Detection of genome-wide polymorphisms in the AT-rich Plasmodium falciparum genome using a high-density microarray.

BMC Genomics
Hongying JiangXin-zhuan Su

Abstract

Genetic mapping is a powerful method to identify mutations that cause drug resistance and other phenotypic changes in the human malaria parasite Plasmodium falciparum. For efficient mapping of a target gene, it is often necessary to genotype a large number of polymorphic markers. Currently, a community effort is underway to collect single nucleotide polymorphisms (SNP) from the parasite genome. Here we evaluate polymorphism detection accuracy of a high-density 'tiling' microarray with 2.56 million probes by comparing single feature polymorphisms (SFP) calls from the microarray with known SNP among parasite isolates. We found that probe GC content, SNP position in a probe, probe coverage, and signal ratio cutoff values were important factors for accurate detection of SFP in the parasite genome. We established a set of SFP calling parameters that could predict mSFP (SFP called by multiple overlapping probes) with high accuracy (> or = 94%) and identified 121,087 mSFP genome-wide from five parasite isolates including 40,354 unique mSFP (excluding those from multi-gene families) and approximately 18,000 new mSFP, producing a genetic map with an average of one unique mSFP per 570 bp. Genomic copy number variation (CNV) among the par...Continue Reading

References

Aug 20, 1976·Science·W Trager, J B Jensen
Apr 1, 1989·Proceedings of the National Academy of Sciences of the United States of America·B A BiggsG V Brown
Feb 1, 1994·Proceedings of the National Academy of Sciences of the United States of America·A F CowmanJ K Thompson
Sep 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·K P DayD J Kemp
Aug 1, 1996·Magnetic Resonance in Medicine : Official Journal of the Society of Magnetic Resonance in Medicine·B SiewertR R Edelman
Feb 7, 2001·Genome Research·E Pizzi, C Frontali
Oct 9, 2002·Nature·Malcolm J GardnerBart Barrell
Sep 10, 2003·Nature Biotechnology·Giulia C KennedyKeith W Jones
Dec 31, 2003·Cell·L AravindLouis H Miller
Feb 6, 2004·Genome Research·Graham R BignellRichard Wooster
Feb 13, 2004·Bioinformatics·Laurent GautierRafael A Irizarry
Apr 20, 2005·Nature Genetics·Kevin L GundersonMark S Chee
Sep 22, 2005·Molecular and Biochemical Parasitology·Céline Karine CarretAlasdair Ivens
Jun 23, 2006·PLoS Pathogens·Claire KidgellElizabeth A Winzeler
Dec 13, 2006·Nature Genetics·Daniel C JeffaresMatthew Berriman
Dec 13, 2006·Nature Genetics·Sarah K VolkmanDyann F Wirth
Dec 26, 2006·Biostatistics·Benilton CarvalhoRafael A Irizarry
Jan 17, 2007·Biotechnology Journal·Frank J Steemers, Kevin L Gunderson
Mar 6, 2007·Biotechnology and Bioengineering·Hiroko HagiwaraMasayuki Machida
Apr 28, 2007·Science·UNKNOWN Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical RShaun Purcell
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Jun 19, 2007·Nature Reviews. Genetics·Xinzhuan SuThomas E Wellems
Jun 30, 2007·Molecular and Biochemical Parasitology·Ulf RibackeMats Wahlgren
Jul 17, 2007·Nature·Hakon HakonarsonConstantin Polychronakos

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Citations

Sep 20, 2008·Current Genetics·Karen Hayton, Xin-Zhuan Su
Nov 13, 2013·Trends in Parasitology·Jian LiXin-zhuan Su
Aug 28, 2009·BMC Genetics·Wayne Wenzhong XuGary J Muehlbauer
Aug 6, 2009·BMC Genomics·Ian H CheesemanDavid J Conway
Oct 27, 2010·BMC Genomics·Amit BahlDavid S Roos
Apr 6, 2011·Genome Biology·Hongying JiangXin-zhuan Su
Oct 31, 2009·PLoS Pathogens·Elizabeth A Winzeler
Dec 23, 2010·Pharmacogenomics·Tim AndersonDavid Fidock
Nov 29, 2015·Molecular Biology and Evolution·Ian H CheesemanTim Jc Anderson
Oct 7, 2009·Expert Review of Anti-infective Therapy·Liwang Cui, Xin-zhuan Su
Jun 30, 2009·Trends in Parasitology·Tim J C AndersonMichael T Ferdig
Feb 20, 2015·Annals of the New York Academy of Sciences·Adina Heinberg, Laura Kirkman
Nov 6, 2008·International Journal for Parasitology·Hans-Peter BeckWillie Weir
Apr 6, 2012·International Journal for Parasitology·Lisa C Ranford-Cartwright, Jonathan M Mwangi
Jun 3, 2009·The Korean Journal of Parasitology·Xin-Zhuan SuRobert M Stephens
Feb 10, 2017·Trends in Parasitology·Sarah K VolkmanDaniel L Hartl
Mar 31, 2016·PloS One·Cristina K MoreiraThomas J Templeton
Apr 13, 2012·Nature Reviews. Genetics·Sarah K VolkmanDyann F Wirth
Apr 6, 2019·Frontiers in Immunology·Janna HeideJulian Schulze Zur Wiesch

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Methods Mentioned

BETA
genotyping
PCR
chip
electrophoresis
chips

Software Mentioned

mSFP
house
R
affy BioConductor package
LPE
GBrowse browser
PladmoDB
Partek Genomics Suite
R programming environment
Bioconductor

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