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Harnessing Whole Genome Sequencing in Medical Mycology

PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically impo...

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Autor principal: Cuomo, Christina A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570814/
https://www.ncbi.nlm.nih.gov/pubmed/28904649
http://dx.doi.org/10.1007/s12281-017-0276-7
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author Cuomo, Christina A.
author_facet Cuomo, Christina A.
author_sort Cuomo, Christina A.
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description PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. RECENT FINDINGS: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. SUMMARY: Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.
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spelling pubmed-55708142017-09-11 Harnessing Whole Genome Sequencing in Medical Mycology Cuomo, Christina A. Curr Fungal Infect Rep Advances in Diagnosis of Invasive Fungal Infections (S Chen, Section Editor) PURPOSE OF REVIEW: Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. RECENT FINDINGS: Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. SUMMARY: Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples. Springer US 2017-06-09 2017 /pmc/articles/PMC5570814/ /pubmed/28904649 http://dx.doi.org/10.1007/s12281-017-0276-7 Text en © Springer Science+Business Media New York 2017
spellingShingle Advances in Diagnosis of Invasive Fungal Infections (S Chen, Section Editor)
Cuomo, Christina A.
Harnessing Whole Genome Sequencing in Medical Mycology
title Harnessing Whole Genome Sequencing in Medical Mycology
title_full Harnessing Whole Genome Sequencing in Medical Mycology
title_fullStr Harnessing Whole Genome Sequencing in Medical Mycology
title_full_unstemmed Harnessing Whole Genome Sequencing in Medical Mycology
title_short Harnessing Whole Genome Sequencing in Medical Mycology
title_sort harnessing whole genome sequencing in medical mycology
topic Advances in Diagnosis of Invasive Fungal Infections (S Chen, Section Editor)
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570814/
https://www.ncbi.nlm.nih.gov/pubmed/28904649
http://dx.doi.org/10.1007/s12281-017-0276-7
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