Whole genome sequencing analysis of Plasmodium vivax using whole genome capture

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Bright, A T ^a,b   Tewhey, Ryan ^b,c   Abeles, Shira ^d   Chuquiyauri, Raul ^d,e   Llanos Cuentas, Alejandro ^e   Ferreira, Marcelo U ^f   Schork, Nicholas J ^b   Vinetz, Joseph M ^d   Winzeler, Elizabeth A ^b,g  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^e INSTITUTO DE MEDICINA TROPICAL ALEXANDER VON HUMBOLDT   (Peru)

^f UNIVERSITY OF SÃO PAULO   (Brazil)

^g GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

Malaria

Indexed keywords

GENOMIC DNA; PROTOZOAL DNA;

ANALYTIC METHOD; ARTICLE; CELL INFILTRATION; DNA HYBRIDIZATION; DNA SEQUENCE; FEASIBILITY STUDY; GENOME; GENOME ANALYSIS; IN SOLUTION HYBRIDIZATION CAPTURE METHOD; LEUKOCYTE; NONHUMAN; PERU; PLASMODIUM VIVAX; SAMPLING; SEQUENCE ANALYSIS; WHOLE GENOME CAPTURE METHOD; CHEMISTRY; GENETICS; NUCLEIC ACID HYBRIDIZATION;

PLASMODIUM VIVAX;

DNA, PROTOZOAN; GENOME, HELMINTH; NUCLEIC ACID HYBRIDIZATION; PLASMODIUM VIVAX; SEQUENCE ANALYSIS, DNA;

EID: 84862492581     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-262     Document Type: Article

References (12)

1. Baird JK. Resistance to therapies for infection by Plasmodium vivax. Clin Microbiol Rev 2009, 22:508-534. 10.1128/CMR.00008-09, 2708388, 19597012.
2. Tjitra E, Anstey NM, Sugiarto P, et al. Multidrug-resistant Plasmodium vivax associated with severe and fatal malaria: a prospective study in Papua. Indonesia. PLoS medicine 2008, 5:e128.
3. Trager W, Jensen JB. Cultivation of erythrocytic stages. Bulletin of the World Health Organization 1977, 55:363-365. 2366733, 338187.
4. Dharia NV, Bright AT, Westenberger SJ, et al. Whole-genome sequencing and microarray analysis of ex vivo Plasmodium vivax reveal selective pressure on putative drug resistance genes. Proc Natl Acad Sci U S A 2010, 107:20045-20050. 10.1073/pnas.1003776107, 2993397, 21037109.
5. Sriprawat K, Kaewpongsri S, Suwanarusk R, et al. Effective and cheap removal of leukocytes and platelets from Plasmodium vivax infected blood. Malar J 2009, 8:115. 10.1186/1475-2875-8-115, 2694833, 19490618.
6. Tewhey R, Nakano M, Wang X, et al. Enrichment of sequencing targets from the human genome by solution hybridization. Genome Biol 2009, 10:R116. 10.1186/gb-2009-10-10-r116, 2784331, 19835619.
7. Gnirke A, Melnikov A, Maguire J, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27:182-189. 10.1038/nbt.1523, 2663421, 19182786.
8. Melnikov A, Galinsky K, Rogov P, et al. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol 2011, 12:R73. 10.1186/gb-2011-12-8-r73, 3245613, 21835008.
9. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 2009, 25:1754-1760.
10. DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43:491-498. 10.1038/ng.806, 3083463, 21478889.
11. Bainbridge MN, Wang M, Burgess DL, et al. Whole exome capture in solution with 3 Gbp of data. Genome Biol 2010, 11:R62. 10.1186/gb-2010-11-6-r62, 2911110, 20565776.
12. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England) 2009, 25:2078-2079.