Journal article
SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
PLoS computational biology, Vol.10(8), pp.e1003665-e1003665
08/2014
DOI: 10.1371/journal.pcbi.1003665
PMCID: PMC4125065
PMID: 25102416
Abstract
The sensitivity of massively-parallel sequencing has confirmed that most cancers are oligoclonal, with subpopulations of neoplastic cells harboring distinct mutations. A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications. Single tumor analysis already contributes to understanding these phenomena. However, cryptic subclones are frequently revealed by additional patient samples (e.g., collected at relapse or following treatment), indicating that accurately characterizing a tumor requires analyzing multiple samples from the same patient. To address this need, we present SciClone, a computational method that identifies the number and genetic composition of subclones by analyzing the variant allele frequencies of somatic mutations. We use it to detect subclones in acute myeloid leukemia and breast cancer samples that, though present at disease onset, are not evident from a single primary tumor sample. By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.
Details
- Title: Subtitle
- SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
- Creators
- Christopher A Miller - The Genome Institute, Washington University, St. Louis, Missouri, United States of AmericaMichael H Tomasson - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaBrian S White - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaNathan D Dees - The Genome Institute, Washington University, St. Louis, Missouri, United States of AmericaMalachi Griffith - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of AmericaJohn S Welch - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaObi L Griffith - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaRavi Vij - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaTimothy A Graubert - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of America; Massachusetts General Hospital, Boston, Massachusetts, United States of AmericaMatthew J Walter - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaMatthew J Ellis - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaWilliam Schierding - Liggins Institute, Auckland, New ZealandJohn F DiPersio - Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaTimothy J Ley - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaElaine R Mardis - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaRichard K Wilson - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of AmericaLi Ding - The Genome Institute, Washington University, St. Louis, Missouri, United States of America; Department of Internal Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, Missouri, United States of America; Department of Genetics, Washington University, St. Louis, Missouri, United States of America; Siteman Cancer Center, Barnes-Jewish Hospital, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Resource Type
- Journal article
- Publication Details
- PLoS computational biology, Vol.10(8), pp.e1003665-e1003665
- DOI
- 10.1371/journal.pcbi.1003665
- PMID
- 25102416
- PMCID
- PMC4125065
- NLM abbreviation
- PLoS Comput Biol
- ISSN
- 1553-734X
- eISSN
- 1553-7358
- Grant note
- U54 HG003079 / NHGRI NIH HHS P01 CA101937 / NCI NIH HHS P50 CA171963 / NCI NIH HHS K12 CA167540 / NCI NIH HHS 1K12CA167540 / NCI NIH HHS R01 CA180006 / NCI NIH HHS P50CA171063 / NCI NIH HHS U54HG003079 / NHGRI NIH HHS UL1 TR000448 / NCATS NIH HHS U01 HG006517 / NHGRI NIH HHS U01HG006517 / NHGRI NIH HHS
- Language
- English
- Date published
- 08/2014
- Academic Unit
- Hematology, Oncology, and Blood & Marrow Transplantation; Internal Medicine
- Record Identifier
- 9984094321302771
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