A
Alice S. Whittemore
Researcher at Stanford University
Publications - 447
Citations - 48431
Alice S. Whittemore is an academic researcher from Stanford University. The author has contributed to research in topics: Breast cancer & Cancer. The author has an hindex of 96, co-authored 436 publications receiving 43749 citations. Previous affiliations of Alice S. Whittemore include Vanderbilt University & Harvard University.
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Journal ArticleDOI
Finding the missing heritability of complex diseases
Teri A. Manolio,Francis S. Collins,Nancy J. Cox,David Goldstein,Lucia A. Hindorff,David J. Hunter,Mark I. McCarthy,Erin M. Ramos,Lon R. Cardon,Aravinda Chakravarti,Judy H. Cho,Alan E. Guttmacher,Augustine Kong,Leonid Kruglyak,Leonid Kruglyak,Elaine R. Mardis,Charles N. Rotimi,Montgomery Slatkin,David Valle,Alice S. Whittemore,Michael Boehnke,Andrew G. Clark,Evan E. Eichler,Greg Gibson,Jonathan L. Haines,Trudy F. C. Mackay,Steven A. McCarroll,Peter M. Visscher +27 more
TL;DR: This paper examined potential sources of missing heritability and proposed research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.
Journal ArticleDOI
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
Nilah M. Ioannidis,Joseph H. Rothstein,Joseph H. Rothstein,Vikas Pejaver,Sumit Middha,Shannon K. McDonnell,Saurabh Baheti,Anthony M. Musolf,Qing Li,Emily R. Holzinger,Danielle M. Karyadi,Lisa A. Cannon-Albright,Craig C. Teerlink,Janet L. Stanford,William B. Isaacs,Jianfeng Xu,Kathleen A. Cooney,Kathleen A. Cooney,Ethan M. Lange,Johanna Schleutker,John D. Carpten,Isaac J. Powell,Olivier Cussenot,Geraldine Cancel-Tassin,Graham G. Giles,Graham G. Giles,Robert J. MacInnis,Robert J. MacInnis,Christiane Maier,Chih-Lin Hsieh,Fredrik Wiklund,William J. Catalona,William D. Foulkes,Diptasri Mandal,Rosalind A. Eeles,Zsofia Kote-Jarai,Carlos Bustamante,Daniel J. Schaid,Trevor Hastie,Elaine A. Ostrander,Joan E. Bailey-Wilson,Predrag Radivojac,Stephen N. Thibodeau,Alice S. Whittemore,Weiva Sieh,Weiva Sieh +45 more
TL;DR: This work developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, LRT, GERP, SiPhy, phyloP, and phastCons.
Journal ArticleDOI
Common variants on chromosome 6p22.1 are associated with schizophrenia
Jianxin Shi,Douglas F. Levinson,Jubao Duan,Alan R. Sanders,Yonglan Zheng,Itsik Pe'er,Frank Dudbridge,Peter Holmans,Alice S. Whittemore,Bryan J. Mowry,Ann Olincy,Farooq Amin,C. Robert Cloninger,Jeremy M. Silverman,Nancy G. Buccola,William Byerley,Donald W. Black,Raymond R. Crowe,Jorge R. Oksenberg,Daniel B. Mirel,Kenneth S. Kendler,Robert Freedman,Pablo V. Gejman +22 more
TL;DR: It is demonstrated that common schizophrenia susceptibility alleles can be detected and the characterization of these signals will suggest important directions for research on susceptibility mechanisms.
Journal ArticleDOI
Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk
Ganna Chornokur,Hui-Yi Lin,Jonathan Tyrer,Kate Lawrenson,Joe Dennis,Ernest K. Amankwah,Xiaotao Qu,Ya-Yu Tsai,Heather S.L. Jim,Zhihua Chen,Ann Y. Chen,Jennifer Permuth-Wey,Katja K.H. Aben,Hoda Anton-Culver,Natalia Antonenkova,Fiona Bruinsma,Elisa V. Bandera,Yukie Bean,Matthias W. Beckmann,Maria Bisogna,Line Bjørge,Natalia Bogdanova,Louise A. Brinton,Angela Brooks-Wilson,Clareann H. Bunker,Ralf Bützow,Ian G. Campbell,Karen Carty,Jenny Chang-Claude,Linda S. Cook,Daniel W. Cramer,Julie M. Cunningham,Cezary Cybulski,Agnieszka Dansonka-Mieszkowska,Andreas du Bois,Evelyn Despierre,Ed Dicks,Jennifer A. Doherty,Thilo Dörk,Matthias Dürst,Douglas F. Easton,Diana Eccles,Robert P. Edwards,Arif B. Ekici,Peter A. Fasching,Brooke L. Fridley,Yu-Tang Gao,Aleksandra Gentry-Maharaj,Graham G. Giles,Rosalind Glasspool,Marc T. Goodman,Jacek Gronwald,Patricia Harrington,Philipp Harter,Alexander Hein,Florian Heitz,Michelle A.T. Hildebrandt,Peter Hillemanns,Claus Høgdall,Estrid Høgdall,Satoyo Hosono,Anna Jakubowska,Allan Jensen,Bu-Tian Ji,Beth Y. Karlan,Linda E. Kelemen,Mellissa Kellar,Lambertus A. Kiemeney,Camilla Krakstad,Susanne K. Kjaer,Jolanta Kupryjanczyk,Diether Lambrechts,Sandrina Lambrechts,Nhu D. Le,Alice W. Lee,Shashi Lele,Arto Leminen,Jenny Lester,Douglas A. Levine,Dong Liang,Boon Kiong Lim,Jolanta Lissowska,Karen Lu,Jan Lubinski,Lene Lundvall,Leon F.A.G. Massuger,Keitaro Matsuo,Valerie McGuire,John R. McLaughlin,Iain A. McNeish,Usha Menon,Roger L. Milne,Francesmary Modugno,Kirsten B. Moysich,Roberta B. Ness,Heli Nevanlinna,Ursula Eilber,Kunle Odunsi,Sara H. Olson,Irene Orlow,Sandra Orsulic,Rachel Palmieri Weber,James Paul,Celeste Leigh Pearce,Tanja Pejovic,Liisa M. Pelttari,Malcolm C. Pike,Elizabeth M. Poole,Harvey A. Risch,Barry P. Rosen,Mary Anne Rossing,Joseph H. Rothstein,Anja Rudolph,Ingo B. Runnebaum,Iwona K. Rzepecka,Helga B. Salvesen,Eva S. Schernhammer,Ira Schwaab,Xiao-Ou Shu,Yurii B. Shvetsov,Nadeem Siddiqui,Weiva Sieh,Honglin Song,Melissa C. Southey,Beata Spiewankiewicz,Lara Sucheston,Soo-Hwang Teo,Kathryn L. Terry,Pamela J. Thompson,Lotte Ansgaard Thomsen,Ingvild L. Tangen,Shelley S. Tworoger,Anne M. van Altena,Robert A. Vierkant,Ignace Vergote,Christine Walsh,Shan Wang-Gohrke,Nicolas Wentzensen,Alice S. Whittemore,Kristine G. Wicklund,Lynne R. Wilkens,Anna H. Wu,Xifeng Wu,Yin Ling Woo,Hannah P. Yang,Wei Zheng,Argyrios Ziogas,Hanis Nazihah Hasmad,Andrew Berchuck,Edwin S. Iversen,Joellen M. Schildkraut,Susan J. Ramus,Ellen L. Goode,Alvaro N.A. Monteiro,Simon A. Gayther,Steven A. Narod,Paul D.P. Pharoah,Thomas A. Sellers,Catherine M. Phelan +158 more
TL;DR: Associations between inherited cellular transport gene variants and risk of EOC histologic subtypes are revealed on a large cohort of women.
Journal ArticleDOI
Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores
Bjarni J. Vilhjálmsson,Jian Yang,Hilary K. Finucane,Alexander Gusev,Sara Lindström,Stephan Ripke,Giulio Genovese,Po-Ru Loh,Gaurav Bhatia,Ron Do,Tristan J. Hayeck,Hong-Hee Won,Benjamin M. Neale,Aiden Corvin,James T.R. Walters,Kai How Farh,Peter Holmans,Phil Lee,Brendan Bulik-Sullivan,David A. Collier,Hailiang Huang,Tune H. Pers,Ingrid Agartz,E. Agerbo,Margot Albus,Madeline Alexander,Farooq Amin,Silviu Alin Bacanu,Martin Begemann,Richard A. Belliveau,Judit Bene,Sarah E. Bergen,Elizabeth Bevilacqua,Tim B. Bigdeli,Donald W. Black,Richard Bruggeman,Nancy G. Buccola,Randy L. Buckner,William Byerley,Wiepke Cahn,Guiqing Cai,Dominique Campion,Rita M. Cantor,Vaughan J. Carr,Noa Carrera,Stanley V. Catts,Kimberly Chambert,Raymond C.K. Chan,Ronald Y.L. Chen,Eric Y.H. Chen,Wei Cheng,Eric F. C. Cheung,Siow Ann Chong,C. Robert Cloninger,David Cohen,Nadine Cohen,Paul Cormican,Nicholas John Craddock,James J. Crowley,David Curtis,Michael Davidson,Kenneth L. Davis,Franziska Degenhardt,Jurgen Del Favero,Lynn E. DeLisi,Ditte Demontis,Dimitris Dikeos,Timothy G. Dinan,Srdjan Djurovic,Gary Donohoe,Elodie Drapeau,Jubao Duan,Frank Dudbridge,Naser Durmishi,Peter Eichhammer,Johan G. Eriksson,Valentina Escott-Price,Laurent Essioux,Ayman H. Fanous,Martilias S. Farrell,Josef Frank,Lude Franke,Robert Freedman,Nelson B. Freimer,Marion Friedl,Joseph I. Friedman,Menachem Fromer,Lyudmila Georgieva,Elliot S. Gershon,Ina Giegling,Paola Giusti-Rodrguez,Stephanie Godard,Jacqueline I. Goldstein,Vera Golimbet,Srihari Gopal,Jacob Gratten,Jakob Grove,Lieuwe de Haan,Christian Hammer,Marian L. Hamshere,Mark Hansen,Thomas Hansen,Vahram Haroutunian,Annette M. Hartmann,Frans Henskens,Stefan Herms,Joel N. Hirschhorn,Per Hoffmann,A. Hofman,Mads V. Hollegaard,David M. Hougaard,Masashi Ikeda,Inge Joa,Antonio Julià,René S. Kahn,Luba Kalaydjieva,Sena Karachanak-Yankova,Juha Karjalainen,David J. Kavanagh,Matthew C. Keller,Brian Kelly,James L. Kennedy,Andrey Khrunin,Yunjung Kim,Janis Klovins,James A. Knowles,Bettina Konte,Vaidutis Kučinskas,Zita Ausrele Kucinskiene,Hana Kuzelova-Ptackova,Anna K. Kähler,Claudine Laurent,Jimmy Lee Chee Keong,S. Hong Lee,Sophie E. Legge,Bernard Lerer,Miaoxin Li,Tao Li,Kung Yee Liang,Jeffrey A. Lieberman,Svetlana A. Limborska,Carmel M. Loughland,Jan Lubinski,Jouko K. Lnnqvist,Milan Macek,Patrik K. E. Magnusson,Brion S. Maher,Wolfgang Maier,Jacques Mallet,Sara Marsal,Manuel Mattheisen,Morten Mattingsdal,Robert W. McCarley,Colm McDonald,Andrew M. McIntosh,Sandra Meier,Carin J. Meijer,Béla Melegh,Ingrid Melle,Raquelle I. Mesholam-Gately,Andres Metspalu,Patricia T. Michie,Lili Milani,Vihra Milanova,Younes Mokrab,Derek W. Morris,Ole Mors,Preben Bo Mortensen,Kieran C. Murphy,Robin M. Murray,Inez Myin-Germeys,Bertram Mller-Myhsok,Mari Nelis,Igor Nenadic,Deborah A. Nertney,Gerald Nestadt,Kristin K. Nicodemus,Liene Nikitina-Zake,Laura Nisenbaum,Annelie Nordin,Eadbhard O'Callaghan,Colm O'Dushlaine,F. Anthony O'Neill,Sang Yun Oh,Ann Olincy,Line Olsen,Jim van Os,Christos Pantelis,George N. Papadimitriou,Sergi Papiol,Elena Parkhomenko,Michele T. Pato,Tiina Paunio,Milica Pejovic-Milovancevic,Diana O. Perkins,Olli Pietilinen,Jonathan Pimm,Andrew Pocklington,John Powell,Alkes Price,Ann E. Pulver,Shaun Purcell,Digby Quested,Henrik B. Rasmussen,Abraham Reichenberg,Mark Reimers,Alexander Richards,Joshua L. Roffman,Panos Roussos,Douglas M. Ruderfer,Veikko Salomaa,Alan R. Sanders,Ulrich Schall,Christian Schubert,Thomas G. Schulze,Sibylle G. Schwab,Edward M. Scolnick,Rodney J. Scott,Larry J. Seidman,Jianxin Shi,Engilbert Sigurdsson,Teimuraz Silagadze,Jeremy M. Silverman,Kang Sim,Petr Slominsky,Jordan W. Smoller,Hon-Cheong So,Chris C. A. Spencer,Eli A. Stahl,Hreinn Stefansson,Stacy Steinberg,Elisabeth Stögmann,Richard E. Straub,Eric Strengman,Jana Strohmaier,T. Scott Stroup,Mythily Subramaniam,Jaana Suvisaari,Dragan M. Svrakic,Jin P. Szatkiewicz,Erik Sderman,Srinivas Thirumalai,Draga Toncheva,Paul A. Tooney,Sarah Tosato,Juha Veijola,John L. Waddington,Dermot Walsh,Dai Wang,Qiang Wang,Bradley T. Webb,Mark Weiser,Dieter B. Wildenauer,Nigel Williams,Stephanie Williams,Stephanie H. Witt,Aaron R. Wolen,Emily H. M. Wong,Brandon Wormley,Jing Qin Wu,Hualin Simon Xi,Clement C. Zai,Xuebin Zheng,Fritz Zimprich,Naomi R. Wray,Kari Stefansson,Peter M. Visscher,Rolf Adolfsson,Ole A. Andreassen,Douglas Blackwood,Elvira Bramon,Joseph D. Buxbaum,Anders D. Børglum,Sven Cichon,Ariel Darvasi,Enrico Domenici,Hannelore Ehrenreich,Tõnu Esko,Pablo V. Gejman,Michael Gill,Hugh Gurling,Christina M. Hultman,Nakao Iwata,Assen Jablensky,Erik G. Jönsson,Kenneth S. Kendler,George Kirov,Jo Knight,Todd Lencz,Douglas F. Levinson,Qingqin S. Li,Jianjun Liu,Anil K. Malhotra,Steven A. McCarroll,Andrew McQuillin,Jennifer L. Moran,Bryan J. Mowry,Markus M. Nthen,Roel A. Ophoff,Michael John Owen,A. Palotie,Carlos N. Pato,Tracey L. Petryshen,Danielle Posthuma,Marcella Rietschel,Brien P. Riley,Dan Rujescu,Pak C. Sham,Pamela Sklar,David St Clair,Daniel R. Weinberger,Jens R. Wendland,Thomas Werge,Mark J. Daly,Patrick F. Sullivan,Michael Conlon O'Donovan,Peter Kraft,David J. Hunter,Muriel A. Adank,Habibul Ahsan,Kristiina Aittomäki,Laura Baglietto,Sonja I. Berndt,Carl Blomquist,Federico Canzian,Jenny Chang-Claude,Stephen J. Chanock,Laura Crisponi,Kamila Czene,Norbert Dahmen,Isabel dos Santos Silva,Douglas F. Easton,A. Heather Eliassen,Jonine D. Figueroa,Olivia Fletcher,Montserrat Garcia-Closas,Mia M. Gaudet,Lorna Gibson,Christopher A. Haiman,Per Hall,Aditi Hazra,Rebecca Hein,Brian E. Henderson,Albert Hofman,John L. Hopper,Astrid Irwanto,Mattias Johansson,Rudolf Kaaks,Muhammad G. Kibriya,Peter Lichtner,Eiliv Lund,Enes Makalic,Alfons Meindl,Hanne Meijers-Heijboer,Bertram Müller-Myhsok,Taru A. Muranen,Heli Nevanlinna,Petra H.M. Peeters,Julian Peto,Ross L. Prentice,Nazneen Rahman,María José Sánchez,Daniel F. Schmidt,Rita K. Schmutzler,Melissa C. Southey,Rulla M. Tamimi,Ruth C. Travis,Clare Turnbull,André G. Uitterlinden,Rob B. van der Luijt,Quinten Waisfisz,Zhaoming Wang,Alice S. Whittemore,Rose Yang,Wei Zheng,Wei Zheng,Sekar Kathiresan,Michele T. Pato,Carlos N. Pato,E Stahl,Noah Zaitlen,Bogdan Pasaniuc,Gillian M. Belbin,Eimear E. Kenny,Mikkel H. Schierup,Phillip L. De Jager,Nikolaos A. Patsopoulos,Steve McCarroll,Mark J. Daly,Shaun M. Purcell,Daniel I. Chasman,Benjamin M. Neale,Michael E. Goddard,Nick Patterson,Alkes L. Price +394 more
TL;DR: LDpred is introduced, a method that infers the posterior mean effect size of each marker by using a prior on effect sizes and LD information from an external reference panel, and outperforms the approach of pruning followed by thresholding, particularly at large sample sizes.