The use of phenome-wide association studies (PheWAS) for exploration of novel genotype-phenotype relationships and pleiotropy discovery.

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Published in Genet Epidemiol on May 18, 2011

Authors

S A Pendergrass1, K Brown-Gentry, S M Dudek, E S Torstenson, J L Ambite, C L Avery, S Buyske, C Cai, M D Fesinmeyer, C Haiman, G Heiss, L A Hindorff, C-N Hsu, R D Jackson, C Kooperberg, L Le Marchand, Y Lin, T C Matise, L Moreland, K Monroe, A P Reiner, R Wallace, L R Wilkens, D C Crawford, M D Ritchie

Author Affiliations

1: Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232-0700, USA.

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Letter: Colonial morphology of Neisseria gonorrhoeae. JAMA (1974) 2.00

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