About the Authors

Zhifu Sun

Affiliation Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America

Yan W. Asmann

Affiliation Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America

Krishna R. Kalari

Affiliations Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America, Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America

Brian Bot

Affiliation Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America

Jeanette E. Eckel-Passow

Affiliation Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America

Tiffany R. Baker

Affiliation Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America

Jennifer M. Carr

Affiliation Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America

Irina Khrebtukova

Affiliation Illumina, Inc., Hayward, California, United States of America

Shujun Luo

Affiliation Illumina, Inc., Hayward, California, United States of America

Lu Zhang

Affiliation Illumina, Inc., Hayward, California, United States of America

Gary P. Schroth

Affiliation Illumina, Inc., Hayward, California, United States of America

Edith A. Perez

Affiliation Department of Medicine, Mayo Clinic, Jacksonville, Florida, United States of America

E. Aubrey Thompson

thompson.aubrey@mayo.edu

Affiliation Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America

Competing Interests

Z. Sun, Y. Asmann, K.R. Kalari, B. Bot, J. Eckel-Passow, T.R. Baker, J.M. Carr, E.A. Perez, and E.A. Thompson declare no conflict of interest. I. Khrebtukova, S. Luo, L. Zhang, and G.P. Schroth were employed by Illumina, Inc. at the time these experiments were carried out. Although all sequencing protocols were carried out on the Illumina Genome Analyzer, the central focus of this project is on library construction and data analysis, with no attempt to favor any particular next generation sequencing platform. Although they had roles in the study, this does not alter our adherence to all the PLoS ONE policies on sharing data and materials.

Author Contributions

Conceived and designed the experiments: EAT YWA GPS. Performed the experiments: TRB JMC SL. Analyzed the data: ZS EAT. Wrote the manuscript: ZS EAT. Provided overall guidance for the project: YWA. Adapted the CNV-seq protocols: KRK. Provided statistical support: BB JEP. Provided the initial analyses of the sequence data: IK LZ. Guided our analysis of breast tumor samples and contributed to data interpretation and re-evaluation of our conclusions: EAP.