Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing

被引：388

作者：

Manske, Magnus ^{[1
,2
]}

Miotto, Olivo ^{[2
,3
]}

Campino, Susana ^{[1
,2
]}

Auburn, Sarah ^{[1
,2
,4
]}

Almagro-Garcia, Jacob ^{[1
,2
,5
]}

Maslen, Gareth ^{[1
,2
]}

O'Brien, Jack ^{[2
,5
]}

Djimde, Abdoulaye ^{[6
]}

Doumbo, Ogobara ^{[6
]}

Zongo, Issaka ^{[7
]}

Ouedraogo, Jean-Bosco ^{[7
]}

Michon, Pascal ^{[8
]}

Mueller, Ivo ^{[8
]}

Siba, Peter ^{[8
]}

Nzila, Alexis ^{[9
]}

Borrmann, Steffen ^{[9
]}

Kiara, Steven M. ^{[9
]}

Marsh, Kevin ^{[9
]}

Jiang, Hongying ^{[10
]}

Su, Xin-Zhuan ^{[10
]}

Amaratunga, Chanaki ^{[10
]}

Fairhurst, Rick ^{[10
]}

Socheat, Duong ^{[11
]}

Nosten, Francois ^{[3
,12
,13
]}

Imwong, Mallika ^{[14
]}

White, Nicholas J. ^{[3
,13
]}

Sanders, Mandy ^{[1
]}

Anastasi, Elisa ^{[1
]}

Alcock, Dan ^{[1
]}

Drury, Eleanor ^{[1
]}

Oyola, Samuel ^{[1
]}

Quail, Michael A. ^{[1
]}

Turner, Daniel J. ^{[1
]}

Ruano-Rubio, Valentin ^{[1
,2
,5
]}

Jyothi, Dushyanth ^{[1
,2
]}

Amenga-Etego, Lucas ^{[2
,5
,15
]}

Hubbart, Christina ^{[5
]}

Jeffreys, Anna ^{[5
]}

Rowlands, Kate ^{[5
]}

Sutherland, Colin ^{[16
]}

Roper, Cally ^{[16
]}

Mangano, Valentina ^{[17
]}

Modiano, David ^{[17
]}

Tan, John C. ^{[18
]}

Ferdig, Michael T. ^{[18
]}

Amambua-Ngwa, Alfred ^{[19
]}

Conway, David J. ^{[16
,19
]}

Takala-Harrison, Shannon ^{[20
]}

Plowe, Christopher V. ^{[20
]}

Rayner, Julian C. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Univ Oxford, MRC Ctr Genom & Global Hlth, Oxford OX3 7BN, England

[3] Mahidol Univ, Mahidol Oxford Trop Med Res Unit, Bangkok 10400, Thailand

[4] Charles Darwin Univ, Menzies Sch Hlth Res, Darwin, NT 0811, Australia

[5] Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England

[6] Univ Bamako, Fac Med, Malaria Res & Training Ctr, Bamako, Mali

[7] Inst Rech Sci Sante, Direct Reg Ouest, Bobo Dioulasso, Burkina Faso

[8] Papua New Guinea Inst Med Res, Madang 511, Papua N Guinea

[9] KEMRI Wellcome Trust Res Program, Kilifi, Kenya

[10] Nat Inst Allergy & Infect Dis, NIH, Rockville, MD 20892 USA

[11] Cambodia Natl Malaria Ctr, Phnom Penh, Cambodia

[12] Shoklo Malaria Res Unit, Mae Sot 63110, Tak, Thailand

[13] Univ Oxford, Ctr Trop Med, Oxford OX3 7LJ, England

[14] Mahidol Univ, Fac Trop Med, Dept Mol Trop Med & Genet, Bangkok 10400, Thailand

[15] Navrongo Hlth Ctr, Navrongo, Ghana

[16] London Sch Hyg & Trop Med, London WC1E 7HT, England

[17] Univ Roma La Sapienza, Dept Publ Hlth Sci, I-00185 Rome, Italy

[18] Univ Notre Dame, Eck Inst Global Hlth, Dept Biol Sci, Notre Dame, IN 46556 USA

[19] MRC Labs, Fajara, Gambia

[20] Univ Maryland, Ctr Vaccine Dev, Baltimore, MD 21201 USA

[21] Univ Oxford, Weatherall Inst Mol Med, Oxford OX3 9DS, England

来源：

NATURE | 2012年 / 487卷 / 7407期

基金：

美国国家卫生研究院; 英国惠康基金; 英国医学研究理事会;

关键词：

PAPUA-NEW-GUINEA; MALARIA PARASITE; LIBRARY PREPARATION; GENOME; RESISTANCE; TRANSMISSION; POLYMORPHISM; EVOLUTION; SELECTION; PATTERNS;

D O I：

10.1038/nature11174

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance(1,2). Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.

引用

页码：375 / 379

页数：5

共 30 条

[1]

Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum [J].

Anderson, TJC ;

Haubold, B ;

Williams, JT ;

Estrada-Franco, JG ;

Richardson, L ;

Mollinedo, R ;

Bockarie, M ;

Mokili, J ;

Mharakurwa, S ;

French, N ;

Whitworth, J ;

Velez, ID ;

Brockman, AH ;

Nosten, F ;

Ferreira, MU ;

Day, KP .

MOLECULAR BIOLOGY AND EVOLUTION, 2000, 17 (10) :1467-1482

[2]

[Anonymous], 2007, PRINCIPLES POPULATIO

[3]

Evidence of non-neutral polymorphism in Plasmodium falciparum gamete surface protein genes Pfs47 and Pfs48/45 [J].

Anthony, Thomas G. ;

Polley, Spencer D. ;

Vogler, Alfried P. ;

Conway, David J. .

MOLECULAR AND BIOCHEMICAL PARASITOLOGY, 2007, 156 (02) :117-123

[4]

Characterization of Within-Host Plasmodium falciparum Diversity Using Next-Generation Sequence Data [J].

Auburn, Sarah ;

Campino, Susana ;

Miotto, Olivo ;

Djimde, Abdoulaye A. ;

Zongo, Issaka ;

Manske, Magnus ;

Maslen, Gareth ;

Mangano, Valentina ;

Alcock, Daniel ;

MacInnis, Bronwyn ;

Rockett, Kirk A. ;

Clark, Taane G. ;

Doumbo, Ogobara K. ;

Ouedraogo, Jean Bosco ;

Kwiatkowski, Dominic P. .

PLOS ONE, 2012, 7 (02)

[5]

An Effective Method to Purify Plasmodium falciparum DNA Directly from Clinical Blood Samples for Whole Genome High-Throughput Sequencing [J].

Auburn, Sarah ;

Campino, Susana ;

Clark, Taane G. ;

Djimde, Abdoulaye A. ;

Zongo, Issaka ;

Pinches, Robert ;

Manske, Magnus ;

Mangano, Valentina ;

Alcock, Daniel ;

Anastasi, Elisa ;

Maslen, Gareth ;

MacInnis, Bronwyn ;

Rockett, Kirk ;

Modiano, David ;

Newbold, Christopher I. ;

Doumbo, Ogobara K. ;

Ouedraogo, Jean Bosco ;

Kwiatkowski, Dominic P. .

PLOS ONE, 2011, 6 (07)

[6]

The novel putative transporter NPT1 plays a critical role in early stages of Plasmodium berghei sexual development [J].

Boisson, Bertrand ;

Lacroix, Celine ;

Bischoff, Emmanuel ;

Gueirard, Pascale ;

Bargieri, Daniel Y. ;

Franke-Fayard, Blandine ;

Janse, Chris J. ;

Menard, Robert ;

Baldacci, Patricia .

MOLECULAR MICROBIOLOGY, 2011, 81 (05) :1343-1357

[7]

Artemisinin Resistance in Plasmodium falciparum Malaria. [J].

Dondorp, Arjen M. ;

Nosten, Francois ;

Yi, Poravuth ;

Das, Debashish ;

Phyo, Aung Phae ;

Tarning, Joel ;

Lwin, Khin Maung ;

Ariey, Frederic ;

Hanpithakpong, Warunee ;

Lee, Sue J. ;

Ringwald, Pascal ;

Silamut, Kamolrat ;

Imwong, Mallika ;

Chotivanich, Kesinee ;

Lim, Pharath ;

Herdman, Trent ;

An, Sen Sam ;

Yeung, Shunmay ;

Singhasivanon, Pratap ;

Day, Nicholas P. J. ;

Lindegardh, Niklas ;

Socheat, Duong ;

White, Nicholas J. .

NEW ENGLAND JOURNAL OF MEDICINE, 2009, 361 (05) :455-467

[8]

Multigenic drug resistance among inbred malaria parasites [J].

Dye, C ;

Williams, BG .

PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 1997, 264 (1378) :61-67

[9]

Genome sequence of the human malaria parasite Plasmodium falciparum [J].

Gardner, MJ ;

Hall, N ;

Fung, E ;

White, O ;

Berriman, M ;

Hyman, RW ;

Carlton, JM ;

Pain, A ;

Nelson, KE ;

Bowman, S ;

Paulsen, IT ;

James, K ;

Eisen, JA ;

Rutherford, K ;

Salzberg, SL ;

Craig, A ;

Kyes, S ;

Chan, MS ;

Nene, V ;

Shallom, SJ ;

Suh, B ;

Peterson, J ;

Angiuoli, S ;

Pertea, M ;

Allen, J ;

Selengut, J ;

Haft, D ;

Mather, MW ;

Vaidya, AB ;

Martin, DMA ;

Fairlamb, AH ;

Fraunholz, MJ ;

Roos, DS ;

Ralph, SA ;

McFadden, GI ;

Cummings, LM ;

Subramanian, GM ;

Mungall, C ;

Venter, JC ;

Carucci, DJ ;

Hoffman, SL ;

Newbold, C ;

Davis, RW ;

Fraser, CM ;

Barrell, B .

NATURE, 2002, 419 (6906) :498-511

[10]

ESTIMATION OF INBREEDING COEFFICIENTS FROM GENOTYPIC DATA ON MULTIPLE ALLELES, AND APPLICATION TO ESTIMATION OF CLONALITY IN MALARIA PARASITES [J].

HILL, WG ;

BABIKER, HA ;

RANFORDCARTWRIGHT, LC ;

WALLIKER, D .

GENETICAL RESEARCH, 1995, 65 (01) :53-61

← 1 2 3 →