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Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.

Publication ,  Journal Article
Levitt, B; Obala, A; Langdon, S; Corcoran, D; O'Meara, WP; Taylor, SM
Published in: Sci Rep
January 24, 2017

Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets. Therefore, we designed, validated, and applied to field parasites an approach that leverages sequencing of individually barcoded samples in a multiplex manner. We utilize variant barcodes, invariant linker sequences and modular template-specific primers to allow for the simultaneous generation of high-dimensional sequencing data of multiple gene targets. This modularity permits a cost-effective and reproducible way to query many genes at once. In mixtures of reference parasite genomes, we quantitatively detected unique haplotypes comprising as little as 2% of a polyclonal infection. We applied this genotyping approach to field-collected parasites collected in Western Kenya in order to simultaneously obtain parasites genotypes at three unlinked loci. In summary, we present a rapid, scalable, and flexible method for genotyping individual parasites that enables molecular epidemiologic studies of parasite evolution, population structure and transmission.

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Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

January 24, 2017

Volume

7

Start / End Page

41108

Location

England

Related Subject Headings

  • Polymorphism, Genetic
  • Plasmodium falciparum
  • Malaria, Falciparum
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genotyping Techniques
  • DNA Barcoding, Taxonomic
 

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Levitt, B., Obala, A., Langdon, S., Corcoran, D., O’Meara, W. P., & Taylor, S. M. (2017). Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya. Sci Rep, 7, 41108. https://doi.org/10.1038/srep41108
Levitt, Brandt, Andrew Obala, Scott Langdon, David Corcoran, Wendy Prudhomme O’Meara, and Steve M. Taylor. “Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.Sci Rep 7 (January 24, 2017): 41108. https://doi.org/10.1038/srep41108.
Levitt B, Obala A, Langdon S, Corcoran D, O’Meara WP, Taylor SM. Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya. Sci Rep. 2017 Jan 24;7:41108.
Levitt, Brandt, et al. “Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.Sci Rep, vol. 7, Jan. 2017, p. 41108. Pubmed, doi:10.1038/srep41108.
Levitt B, Obala A, Langdon S, Corcoran D, O’Meara WP, Taylor SM. Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya. Sci Rep. 2017 Jan 24;7:41108.

Published In

Sci Rep

DOI

EISSN

2045-2322

Publication Date

January 24, 2017

Volume

7

Start / End Page

41108

Location

England

Related Subject Headings

  • Polymorphism, Genetic
  • Plasmodium falciparum
  • Malaria, Falciparum
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genotyping Techniques
  • DNA Barcoding, Taxonomic