Quantitative Trait Loci (QTL) References

QTL References with Links

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QTL References by Subject Areas

Genetic Linkage & Linkage Maps

Meiosis and Crossover Biology
Zickler, Kleckner (1999)
Map Construction
Lander et al. (1987); Lander, Green (1987); Stam (1993); Stephens, Smith (1993); Thompson (1994); Morton (1995); Kruglyak (1997); Jones (2000); van Os et al. (2005); Shifman et al. (2006); West et al. (2006)
Genotyping Errors
Lincoln, Lander (1992); Ehm, Kimmel, Cottingham (1996); Stringham, Boehnke (1996); Sybenga (1996); Goldstein, Zhao, Speed (1997); Broman, Weber (1998); Broman (1999); Keller (1999); Goring, Terwilliger (2000); Thallman et al. (2001a, 2001b); Rosa, Yandell, Gianola (2002)

QTL Overview

Tanksley (1993); Lander, Schork (1994); Basten, Weir, Zeng (1995); Paterson (1995); Doerge, Zeng, Weir (1997); Kearsey, Farquhar (1998); Broman (2001); Mackay (2001a,b); Mauricio (2001); Asíns (2002); Boake et al. (2002); Phillips, Belknap (2002); Hackett (2003); FAO (2004); Collard et al. (2005); Swertz, Jansen (2007); Stein (2008); Xu, Crouch (2008)

From QTL to Gene

Guo, Lange (2000); Nadeau, Frankel (2000); Flint, Mott (2001); Glazier, Nadeau, Aitman (2002); Korstanje, Paigen (2002); Botstein, Risch (2003); Page et al. (2003); Rebbeck, Spitz, Wu (2004); Barendse (2005); Darvasi (2005); Hirschorn, Daly (2005); Petretto, Liu, Aitman (2007); Verdugo et al. (2010) [see Fine mapping under Linkage Disequilibrium]

Experimental Design

Soller, Brody, Genizi (1976); Weller, Kashi, Soller (1990); Cockerham, Zeng (1996); Liu, Zeng (2000); Schork (2002); Bueno Filho, Gilmour (2003); Jin et al. (2004); Vision et al. (2004); Howad et al. (2005); Jannick (2005); Wang et al. (2005); Xu, Zou, Vision (2005); Fu, Jansen (2006); Nettleton, Wang (2006); Rosa, de Leon, Rosa (2006); Wang, Nettleton (2006); Zou, Xu, Vision (2006); Sen et al. (2007); Lam et al. (2008)

Marker Regression Analysis

Single Marker Analysis

Sax K (1923); Rasmusson JM (1933); McMillan I, Robertson A (1974); Soller, Brody, Genizi (1976); Cowen (1989); Moreno-Gonzalez (1992, 1993); Kearsey MJ, Hyne V (1994); Hyne V, Kearsey MJ (1995)

Least Squares Mapping

Lande, Thompson (1990); Knapp (1991); Haley, Knott (1992); Martinez, Curnow (1992); Zeng (1993); Haley, Knott, Elsen (1994); Rebaï, Goffinet, Mangin (1995); Whittaker, Thompson, Visscher (1996); Xu (1997); Feenstra, Skovgaard (2004); Feenstra, Skovgaard, Broman (2006);

Interval Mapping (IM) for Single QTL

Interval Mapping (IM)

Paterson et al. (1988); Lander, Botstein (1989); Carbonell, Gerig (1991); Carbonell, Gerig, Balansard, Asin (1992); Luo, Kearsey (1992); van Ooijen (1992); Jansen (1993); Luo, Williams (1993)

Composite Interval Mapping (CIM or MQM)

Jansen, Stam (1994); Zeng (1994); Jiang, Zeng (1997) Piepho, Gauch (2001); Hayashi, Awata, Yasue (2002); Gao, Yang (2006)

Cautions about Interval Mapping

Beavis (1994); Georges et al. (1995); Beavis (1998); Beavis, Keim (1996); Melchinger, Utz, Schon (1998); Kao (2000); Utz, Melchinger, Schon (2000); Bernardo (2001); Xu (2003)

Multiple Interval Mapping (MIM)

Haley, Knott (1992); Frankel, Schork (1996); Jansen (1996); Liu et al. (1996); Kao, Zeng (1997); Kao, Zeng, Teasdale (1999); Weber et al. (1999); Zeng, Kao, Basten (1999); Carlborg et al. (2000); Kao (2000); Otto, Jones (2000); Zeng et al. (2000); Cordella et al. (2001); Jannink, Jansen (2001); Corander, Sillanpää (2002); Kao, Zeng (2002); Chen (2004); Chen, Chen (2005); Zeng, Wang, Zou (2005).

Bayesian Interval Mapping

Thomas, Cortessis (1992); Hoeschele, van Raden (1993a, 1993b); Satagopan, Yandell (1996); Satagopan, Yandell, Newton, Osborn (1996); Heath (1997); Hoeschele et al. (1997); Uimari, Hoeschele (1997); Berry (1998); Sillanpää, Arjas (1998); Stephens, Fisch (1998); Sillanpää, Arjas (1999); Bink, Janss, Quaas (2000); Sen, Churchill (2001); Corander, Sillanpää (2002); Sillanpää, Corander (2002); van de Ven (2004); Wang et al. (2005); Yi et al. (2005); Yandell et al. (2007); Yi, Shriner et al. (2007); Zhang, Zhang (2007)

Model Selection for Multiple QTL

Ball (2001); Broman, Speed (2002); Sillanpää, Corander (2002)

Epistasis & Multiple QTL

Bateson (1909, 1913); Fisher (1918); Falconer (1952); Cockerham (1954); Haley, Knott (1992); Cheverud, Routman (1995); Doebley, Stec, Gustus (1995); Gibson (1996); Chase, Adler, Lark (1997); Routman, Cheverud (1997); -Phillips (1998); Lukens, Doebley (1999); Wang, Zhu, Paterson (1999); -Phillips, Otto, Witlock (2000); Zeng et al. (2000); Cordella et al. (2001); Hansen, Wagner (2001); -Nadeau (2001); Jannink, Jansen (2001); Sen, Churchill (2001); Shimomura et al. (2001); Sugiyama et al. (2001); -Wade (2001); Boer et al. (2002); Carlborg (2002);' Carlborg et al. (2002); Cordell (2002); Kao, Zeng (2002); Ljungberg et al. (2002); Yi, Xu (2002); Carlborg et al. (2003); Ljungberg et al. (2003); -Moore (2003); Barton, Turelli (2004); Carlborg, Haley (2004); Narita, Sasaki (2004); Yang (2004); -Malmberg, Mauricio (2005); -Marchini, Donnelly, Cardon (2005); Moore (2005); Wang, Zeng (2005); -Weinrich, Watson, Chao (2005); Yi et al. (2005); Zeng, Wang, Zou (2005); Zhang et al. (2005); Zhang, Xu (2005); -Azevedo et al. (2006); -Demuth, Wade (2006); Hansen (2006); Mao et al. (2006); -McKinney et al. (2006); -Otto, Gerstein (2006); Turelli, Barton (2006); Álvarez-Castro, Carlborg (2007); -Holland (2007); -Musani (2007); Phillips (2008); Wang, Elston, Zhu (2010)

Segregation Distortion Loci (SDL)

Vogl, Xu (2000); Carr, Dudash (2003); Luo, Xu (2003)

Thresholds & Resampling

Permutation Thresholds

Goffinet, Loisel, Lawrent (1992); Churchill, Doerge (1994); Lander, Kruglyak (1995); Doerge, Churchill (1996); Mangin, Goffinet (1997); Nettleton, Doerge (2000); Zou et al. (2004); Jin, Fine, Yandell (2006); Churchill, Doerge (2008)

Threshold Theory

Lander, Botstein (1989); Feingold, Brown, Siegmund (1993); Mangin, Goffinet, Rebaï (1994); Rebaï, Goffinet, Mangin (1994); Goffinet, Mangin (1998); Dupuis, Siegmund (1999); Kao (2000); Zou et al. (2004); Shi, Siegmund, Yakir (2007)

Cross-validation and Bootstrap

Visscher, Thompson, Haley (1996); Melchinger, Utz, Schon (1998); Utz, Melchinger, Schon (2000)

Multiple Correlated Traits

Multiple Trait Mapping

Jiang, Zeng (1995); Korol, Ronin, Kirzhner (1995); Almasy et al. (1997) Henshall, Goddard (1999); Knott, Haley (2000); Vieira et al. (2000); Ma, Casella, Wu (2002); Chesler et al. (2003); Gilbert, Le Roy (2003); Jansen (2003); Kraft, Horvath (2003); Lund et al. (2003); Gilbert, Le Roy (2004)

Principal Components

Liu et al. (1996); Mangin, Thoquet, Grimsley (1998); Zeng et al. (2000); Korol et al. (2001); Mahler et al. (2002)

eQTL & Microarray Gene Expression

Cis-action: Brem et al. (2002); Rockman, Wray (2002); Lan et al. (2003); Schadt et al. (2003); Pastinen, Hudson (2004); Doss et al. (2005); Ronald et al. (2005); Costanzo et al. Andrews (2006); GuhaThakurta et al. (2006); Hughes et al. (2006); Kiekens et al. (2006); Zhang et al. (2006); Boone, Bussey, Andrews (2007); Liang et al. (2007); Liu, Lin, Ghosh (2007); Luo et al. (2007); Akavia, Benayahu ( Chaibub Neto et al. (2008); Ferrara et al. (2008); Quigley et al. (2009)

Non-Normal, Non-parametric & Semi-parametric QTL

Non-Normal

General
Jansen (1992); Hackett (1997); von Rohr, Hoeschele (2002); Yang, Yi, Xu (2006)
Counts/poisson/negative binomial
Wright (1934a,b); Mackay, Fry (1996); Shepel et al. (1998); Lan et al. (2001); Mao, Xu (2004)
Categorical/ordinal/binomial
Falconer (1965); Hackett, Weller (1995); Visscher, Haley, Knott (1996); Xu et al. (1998); Xu, Atchley (1996); Xu, Yi (1999a,b); McIntyre, Coffman, Doerge (2000); Rao, Li (2000); Yi, Xu (2000a); Broman (2003); Coffman et al. McIntyre (2005); Li, Wang, Zeng (2006); Huang et al. Zou (2007); Yi, Banerjee et al. Yandell (2007)

Semi-Parametric & Non-Parametric

Ordered alternative/stochastic ordering
Nettleton, Praestgaard (1998); Nettleton (1999); Hoff et al. (2002); Nettleton (2002)
Semi-parametric
Zou, Fine, Yandell (2000); Lange, Whittaker (2001); Symons et al. (2002); Zou, Fine (2002); Diao, Lin (2005); Jin, Fine, Yandell (2006); Cheng, Tzeng (2009)
Survival/censoring
Symons et al. (2002); Epstein et al. (2003); Diao et al. (2004); Fine, Zou, Yandell (2004)
Non-parametric
Kruglyak, Lander (1995); Poole, Drinkwater (1996); Broman (2003); Basrak et al. (2004); Fine, Zou, Yandell (2004); Li, Boehnke, Abecasis, Song (2006); Zak et al. (2007)

Quantitative and Qualitative Traits

Williams et al. (1999); Broman (2003); Lund et al. (2003)

Outbred Populations / Combining Multiple Crosses

Genome-wide Association Studies

Stranger et al. Dermitzakis (2005); Cheung et al. Burdick (2005) Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University and Novartis Institutes for BioMedical Research et al. Purcell (2007); Dixon et al. Cookson (2007); Frayling (2007); Gudmundsson et al. (2007); Scott et al. Boehnke (2007); Shi, Lee, Wahba (2007); Sladek et al. Frogue (2007); Zeggini et al. Hattersley (2007); Zhu et al. Schadt (2007); Geiger et al. Suhre (2008); Kwee et al. Epstein (2008); Melzer et al. Ferrucci (2008); Moskvina, Schmidt (2008); Shi et al. Klein (2008); Slegen et al. Langefeld (2008)

Linkage Disequilibrium & Association Mapping

Quantitative traits
Risch, Merikangus (1996); Andersson (2001); Meuwissen et al. (2002); Perez-Enciso (2003); Andersson, Georges (2004); Grapes et al. (2004); Goddard, Meuwissen (2005); Slate(2005); Zhao et al. (2007); Lee et al. (2008)
Qualitative traits
Ohta, Kimura (1971); Sved (1971); Hill (1975); Kingman (1982); Hill, Weir (1994); Devlin, Risch (1995); Kaplan, Weir (1995); Guo, Xiong (1997); Laitinen et al. (1997); Thompson, Neel (1997); Slatkin (1999); Huang, Jiang (2000); Jorde (2000); McVean (2002); Morton (2005); Prentice, Qi (2006)
Population substructure and TDT
Spielman et al. (1993); Devlin, Roeder (1999); Pritchard, Stephens, Donnelly (2000); Pritchard et al. Donnelly (2000); Devlin, Roeder, Wasserman (2001); Pritchard and Donnelly (2001); Hanson et al. Sandkuijl (2006)
LD mapping for qualitative traits via multipoint mapping from case-control data
Service et al. (1999); McPeek and Strahs (1999); Morris, Whittaker Balding (2000); Lam, Roeder, Devlin (2000); Liu et al. Risch (2001); Rannala, Reeve (2001); Morris, Whittaker, Balding (2002); Morris et al. Balding (2003); Strahs and McPeek (2003); Morris, Whittaker, Balding (2004)
Fine mapping [see From QTL to Gene]
Lai et al. (1994) Nachman, Hoekstra, D'Agostino (2003); Wilson et al. (2004); Hirschhorn, Daly (2005); Cline, Kent (2009)

Isolated Founder Populations

Hastbacka et al. (1992); Hastbacka et al (1994); Abney, McPeek, Ober (2000); Abney, McPeek, Ober (2001); Abney, Ober, McPeek (2002).

Outbred Pedigrees

Elston, Stewart (1971); Amos (1994); Almasy et al. (1997); Almasy, Blangero (1998); Blangero, Williams, Almasy (2000); Xu, Yi (2000); Yi, Xu (2000b); Blangero, Williams, Almasy (2001); Hoeschele (2001); Wu, Zeng (2001); Wu, Ma, Casella (2002)

Outbred Crosses

Xu (1996); Butcher et al. (2002)

Combining Data Across Experiments

Fernando, Grossman (1989); Bernardo (1994); Fernando, Stricker, Elston (1994); Bernardo (1995); Jiang, Zeng (1995); Stricker, Fernando, Elston (1995); Fisch, Ragot, Gay (1996); Grignola et al. (1996); Goffinet, Gerber (2000); Liu, Zeng (2000); Piepho (2000); Zou, Yandell, Fine (2001)

Epistasis and Sewall Wright's Shifting Balance Theory

Wright (1931) Fisher, Ford (1950); Wright (1988); Coyne, Barton, Turelli (1997); Wade, Goodnight (1997); Peck, Ellner, Gould (1998); Coyne, Barton, Turelli (2000); Peck, Ellner, Gould (2000); Wade, Goodnight (2000)
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Brian Yandell (yandell@stat.wisc.edu)