Evaluating potential for whole-genome studies in Kosrae, an isolated population in Micronesia

被引：52

作者：

Bonnen, PE

Pe'er, I

Plenge, RM

Salit, J

Lowe, JK

Shapero, MH

Lifton, RP

Breslow, JL

Daly, MJ

Reich, DE

Jones, KW

Stoffel, M

Altshuler, D

Friedman, JM

机构：

[1] Rockefeller Univ, New York, NY 10021 USA

[2] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

[3] Harvard Univ, Broad Inst, Cambridge, MA 02138 USA

[4] MIT, Cambridge, MA 02139 USA

[5] Harvard Univ, Sch Med, Dept Med, Boston, MA 02115 USA

[6] Affymetrix Inc, Santa Clara, CA 95051 USA

[7] Yale Univ, Sch Med, Dept Med, New Haven, CT 06510 USA

[8] Yale Univ, Sch Med, Dept Genet, New Haven, CT 06510 USA

[9] Harvard Univ, Sch Med, Howard Hughes Med Inst, Boston, MA 02115 USA

[10] Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA

来源：

NATURE GENETICS | 2006年 / 38卷 / 02期

关键词：

D O I：

10.1038/ng1712

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Whole-genome association studies are predicted to be especially powerful in isolated populations owing to increased linkage disequilibrium (LD) and decreased allelic diversity, but this possibility has not been empirically tested(1-3). We compared genome-wide data on 113,240 SNPs typed on 30 trios from the Pacific island of Kosrae to the same markers typed in the 270 samples from the International HapMap Project(4,5). The extent of LD is longer and haplotype diversity is lower in Kosrae than in the HapMap populations. More than 98% of Kosraen haplotypes are present in HapMap populations, indicating that HapMap will be useful for genetic studies on Kosrae. The long-range LD around common alleles and limited diversity result in improved efficiency in genetic studies in this population and augments the power to detect association of 'hidden SNPs'.

引用

页码：214 / 217

页数：4

共 27 条

[1] A haplotype map of the human genome [J].

Altshuler, D ;

Brooks, LD ;

Chakravarti, A ;

Collins, FS ;

Daly, MJ ;

Donnelly, P ;

Gibbs, RA ;

Belmont, JW ;

Boudreau, A ;

Leal, SM ;

Hardenbol, P ;

Pasternak, S ;

Wheeler, DA ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Zeng, CQ ;

Gao, Y ;

Hu, HR ;

Hu, WT ;

Li, CH ;

Lin, W ;

Liu, SQ ;

Pan, H ;

Tang, XL ;

Wang, J ;

Wang, W ;

Yu, J ;

Zhang, B ;

Zhang, QR ;

Zhao, HB ;

Zhao, H ;

Zhou, J ;

Gabriel, SB ;

Barry, R ;

Blumenstiel, B ;

Camargo, A ;

Defelice, M ;

Faggart, M ;

Goyette, M ;

Gupta, S ;

Moore, J ;

Nguyen, H ;

Onofrio, RC ;

Parkin, M ;

Roy, J ;

Stahl, E ;

Winchester, E ;

Ziaugra, L ;

Shen, Y .

NATURE, 2005, 437 (7063) :1299-1320

[2] Not all isolates are equal: linkage disequilibrium analysis on Xq13.3 reveals different patterns in Sardinian sub-populations [J].

Angius, A ;

Bebbere, D ;

Petretto, E ;

Falchi, M ;

Forabosco, P ;

Maestrale, GB ;

Casu, G ;

Persico, I ;

Melis, PM ;

Pirastu, M .

HUMAN GENETICS, 2002, 111 (01) :9-15

[3] Haploview: analysis and visualization of LD and haplotype maps [J].

Barrett, JC ;

Fry, B ;

Maller, J ;

Daly, MJ .

BIOINFORMATICS, 2005, 21 (02) :263-265

[4] Mapping complex disease loci in whole-genome association studies [J].

Carlson, CS ;

Eberle, MA ;

Kruglyak, L ;

Nickerson, DA .

NATURE, 2004, 429 (6990) :446-452

[5]

CHURCHILL GA, 1994, GENETICS, V138, P963

[6] Linkage disequilibrium mapping in isolated populations: The example of Finland revisited [J].

De La Chapelle, A ;

Wright, FA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (21) :12416-12423

[7]

Doerge RW, 1996, GENETICS, V142, P285

[8]

Eaves IA, 2000, NAT GENET, V25, P320

[9] The International HapMap Project [J].

Gibbs, RA ;

Belmont, JW ;

Hardenbol, P ;

Willis, TD ;

Yu, FL ;

Yang, HM ;

Ch'ang, LY ;

Huang, W ;

Liu, B ;

Shen, Y ;

Tam, PKH ;

Tsui, LC ;

Waye, MMY ;

Wong, JTF ;

Zeng, CQ ;

Zhang, QR ;

Chee, MS ;

Galver, LM ;

Kruglyak, S ;

Murray, SS ;

Oliphant, AR ;

Montpetit, A ;

Hudson, TJ ;

Chagnon, F ;

Ferretti, V ;

Leboeuf, M ;

Phillips, MS ;

Verner, A ;

Kwok, PY ;

Duan, SH ;

Lind, DL ;

Miller, RD ;

Rice, JP ;

Saccone, NL ;

Taillon-Miller, P ;

Xiao, M ;

Nakamura, Y ;

Sekine, A ;

Sorimachi, K ;

Tanaka, T ;

Tanaka, Y ;

Tsunoda, T ;

Yoshino, E ;

Bentley, DR ;

Deloukas, P ;

Hunt, S ;

Powell, D ;

Altshuler, D ;

Gabriel, SB ;

Qiu, RZ .

NATURE, 2003, 426 (6968) :789-796

[10]

JORDE LB, 1995, AM J HUM GENET, V56, P11

← 1 2 3 →