ArticleGenomics2009
Optimizing comparative genomic hybridization probes for genotyping and SNP detection in Plasmodium falciparum.
Article in Genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 33 citations in OpenAlex.
- Bridging biological samples to functional nucleic acid biosensor applications: current enzymatic-based strategies for single-stranded DNA generation.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2024Review
- One-step colorimetric genotyping of single nucleotide polymorphism using probe-enhanced loop-mediated isothermal amplification (PE-LAMP).Theranostics · 2019Article
- Article
- Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.BMC genomics · 2014Article
- Comprehensive analysis of prokaryotes in environmental water using DNA microarray analysis and whole genome amplification.Pathogens (Basel, Switzerland) · 2013Article
- Using genetic methods to define the targets of compounds with antimalarial activity.Journal of medicinal chemistry · 2013Review
- Asexual populations of the human malaria parasite, Plasmodium falciparum, use a two-step genomic strategy to acquire accurate, beneficial DNA amplifications.PLoS pathogens · 2013Article
- Signal oscillation is another reason for variability in microarray-based gene expression quantification.PloS one · 2013Article
- Comparative Genomics and Systems Biology of Malaria ParasitesCurrent bioinformatics · 2012Article
- Harnessing genomics and genome biology to understand malaria biology.Nature reviews. Genetics · 2012Review
- Application of genomics to field investigations of malaria by the international centers of excellence for malaria research.Acta tropica · 2012Review
- Molecular-beacon-based tricomponent probe for SNP analysis in folded nucleic acids.Chemistry (Weinheim an der Bergstrasse, Germany) · 2011Article
- The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross.BMC genomics · 2011Article
- Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum.PLoS genetics · 2011Article
- High-throughput 454 resequencing for allele discovery and recombination mapping in Plasmodium falciparum.BMC genomics · 2011Article
- An optimized microarray platform for assaying genomic variation in Plasmodium falciparum field populations.Genome biology · 2011Article
- How can we identify parasite genes that underlie antimalarial drug resistance?Pharmacogenomics · 2011Review
- Real-time SNP analysis in secondary-structure-folded nucleic acids.Angewandte Chemie (International ed. in English) · 2010Article
- Genome scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin-resistant parasites.Genome research · 2010Article
- Variable numbers of tandem repeats in Plasmodium falciparum genes.Journal of molecular evolution · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Microarray-based comparative genomic hybridizations (CGH) interrogate genomic DNA to identify structural differences such as amplifications and deletions that are easily detected as large signal aberrations. Subtle signal deviations caused by single nucleotide polymorphisms (SNPs) can also be detected but is challenged by a high AT content (81%) in P. falciparum. We compared genome-wide CGH signal to sequence polymorphisms between parasite strains 3D7, HB3, and Dd2 using NimbleGen microarrays. From 23,191 SNPs (excluding var/rif/stevor genes), our CGH probe set detected SNPs with >99.9% specificity but low (<10%) sensitivity. Probe length, melting temperature, GC content, SNP location in the probe, mutation type, and hairpin structures affected SNP sensitivity. Previously unrecognized variable number tandem repeats (VNTRs) also were detected by this method. These findings will guide the redesign of a probe set to optimize an openly available CGH microarray platform for high-resolution genotyping suitable for population genomics studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.