title: Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
abstract: Sequencing studies of breast tumour cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumours. Here we developed a whole-genome and exome single cell sequencing approach called nuc-seq that uses G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumour nuclei from an oestrogen-receptor-positive (ER(+)) breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumour evolution and remained highly stable as the tumour masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Using targeted single-molecule sequencing, many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumour mass. Using mathematical modelling we found that the triple-negative tumour cells had an increased mutation rate (13.3×), whereas the ER(+) tumour cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Yong
authors: Y
authors: Wang
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Jill
authors: J
authors: Waters
authors: 1] The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA [2] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA.
authors: Marco L
authors: ML
authors: Leung
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Anna
authors: A
authors: Unruh
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Whijae
authors: W
authors: Roh
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Xiuqing
authors: X
authors: Shi
authors: The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA.
authors: Ken
authors: K
authors: Chen
authors: 1] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [2] The University of Texas MD Anderson Cancer Center, Department of Epidemiology, Houston, Texas 77030, USA.
authors: Paul
authors: P
authors: Scheet
authors: 1] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [2] The University of Texas MD Anderson Cancer Center, Department of Epidemiology, Houston, Texas 77030, USA.
authors: Selina
authors: S
authors: Vattathil
authors: The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA.
authors: Han
authors: H
authors: Liang
authors: The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA.
authors: Asha
authors: A
authors: Multani
authors: The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, Texas 77030, USA.
authors: Hong
authors: H
authors: Zhang
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02215, USA.
authors: Rui
authors: R
authors: Zhao
authors: Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02215, USA.
authors: Franziska
authors: F
authors: Michor
authors: The University of Texas MD Anderson Cancer Center Department of Investigational Cancer Therapeutics, Houston, Texas 77030, USA.
authors: Funda
authors: F
authors: Meric-Bernstam
authors: 1] The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA [2] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [3] The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA.
authors: Nicholas E
authors: NE
authors: Navin
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D060965:Clonal Evolution; D016172:DNA Fingerprinting; D005260:Female; D014644:Genetic Variation; D016678:Genome / Q000235:genetics*; D006801:Humans; D008962:Models, Theoretical; D009154:Mutation / Q000235:genetics; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis; D064726:Triple Negative Breast Neoplasms / Q000235:genetics