Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

doi:10.1186/gb-2008-9-12-r171

Genome Biology

Volume 9
Issue 12

Viewing options:

Abstract
Full text
PDF (671KB)
Additional files

Associated material:

PubMed record

Related literature:

Articles citing this article
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Neafsey DE
Schaffner SF
Volkman SK
Park D
Montgomery P
Milner DA
Lukens A
Rosen D
Daniels R
Houde N
Cortese JF
Tyndall E
Gates C
Stange-Thomann N
Sarr O
Ndiaye D
Ndir O
Mboup S
Ferreira MU
Moraes Sd
Dash AP
Chitnis CE
Wiegand RC
Hartl DL
Birren BW
Lander ES
Sabeti PC
Wirth DF

on PubMed

Neafsey DE
Schaffner SF
Volkman SK
Park D
Montgomery P
Milner DA
Lukens A
Rosen D
Daniels R
Houde N
Cortese JF
Tyndall E
Gates C
Stange-Thomann N
Sarr O
Ndiaye D
Ndir O
Mboup S
Ferreira MU
Moraes Sd
Dash AP
Chitnis CE
Wiegand RC
Hartl DL
Birren BW
Lander ES
Sabeti PC
Wirth DF
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research

Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence

Daniel E Neafsey¹^* , Stephen F Schaffner¹^* , Sarah K Volkman²^,3 , Daniel Park¹ , Philip Montgomery¹ , Danny A Milner Jr² , Amanda Lukens² , David Rosen² , Rachel Daniels¹ , Nathan Houde¹ , Joseph F Cortese¹ , Erin Tyndall¹ , Casey Gates¹ , Nicole Stange-Thomann¹ , Ousmane Sarr⁴ , Daouda Ndiaye⁴ , Omar Ndir⁴ , Soulyemane Mboup⁴ , Marcelo U Ferreira⁵ , Sandra do Lago Moraes⁶ , Aditya P Dash⁷ , Chetan E Chitnis⁸ , Roger C Wiegand¹ , Daniel L Hartl⁹ , Bruce W Birren¹ , Eric S Lander¹ , Pardis C Sabeti¹ and Dyann F Wirth²

¹Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA

²Department of Immunology and Infectious Diseases, Harvard School of Public Health, 677 Huntington Ave, Boston, MA 02115, USA

³School for Health Studies, Simmons College, 300 The Fenway, Boston, MA 02115, USA

⁴Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, BP 7325 Dakar, Senegal

⁵Departamento de Parasitologia, Instituto de Ciencias Biomedicas da USP, Av. Prof. Lineu Prestes 1374, Cidade Universitaria, 05508-900 Sao Paulo, SP, Brazil

⁶Instituto de Medicina Tropical de Sao Paulo, Universidade de Sao Paulo, Av Dr. Eneas de Carvalho Aguiar 470, 05403-907 Sao Paulo, SP, Brazil

⁷National Institute of Malaria Research, 22, Sham Nath Marg, Delhi-110054, India

⁸International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi-110067, India

⁹Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R171doi:10.1186/gb-2008-9-12-r171


Published:	15 December 2008

Subject areas: Genetics, Genome studies, Microbiology and parasitology

Additional files

Additional data file 1:

Lines indicate the number of SNPs exhibiting various call rates using the DM, BRLMM, and BRLMM-P SNP calling algorithms. BRLMM-P SNP calls were used for analysis.

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

Array performance in the presence of human DNA and malaria DNA from mixed (non-clonal) infections.

Format: DOC Size: 22KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional data file 3:

Reported results are for SNP loci known to exhibit different alleles between the HB3 and Dd2 lines. The highest proportion of heterozygous calls was observed for the even (1:1) mixture of malaria.

Format: PDF Size: 10KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 4:

Concordance with known genotype can be improved using more stringent confidence cutoff values with the BRLMM-P calling algorithm.

Format: PDF Size: 10KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 5:

Genomic location and genotype data for SNPs assayed on the array with a call rate of at least 80%.

Format: XLS Size: 1.7MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 6:

(a) High MAF (MAF > 0.25) topology. (b) Low MAF (MAF < 0.25) topology. Nodes exhibiting bootstrap support levels of at least 50% or 90% are indicated by gray dots and black dots, respectively. Bootstrap support and branch length differ between the topologies, but the American and Asian parasites form congruent clades.

Format: PDF Size: 19KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 7:

(a) Plot of the likelihood of the genotyping data given that the samples derive from K = 1-5 populations. (b) Plot of the posterior probability of population membership for each sample hybridized to the array, assuming three underlying populations.

Format: PDF Size: 16KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 8:

(a) First two principal components for Brazil data; clusters suggest population structure. (b) First two components for worldwide data set. (c) First and third components for worldwide data set.

Format: PDF Size: 15KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 9:

Significantly greater nonsynonymous divergence (determined by bootstrapping) is indicated by asterisks: **P < 0.001.

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 10:

Nonsynonymous and silent SNP DAF correlation between Senegal and Thailand.

Format: PDF Size: 20KB Download file

This file can be viewed with: Adobe Acrobat Reader