Tumour evolution inferred by single-cell sequencing
Nicholas Navin,Jude Kendall,Jennifer Troge,Peter Andrews,Linda Rodgers,Jeanne McIndoo,Kerry Cook,Asya Stepansky,Dan Levy,Diane Esposito,Lakshmi Muthuswamy,Alexander Krasnitz,W. Richard McCombie,James W. Hicks,Michael Wigler +14 more
Reads0
Chats0
TLDR
It is shown that with flow-sorted nuclei, whole genome amplification and next generation sequencing the authors can accurately quantify genomic copy number within an individual nucleus and indicate that tumours grow by punctuated clonal expansions with few persistent intermediates.Abstract:
Genomic analysis provides insights into the role of copy number variation in disease, but most methods are not designed to resolve mixed populations of cells. In tumours, where genetic heterogeneity is common, very important information may be lost that would be useful for reconstructing evolutionary history. Here we show that with flow-sorted nuclei, whole genome amplification and next generation sequencing we can accurately quantify genomic copy number within an individual nucleus. We apply single-nucleus sequencing to investigate tumour population structure and evolution in two human breast cancer cases. Analysis of 100 single cells from a polygenomic tumour revealed three distinct clonal subpopulations that probably represent sequential clonal expansions. Additional analysis of 100 single cells from a monogenomic primary tumour and its liver metastasis indicated that a single clonal expansion formed the primary tumour and seeded the metastasis. In both primary tumours, we also identified an unexpectedly abundant subpopulation of genetically diverse 'pseudodiploid' cells that do not travel to the metastatic site. In contrast to gradual models of tumour progression, our data indicate that tumours grow by punctuated clonal expansions with few persistent intermediates.read more
Citations
More filters
Journal ArticleDOI
Revealing the vectors of cellular identity with single-cell genomics
TL;DR: In this paper, a cell is represented as a superposition of "basis vectors", each determining a different (but possibly dependent) aspect of cellular organization and function, which can be used for constructing and characterizing a reference map of cell identities.
Journal ArticleDOI
Advances and applications of single-cell sequencing technologies.
Yong Wang,Nicholas Navin +1 more
TL;DR: In this review, single-cell sequencing technologies and applications, as well as translational applications in the clinic are discussed.
Journal ArticleDOI
Mosaic Copy Number Variation in Human Neurons
Michael J. McConnell,Michael R. Lindberg,Kristen J. Brennand,Julia C. Piper,Thierry Voet,Thierry Voet,Chris Cowing-Zitron,Svetlana Shumilina,Roger S. Lasken,Roger S. Lasken,Joris Vermeesch,Ira M. Hall,Fred H. Gage +12 more
TL;DR: Single-cell sequencing of endogenous human frontal cortex neurons revealed that 13 to 41% of neurons have at least one megabase-scale de novo CNV, that deletions are twice as common as duplications, and that a subset of neurons has highly aberrant genomes marked by multiple alterations.
Journal ArticleDOI
Somatic Mutation, Genomic Variation, and Neurological Disease
Annapurna Poduri,Gilad D. Evrony,Gilad D. Evrony,Xuyu Cai,Xuyu Cai,Christopher A. Walsh,Christopher A. Walsh +6 more
TL;DR: Findings suggest that somatic, perhaps brain-only, mosaic mutations may be important for other neurodevelopmental diseases, however, finding the mutations and the affected cells may require special study designs and technology.
Journal ArticleDOI
Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain.
Gilad D. Evrony,Xuyu Cai,Xuyu Cai,Xuyu Cai,Eunjung Lee,Eunjung Lee,L. Benjamin Hills,L. Benjamin Hills,Princess C. Elhosary,Hillel S. Lehmann,Hillel S. Lehmann,J.J. Parker,J.J. Parker,Kutay Deniz Atabay,Kutay Deniz Atabay,Edward C. Gilmore,Annapurna Poduri,Annapurna Poduri,Peter J. Park,Peter J. Park,Peter J. Park,Christopher A. Walsh +21 more
TL;DR: A method to amplify genomes of single neurons from human brains allows systematic assessment of genomic diversity in the human brain and describes the mosaicism of a somatic AKT3 mutation identified in a child with hemimegalencephaly.
References
More filters
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TL;DR: Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds.
Journal ArticleDOI
The clonal evolution of tumor cell populations
TL;DR: Each patient's cancer may require individual specific therapy, and even this may be thwarted by emergence of a genetically variant subline resistant to the treatment, which should be directed toward understanding and controlling the evolutionary process in tumors before it reaches the late stage usually seen in clinical cancer.
Journal ArticleDOI
Distant metastasis occurs late during the genetic evolution of pancreatic cancer
Shinichi Yachida,Siân Jones,Ivana Bozic,Tibor Antal,Tibor Antal,Rebecca J. Leary,Baojin Fu,Mihoko Kamiyama,Ralph H. Hruban,James R. Eshleman,Martin A. Nowak,Victor E. Velculescu,Kenneth W. Kinzler,Bert Vogelstein,Christine A. Iacobuzio-Donahue +14 more
TL;DR: In this article, the authors rely on data generated by sequencing the genomes of seven pancreatic cancer metastases to evaluate the clonal relationships among primary and metastatic cancers and find that clonal populations that give rise to distant metastases are represented within the primary carcinoma, but these clones are genetically evolved from the original parental, non-metastatic clone.
SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer
TL;DR: A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.
Related Papers (5)
Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger,Andrew Rowan,Stuart Horswell,James Larkin,David Endesfelder,Eva Grönroos,Pierre Martinez,Nicholas Matthews,Aengus Stewart,Patrick S. Tarpey,Ignacio Varela,Benjamin Phillimore,Sharmin Begum,Neil Q. McDonald,Adam Butler,David T. Jones,Keiran Raine,Calli Latimer,Claudio R. Santos,Mahrokh Nohadani,Aron Charles Eklund,Bradley Spencer-Dene,Graham Clark,Lisa Pickering,Gordon Stamp,Martin Gore,Zoltan Szallasi,Zoltan Szallasi,Julian Downward,P. Andrew Futreal,Charles Swanton +30 more