Recent Publications

Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W.
DeMix: deconvolution for mixed cancer transcriptomes using raw measured data.
Bioinformatics.  2013 Aug 1;29(15):1865-71. doi: 10.1093/bioinformatics/btt301. Epub 2013 May 27.


Bhatia G, Patterson NJ, Sankararaman S, Price AL.
Estimating and interpreting Fst: the impact of rare variants.
Genome Res.  2013 Jul 16. [Epub ahead of print]


Qiao D, Mattheisen M, Lange C.
On association analysis of rare variants under population substructure: an approach for the detection of subjects that can cause bias in the analysis-topt: an outlier detection method.
Genet Epidemiol. 2013 Jul;37(5):431-9. doi: 10.1002/gepi.21734. Epub 2013 May 14.


Zhang M, Song F, Liang L, Nan H, Zhang J, Liu H, Wang LE, Wei Q, Lee JE, Amos CI, Kraft P, Qureshi AA, Han J.
Genome-wide association studies identify several new loci associated with pigmentation traits and skin cancer risk in European Americans.
Hum Mol Genet.  2013 Jul 15;22(14):2948-59. doi: 10.1093/hmg/ddt142. Epub 2013 Apr 1.


Lee S, Teslovich TM, Boehnke M, Lin X.
General Framework for Meta-analysis of Rare Variants in Sequencing Association Studies.
Am J Hum Genet.  2013 Jul 11;93(1):42-53. doi: 10.1016/j.ajhg.2013.05.010. Epub 2013 Jun 13.


Huang YT, Lin X.
Gene set analysis using variance component tests.
BMC Bioinformatics.  2013 Jun 28;14:210. doi: 10.1186/1471-2105-14-210.


Biswas S, Atienza P, Chipman J, Hughes K, Barrera AM, Amos CI, Arun B, Parmigiani G.
Simplifying clinical use of the genetic risk prediction model BRCAPRO.
Breast Cancer Res Treat.  2013 Jun;139(2):571-9. doi: 10.1007/s10549-013-2564-4. Epub 2013 May 21.


Won S, Lange C.
A general framework for robust and efficient association analysis in family-based designs: quantitative and dichotomous phenotypes.
Stat Med.  2013 Jun 6. doi: 10.1002/sim.5865. [Epub ahead of print]


Huang J, Chen J, Lathrop M, Liang L.
A tool for RNA sequencing sample identity check.
Bioinformatics.  2013 Jun 1;29(11):1463-4. doi: 10.1093/bioinformatics/btt155. Epub 2013 Apr 4.


Chen CY, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL.
Improved ancestry inference using weights from external reference panels.
Bioinformatics. 2013 June 1;29(11):1399-406.


Zaitlen N, Kraft P, Patterson N, Pasaniuc B, Bhatia G, Pollack S, Price AL.
Using extended genealogy to estimate components of heritability for 23 quantitative and dichotomous traits.
PLoS Genet.  2013 May;9(5):e1003520. doi: 10.1371/journal.pgen.1003520. Epub 2013 May 30.


Gorfine M, Hsu L, Zucker DM, Parmigiani G.
Calibrated predictions for multivariate competing risks models.
Lifetime Data Anal.  2013 May 31. [Epub ahead of print]


Fung WL, Naylor MG, Bennett DA, Lange C, Blacker D.
Principal Components Methods for Narrow-Sense Heritability in the Analysis of Multidimensional Longitudinal Cognitive Phenotypes.
Am J Med Genet B Neuropsychiatr Genet.  2013 May 6. doi: 10.1002/ajmg.b.32151. [Epub ahead of print]


Li L, Kabesch M, Bouzigon E, Demenais F, Farrall M, Moffatt MF, Lin X, Liang L.
Using eQTL Weights to Improve Power for Genome-wide Association Studies; A Genetic Study of Childhood Asthma.
Front Genet.  2013 May 31;4:103. doi: 10.3389/fgene.2013.00103.


Wu C, Chang J, Ma B, Miao X, Zhou Y, Liu Y, Li Y, Wu T, Hu Z, Shen H, Jia W, Zeng Y, Lin D, Kraft P.
The case-only test for gene-environment interaction is not uniformly powerful: an empirical example.
Genet Epidemiol.  2013 May;37(4):402-7. doi: 10.1002/gepi.21713. Epub 2013 Mar 13.


Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X.
Sequence Kernel Association Tests for the Combined Effect of Rare and Common Variants.
Am J Hum Genet.  2013 May 14. pii: S0002-9297(13)00176-6. doi: 10.1016/j.ajhg.2013.04.015. [Epub ahead of print]


Aschard H, Zaitlen N, Tamimi RM, Lindström S, Kraft P.
A Nonparametric Test to Detect Quantitative Trait Loci Where the Phenotypic Distribution Differs by Genotypes.
Genet Epidemiol. 2013 May;37(4):323-33. doi: 10.1002/gepi.21716. Epub 2013 Mar 19


Schifano ED, Li L, Christiani DC, Lin X.
Genome-wide association analysis for multiple continuous secondary phenotypes.
Am J Hum Genet.  2013 May 2;92(5):744-59. doi: 10.1016/j.ajhg.2013.04.004.


Kantor DB, Palmer CD, Young TR, Meng Y, Gajdos ZK, Lyon H, Price AL, Pollack S, London SJ, Loehr LR, Smith LJ, Kumar R, Jacobs Jr DR, Petrini MF, O’Connor GT, White WB, Papanicolaou G, Burkart KM, Heckbert SR, Barr RG, Hirschhorn JN.
Replication and fine-mapping of asthma-associated loci in individuals of African ancestry.
Hum Genet. 2013 May [Epub ahead of print]


Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA.
Using population admixture to help complete maps of the human genome.
Nat Genet. 2013 Apr;45(4):406-14.


Siedlinski M, Tingley D, Lipman PJ, Cho MH, Litonjua AA, Sparrow D, Bakke P, Gulsvik A, Lomas DA, Anderson W, Kong X, Rennard SI, Beaty TH, Hokanson JE, Crapo JD, Lange C, Silverman EK; and the COPDGene and ECLIPSE Investigators.
Dissecting direct and indirect genetic effects on chronic obstructive pulmonary disease (COPD) susceptibility.
Hum Genet.  2013 Apr;132(4):431-41. doi: 10.1007/s00439-012-1262-3. Epub 2013 Jan 9.


Lin X, Lee S, Christiani DC, Lin X.
Test for interactions between a genetic marker set and environment in generalized linear models.
Biostatistics.  2013 Mar 5. [Epub ahead of print]


Dicker L, Lin X.
Parallelism, uniqueness, and large-sample asymptotics for the Dantzig selector.
Can J Stat.  2013 Mar 1;41(1):23-35.


Lutz S, Yip WK, Hokanson J, Laird N, Lange C.
A general semi-parametric approach to the analysis of genetic association studies in population-based designs.
BMC Genet.  2013 Feb 28;14:13. doi: 10.1186/1471-2156-14-13.


Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X.
Family-based association tests for sequence data, and comparisons with population-based association tests.
Eur J Hum Genet.  2013 Feb 6.  doi: 10.1038/ejhg.2012.308 [Epub ahead of print]


Pasquale LR, Loomis SJ, Aschard H, Kang JH, Cornelis MC, Qi L, Kraft P, Hu FB.
Exploring genome-wide- dietary heme iron intake interactions and the risk of type 2 diabetes.
Front Genet.  2013;4:7. doi: 10.3389/fgene.2013.00007. Epub 2013 Jan 30.


Thompson JR, Gögele M, Weichenberger CX, Modenese M, Attia J, Barrett JH, Boehnke M, De Grandi A, Domingues FS, Hicks AA, Marroni F, Pattaro C, Ruggeri F, Borsani G, Casari G, Parmigiani G, Pastore A, Pfeufer A, Schwienbacher C, Taliun D, Consortium C, Fox CS, Pramstaller PP, Minelli C.
SNP prioritization using a Bayesian probability of association.
Genet Epidemiol.  2013 Feb;37(2):214-21. 


Minelli C, De Grandi A, Weichenberger CX, Gögele M, Modenese M, Attia J, Barrett JH, Boehnke M, Borsani G, Casari G, Fox CS, Freina T, Hicks AA, Marroni F, Parmigiani G, Pastore A, Pattaro C, Pfeufer A, Ruggeri F, Schwienbacher C, Taliun D, Pramstaller PP, Domingues FS, Thompson JR.
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up.
Genet Epidemiol.  2013 Feb;37(2):205-13.


Barnett IJ, Lee S, Lin X.
Detecting rare variant effects using extreme phenotype sampling in sequencing association studies.
Genet Epidemiol.  2013 Feb;37(2):142-51. 


De G, Yip WK, Ionita-Laza I, Laird NM.
Rare variant analysis for family-based design.
PLoS One.  2013;8(1):e48495.  doi: 10.1371/journal.pone.0048495.  PMCID: PMC3546113.


Hiraki LT, Major JM, Chen C, Cornelis MC, Hunter DJ, Rimm EB, Simon KC, Weinstein SJ, Purdue MP, Yu K, Albanes D, Kraft P.
Exploring the genetic architecture of circulating 25-hydroxyvitamin D.
Genet Epidemiol. 2013 Jan;31(1):92-8.


Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Diaz LA Jr, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD.
Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. 
Nat Genet.  2013 Jan;45(1):12-7.  PMCID: PMC3557959.


Fier H, Won S, Prokopenko D, AlChawa T, Ludwig KU, Fimmers R, Silverman EK, Pagano M, Mangold E, Lange C.
‘Location, Location, Location’: A spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate.
Bioinformatics.  2012 Dec;28(23):3027-33.  PMCID: PMC3516147.


Sofer T, Maity A, Coull B, Baccarelli A, Schwartz J, Lin X.
Multivariate gene selection and testing in studying the exposure effects on a gene set.
Stat Biosci.  2012 Nov;4(2):319-338.  PMCID: PMC3524591.


Zaitlen N, Lindström S, Pasaniuc B, Cornelis M, Genovese G, Pollack S, Barton A, Bickeböller H, Bowden DW, Eyre S, Freedman BI, Friedman DJ, Field JK, Groop L, Haugen A, Heinrich J, Henderson BE, Hicks PJ, Hocking LJ, Kolonel LN, Landi MT, Langefeld CD, Le Marchand L, Meister M, Morgan AW, Raji OY, Risch A, Rosenberger A, Scherf D, Steer S, Walshaw M, Waters KM, Wilson AG, Wordsworth P, Zienolddiny S, Tchetgen ET, Haiman C, Hunter DJ, Plenge RM, Worthington J, Christiani DC, Schaumberg DA, Chasman DI, Altshuler D, Voight B, Kraft P, Patterson N, Price AL.
Informed conditioning on clinical covariates increases power in case-control association studies.
PLoS Genet.  2012 Nov;8(11):e1003032. doi: 10.1371/journal.pgen.1003032.


Vansteelandt S, Lange C.
Causation and causal inference for genetic effects.
Hum Genet.  2012 Oct;131(10):1665-76.


Cai T, Lin X, Carroll RJ.
Identifying genetic marker sets associated with phenotypes via an efficient adaptive score test.
Bioinformatics.  2012 Sep;13(4):776-90.  PMCID: PMC3440238.


Wang C, Parmigiani G, Dominici F.
Bayesian effect estimation accounting for adjustment uncertainty
Biometrics.  2012 Sep;68(3):661-71.


Ludwig KU, Mangold E, Herms S, Nowak S, Reutter H, Paul A, Becker J, Herberz R, AlChawa T, Nasser E, Böhmer AC, Mattheisen M, Alblas MA, Barth S, Kluck N, Lauster C, Braumann B, Reich RH, Hemprich A, Pötzsch S, Blaumeiser B, Daratsianos N, Kreusch T, Murray JC, Marazita ML, Ruczinski I, Scott AF, Beaty TH, Kramer FJ, Wienker TF, Steegers-Theunissen RP, Rubini M, Mossey PA, Hoffmann P, Lange C, Cichon S, Propping P, Knapp M, Nöthen MM.
Genome-wide meta-analyses of nonsyndromic cleft clip with or without cleft palate identify six new risk loci.
Nat Genet.  2012 Sep;44(9):968-71. 


Lee S, Wu MC, Lin X.
Optimal tests for rare variant effects in sequencing association studies.
Biostatistics.  2012 Sep;13(4):762-75.  PMCID: PMC3440237.


Schifano ED, Epstein MP, Bielak LF, Jhun MA, Kardia SL, Peyser PA, Lin X.
SNP set association analysis for familial data.
Genet Epidemiol.  2012 Sep 11.  doi: 10.1002/gepi.21676.


Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA; NHLBI GO Exome Sequencing Project—ESP Lung Project Team, Christiani DC, Wurfel MM, Lin X.
Optimal unified approach for rare-variant association testing with application to small-sample case-control whole-exome sequencing studies.
Am J Hum Genet.  2012 Aug;91(2):224-237. 


Coviello AD, Haring R, Wellons M, Vaidya D, Lehtimäki T, Keildson S, Lunetta KL, He C, Fornage M, Lagou V, Mangino M, Onland-Moret NC, Chen B, Eriksson J, Garcia M, Liu YM, Koster A, Lohman K, Lyytikäinen LP, Petersen AK, Prescott J, Stolk L, Vandenput L, Wood AR, Zhuang WV, Ruokonen A, Hartikainen AL, Pouta A, Bandinelli S, Biffar R, Brabant G, Cox DG, Chen Y, Cummings S, Ferrucci L, Gunter MJ, Hankinson SE, Martikainen H, Hofman A, Homuth G, Illig T, Jansson JO, Johnson AD, Karasik D, Karlsson M, Kettunen J, Kiel DP, Kraft P, Liu J, Ljunggren O, Lorentzon M, Maggio M, Markus MR, Mellström D, Miljkovic I, Mirel D, Nelson S, Morin Papunen L, Peeters PH, Prokopenko I, Raffel L, Reincke M, Reiner AP, Rexrode K, Rivadeneira F, Schwartz SM, Siscovick D, Soranzo N, Stöckl D, Tworoger S, Uitterlinden AG, van Gils CH, Vasan RS, Wichmann HE, Zhai G, Bhasin S, Bidlingmaier M, Chanock SJ, De Vivo I, Harris TB, Hunter DJ, Kähönen M, Liu S, Ouyang P, Spector TD, van der Schouw YT, Viikari J, Wallaschofski H, McCarthy MI, Frayling TM, Murray A, Franks S, Järvelin MR, de Jong FH, Raitakari O, Teumer A, Ohlsson C, Murabito JM, Perry JR.
A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation.
PLoS Genet.  2012 Jul;8(7):e1002805.  Epub 2012 Jul 19.  PMCID: PMC3400553.


Wang XV, Blades N, Ding J, Sultana R, Parmigiani G.
Estimation of sequencing error rates in short reads.
BMC Bioinformatics.  2012 Jul;13:185. doi: 10.1186/1471-2105-13-185.  PMCID: PMC3495688.


Adhikari K, Alchawa T, Ludwig K, Mangold E, Laird N, Lange C
Is it rare or common?
Genet Epidemiol. 2012 Jul;36(5):419-29


Aschard H, Chen J, Cornelis MC, Chibnik LB, Karlson EW, Kraft P.
Inclusion of gene-gene and gene-environment interactions unlikely to dramatically improve risk prediction for complex diseases.
Am J Hum Genet.  2012 Jun;90(6):962-972.  PMCID: PMC3370279.


Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR.
Exome sequencing and the genetic basis of complex traits.
Nat Genet.  2012 May;44(6):623-630


Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P, Sullivan PF, Bergen S, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Purcell SM, Haas DW, Liang L, Sunyaev S, Patterson N, de Bakker PI, Reich D, Price AL.
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies.
Nat Genet.  2012 May;44(6):631-635.


Perry JR, Voight BF, Yengo L, Amin N, Dupuis J, Ganser M, Grallert H, Navarro P, Li M, Qi L, Steinthorsdottir V, Scott RA, Almgren P, Arking DE, Aulchenko Y, Balkau B, Benediktsson R, Bergman RN, Boerwinkle E, Bonnycastle L, Burtt NP, Campbell H, Charpentier G, Collins FS, Gieger C, Green T, Hadjadj S, Hattersley AT, Herder C, Hofman A, Johnson AD, Kottgen A, Kraft P, Labrune Y, Langenberg C, Manning AK, Mohlke KL, Morris AP, Oostra B, Pankow J, Petersen AK, Pramstaller PP, Prokopenko I, Rathmann W, Rayner W, Roden M, Rudan I, Rybin D, Scott LJ, Sigurdsson G, Sladek R, Thorleifsson G, Thorsteinsdottir U, Tuomilehto J, Uitterlinden AG, Vivequin S, Weedon MN, Wright AF; MAGIC; DIAGRAM Consortium; GIANT Consortium, Hu FB, Illig T, Kao L, Meigs JB, Wilson JF, Stefansson K, van Duijn C, Altschuler D, Morris AD, Boehnke M, McCarthy MI, Froguel P, Palmer CN, Wareham NJ, Groop L, Frayling TM, Cauchi S.
Stratifying type 2 diabetes cases by BMI identifies genetic risk variants in LAMA1 and enrichment for risk variants in lean compared to obese cases.
PLoS Genet.  2012 May;8(5):e1002741.  PMCID: PMC3364960.


Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET.
Patterns of cis regulatory variation in diverse human populations.
PLoS Genet.  2012 Apr;8(4):e1002639.  PMCID: PMC3330104.


Stahl EA, Wegmann D, Trynka G, Gutierrez-Achury J, Do R, Voight BF, Kraft P, Chen R, Kallberg HJ, Kurreeman FA; Diabetes Genetics Replication and Meta-analysis Consortium; Myocardial Infarction Genetics Consortium, Kathiresan S, Wijmenga C, Gregersen PK, Alfredsson L, Siminovitch KA, Worthington J, de Bakker PI, Raychaudhuri S, Plenge RM.
Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis.
Nat Genet.  2012 Mar;44(5):483-489. 


Sebro R, Lange C, Laird NM, Rogus JJ, Risch NJ.
Differentiating population stratification from genotyping error using family data.
Ann Hum Genet. 2012 Jan;76(1):42-52.


Dastani Z, Hivert MF, Timpson N, Perry JR, Yuan X, other authors, Kraft P, other authors, Cupples LA, Sandhu MS, Ridker PM, Rader DJ, Kathiresan S.
Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
PLoS Genet.  2012;8(3):e1002607.  PMCID: PMC3315470.


Castaldi PJ, Cho MH, Litonjua AA, Bakke P, Gulsvik A, Lomas DA, Anderson W, Beaty TH, Hokanson JE, Crapo JD, Laird N, Silverman EK; COPDGene and Eclipse Investigators.
The association of genome-wide significant spirometric loci with chronic obstructive pulmonary disease susceptibility.
Am J Respir Cell Mol Biol. 2011 Dec;45(6):1147-53.  PMCID: PMC3262664


Ionita-Laza I, Makarov V, Yoon S, Raby B, Buxbaum J, Nicolae DL, Lin X.
Finding disease variants in Mendelian disorders by using sequence data: methods and applications.
Am J Hum Genet.  2011 Dec;89(6):701-712.  PMCID: PMC3234377.


Hoffmann TJ, Vansteelandt S, Lange C, Silverman EK, DeMeo DL, Laird NM.
Combining disease models to test for gene-environment interaction in nuclear families.
Biometrics. 2011 Dec;67(4):1260-70. doi: 10.1111/j.1541-0420.2011.01581.x. Epub 2011 Mar 14. PMCID: PMC3120904


Yip W, De G, Raby B, and Laird NM.
Identifying Casual Variants Disease Through Family Based Analysis of GAW17 Data Set.
BMC Proc. 2011 Nov 29;5 Suppl 9:S21. PMCID: PMC3287856


Chambers JC, Zhang W, Sehmi J, Li X, Wass MN, Van der Harst P, Holm H, Sanna S, Kavousi M, Baumeister SE, Coin LJ, Deng G, Gieger C, Heard-Costa NL, Hottenga JJ, Kühnel B, Kumar V, Lagou V, Liang L, Luan J, Vidal PM, Mateo Leach I, O’Reilly PF, Peden JF, Rahmioglu N, Soininen P, Speliotes EK, Yuan X, Thorleifsson G, Alizadeh BZ, Atwood LD, Borecki IB, Brown MJ, Charoen P, Cucca F, Das D, de Geus EJ, Dixon AL, Döring A, Ehret G, Eyjolfsson GI, Farrall M, Forouhi NG, Friedrich N, Goessling W, Gudbjartsson DF, Harris TB, Hartikainen AL, Heath S, Hirschfield GM, Hofman A, Homuth G, Hyppönen E, Janssen HL, Johnson T, Kangas AJ, Kema IP, Kühn JP, Lai S, Lathrop M, Lerch MM, Li Y, Liang TJ, Lin JP, Loos RJ, Martin NG, Moffatt MF, Montgomery GW, Munroe PB, Musunuru K, Nakamura Y, O’Donnell CJ, Olafsson I, Penninx BW, Pouta A, Prins BP, Prokopenko I, Puls R, Ruokonen A, Savolainen MJ, Schlessinger D, Schouten JN, Seedorf U, Sen-Chowdhry S, Siminovitch KA, Smit JH, Spector TD, Tan W, Teslovich TM, Tukiainen T, Uitterlinden AG, Van der Klauw MM, Vasan RS, Wallace C, Wallaschofski H, Wichmann HE, Willemsen G, Würtz P, Xu C, Yerges-Armstrong LM; Alcohol Genome-wide Association (AlcGen) Consortium; Diabetes Genetics Replication and Meta-analyses (DIAGRAM+) Study; Genetic Investigation of Anthropometric Traits (GIANT) Consortium; Global Lipids Genetics Consortium; Genetics of Liver Disease (GOLD) Consortium; International Consortium for Blood Pressure (ICBP-GWAS); Meta-analyses of Glucose and Insulin-Related Traits Consortium (MAGIC), Abecasis GR, Ahmadi KR, Boomsma DI, Caulfield M, Cookson WO, van Duijn CM, Froguel P, Matsuda K, McCarthy MI, Meisinger C, Mooser V, Pietiläinen KH, Schumann G, Snieder H, Sternberg MJ, Stolk RP, Thomas HC, Thorsteinsdottir U, Uda M, Waeber G, Wareham NJ, Waterworth DM, Watkins H, Whitfield JB, Witteman JC, Wolffenbuttel BH, Fox CS, Ala-Korpela M, Stefansson K, Vollenweider P, Völzke H, Schadt EE, Scott J, Järvelin MR, Elliott P, Kooner JS.
Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
Nat Genet.  2011 Oct;43(11):1131-1138. 


Haiman CA, Chen GK, Vachon CM, Canzian F, Dunning A, Millikan RC, Wang X, Ademuyiwa F, Ahmed S, Ambrosone CB, Baglietto L, Balleine R, Bandera EV, Beckmann MW, Berg CD, Bernstein L, Blomqvist C, Blot WJ, Brauch H, Buring JE, Carey LA, Carpenter JE, Chang-Claude J, Chanock SJ, Chasman DI, Clarke CL, Cox A, Cross SS, Deming SL, Diasio RB, Dimopoulos AM, Driver WR, Dünnebier T, Durcan L, Eccles D, Edlund CK, Ekici AB, Fasching PA, Feigelson HS, Flesch-Janys D, Fostira F, Försti A, Fountzilas G, Gerty SM; Gene Environment Interaction and Breast Cancer in Germany (GENICA) Consortium, Giles GG, Godwin AK, Goodfellow P, Graham N, Greco D, Hamann U, Hankinson SE, Hartmann A, Hein R, Heinz J, Holbrook A, Hoover RN, Hu JJ, Hunter DJ, Ingles SA, Irwanto A, Ivanovich J, John EM, Johnson N, Jukkola-Vuorinen A, Kaaks R, Ko YD, Kolonel LN, Konstantopoulou I, Kosma VM, Kulkarni S, Lambrechts D, Lee AM, Marchand LL, Lesnick T, Liu J, Lindstrom S, Mannermaa A, Margolin S, Martin NG, Miron P, Montgomery GW, Nevanlinna H, Nickels S, Nyante S, Olswold C, Palmer J, Pathak H, Pectasides D, Perou CM, Peto J, Pharoah PD, Pooler LC, Press MF, Pylkäs K, Rebbeck TR, Rodriguez-Gil JL, Rosenberg L, Ross E, Rüdiger T, Silva Idos S, Sawyer E, Schmidt MK, Schulz-Wendtland R, Schumacher F, Severi G, Sheng X, Signorello LB, Sinn HP, Stevens KN, Southey MC, Tapper WJ, Tomlinson I, Hogervorst FB, Wauters E, Weaver J, Wildiers H, Winqvist R, Van Den Berg D, Wan P, Xia LY, Yannoukakos D, Zheng W, Ziegler RG, Siddiq A, Slager SL, Stram DO, Easton D, Kraft P, Henderson BE, Couch FJ.
A common variant at the TERT-CLPTM1L locus is associated with estrogen receptor-negative breast cancer.
Nat Genet.  2011 Oct;43(12):1210-1214.  PMCID: PMC3279120.


Bhatia G, Patterson N, Pasaniuc B, Zaitlen N, Genovese G, Pollack S, Mallick S, Myers S, Tandon A, Spencer C, Palmer CD, Adeyemo AA, Akylbekova EL, Cupples LA, Divers J, Fornage M, Kao WH, Lange L, Li M, Musani S, Mychaleckyj JC, Ogunniyi A, Papanicolaou G, Rotimi CN, Rotter JI, Ruczinski I, Salako B, Siscovick DS, Tayo BO, Yang Q, McCarroll S, Sabeti P, Lettre G, De Jager P, Hirschhorn J, Zhu X, Cooper R, Reich D, Wilson JG, Price AL.
Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection.
Am J Hum Genet.  2011 Sep;89(3):368-381.  PMCID: PMC3169818.


Chu X, Pan CM, Zhao SX, Liang J, Gao GQ, Zhang XM, Yuan GY, Li CG, Xue LQ, Shen M, Liu W, Xie F, Yang SY, Wang HF, Shi JY, Sun WW, Du WH, Zuo CL, Shi JX, Liu BL, Guo CC, Zhan M, Gu ZH, Zhang XN, Sun F, Wang ZQ, Song ZY, Zou CY, Sun WH, Guo T, Cao HM, Ma JH, Han B, Li P, Jiang H, Huang QH, Liang L, Liu LB, Chen G, Su Q, Peng YD, Zhao JJ, Ning G, Chen Z, Chen JL, Chen SJ, Huang W, Song HD; China Consortium for Genetics of Autoimmune Thyroid Disease.
A genome-wide association study identifies two new risk loci for Graves’ disease.
Nat Genet.  2011 Aug;43(9):897-901.


Torgerson DG, Ampleford EJ, Chiu GY, Gauderman WJ, Gignoux CR, Graves PE, Himes BE, Levin AM, Mathias RA, Hancock DB, Baurley JW, Eng C, Stern DA, Celedón JC, Rafaels N, Capurso D, Conti DV, Roth LA, Soto-Quiros M, Togias A, Li X, Myers RA, Romieu I, Van Den Berg DJ, Hu D, Hansel NN, Hernandez RD, Israel E, Salam MT, Galanter J, Avila PC, Avila L, Rodriquez-Santana JR, Chapela R, Rodriguez-Cintron W, Diette GB, Adkinson NF, Abel RA, Ross KD, Shi M, Faruque MU, Dunston GM, Watson HR, Mantese VJ, Ezurum SC, Liang L, Ruczinski I, Ford JG, Huntsman S, Chung KF, Vora H, Li X, Calhoun WJ, Castro M, Sienra-Monge JJ, del Rio-Navarro B, Deichmann KA, Heinzmann A, Wenzel SE, Busse WW, Gern JE, Lemanske RF Jr, Beaty TH, Bleecker ER, Raby BA, Meyers DA, London SJ; Mexico City Childhood Asthma Study (MCAAS), Gilliland FD; Children’s Health Study (CHS) and HARBORS study, Burchard EG; Genetics of Asthma in Latino Americans (GALA) Study, Study of Genes-Environment and Admixture in Latino Americans (GALA2) and Study of African Americans, Asthma, Genes & Environments (SAGE), Martinez FD; Childhood Asthma Research and Education (CARE) Network, Weiss ST; Childhood Asthma Management Program (CAMP), Williams LK; Study of Asthma Phenotypes and Pharmacogenomic Interactions by Race-Ethnicity (SAPPHIRE), Barnes KC; Genetic Research on Asthma in African Diaspora (GRAAD) Study, Ober C, Nicolae DL.
Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations.
Nat Genet.  2011 July;43(9):887-892.


Kote-Jarai Z, Olama AA, Giles GG, Severi G, Schleutker J, Weischer M, Campa D, Riboli E, Key T, Gronberg H, Hunter DJ, Kraft P, Thun MJ, Ingles S, Chanock S, Albanes D, Hayes RB, Neal DE, Hamdy FC, Donovan JL, Pharoah P, Schumacher F, Henderson BE, Stanford JL, Ostrander EA, Sorensen KD, Dörk T, Andriole G, Dickinson JL, Cybulski C, Lubinski J, Spurdle A, Clements JA, Chambers S, Aitken J, Gardiner RA, Thibodeau SN, Schaid D, John EM, Maier C, Vogel W, Cooney KA, Park JY, Cannon-Albright L, Brenner H, Habuchi T, Zhang HW, Lu YJ, Kaneva R, Muir K, Benlloch S, Leongamornlert DA, Saunders EJ, Tymrakiewicz M, Mahmud N, Guy M, O’Brien LT, Wilkinson RA, Hall AL, Sawyer EJ, Dadaev T, Morrison J, Dearnaley DP, Horwich A, Huddart RA, Khoo VS, Parker CC, Van As N, Woodhouse CJ, Thompson A, Christmas T, Ogden C, Cooper CS, Lophatonanon A, Southey MC, Hopper JL, English DR, Wahlfors T, Tammela TL, Klarskov P, Nordestgaard BG, Røder MA, Tybjærg-Hansen A, Bojesen SE, Travis R, Canzian F, Kaaks R, Wiklund F, Aly M, Lindstrom S, Diver WR, Gapstur S, Stern MC, Corral R, Virtamo J, Cox A, Haiman CA, Le Marchand L, Fitzgerald L, Kolb S, Kwon EM, Karyadi DM, Orntoft TF, Borre M, Meyer A, Serth J, Yeager M, Berndt SI, Marthick JR, Patterson B, Wokolorczyk D, Batra J, Lose F, McDonnell SK, Joshi AD, Shahabi A, Rinckleb AE, Ray A, Sellers TA, Lin HY, Stephenson RA, Farnham J, Muller H, Rothenbacher D, Tsuchiya N, Narita S, Cao GW, Slavov C, Mitev V, Easton DF, Eeles RA; UK Genetic Prostate Cancer Study Collaborators/British Association of Urological Surgeons’ Section of Oncology; UK ProtecT Study Collaborators, The Australian Prostate Cancer BioResource; PRACTICAL Consortium.
Seven prostate cancer susceptibility loci identified by a multi-stage genome-wide association study.
Nat Genet.  2011 Jul;43(8):785-791.  PMCID: PMC3396006.


Wu MC, Lee S, Cai T, Li Y, Boehnke M, Lin X.
Rare-variant association testing for sequencing data with the sequence kernel association test.
Am J Hum Genet.  2011 July;89(1):82-93.  PMCID: PMC3135811.


Cornelis MC, Monda KL, Yu K, Paynter N, Azzato EM, Bennett SN, Berndt SI, Boerwinkle E, Chanock S, Chatterjee N, Couper D, Curhan G, Heiss G, Hu FB, Hunter DJ, Jacobs K, Jensen MK, Kraft P, Landi MT, Nettleton JA, Purdue MP, Rajaraman P, Rimm EB, Rose LM, Rothman N, Silverman D, Stolzenberg-Solomon R, Subar A, Yeager M, Chasman DI, van Dam RM, Caporaso NE.
Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. 
PLoS Genet.  2011 Apr;7(4):e1002033.  PMCID: PMC3071630.


Lindström S, Vachon CM, Li J, Varghese J, Thompson D, Warren R, Brown J, Leyland J, Audley T, Wareham NJ, Loos RJ, Paterson AD, Rommens J, Waggott D, Martin LJ, Scott CG, Pankratz VS, Hankinson SE, Hazra A, Hunter DJ, Hopper JL, Southey MC, Chanock SJ, Silva Idos S, Liu J, Eriksson L, Couch FJ, Stone J, Apicella C, Czene K, Kraft P, Hall P, Easton DF, Boyd NF, Tamimi RM.
Common variants in ZNF365 are associated with both mammographic density and breast cancer risk.
Nat Genet.  2011 Mar;43(3):185-187.  PMCID: PMC3076615.


Ionita-Laza I, Buxbaum JD, Laird NM, Lange C.
A new testing strategy to identify rare variants with either risk or protective effect on disease.
PLoS Genet.  2011 Feb;7(2):e1001289.  PMCID: PMC3033379.


Price AL, Helgason A, Thorleifsson G, McCarroll SA, Kong A, Stefansson K.
Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals.
PLoS Genet.  2011 Feb;7(2):e1001317.  PMCID: PMC3044684.


Painter JN, Anderson CA, Nyholt DR, Macgregor S, Lin J, Lee SH, Lambert A, Zhao ZZ, Roseman F, Guo Q, Gordon SD, Wallace L, Henders AK, Visscher PM, Kraft P, Martin NG, Morris AP, Treloar SA, Kennedy SH, Missmer SA, Montgomery GW, Zondervan KT.
Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis.
Nat Genet.  2011 Jan;43(1):51-54.  PMCID: PMC3019124.


Sato Y, Yamamoto N, Kunitoh H, Ohe Y, Minami H, Laird NM, Katori N, Saito Y, Ohnami S, Sakamoto H, Sawada J, Saijo N, Yoshida T, Tamura T.
Genome-wide association study on overall survival of advanced non-small cell lung cancer patients treated with carboplatin and paclitaxel.
J Thorac Oncol. 2011 Jan;6(1):132-8. PMID: 21079520


Heid IM, Jackson AU, Randall JC, Winkler TW, Qi L, other authors, Liang L, other authors, Kraft P, other authors, Hunter DJ, Kaplan RC, North KE, O’Connell JR, Peltonen L, Schlessinger D, Strachan DP, Hirschhorn JN, Assimes TL, Wichmann HE, Thorsteinsdottir U, van Duijn CM, Stefansson K, Cupples LA, Loos RJ, Barroso I, McCarthy MI, Fox CS, Mohlke KL, Lindgren CM.
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
Nat Genet.  2010 Nov;42(11):949-960.  PMCID: PMC3000924.


Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Allen HL, Lindgren CM, Luan J, Mägi R, Randall JC, Vedantam S, Winkler TW, Qi L, Workalemahu T, Heid IM, Steinthorsdottir V, Stringham HM, Weedon MN, Wheeler E, Wood AR, Ferreira T, Weyant RJ, Segrè AV, Estrada K, Liang L, other authors, Kraft P, other authors, Hunter DJ, Kaplan RC, Mohlke KL, O’Connell JR, Peltonen L, Schlessinger D, Strachan DP, van Duijn CM, Wichmann HE, Frayling TM, Thorsteinsdottir U, Abecasis GR, Barroso I, Boehnke M, Stefansson K, North KE, McCarthy MI, Hirschhorn JN, Ingelsson E, Loos RJ.
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index.
Nat Genet.  2010 Nov;42(11):937-948.  PMCID: PMC3014648.


Kraft P, Haiman CA.
GWAS identifies a common breast cancer risk allele among BRCA1 carriers.
Nat Genet.  2010 Oct;42(10):819-820.


Saccone NL, Culverhouse RC, Schwantes-An TH, Cannon DS, Chen X, Cichon S, Giegling I, Han S, Han Y, Keskitalo-Vuokko K, Kong X, Landi MT, Ma JZ, Short SE, Stephens SH, Stevens VL, Sun L, Wang Y, Wenzlaff AS, Aggen SH, Breslau N, Broderick P, Chatterjee N, Chen J, Heath AC, Heliövaara M, Hoft NR, Hunter DJ, Jensen MK, Martin NG, Montgomery GW, Niu T, Payne TJ, Peltonen L, Pergadia ML, Rice JP, Sherva R, Spitz MR, Sun J, Wang JC, Weiss RB, Wheeler W, Witt SH, Yang BZ, Caporaso NE, Ehringer MA, Eisen T, Gapstur SM, Gelernter J, Houlston R, Kaprio J, Kendler KS, Kraft P, Leppert MF, Li MD, Madden PA, Nöthen MM, Pillai S, Rietschel M, Rujescu D, Schwartz A, Amos CI, Bierut LJ.
Multiple independent loci at chromosome 15q25.1 affect smoking quantity: a meta-analysis and comparison with lung cancer and COPD.
PLoS Genet.  2010 Aug;6(8):e1001053.  PMCID: PMC2916847.


Ionita-Laza I, Laird NM.
On the optimal design of genetic variant discovery studies.
Stat Appl Genet Mol Biol. 2010;9(1):Article33. Epub 2010 Aug 27. PMCID: PMC 2942028


Sanna S, Pitzalis M, Zoledziewska M, Zara I, Sidore C, Murru R, Whalen MB, Busonero F, Maschio A, Costa G, Melis MC, Deidda F, Poddie F, Morelli L, Farina G, Li Y, Dei M, Lai S, Mulas A, Cuccuru G, Porcu E, Liang L, Zavattari P, Moi L, Deriu E, Urru MF, Bajorek M, Satta MA, Cocco E, Ferrigno P, Sotgiu S, Pugliatti M, Traccis S, Angius A, Melis M, Rosati G, Abecasis GR, Uda M, Marrosu MG, Schlessinger D, Cucca F.
Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis.
Nat Genet.  2010 Jun;42(6):495-497.


Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR.
Pooled association tests for rare variants in exon-resequencing studies.
Am J Hum Genet.  2010 Jun;86(6):832-838. PMCID: PMC3032073.


Wu MC, Kraft P, Epstein MP, Taylor DM, Chanock SJ, Hunter DJ, Lin X.
Powerful SNP-set analysis for case-control genome-wide association studies.
Am J Hum Genet.  2010 Jun;86(6):929-942.  PMCID: PMC3032061. 


Lasky-Su J, Won S, Mick E, Anney RJ, Franke B, Neale B, Biederman J, Smalley SL, Loo SK, Todorov A, Faraone SV, Weiss ST, Lange C.
On genome-wide association studies for family-based designs: an integrative analysis approach combining ascertained family samples with unselected controls.
Am J Hum Genet.  2010 Apr;86(4):573-580.  PMCID: PMC2850439.


Derti A, Cenik C, Kraft P, Roth FP.
Absence of evidence for MHC-dependent mate selection within HapMap populations.
PLoS Genet.  2010 Apr;6(4):e1000925.  PMCID: PMC2861700.


Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Hersh CP, DeMeo DL, Hunninghake GM, Litonjua AA, Sparrow D, Lange C, Won S, Murphy JR, Beaty TH, Regan EA, Make BJ, Hokanson JE, Crapo JD, Kong X, Anderson WH, Tal-Singer R, Lomas DA, Bakke P, Gulsvik A, Pillai SG, Silverman EK. 
Variants in FAM13A are associated with chronic obstructive pulmonary disease
Nat Genet.  2010 Mar;42(3):200-202.  PMCID: PMC2828499.


Bhattacharjee S, Wang Z, Ciampa J, Kraft P, Chanock S, Yu K, Chatterjee N.
Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies.
Am J Hum Genet.  2010 Mar;86(3):331-342.  PMCID: PMC2833365.


Petersen GM, Amundadottir L, Fuchs CS, Kraft P, Stolzenberg-Solomon RZ, Jacobs KB, Arslan AA, Bueno-de-Mesquita HB, Gallinger S, Gross M, Helzlsouer K, Holly EA, Jacobs EJ, Klein AP, LaCroix A, Li D, Mandelson MT, Olson SH, Risch HA, Zheng W, Albanes D, Bamlet WR, Berg CD, Boutron-Ruault MC, Buring JE, Bracci PM, Canzian F, Clipp S, Cotterchio M, de Andrade M, Duell EJ, Gaziano JM, Giovannucci EL, Goggins M, Hallmans G, Hankinson SE, Hassan M, Howard B, Hunter DJ, Hutchinson A, Jenab M, Kaaks R, Kooperberg C, Krogh V, Kurtz RC, Lynch SM, McWilliams RR, Mendelsohn JB, Michaud DS, Parikh H, Patel AV, Peeters PH, Rajkovic A, Riboli E, Rodriguez L, Seminara D, Shu XO, Thomas G, Tjønneland A, Tobias GS, Trichopoulos D, Van Den Eeden SK, Virtamo J, Wactawski-Wende J, Wang Z, Wolpin BM, Yu H, Yu K, Zeleniuch-Jacquotte A, Fraumeni JF Jr, Hoover RN, Hartge P, Chanock SJ.
A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1, and 5p15.33.
Nat Genet.  2010 Mar;42(3):224-228.  PMCID: PMC2853179.