Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Pulido-Tamayo, Sergio; Sánchez-Rodríguez, Aminael; Swings, Toon; Bergh, Bram Van den; Dubey, Akhilesh; Steenackers, Hans; Michiels, Jan; Fostier, Jan; Marchal, Kathleen

doi:10.1093/nar/gkv478

Cited by 53 publications

(53 citation statements)

References 26 publications

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“…The haplotypes were constructed using EVORhA 63 , a frequency based haplotype reconstruction method, with 4 wOv samples excluded because of low depth of coverage (F7, E17, E21 and E24; average depth <30). For quality filtering, any reads with >1 base with quality <23 were discarded, as previously described 64 .…”

Section: Methodsmentioning

confidence: 99%

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

et al. 2016

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Ongoing elimination efforts have altered the global distribution of Onchocerca volvulus, the agent of river blindness, and further population restructuring is expected as efforts continue. Therefore, a better understanding of population-genetic processes and their effect on biogeography is needed to support elimination goals. We describe O. volvulus genome variation in 27 isolates from early 1990s (before widespread mass treatment) from four distinct locales: Ecuador, Uganda, the West African forest, and the West African savanna. We observed genetic substructuring between Ecuador and West Africa and between the West African forest and savanna bioclimes, with evidence of unidirectional gene flow from savanna to forest strains. We identified forest:savanna-discriminatory genomic regions and report a set of ancestry informative loci that can be used to differentiate between forest, savanna and admixed isolates, which has not previously been possible. We observed mito-nuclear discordance possibly stemming from incomplete lineage sorting. The catalog of the nuclear, mitochondrial and endosymbiont DNA variants generated in this study will support future basic and translational onchocerciasis research, with particular relevance for ongoing control programs and boost efforts to characterize drug, vaccine, and diagnostic targets.

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Section: Methodsmentioning

confidence: 99%

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

et al. 2016

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“…While these methods allow for the identification of major resistance alleles, they may miss minor alleles (15) or provide an inaccurate picture of mixed infection haplotypes. In comparison, next-generation sequencing (NGS) can accurately capture mixed infection haplotypes and detect minor allele frequencies (MAFs) as low as 1% (16,17). This sensitivity is particularly important for identification of naturally circulating drug-resistant alleles in individual patient samples before they are selected by drug pressure in countries where malaria is endemic.…”

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confidence: 99%

Molecular Epidemiology of Plasmodium falciparum kelch13 Mutations in Senegal Determined by Using Targeted Amplicon Deep Sequencing

Talundzic

Ndiaye

Déme

et al. 2017

Antimicrob Agents Chemother

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The emergence of Plasmodium falciparum resistance to artemisinin in Southeast Asia threatens malaria control and elimination activities worldwide. Multiple polymorphisms in the P. falciparum kelch gene found in chromosome 13 (Pfk13) have been associated with artemisinin resistance. Surveillance of potential drug resistance loci within a population that may emerge under increasing drug pressure is an important public health activity. In this context, P. falciparum infections from an observational surveillance study in Senegal were genotyped using targeted amplicon deep sequencing (TADS) for Pfk13 polymorphisms. The results were compared to previously reported Pfk13 polymorphisms from around the world. A total of 22 Pfk13 propeller domain polymorphisms were identified in this study, of which 12 have previously not been reported. Interestingly, of the 10 polymorphisms identified in the present study that were also previously reported, all had a different amino acid substitution at these codon positions. Most of the polymorphisms were present at low frequencies and were confined to single isolates, suggesting they are likely transient polymorphisms that are part of naturally evolving parasite populations. The results of this study underscore the need to identify potential drug resistance loci existing within a population, which may emerge under increasing drug pressure.

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“…The resulting diversity is especially large for RNA viruses (Holmes, 2009 immune escape (Luciani et al, 2012), or affect virulence (T€ opfer et al, 2013). Estimating intrahost viral genetic diversity and reconstructing the individual haplotype sequences relies on both error correction and read assembly (Pulido-Tamayo et al, 2015). It can be performed on different spatial scales, including single sites of the genome (single-nucleotide-variant calling), small sliding windows (local reconstruction), or complete genomes (global reconstruction).…”

Section: Viral Quasispeciesmentioning

confidence: 99%

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

Hölzer

2017

In Loeffler’s Footsteps – Viral Genomics in the Era of High-Throughput Sequencing

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Computer-assisted technologies of the genomic structure, biological function, and evolution of viruses remain a largely neglected area of research. The attention of bioinformaticians to this challenging field is currently unsatisfying in respect to its medical and biological importance. The power of new genome sequencing technologies, associated with new tools to handle "big data", provides unprecedented opportunities to address fundamental questions in virology. Here, we present an overview of the current technologies, challenges, and advantages of Next-Generation Sequencing (NGS) in relation to the field of virology. We present how viral sequences can be detected de novo out of current short-read NGS data. Furthermore, we discuss the challenges and applications of viral quasispecies and how secondary structures, commonly shaped by RNA viruses, can be computationally predicted. The phylogenetic analysis of viruses, as another ubiquitous field in virology, forms an essential element of describing viral epidemics and challenges current algorithms. Recently, the first specialized virus-bioinformatic organizations have been established. We need to bring together virologists and bioinformaticians and provide a platform for the implementation of interdisciplinary collaborative projects at local and international scales. Above all, there is an urgent need for dedicated software tools to tackle various challenges in virology.

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Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

Cited by 53 publications

References 26 publications

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

Molecular Epidemiology of Plasmodium falciparum kelch13 Mutations in Senegal Determined by Using Targeted Amplicon Deep Sequencing

Software Dedicated to Virus Sequence Analysis “Bioinformatics Goes Viral”

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