIDS, of which 19,528 publications relating to Big Data were included in bibliometric analysis. Results showed that (1) the number of Big Data publications has been increasing since 2000, (2) US institutes have been in close collaborations with China, Canada, and Germany, (3) some institutes (e.g., University of California system, MD Anderson Cancer Center, and Harvard Medical School) are among the most productive institutes and started using Big Data in HIV/AIDS research early, (4) Big Data research was not active in public health disciplines until 2015, (5) research topics such as genomics, HIV comorbidities, population-based studies, Electronic Health Records (EHR), social media, precision medicine, and methodologies such as machine learning, Deep Learning, radiomics, and data mining emerge quickly in recent years. CONCLUSIONS We identified a rapid growth in the cross-disciplinary research of HIV/AIDS and Big Data over the past two decades. Our findings demonstrated patterns and trends of prevailing research topics and Big Data applications in HIV/AIDS research and suggested a number of fast-evolving areas of Big Data Science in HIV/AIDS research including secondary analysis of EHR, machine learning, Deep Learning, predictive analysis, and NLP.
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Affiliation(s)
- Chen Liang
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
| | - Shan Qiao
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Bankole Olatosi
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Tianchu Lyu
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Xiaoming Li
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
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Rasmussen SA, Pomputius A, Amberger JS, Hamosh A. Viewing Victor McKusick's legacy through the lens of his bibliography. Am J Med Genet A 2021; 185:3212-3223. [PMID: 34159717 DOI: 10.1002/ajmg.a.62394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/13/2021] [Accepted: 05/22/2021] [Indexed: 11/09/2022]
Abstract
Victor McKusick's contributions to the field of medical genetics are legendary and include his contributions as a mentor, as creator of Mendelian Inheritance in Man (now Online Mendelian Inheritance in Man [OMIM®]), and as a leader in the field of medical genetics. McKusick's full bibliography includes 772 publications. Here we review the 453 papers authored by McKusick and indexed in PubMed, from his earliest paper published in the New England Journal of Medicine in 1949 to his last paper published in American Journal of Medical Genetics Part A in 2008. This review of his bibliography chronicles McKusick's evolution from an internist and cardiologist with an interest in genetics to an esteemed leader in the growing field of medical genetics. Review of his bibliography also provides a historical perspective of the development of the discipline of medical genetics. This field came into its own during his lifetime, transitioning from the study of interesting cases and families used to codify basic medical genetics principles to an accredited medical specialty that is expected to transform healthcare. Along the way, he helped to unite the fields of medical and human genetics to focus on mapping the human genome, culminating in completion of the Human Genome Project. This review confirms the critical role played by Victor McKusick as the founding father of medical genetics.
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Affiliation(s)
- Sonja A Rasmussen
- Department of Pediatrics, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Obstetrics and Gynecology, University of Florida College of Medicine, Gainesville, Florida, USA.,Department of Epidemiology, University of Florida, College of Public Health and Health Professions and College of Medicine, Gainesville, Florida, USA
| | - Ariel Pomputius
- Health Science Center Libraries, University of Florida, Gainesville, Florida, USA
| | - Joanna S Amberger
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
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Juengst ET. Anticipating the ethical, legal, and social implications of human genome research: An ongoing experiment. Am J Med Genet A 2021; 185:3369-3376. [PMID: 34155808 DOI: 10.1002/ajmg.a.62405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/05/2021] [Indexed: 11/11/2022]
Abstract
Dr. Victor McKusick was a founding member of the joint NIH-DOE working group that designed the federal effort to address the ethical, legal, and social implications of the US Human Genome Project in 1989. A key feature of this effort was its commitment to anticipating genomics-driven questions before they became urgent practical dilemmas, by complementing the scientific effort to map and sequence the human genome with projects by a wide range of social scientists, humanities scholars, legal experts, and public educators designed to equip society with the foresight required to optimize the public welfare benefits of new genomic information. This article describes the origins of that experiment and the model of anticipatory science policy that it produced, as one piece of Dr. McKusick's extraordinary intellectual legacy.
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Affiliation(s)
- Eric T Juengst
- UNC Center for Bioethics, Department of Social Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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Massaiu I, Songia P, Chiesa M, Valerio V, Moschetta D, Alfieri V, Myasoedova VA, Schmid M, Cassetta L, Colombo GI, D’Alessandra Y, Poggio P. Evaluation of Oxford Nanopore MinION RNA-Seq Performance for Human Primary Cells. Int J Mol Sci 2021; 22:ijms22126317. [PMID: 34204756 PMCID: PMC8231517 DOI: 10.3390/ijms22126317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Transcript sequencing is a crucial tool for gaining a deep understanding of biological processes in diagnostic and clinical medicine. Given their potential to study novel complex eukaryotic transcriptomes, long-read sequencing technologies are able to overcome some limitations of short-read RNA-Seq approaches. Oxford Nanopore Technologies (ONT) offers the ability to generate long-read sequencing data in real time via portable protein nanopore USB devices. This work aimed to provide the user with the number of reads that should be sequenced, through the ONT MinION platform, to reach the desired accuracy level for a human cell RNA study. We sequenced three cDNA libraries prepared from poly-adenosine RNA of human primary cardiac fibroblasts. Since the runs were comparable, they were combined in a total dataset of 48 million reads. Synthetic datasets with different sizes were generated starting from the total and analyzed in terms of the number of identified genes and their expression levels. As expected, an improved sensitivity was obtained, increasing the sequencing depth, particularly for the non-coding genes. The reliability of expression levels was assayed by (i) comparison with PCR quantifications of selected genes and (ii) by the implementation of a user-friendly multiplexing method in a single run.
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Affiliation(s)
- Ilaria Massaiu
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Paola Songia
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Mattia Chiesa
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Vincenza Valerio
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
- Dipartimento di Medicina Clinica e Chirurgia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Donato Moschetta
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, 20133 Milano, Italy
| | - Valentina Alfieri
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Veronika A. Myasoedova
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Michael Schmid
- Genexa AG, Dienerstrasse 7, CH-8004 Zürich, Switzerland;
| | - Luca Cassetta
- The Queen’s Medical Research Council Centre for Reproductive Health, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Gualtiero I. Colombo
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Yuri D’Alessandra
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
| | - Paolo Poggio
- Centro Cardiologico Monzino IRCCS, 20131 Milan, Italy; (I.M.); (P.S.); (M.C.); (V.V.); (D.M.); (V.A.); (V.A.M.); (G.I.C.); (Y.D.)
- Correspondence:
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Dutta K, Das R, Medeiros J, Kanjilal P, Thayumanavan S. Charge-Conversion Strategies for Nucleic Acid Delivery. ADVANCED FUNCTIONAL MATERIALS 2021; 31:2011103. [PMID: 35832306 PMCID: PMC9275120 DOI: 10.1002/adfm.202011103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Indexed: 05/05/2023]
Abstract
Nucleic acids are now considered as one of the most potent therapeutic modalities, as their roles go beyond storing genetic information and chemical energy or as signal transducer. Attenuation or expression of desired genes through nucleic acids have profound implications in gene therapy, gene editing and even in vaccine development for immunomodulation. Although nucleic acid therapeutics bring in overwhelming possibilities towards the development of molecular medicines, there are significant loopholes in designing and effective translation of these drugs into the clinic. One of the major pitfalls lies in the traditional design concepts for nucleic acid drug carriers, viz. cationic charge induced cytotoxicity in delivery pathway. Targeting this bottleneck, several pioneering research efforts have been devoted to design innovative carriers through charge-conversion approaches, whereby built-in functionalities convert from cationic to neutral or anionic, or even from anionic to cationic enabling the carrier to overcome several critical barriers for therapeutics delivery, such as serum deactivation, instability in circulation, low transfection and poor endosomal escape. This review will critically analyze various molecular designs of charge-converting nanocarriers in a classified approach for the successful delivery of nucleic acids. Accompanied by the narrative on recent clinical nucleic acid candidates, the review concludes with a discussion on the pitfalls and scope of these interesting approaches.
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Affiliation(s)
- Kingshuk Dutta
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Corteva Agriscience, 9330 Zionsville Road, Indianapolis 46268, United States
| | - Ritam Das
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Jewel Medeiros
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Pintu Kanjilal
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department of Biomedical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, United States
- The Center for Bioactive Delivery- Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, United States
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Corson VL, Bernhardt BA. The evolution of genetic counseling at Johns Hopkins Hospital and beyond. Am J Med Genet A 2021; 185:3230-3235. [PMID: 34061451 DOI: 10.1002/ajmg.a.62374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 02/03/2023]
Abstract
In celebration of the 100th birthday of Dr. Victor A. McKusick, we look back at the history of genetic counseling at Johns Hopkins Hospital and at some milestones for the profession. With the first students graduating from the Human Genetics program at Sarah Lawrence College in 1971, the genetic counseling profession is celebrating its 50th anniversary this year. The profession has seen growth in numbers and scope of practice, the evolution of a national society, the advent of certification and accreditation, the proliferation of graduate programs, the pursuit of state licensure, and collaboration with fellow genetics professionals. Many of the early jobs were at academic centers, such as Johns Hopkins Hospital, while today counselors are employed in a multitude of settings and engaged in a variety of roles.
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Affiliation(s)
- Virginia L Corson
- Department of Gynecology and Obstetrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Barbara A Bernhardt
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Gene expression regulates metabolite homeostasis during the Crabtree effect: Implications for the adaptation and evolution of Metabolism. Proc Natl Acad Sci U S A 2021; 118:2014013118. [PMID: 33372135 DOI: 10.1073/pnas.2014013118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A key issue in both molecular and evolutionary biology has been to define the roles of genes and phenotypes in the adaptation of organisms to environmental changes. The dominant view has been that an organism's metabolic adaptations are driven by gene expression and that gene mutations, independent of the starting phenotype, are responsible for the evolution of new metabolic phenotypes. We propose an alternate hypothesis, in which the phenotype and genotype together determine metabolic adaptation both in the lifetime of the organism and in the evolutionary selection of adaptive metabolic traits. We tested this hypothesis by flux-balance and metabolic-control analysis of the relative roles of the starting phenotype and gene expression in regulating the metabolic adaptations during the Crabtree effect in yeast, when they are switched from a low- to high-glucose environment. Critical for successful short-term adaptation was the ability of the glycogen/trehalose shunt to balance the glycolytic pathway. The role of later gene expression of new isoforms of glycolytic enzymes, rather than flux control, was to provide additional homeostatic mechanisms allowing an increase in the amount and efficiency of adenosine triphosphate and product formation while maintaining glycolytic balance. We further showed that homeostatic mechanisms, by allowing increased phenotypic plasticity, could have played an important role in guiding the evolution of the Crabtree effect. Although our findings are specific to Crabtree yeast, they are likely to be broadly found because of the well-recognized similarities in glucose metabolism across kingdoms and phyla from yeast to humans.
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Mahmood U, Bukhari SA, Ali M, Ahmed ZM, Riazuddin S. Identification of Hearing Loss-Associated Variants of PTPRQ, MYO15A, and SERPINB6 in Pakistani Families. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5584788. [PMID: 33997018 PMCID: PMC8080868 DOI: 10.1155/2021/5584788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/12/2021] [Accepted: 03/30/2021] [Indexed: 12/30/2022]
Abstract
The inner ear is an essential part of a well-developed and well-coordinated hearing system. However, hearing loss can make communication and interaction more difficult. Inherited hearing loss (HL) can occur from pathogenic genetic variants that negatively alter the intricate inner ear sensory mechanism. Recessively inherited forms of HL are highly heterogeneous and account for a majority of prelingual deafness. The current study is designed to investigate genetic causes of HL in three consanguineous Pakistani families. After IRB approval, the clinical history and pure tone audiometric data was obtained for the clinical diagnosis of HL segregating in these three Pakistani families. We performed whole exome sequencing (WES) followed by Sanger sequencing in order to identify and validate the HL-associated pathogenic variants, respectively. The 3-D molecular modeling and the Ramachandran analysis of the identified missense variants were compiled to evaluate the impact of the variants on the encoded proteins. Clinical evaluation revealed prelingual severe to profound sensorineural HL segregating among the affected individuals in all three families. Genetic analysis revealed segregation of several novel variants associated with HL, including a canonical splice-site variant (c.55-2A>G) of PTPRQ in family GCFHL-01, a missense variant [c.1079G>A; p.(Arg360Gln)] of SERPINB6 in family LUHL-01, and an insertion variant (c.10208-10211insCCACCAGGCCCGTGCCTC) within MYO15A in family LUHL-011. All the identified variants had very low frequencies in the control databases. The molecular modeling of p.Arg360Gln missense variant also predicted impaired folding of SERPINB6 protein. This study reports the identification of novel disease-causing variants in three known deafness genes and further highlights the genetic heterogeneity of HL in Pakistani population.
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Affiliation(s)
- Umair Mahmood
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Shazia A. Bukhari
- Department of Biochemistry, Government College University, Faisalabad 38000, Pakistan
| | - Muhammad Ali
- Department of Animal Sciences, Quaid Azam University, Islamabad 46000, Pakistan
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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Zhang R, Wang M, Wang M, Zhang L, Ding Y, Tang Z, Fu Z, Fan H, Zhang W, Wang J. Vitamin D Level and Vitamin D Receptor Genetic Variation Were Involved in the Risk of Non-Alcoholic Fatty Liver Disease: A Case-Control Study. Front Endocrinol (Lausanne) 2021; 12:648844. [PMID: 34421816 PMCID: PMC8377425 DOI: 10.3389/fendo.2021.648844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND It has been demonstrated that vitamin D receptor (VDR), a key gene in the metabolism of vitamin D (VD), may affect the development of Non-alcoholic fatty liver disease (NAFLD) by regulating VD level and its biological effects. OBJECTIVES To investigate the effects of serum VD level, VDR variation, and a combination of VDR SNP and environmental behavior factor on the risk of NAFLD. METHODS A total of 3023 subjects from a community in Nanjing were enrolled, including 1120 NAFLD cases and 1903 controls. Serum 25(OH)D3 levels were measured and eight single nucleotide polymorphisms (SNPs) in VDR gene were genotyped. RESULTS Logistic regression analyses indicated that VD sufficiency and VD insufficiency were significantly associated with a low risk of NAFLD (all P<0.05; all Ptrend<0.05, in a locus-dosage manner). After adjusting for gender and age, VDR rs2228570-A and rs11168287-A alleles were all reduced the risk of NAFLD (all PFDR=0.136, in dominant model; Ptrend =0.039, combined effects in a locus-dosage manner). The protective effects of two favorable alleles were more evident among subjects ≤40 years, non-hypertension, non-hyperglycemia and non-low high density lipoprotein-cholesterol (all P<0.05). The area under the receiver operating curve of the combination of VDR SNP and exercise time for assessing NAFLD risk was slightly higher than that of only including exercise time or neither (all P<0.05). CONCLUSION High serum VD levels and VDR variants (rs2228570-A and rs11168287-A) might contribute to a low risk of NAFLD in Chinese Han population. The inclusion of VDR SNP and exercise time could improve the efficiency in assessment of NAFLD risk, which might provide a novel perspective for early screening and preventing NAFLD.
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Affiliation(s)
- Ru Zhang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Minxian Wang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Min Wang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Liuxin Zhang
- Department of Nursing, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China
| | - Yajie Ding
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Zongzhe Tang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
| | - Zuqiang Fu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haozhi Fan
- Department of Information, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China
| | - Jie Wang
- Department of Fundamental and Community Nursing, School of Nursing, Nanjing Medical University, Nanjing, China
- *Correspondence: Jie Wang,
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Dillman A, Zoratti MJ, Park JJH, Hsu G, Dron L, Smith G, Harari O, Rayner CR, Zannat NE, Gupta A, Mackay E, Arora P, Lee Z, Mills EJ. The Landscape of Emerging Randomized Clinical Trial Evidence for COVID-19 Disease Stages: A Systematic Review of Global Trial Registries. Infect Drug Resist 2020; 13:4577-4587. [PMID: 33376364 PMCID: PMC7764888 DOI: 10.2147/idr.s288399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose A multitude of randomized controlled trials (RCTs) have emerged in response to the novel coronavirus disease (COVID-19) pandemic. Understanding the distribution of trials among various settings is important to guide future research priorities and efforts. The purpose of this review was to describe the emerging evidence base of COVID-19 RCTs by stages of disease progression, from pre-exposure to hospitalization. Methods We collated trial data across international registries: ClinicalTrials.gov; International Standard Randomised Controlled Trial Number Registry; Chinese Clinical Trial Registry; Clinical Research Information Service; EU Clinical Trials Register; Iranian Registry of Clinical Trials; Japan Primary Registries Network; German Clinical Trials Register (up to 7 October 2020). Active COVID-19 RCTs in international registries were eligible for inclusion. We extracted trial status, intervention(s), control, sample size, and clinical context to generate descriptive frequencies, network diagram illustrations, and statistical analyses including odds ratios and the Mann–Whitney U-test. Results Our search identified 11503 clinical trials registered for COVID-19 and identified 2388 RCTs. After excluding 45 suspended RCTs and 480 trials with unclear or unreported disease stages, 1863 active RCTs were included and categorized into four broad disease stages: pre-exposure (n=107); post-exposure (n=208); outpatient treatment (n=266); hospitalization, including the intensive care unit (n=1376). Across all disease stages, most trials had two arms (n=1500/1863, 80.52%), most often included (hydroxy)chloroquine (n=271/1863, 14.55%) and were US-based (n=408/1863, 21.90%). US-based trials had lower odds of including (hydroxy)chloroquine than trials in other countries (OR: 0.63, 95% CI: 0.45–0.90) and similar odds of having two arms compared to other geographic regions (OR: 1.05, 95% CI: 0.80–1.38). Conclusion There is a marked difference in the number of trials across settings, with limited studies on non-hospitalized persons. Focus on pre- and post-exposure, and outpatients, is worthwhile as a means of reducing infections and lessening the health, social, and economic burden of COVID-19.
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Affiliation(s)
- Alison Dillman
- School of Public Health, Faculty of Medicine, Imperial College London, London, England
| | - Michael J Zoratti
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Jay J H Park
- Department of Experimental Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Grace Hsu
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Louis Dron
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Gerald Smith
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Ofir Harari
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Craig R Rayner
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
| | - Noor-E Zannat
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Alind Gupta
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - Eric Mackay
- Department of Statistical Sciences, University of Toronto, Toronto, Canada
| | - Paul Arora
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Zelyn Lee
- Department of Physiology & Department of Neuroscience, University of Toronto, Toronto, Canada
| | - Edward J Mills
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
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Stone DL, Beck DB, Manthiram K, Park YH, Chae JJ, Remmers E, Kastner DL. The systemic autoinflammatory diseases: Coming of age with the human genome. J Allergy Clin Immunol 2020; 146:997-1001. [PMID: 32987090 PMCID: PMC11008603 DOI: 10.1016/j.jaci.2020.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022]
Affiliation(s)
| | - David B Beck
- National Human Genome Research Institute, Bethesda, Md
| | | | | | - Jae Jin Chae
- National Human Genome Research Institute, Bethesda, Md
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Abstract
Genomic testing is increasingly common in the consumer marketplace. The role of nurses in educating and counseling patients requires them to be prepared to respond to questions about the results of direct-to-consumer genomic testing. This article describes one individual's reflections upon undergoing this testing, the challenges of interpreting the results, and nursing considerations for integrating these results into clinical practice.
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Abstract
This editorial provides an overview of secondary data analysis in nursing science and its application in a range of contemporary research. The practice of undertaking secondary analysis of qualitative and quantitative data is also discussed, along with the benefits, risks and limitations of this analytical method.
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Affiliation(s)
- Siobhan O'Connor
- School of Health in Social Science, The University of Edinburgh, Edinburgh, UK
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Burman A, Garcia-Milian R, Whirledge S. Gene X environment: the cellular environment governs the transcriptional response to environmental chemicals. Hum Genomics 2020; 14:19. [PMID: 32448403 PMCID: PMC7247264 DOI: 10.1186/s40246-020-00269-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 05/13/2020] [Indexed: 12/31/2022] Open
Abstract
Background An individual’s response to environmental exposures varies depending on their genotype, which has been termed the gene-environment interaction. The phenotype of cell exposed can also be a key determinant in the response to physiological cues, indicating that a cell-gene-environment interaction may exist. We investigated whether the cellular environment could alter the transcriptional response to environmental chemicals. Publicly available gene expression array data permitted a targeted comparison of the transcriptional response to a unique subclass of environmental chemicals that alter the activity of the estrogen receptor, xenoestrogens. Results Thirty xenoestrogens were included in the analysis, for which 426 human gene expression studies were identified. Comparisons were made for studies that met the predefined criteria for exposure length, concentration, and experimental replicates. The cellular response to the phytoestrogen genistein resulted in remarkably unique transcriptional profiles in breast, liver, and uterine cell-types. Analysis of gene regulatory networks and molecular pathways revealed that the cellular context mediated the activation or repression of functions important to cellular organization and survival, including opposing effects by genistein in breast vs. liver and uterine cell-types. When controlling for cell-type, xenoestrogens regulate unique gene networks and biological functions, despite belonging to the same class of environmental chemicals. Interestingly, the genetic sex of the cell-type also strongly influenced the transcriptional response to xenoestrogens in the liver, with only 22% of the genes significantly regulated by genistein common between male and female cells. Conclusions Our results demonstrate that the transcriptional response to environmental chemicals depends on a variety of factors, including the cellular context, the genetic sex of a cell, and the individual chemical. These findings highlight the importance of evaluating the impact of exposure across cell-types, as the effect is responsive to the cellular environment. These comparative genetic results support the concept of a cell-gene-environment interaction.
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Affiliation(s)
- Andreanna Burman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, 310 Cedar St, PO Box 208063, New Haven, CT, 06520, USA
| | - Rolando Garcia-Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Shannon Whirledge
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, 310 Cedar St, PO Box 208063, New Haven, CT, 06520, USA.
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Namerow LB, Walker SA, Loftus M, Bishop JR, Ruaño G, Malik S. Pharmacogenomics: an Update for Child and Adolescent Psychiatry. Curr Psychiatry Rep 2020; 22:26. [PMID: 32377970 DOI: 10.1007/s11920-020-01145-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PURPOSE OF REVIEW This paper aims to acquaint child and adolescent psychiatrists with the field of pharmacogenomics (PGX) and review the most up-to-date evidence-based practices to guide the application of this field in clinical care. RECENT FINDINGS Despite much research being done in this area, the field of PGX continues to yield controversial findings. In the adult world, studies have focused on the impact of combinatorial gene panels that guide medication selection by providing reports that estimate the impact of multiple pharmacodynamic and pharmacokinetic genes, but to date, these have not been directly examined in younger patient populations. Pharmacokinetic genes, CYP2D6 and CYP2C19, and hypersensitivity genes, HLA-A and HLA-B, have the strongest evidence base for application to pharmacotherapy in children. Although the field is evolving, and the evidence is mixed, there may be a role for PGX testing in children to help guide dosing and monitoring strategies. However, evidence-based medicine, rather than PGX testing, continues to play the lead role in guiding medication selection in pediatric psychopharmacology.
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Affiliation(s)
- Lisa B Namerow
- Associate Professor of Pediatrics and Psychiatry, University of Connecticut School of Medicine, Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, 200 Retreat Ave, Hartford, CT, 06019, USA.
| | - Sophia A Walker
- Department of Psychiatry, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06032, USA
| | - Mirela Loftus
- Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, 200 Retreat Ave, Hartford, CT, 06019, USA
| | - Jeffrey R Bishop
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Department of Psychiatry, University of Minnesota Medical School, 508 Harvard St SE, Minneapolis, MN, 55455, USA
| | - Gualberto Ruaño
- Department of Psychiatry, University of Connecticut School of Medicine, 263 Farmington Ave, Farmington, CT, 06032, USA.,Institute of Living at Hartford Hospital, Genomas Laboratory of Personalized Health, 67 Jefferson Street, Hartford, CT, 06106, USA
| | - Salma Malik
- Division of Child and Adolescent Psychiatry, Institute of Living/Hartford Hospital, 200 Retreat Ave, Hartford, CT, 06019, USA
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McClaren BJ, Crellin E, Janinski M, Nisselle AE, Ng L, Metcalfe SA, Gaff CL. Preparing Medical Specialists for Genomic Medicine: Continuing Education Should Include Opportunities for Experiential Learning. Front Genet 2020; 11:151. [PMID: 32194628 PMCID: PMC7063730 DOI: 10.3389/fgene.2020.00151] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 02/10/2020] [Indexed: 12/30/2022] Open
Abstract
With the demand for genomic investigations increasing, medical specialists will need to, and are beginning to, practice genomic medicine. The need for medical specialists from diverse specialties to be ready to appropriately practice genomic medicine is widely recognised, but existing studies focus on single specialties or clinical settings. We explored continuing education needs in genomic medicine of a wide range of medical specialists (excluding genetic specialists) from across Australia. Interviews were conducted with 86 medical specialists in Australia from diverse medical specialties. Inductive content analysis categorized participants by career stage and genomics experience. Themes related to education needs were identified through constant comparison and discussion between authors of emerging concepts. Our findings show that participants believe that experiential learning in genomic medicine is necessary to develop the confidence and skills needed for clinical care. The main themes reported are: tailoring of education to the specialty and the individual; peer interactions contextualizes knowledge; experience will aid in developing confidence and skills. In fact, avenues of gaining experience may result in increased engagement with continuing education in genomic medicine as specialists are exposed to relevant applications in their clinical practice. Participants affirmed the need for continuing education in genomic medicine but identified that it would need to be tailored to the specialty and the individual: one size does not fit all, so a multifaceted approached is needed. Participants infrequently attended formal continuing education in genomic medicine. More commonly, they reported experiential learning by observation, case-review or interacting with a "genomics champion" in their specialty, which contextualized their knowledge. Medical specialists anticipate that genomic medicine will become part of their practice which could lessen demand on the specialist genetic workforce. They expect to look to experts within their own medical specialty who have gained genomics expertise for specific and contextualized support as they develop the skills and confidence to practice genomic medicine. These findings highlight the need to include opportunities for experiential learning in continuing education. Concepts identified in these interviews can be tested with a larger sample of medical specialists to ascertain representativeness.
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Affiliation(s)
- Belinda J. McClaren
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Erin Crellin
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Monika Janinski
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Amy E. Nisselle
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Larissa Ng
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Sylvia A. Metcalfe
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
| | - Clara L. Gaff
- Australian Genomics Health Alliance, Melbourne, VIC, Australia
- Genomics in Society, Murdoch Children’s Research Institute, Melbourne, VIC, Australia
- Department of Paediatrics, The University of Melbourne, VIC, Australia
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The Current Status of Genes and Genetic Testing in Emergency Medicine: A Narrative Review. ADVANCED JOURNAL OF EMERGENCY MEDICINE 2020; 4:e10. [PMID: 31938779 PMCID: PMC6955026 DOI: 10.22114/ajem.v0i0.216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Context: An emergency is any medical problem that could cause death or permanent injury if not treated quickly. In some occasions, the kind of urgent intervention depends on patient’s exact genetic background. Unfortunately, the importance of genes in medical emergencies has been forgotten in recent decades. Evidence acquisition: In order to find relevant articles, we searched two databases of Pubmed and Embase. The exact words of “genes”, “genetics”, “epigenetics”, “DNA”, and “emergency” were used alone and in combination. All studies like randomized clinical trials (RCT), case/controls, case series, case reports, and review articles were studied to find the related data. No time limitation was considered for the studies. Results: Several aspects of genetic testing are newly considered in emergency departments including cell-free DNA (cfDNA) for disease diagnosis, pharmacogenetics for decreasing the adverse drug effects, and personalized medicine for exact emergency interventions in diseases like Vascular Ehlers-Danlos syndrome (vEDS). Data from genetic testing and genome wide association studies have yielded promising results to make medical emergency interventions more beneficial in the near future. Conclusion: Taking everything into consideration, several advanced genetic and epigenetic alteration technologies can change emergency medicine for the better. Personalized genetic data of patients can turn emergency medicine to personalized medicine.
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Singh AV, Ansari MHD, Laux P, Luch A. Micro-nanorobots: important considerations when developing novel drug delivery platforms. Expert Opin Drug Deliv 2019; 16:1259-1275. [DOI: 10.1080/17425247.2019.1676228] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ajay Vikram Singh
- Physical Intelligence Department, Max Planck Institute for Intelligent Systems, Stuttgart, Germany
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | | | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
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Sivasubbu S, Scaria V. Genomics of rare genetic diseases-experiences from India. Hum Genomics 2019; 14:52. [PMID: 31554517 PMCID: PMC6760067 DOI: 10.1186/s40246-019-0215-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Home to a culturally heterogeneous population, India is also a melting pot of genetic diversity. The population architecture characterized by multiple endogamous groups with specific marriage patterns, including the widely prevalent practice of consanguinity, not only makes the Indian population distinct from rest of the world but also provides a unique advantage and niche to understand genetic diseases. Centuries of genetic isolation of population groups have amplified the founder effects, contributing to high prevalence of recessive alleles, which translates into genetic diseases, including rare genetic diseases in India.Rare genetic diseases are becoming a public health concern in India because a large population size of close to a billion people would essentially translate to a huge disease burden for even the rarest of the rare diseases. Genomics-based approaches have been demonstrated to accelerate the diagnosis of rare genetic diseases and reduce the socio-economic burden. The Genomics for Understanding Rare Diseases: India Alliance Network (GUaRDIAN) stands for providing genomic solutions for rare diseases in India. The consortium aims to establish a unique collaborative framework in health care planning, implementation, and delivery in the specific area of rare genetic diseases. It is a nation-wide collaborative research initiative catering to rare diseases across multiple cohorts, with over 240 clinician/scientist collaborators across 70 major medical/research centers. Within the GUaRDIAN framework, clinicians refer rare disease patients, generate whole genome or exome datasets followed by computational analysis of the data for identifying the causal pathogenic variations. The outcomes of GUaRDIAN are being translated as community services through a suitable platform providing low-cost diagnostic assays in India. In addition to GUaRDIAN, several genomic investigations for diseased and healthy population are being undertaken in the country to solve the rare disease dilemma.In summary, rare diseases contribute to a significant disease burden in India. Genomics-based solutions can enable accelerated diagnosis and management of rare diseases. We discuss how a collaborative research initiative such as GUaRDIAN can provide a nation-wide framework to cater to the rare disease community of India.
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Affiliation(s)
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Delhi, 110025, India.
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Crellin E, McClaren B, Nisselle A, Best S, Gaff C, Metcalfe S. Preparing Medical Specialists to Practice Genomic Medicine: Education an Essential Part of a Broader Strategy. Front Genet 2019; 10:789. [PMID: 31572433 PMCID: PMC6749815 DOI: 10.3389/fgene.2019.00789] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/26/2019] [Indexed: 12/25/2022] Open
Abstract
Developing a competent workforce will be crucial to realizing the promise of genomic medicine. The preparedness of medical specialists without specific genetic qualifications to play a role in this workforce has long been questioned, prompting widespread calls for education across the spectrum of medical training. Adult learning theory indicates that for education to be effective, a perceived need to learn must first be established. Medical specialists have to perceive genomic medicine as relevant to their clinical practice. Here, we review what is currently known about medical specialists’ perceptions of genomics, compare these findings to those from the genetics era, and identify areas for future research. Previous studies reveal that medical specialists’ views on the clinical utility of genomic medicine are mixed and are often tempered by several concerns. Specialists generally perceive their confidence and understanding to be lacking; subsequently, they welcome additional educational support, although specific needs are rarely detailed. Similar findings from the genetics era suggest that these challenges are not necessarily new but on a different scale and relevant to more specialties as genomic applications expand. While existing strategies developed for genetic education and training may be suitable for genomic education and training, investigating the educational needs of a wider range of specialties is critically necessary to determine if tailored approaches are needed and, if so, to facilitate these. Other interventions are also required to address some of the additional challenges identified in this review, and we encourage readers to see education as part of a broader implementation strategy.
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Affiliation(s)
- Erin Crellin
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Belinda McClaren
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Amy Nisselle
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Stephanie Best
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Australian Institute of Health Innovation, Macquarie University, Sydney, NSW, Australia
| | - Clara Gaff
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
| | - Sylvia Metcalfe
- Australian Genomics Health Alliance, Melbourne, VIC, Australia.,Genomics in Society, Murdoch Children's Research Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia
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