DOI: 10.5061/dryad.d7wm37pxz
title: Selection and exploitation of prevalent, tandemly repeated genomic targets for improved real-time PCR-based detection of Wuchereria bancrofti and Plasmodium falciparum in mosquitoes

description: Background Optimization of polymerase chain reaction (PCR)-based
 diagnostics requires the careful selection of molecular targets that are
 both highly repetitive and pathogen-specific.  Advances in both
 next-generation sequencing (NGS) technologies and bioinformatics-based
 analysis tools are facilitating this selection process, informing target
 choices and reducing labor.  Once developed, such assays provide
 disease control and elimination programs with an additional set of tools
 capable of evaluating and monitoring intervention successes.  The
 importance of such tools is heightened as intervention efforts approach
 their endpoints, as accurate and complete information is an essential
 component of the informed decision-making process.  As global
 efforts for the control and elimination of both lymphatic filariasis and
 malaria continue to make significant gains, the benefits of diagnostics
 with improved analytical and clinical/field-based sensitivities and
 specificities will become increasingly apparent. Methodology/Principal
 Findings       
 Coupling Illumina-based NGS with informatics approaches, we have
 successfully identified the tandemly repeated elements in both the
 Wuchereria bancrofti and Plasmodium falciparum genomes of putatively
 greatest copy number.  Utilizing these sequences as quantitative
 real-time PCR (qPCR)-based targets, we have developed assays capable of
 exploiting the most abundant tandem repeats for both organisms. 
 For the detection of P. falciparum, analysis and development resulted in
 an assay with improved analytical and field-based sensitivity vs. an
 established ribosomal sequence-targeting assay.  Surprisingly,
 analysis of the W. bancrofti genome predicted a ribosomal sequence to be
 the genome’s most abundant tandem repeat.  While resulting cycle
 quantification values comparing a qPCR assay targeting this ribosomal
 sequence and a commonly targeted repetitive DNA sequence from the
 literature supported our finding that this ribosomal sequence was the most
 prevalent tandemly repeated target in the W. bancrofti genome, the
 resulting assay did not significantly improve detection sensitivity in
 conjunction with field sample testing.  Conclusions/Significance
 Examination of pathogen genomes facilitates the development of PCR-based
 diagnostics targeting the most abundant and specific genomic
 elements.  While in some instances currently available tools may
 deliver equal or superior performance, systematic analysis of potential
 targets provides confidence that the selected assays represent the most
 advantageous options available and that informed assay selection is
 occurring in the context of a particular study’s objectives.
description: This dataset is the output from RepeatExplorer and TAREAN-based
 analyses of the genomes of Plasmodium falciparum and Wuchereria
 bancrofti.
description: This dataset is full and complete.  An understanding of the
 output of the RepeatExplorer and TAREAN analysis suites is required to
 interpret this data.