The structure of associations: Method insights from analyzing 28 clinical isolates of Cryptococcus neoformans

Nórida Vélez; Nelson Vega-Vela; Oliver Keatinge Clay; Claudia-Marcela Parra-Giraldo

doi:10.1093/mmy/myad024

The structure of associations: Method insights from analyzing 28 clinical isolates of Cryptococcus neoformans

Nórida Vélez
, Nelson Vega-Vela
, Oliver Keatinge Clay
, Claudia-Marcela Parra-Giraldo

Producción científica: Contribución a revista › Artículo de Investigación › revisión exhaustiva

Resumen

Los aislados clínicos de un patógeno fúngico procedentes de una única región o país suelen presentar clonalidad estructural o agrupación filogenética a nivel de secuencia o MLST; dicha estructura poblacional puede persistir también en muestras más amplias. En un esfuerzo por mejorar la comprensión causal de la patogénesis a nivel molecular, se han aplicado a los hongos métodos de cribado de asociación de todo el genoma diseñados inicialmente para otros reinos. El ejemplo de un conjunto de datos colombianos de 28 aislados clínicos de Cryptococcus neoformans VNI indica dónde puede ser necesario analizar de nuevas formas los resultados de los procesos estándar para extraer de forma eficiente hipótesis para experimentos a partir de datos fúngicos genotipo-fenotipo.

Idioma original	Inglés estadounidense
Publicación	Medical Mycology
Volumen	61
N.º	3
DOI	https://doi.org/10.1093/mmy/myad024
Estado	Publicada - mar. 2 2023

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Microbiología (médica)

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10.1093/mmy/myad024

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@article{ce96671fe46349ec80ae1d06e98a8595,

title = "The structure of associations: Method insights from analyzing 28 clinical isolates of Cryptococcus neoformans",

abstract = "Clinical isolates of a fungal pathogen from a single region or country often exhibit structural clonality or phylogenetic clustering at the sequence or MLST level; such population structure can persist also in larger samples. In efforts to improve causal understanding of pathogenesis at the molecular level, genome-wide association screening methods initially designed for other kingdoms have been applied to fungi. The example of a Colombian dataset of 28 clinical Cryptococcus neoformans VNI isolates indicates where the output from standard pipelines may need to be analyzed in new ways in order to efficiently extract hypotheses for experiments from fungal genotype-phenotype data.",

author = "N{\'o}rida V{\'e}lez and Nelson Vega-Vela and Clay, \{Oliver Keatinge\} and Claudia-Marcela Parra-Giraldo",

note = "{\textcopyright} The Author(s) 2023. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.",

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AU - Vélez, Nórida

AU - Vega-Vela, Nelson

AU - Clay, Oliver Keatinge

AU - Parra-Giraldo, Claudia-Marcela

N1 - © The Author(s) 2023. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology.

PY - 2023/3/2

Y1 - 2023/3/2

N2 - Clinical isolates of a fungal pathogen from a single region or country often exhibit structural clonality or phylogenetic clustering at the sequence or MLST level; such population structure can persist also in larger samples. In efforts to improve causal understanding of pathogenesis at the molecular level, genome-wide association screening methods initially designed for other kingdoms have been applied to fungi. The example of a Colombian dataset of 28 clinical Cryptococcus neoformans VNI isolates indicates where the output from standard pipelines may need to be analyzed in new ways in order to efficiently extract hypotheses for experiments from fungal genotype-phenotype data.

AB - Clinical isolates of a fungal pathogen from a single region or country often exhibit structural clonality or phylogenetic clustering at the sequence or MLST level; such population structure can persist also in larger samples. In efforts to improve causal understanding of pathogenesis at the molecular level, genome-wide association screening methods initially designed for other kingdoms have been applied to fungi. The example of a Colombian dataset of 28 clinical Cryptococcus neoformans VNI isolates indicates where the output from standard pipelines may need to be analyzed in new ways in order to efficiently extract hypotheses for experiments from fungal genotype-phenotype data.

U2 - 10.1093/mmy/myad024

DO - 10.1093/mmy/myad024

M3 - Research Article

C2 - 36882228

SN - 1369-3786

VL - 61

JO - Medical Mycology

JF - Medical Mycology

IS - 3

ER -

The structure of associations: Method insights from analyzing 28 clinical isolates of Cryptococcus neoformans

Resumen

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