Detecting number of clones, and their relative abundance, of a malaria parasite (Plasmodium mexicanum) infecting its vertebrate host

Anne Marie Vardo-Zalik, Alice Flynn Ford, Jos J. Schall

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Microsatellites, short tandem repeats of nucleotides in the genome, are useful markers to detect clonal diversity within Plasmodium infections. However, accuracy in determining number of clones and their relative proportions based on standard genetic analyzer instruments is poorly known. DNA extracted from lizards infected with a malaria parasite, Plasmodium mexicanum, provided template to genotype the parasite based on three microsatellite markers. Replicate genotyping of the same natural infections demonstrated strong repeatability of data from the instrument. Mixing DNA extracted from several infected lizards simulated mixed-clone infections with known clonal diversity and relative proportions of clones (N∈=∈56 simulations). The instrument readily detected at least four alleles (clones), even when DNA concentrations among clones differed up to tenfold, but alleles of similar size can be missed because they fall within the "stutter" artifact, and rarely does an allele fail to be detected. For simulations of infections that changed their relative proportions over time, changes in relative peak heights on the instrument output closely followed the known changes in relative proportions. Such data are useful for a broad range of studies on the ecology of malaria parasites.

Original languageEnglish (US)
Pages (from-to)209-215
Number of pages7
JournalParasitology Research
Volume105
Issue number1
DOIs
StatePublished - Jul 1 2009

Fingerprint

Plasmodium malariae
Plasmodium
malaria
Vertebrates
Parasites
Clone Cells
vertebrates
clones
parasites
Microsatellite Repeats
Lizards
Alleles
microsatellite repeats
alleles
infection
Malaria
lizards
DNA
Infection
Ecology

All Science Journal Classification (ASJC) codes

  • Parasitology
  • veterinary(all)
  • Insect Science
  • Infectious Diseases

Cite this

@article{f2ebc897411944b6962ba7dae4b8152a,
title = "Detecting number of clones, and their relative abundance, of a malaria parasite (Plasmodium mexicanum) infecting its vertebrate host",
abstract = "Microsatellites, short tandem repeats of nucleotides in the genome, are useful markers to detect clonal diversity within Plasmodium infections. However, accuracy in determining number of clones and their relative proportions based on standard genetic analyzer instruments is poorly known. DNA extracted from lizards infected with a malaria parasite, Plasmodium mexicanum, provided template to genotype the parasite based on three microsatellite markers. Replicate genotyping of the same natural infections demonstrated strong repeatability of data from the instrument. Mixing DNA extracted from several infected lizards simulated mixed-clone infections with known clonal diversity and relative proportions of clones (N∈=∈56 simulations). The instrument readily detected at least four alleles (clones), even when DNA concentrations among clones differed up to tenfold, but alleles of similar size can be missed because they fall within the {"}stutter{"} artifact, and rarely does an allele fail to be detected. For simulations of infections that changed their relative proportions over time, changes in relative peak heights on the instrument output closely followed the known changes in relative proportions. Such data are useful for a broad range of studies on the ecology of malaria parasites.",
author = "Vardo-Zalik, {Anne Marie} and Ford, {Alice Flynn} and Schall, {Jos J.}",
year = "2009",
month = "7",
day = "1",
doi = "10.1007/s00436-009-1385-1",
language = "English (US)",
volume = "105",
pages = "209--215",
journal = "Parasitology Research",
issn = "0932-0113",
publisher = "Springer Verlag",
number = "1",

}

Detecting number of clones, and their relative abundance, of a malaria parasite (Plasmodium mexicanum) infecting its vertebrate host. / Vardo-Zalik, Anne Marie; Ford, Alice Flynn; Schall, Jos J.

In: Parasitology Research, Vol. 105, No. 1, 01.07.2009, p. 209-215.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Detecting number of clones, and their relative abundance, of a malaria parasite (Plasmodium mexicanum) infecting its vertebrate host

AU - Vardo-Zalik, Anne Marie

AU - Ford, Alice Flynn

AU - Schall, Jos J.

PY - 2009/7/1

Y1 - 2009/7/1

N2 - Microsatellites, short tandem repeats of nucleotides in the genome, are useful markers to detect clonal diversity within Plasmodium infections. However, accuracy in determining number of clones and their relative proportions based on standard genetic analyzer instruments is poorly known. DNA extracted from lizards infected with a malaria parasite, Plasmodium mexicanum, provided template to genotype the parasite based on three microsatellite markers. Replicate genotyping of the same natural infections demonstrated strong repeatability of data from the instrument. Mixing DNA extracted from several infected lizards simulated mixed-clone infections with known clonal diversity and relative proportions of clones (N∈=∈56 simulations). The instrument readily detected at least four alleles (clones), even when DNA concentrations among clones differed up to tenfold, but alleles of similar size can be missed because they fall within the "stutter" artifact, and rarely does an allele fail to be detected. For simulations of infections that changed their relative proportions over time, changes in relative peak heights on the instrument output closely followed the known changes in relative proportions. Such data are useful for a broad range of studies on the ecology of malaria parasites.

AB - Microsatellites, short tandem repeats of nucleotides in the genome, are useful markers to detect clonal diversity within Plasmodium infections. However, accuracy in determining number of clones and their relative proportions based on standard genetic analyzer instruments is poorly known. DNA extracted from lizards infected with a malaria parasite, Plasmodium mexicanum, provided template to genotype the parasite based on three microsatellite markers. Replicate genotyping of the same natural infections demonstrated strong repeatability of data from the instrument. Mixing DNA extracted from several infected lizards simulated mixed-clone infections with known clonal diversity and relative proportions of clones (N∈=∈56 simulations). The instrument readily detected at least four alleles (clones), even when DNA concentrations among clones differed up to tenfold, but alleles of similar size can be missed because they fall within the "stutter" artifact, and rarely does an allele fail to be detected. For simulations of infections that changed their relative proportions over time, changes in relative peak heights on the instrument output closely followed the known changes in relative proportions. Such data are useful for a broad range of studies on the ecology of malaria parasites.

UR - http://www.scopus.com/inward/record.url?scp=67649600726&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67649600726&partnerID=8YFLogxK

U2 - 10.1007/s00436-009-1385-1

DO - 10.1007/s00436-009-1385-1

M3 - Article

C2 - 19277713

AN - SCOPUS:67649600726

VL - 105

SP - 209

EP - 215

JO - Parasitology Research

JF - Parasitology Research

SN - 0932-0113

IS - 1

ER -