-
Clinical Pharmacology and Therapeutics Jul 2021The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP2B6 gene. Genetic variation within the CYP2B6 gene... (Review)
Review
The Pharmacogene Variation Consortium (PharmVar) catalogs star (*) allele nomenclature for the polymorphic human CYP2B6 gene. Genetic variation within the CYP2B6 gene locus impacts the metabolism or bioactivation of clinically important drugs. Of particular importance are efficacy and safety concerns regarding: efavirenz, which is used for the treatment of HIV type-1 infection; methadone, a mainstay in the treatment of opioid use disorder and as an analgesic; ketamine, used as an antidepressant and analgesic; and bupropion, which is prescribed to treat depression and for smoking cessation. This GeneFocus provides a comprehensive overview and summary of CYP2B6 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
Topics: Alleles; Cytochrome P-450 CYP2B6; Genetic Variation; Haplotypes; Humans; Knowledge Bases; Pharmacogenetics
PubMed: 33448339
DOI: 10.1002/cpt.2166 -
Clinical Pharmacology and Therapeutics Sep 2021The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene... (Review)
Review
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C9 gene. Genetic variation within the CYP2C9 gene locus impacts the metabolism or bioactivation of many clinically important drugs, including nonsteroidal anti-inflammatory drugs, phenytoin, antidiabetic agents, and angiotensin receptor blockers. Variable CYP2C9 activity is of particular importance regarding efficacy and safety of warfarin and siponimod as indicated in their package inserts. This GeneFocus provides a comprehensive overview and summary of CYP2C9 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium.
Topics: Alleles; Cytochrome P-450 CYP2C9; Haplotypes; Humans; Knowledge Bases; Pharmaceutical Preparations; Pharmacogenetics; Polymorphism, Genetic
PubMed: 34109627
DOI: 10.1002/cpt.2333 -
Clinical Pharmacology and Therapeutics Feb 2021The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the... (Review)
Review
The Pharmacogene Variation Consortium (PharmVar) catalogues star (*) allele nomenclature for the polymorphic human CYP2C19 gene. CYP2C19 genetic variation impacts the metabolism of many drugs and has been associated with both efficacy and safety issues for several commonly prescribed medications. This GeneFocus provides a comprehensive overview and summary of CYP2C19 and describes how haplotype information catalogued by PharmVar is utilized by the Pharmacogenomics Knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC).
Topics: Alleles; Cytochrome P-450 CYP2C19; Genetic Variation; Genotype; Haplotypes; Humans; Knowledge Bases; Pharmacogenetics
PubMed: 32602114
DOI: 10.1002/cpt.1973 -
Bone Sep 2017Osteosarcoma is the predominant form of bone cancer, affecting mostly adolescents. Recent progress made in molecular genetic studies of osteosarcoma has changed our view... (Review)
Review
Osteosarcoma is the predominant form of bone cancer, affecting mostly adolescents. Recent progress made in molecular genetic studies of osteosarcoma has changed our view on the cause of the disease and ongoing therapeutic approaches for patients. As we draw closer to gaining more complete catalogs of candidate cancer driver genes in common forms of cancer, the landscape of somatic mutations in osteosarcoma is emerging from its first phase. In this review, we summarize recent whole genome and/or whole exome genomic studies, and then put these findings in the context of genetic hallmarks of somatic mutations and mutational processes in human osteosarcoma. One of the lessons learned here is that the extent of somatic mutations and complexity of the osteosarcoma genome are similar to that of common forms of adult cancer. Thus, a much higher number of samples than those currently obtained are needed to complete the catalog of driver mutations in human osteosarcoma. In parallel, genetic studies in other species have revealed candidate driver genes and their roles in the genesis of osteosarcoma. This review also summarizes newly identified drivers in genetically engineered mouse models (GEMMs) and discusses our understanding of the impact of nature and number of drivers on tumor latency, subtypes, and metastatic potentials of osteosarcoma. It is becoming apparent that a synergistic team composed of three drivers (one 'first driver' and two 'synergistic drivers') may be required to generate an animal model that recapitulates aggressive osteosarcoma with a short latency. Finally, new cancer therapies are urgently needed to improve survival rate and quality of life for osteosarcoma patients. Several vulnerabilities in osteosarcoma are illustrated in this review to exemplify the opportunities for next generation molecularly targeted therapies. However, much work remains in order to complete our understanding of the somatic mutation basis of osteosarcoma, to develop reliable animal models of human disease, and to apply this information to guide new therapeutic approaches for reducing morbidity and mortality of this rare disease.
Topics: Animals; Genomics; High-Throughput Nucleotide Sequencing; Humans; Inheritance Patterns; Models, Biological; Mutation; Osteosarcoma
PubMed: 27760307
DOI: 10.1016/j.bone.2016.10.017 -
The Plant Cell Jan 2020
Topics: Cataloging; Genomics; Lysine; Polyubiquitin; Proteomics; Ubiquitin; Ubiquitination
PubMed: 31748329
DOI: 10.1105/tpc.19.00898 -
Current Issues in Molecular Biology 2018Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with... (Review)
Review
Structural variation (SV) is a type of genetic variation identified through the comparison of genome structures which often have direct and significant associations with phenotypic variations. Building on the next generation sequencing (NGS) technologies, research on plant structural variations are gaining momentum and have revolutionized our view on the functional impact of the 'hidden' diversity that were largely understudied before. Herein, we first describe the current state of plant genomic SV research based on NGS and in particular focus on the biological insights gained from the large-scale identification of various types of plant SVs. Specific examples are chosen to demonstrate the genetic basis for phenotype diversity in model plant and major agricultural crops. Additionally, development of new genomic mapping technologies, including optical mapping and long read sequencing, as well as improved computational algorithms associated with these technologies have helped to pinpoint the exact nature and location of genomic SVs with much better resolution and precision. Future direction of plant research on SVs should focus on the population level to build a comprehensive catalog of SVs, leading to full assessment of their impact on biological diversity.
Topics: Algorithms; Arabidopsis; Chromosome Mapping; Crops, Agricultural; DNA Copy Number Variations; DNA Transposable Elements; Genome, Plant; Genomic Structural Variation; Genotype; High-Throughput Nucleotide Sequencing; Phenotype
PubMed: 28885182
DOI: 10.21775/cimb.027.181 -
Poultry Science Oct 2023The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are...
The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.
Topics: Animals; Metagenome; Gastrointestinal Microbiome; Quail; Chickens; Genes, Microbial
PubMed: 37499616
DOI: 10.1016/j.psj.2023.102931 -
Journal of Medical Internet Research Jan 2022Appointment management in the outpatient setting is important for health care organizations, as waits and delays lead to poor outcomes. Automated patient self-scheduling... (Review)
Review
BACKGROUND
Appointment management in the outpatient setting is important for health care organizations, as waits and delays lead to poor outcomes. Automated patient self-scheduling of outpatient appointments has demonstrable advantages in the form of patients' arrival rates, labor savings, patient satisfaction, and more. Despite evidence of the potential benefits of self-scheduling, the organizational uptake of self-scheduling in health care has been limited.
OBJECTIVE
The objective of this scoping review is to identify and to catalog existing evidence of the barriers to and facilitators of self-scheduling for health care organizations.
METHODS
A scoping review was conducted by searching 4 databases (PubMed, CINAHL, Business Source Ultimate, and Scopus) and systematically reviewing peer-reviewed studies. The Consolidated Framework for Implementation Research was used to catalog the studies.
RESULTS
In total, 30 full-text articles were included in this review. The results demonstrated that self-scheduling initiatives have increased over time, indicating the broadening appeal of self-scheduling. The body of literature regarding intervention characteristics is appreciable. Outer setting factors, including national policy, competition, and the response to patients' needs and technology access, have played an increasing role in influencing implementation over time. Self-scheduling, compared with using the telephone to schedule an appointment, was most often cited as a relative advantage. Scholarly pursuit lacked recommendations related to the framework's inner setting, characteristics of individuals, and processes as determinants of implementation. Future discoveries regarding these Consolidated Framework for Implementation Research domains may help detect, categorize, and appreciate organizational-level barriers to and facilitators of self-scheduling to advance knowledge regarding this solution.
CONCLUSIONS
This scoping review cataloged evidence of the existence, advantages, and intervention characteristics of patient self-scheduling. Automated self-scheduling may offer a solution to health care organizations striving to positively affect access. Gaps in knowledge regarding the uptake of self-scheduling by health care organizations were identified to inform future research.
Topics: Appointments and Schedules; Humans; Organizations; Patient Satisfaction; Text Messaging
PubMed: 35014968
DOI: 10.2196/28323 -
Bioinformation 2020Genomics has become indispensable for research in the last two decades. Completed and ongoing genome projects such as the UK Biobank, ICGC, TCGA and GenomeAsia100K have...
Genomics has become indispensable for research in the last two decades. Completed and ongoing genome projects such as the UK Biobank, ICGC, TCGA and GenomeAsia100K have helped to understand several life-threatening diseases like cancer. Such initiatives from different countries have offered genomics-based diagnostics along with glues for therapies towards personalized healthcare. The Indian Agencies has started initiatives to catalogue the genome sequences of 20,000 individuals. The Department of Biotechnology (DBT) along with other scientific agencies has plans to sequence 10,000 healthy individuals and 10,000 diseased individuals. The Council of Scientific and Industrial Research (CSIR) also developed the "IndiGen" genome project where genome sequences for 1008 individuals are made available in Phase I. This will enable the development of a genome catalogue to introduce novel genomics-based clinical applications in future healthcare plan.
PubMed: 32773988
DOI: 10.6026/97320630016297 -
Frontiers in Oncology 2023Lung cancer is the leading cause of cancer deaths among both men and women, representing approximately 25% of cancer fatalities each year. The treatment landscape for... (Review)
Review
Lung cancer is the leading cause of cancer deaths among both men and women, representing approximately 25% of cancer fatalities each year. The treatment landscape for non-small cell lung cancer (NSCLC) is rapidly evolving due to the progress made in biomarker-driven targeted therapies. While advancements in targeted treatments have improved survival rates for NSCLC patients with actionable biomarkers, long-term survival remains low, with an overall 5-year relative survival rate below 20%. Artificial intelligence/machine learning (AI/ML) algorithms have shown promise in biomarker discovery, yet NSCLC-specific studies capturing the clinical challenges targeted and emerging patterns identified using AI/ML approaches are lacking. Here, we employed a text-mining approach and identified 215 studies that reported potential biomarkers of NSCLC using AI/ML algorithms. We catalogued these studies with respect to BEST (Biomarkers, EndpointS, and other Tools) biomarker sub-types and summarized emerging patterns and trends in AI/ML-driven NSCLC biomarker discovery. We anticipate that our comprehensive review will contribute to the current understanding of AI/ML advances in NSCLC biomarker research and provide an important catalogue that may facilitate clinical adoption of AI/ML-derived biomarkers.
PubMed: 38148837
DOI: 10.3389/fonc.2023.1260374