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We are analyzing https://www.nature.com/articles/nature13600.

Title:
Clonal evolution in breast cancer revealed by single nucleus genome sequencing | Nature
Description:
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. To investigate genomic diversity within tumours, a new type of whole-genome and exome single cell sequencing has been developed using G2/M nuclei; the technique was used to sequence single nuclei from an oestrogen-positive breast cancer and a triple-negative ductal carcinoma—aneuploidy rearrangements emerged as early events in tumour formation and then point mutations evolved gradually over time. Human breast cancers often display intratumour genomic heterogeneity, making clinical diagnosis difficult and complicating the interpretation of research results. This study tackles the problem using a newly developed whole-genome single-cell sequencing technique called nuc-seq that makes use of the natural genome duplication that occurs in the S phase of the cell cycle to achieve 91% mean coverage breadth. The method is applied to sequence single normal and tumour nuclei from an oestrogen-receptor-positive breast cancer and a triple-negative ductal carcinoma. Aneuploid rearrangements emerge as early events, and they remain stable during clonal expansion. In contrast, point mutations appear to evolve gradually, generating extensive clonal diversity. The data also show that no two single tumour cells are genetically identical, raising interesting questions as to the strict definition of a clone.
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Keywords {🔍}

pubmed, scholar, google, cancer, cas, central, nature, data, breast, single, cell, ads, genome, clonal, evolution, sequencing, article, tumour, texas, mutations, usa, genomic, copy, number, supported, human, content, analysis, performed, cells, access, res, information, navin, nuclei, sequence, singlecell, methods, center, department, extended, tnbc, cookies, exome, method, genetics, university, houston, figure, privacy,

Topics {✒️}

permissions reprints nature portfolio privacy policy research results advertising research targeted ultra-deep sequencing cancer development targeted single-molecule sequencing multi-dimensional scaling plot sequence read archive social media oestrogen-receptor-positive breast cancer author information authors generate single-molecule data single-cell exome sequencing triple-negative ductal carcinoma high-throughput sequencing data jak2-negative myeloproliferative neoplasm sequence alignment/map format perform multiple-displacement-amplification single-cell lineage tracing generating duplex libraries alice-reynolds kleberg foundation basal–epithelial subpopulations underlie author correspondence dana-farber cancer institute limited isothermal time-frame age-dependent growth rate shotgun fragment libraries triple-negative tumour cells single-cell sequencing nature protocols 7 nature rev copy number data sequence libraries measuring single-cell ploidy extended data figures copy number profiles lymph node metastases nature methods 7 nature methods 8 springerlink instant access permissions single cell exome copy-number variations institutional subscriptions read primary breast cancer sequence single normal oestrogen-receptor-positive

Schema {🗺️}

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      headline:Clonal evolution in breast cancer revealed by single nucleus genome sequencing
      description: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. To investigate genomic diversity within tumours, a new type of whole-genome and exome single cell sequencing has been developed using G2/M nuclei; the technique was used to sequence single nuclei from an oestrogen-positive breast cancer and a triple-negative ductal carcinoma—aneuploidy rearrangements emerged as early events in tumour formation and then point mutations evolved gradually over time. Human breast cancers often display intratumour genomic heterogeneity, making clinical diagnosis difficult and complicating the interpretation of research results. This study tackles the problem using a newly developed whole-genome single-cell sequencing technique called nuc-seq that makes use of the natural genome duplication that occurs in the S phase of the cell cycle to achieve 91% mean coverage breadth. The method is applied to sequence single normal and tumour nuclei from an oestrogen-receptor-positive breast cancer and a triple-negative ductal carcinoma. Aneuploid rearrangements emerge as early events, and they remain stable during clonal expansion. In contrast, point mutations appear to evolve gradually, generating extensive clonal diversity. The data also show that no two single tumour cells are genetically identical, raising interesting questions as to the strict definition of a clone.
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