Association mapping with single-feature polymorphisms

Genetics
Sung KimPaul Marjoram

Abstract

We develop methods for exploiting "single-feature polymorphism" data, generated by hybridizing genomic DNA to oligonucleotide expression arrays. Our methods enable the use of such data, which can be regarded as very high density, but imperfect, polymorphism data, for genomewide association or linkage disequilibrium mapping. We use a simulation-based power study to conclude that our methods should have good power for organisms like Arabidopsis thaliana, in which linkage disequilibrium is extensive, the reason being that the noisiness of single-feature polymorphism data is more than compensated for by their great number. Finally, we show how power depends on the accuracy with which single-feature polymorphisms are called.

References

Sep 13, 1996·Science·N Risch, K Merikangas
Aug 26, 1998·Science·E A WinzelerR W Davis
Oct 30, 1998·American Journal of Human Genetics·J Graham, E A Thompson
Mar 31, 1999·Proceedings of the National Academy of Sciences of the United States of America·R A KittlesD Goldman
Jun 3, 2000·American Journal of Human Genetics·A P MorrisD J Balding
Jul 14, 2001·Science·J C StephensG F Vovis
Oct 5, 2001·Nature Genetics·M J DalyE S Lander
Oct 5, 2001·Nature Genetics·G C JohnsonJ A Todd
Oct 10, 2001·Genome Research·J S LiuN Risch
Feb 12, 2002·American Journal of Human Genetics·A P MorrisD J Balding
May 25, 2002·Science·Stacey B GabrielDavid Altshuler
Jan 16, 2003·Current Biology : CB·Michael P H Stumpf, David B Goldstein
Mar 6, 2003·Genome Research·Justin O BorevitzJoanne Chory
Nov 14, 2003·Human Heredity·Duncan C ThomasPaul Marjoram
Nov 25, 2003·American Journal of Human Genetics·John MolitorDuncan Thomas
Mar 30, 2004·American Journal of Human Genetics·Nikolas ManiatisNewton E Morton
Mar 31, 2004·Nature Genetics·Jonathan MarchiniPeter Donnelly
May 19, 2004·American Journal of Human Genetics·Caroline DurrantAndrew P Morris
Sep 17, 2004·Genetics·Mikko J Sillanpää, Madhuchhanda Bhattacharjee
Oct 19, 2004·Genetics·Sebastian Zöllner, Jonathan K Pritchard
Dec 14, 2004·Human Genomics·John MolitorDuncan Thomas
Jan 8, 2005·Genetic Epidemiology·Kathryn RoederB Devlin
Jan 8, 2005·Genetic Epidemiology·Alessandro RinaldoKathryn Roeder
Feb 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jonathan D WernerDetlef Weigel
Feb 24, 2005·Genetic Epidemiology·Jung-Ying Tzeng
May 10, 2005·Nature Genetics·Alec J JeffreysPeter Donnelly
May 24, 2005·PLoS Biology·Magnus NordborgJoy Bergelson
Jun 18, 2005·Genome Biology·Nils RostoksRobbie Waugh
Aug 4, 2005·PLoS Biology·Thomas L TurnerSergey V Nuzhdin
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
Feb 3, 2006·BMC Genetics·John MolitorPaul Marjoram

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Citations

Oct 17, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Amir ShermanRon Ophir
Apr 19, 2007·Nucleic Acids Research·Prasanna R BhatTimothy J Close
Aug 28, 2009·BMC Genetics·Wayne Wenzhong XuGary J Muehlbauer
May 10, 2008·BMC Proceedings·Hsuan JungPaul Marjoram
Jul 22, 2006·PLoS Biology·Ayellet V SegrèJun-Yi Leu
Mar 21, 2007·PloS One·Rajesh KumarHenry T Nguyen
May 17, 2006·Genetics·Rong JiangSimon Tavaré
Jul 31, 2007·Genetics·Judith M KolkmanSteven J Knapp
Jul 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Justin O BorevitzJoseph R Ecker
Feb 7, 2009·Current Opinion in Plant Biology·Ritsert C JansenLauren M McIntyre
Jan 24, 2009·Current Opinion in Plant Biology·Joost J B Keurentjes
Apr 10, 2007·Trends in Plant Science·Tong Zhu, John Salmeron
Sep 13, 2012·Molecular Ecology Resources·Matthew L SettlesBarrie D Robison

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