Plasmodium copy number variation scan: gene copy numbers evaluation in haploid genomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-04-12

AUTHORS

Johann Beghain, Anne-Claire Langlois, Eric Legrand, Laura Grange, Nimol Khim, Benoit Witkowski, Valentine Duru, Laurence Ma, Christiane Bouchier, Didier Ménard, Richard E. Paul, Frédéric Ariey

ABSTRACT

BACKGROUND: In eukaryotic genomes, deletion or amplification rates have been estimated to be a thousand more frequent than single nucleotide variation. In Plasmodium falciparum, relatively few transcription factors have been identified, and the regulation of transcription is seemingly largely influenced by gene amplification events. Thus copy number variation (CNV) is a major mechanism enabling parasite genomes to adapt to new environmental changes. METHODS: Currently, the detection of CNVs is based on quantitative PCR (qPCR), which is significantly limited by the relatively small number of genes that can be analysed at any one time. Technological advances that facilitate whole-genome sequencing, such as next generation sequencing (NGS) enable deeper analyses of the genomic variation to be performed. Because the characteristics of Plasmodium CNVs need special consideration in algorithms and strategies for which classical CNV detection programs are not suited a dedicated algorithm to detect CNVs across the entire exome of P. falciparum was developed. This algorithm is based on a custom read depth strategy through NGS data and called PlasmoCNVScan. RESULTS: The analysis of CNV identification on three genes known to have different levels of amplification and which are located either in the nuclear, apicoplast or mitochondrial genomes is presented. The results are correlated with the qPCR experiments, usually used for identification of locus specific amplification/deletion. CONCLUSIONS: This tool will facilitate the study of P. falciparum genomic adaptation in response to ecological changes: drug pressure, decreased transmission, reduction of the parasite population size (transition to pre-elimination endemic area). More... »

PAGES

206

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12936-016-1258-x

DOI

http://dx.doi.org/10.1186/s12936-016-1258-x

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1007547312

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27066902


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85 mitochondrial genome
86 new environmental changes
87 next-generation sequencing
88 nucleotide variations
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92 parasite genome
93 parasite population size
94 population size
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97 qPCR experiments
98 quantitative PCR
99 rate
100 read depth strategy
101 reduction
102 regulation
103 regulation of transcription
104 response
105 results
106 sequencing
107 single nucleotide variations
108 size
109 small number
110 special consideration
111 specific amplification/deletion
112 strategies
113 study
114 technological advances
115 time
116 tool
117 transcription
118 transcription factors
119 transmission
120 variation
121 whole-genome sequencing
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