{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T05:30:31Z","timestamp":1768973431313,"version":"3.49.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1068,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation:\u2003Several cancer types consist of multiple genetically and phenotypically distinct subpopulations. The underlying mechanism for this intra-tumoral heterogeneity can be explained by the clonal evolution model, whereby growth advantageous mutations cause the expansion of cancer cell subclones. The recurrent phenotype of many cancers may be a consequence of these coexisting subpopulations responding unequally to therapies. Methods to computationally infer tumor evolution and subpopulation diversity are emerging and they hold the promise to improve the understanding of genetic and molecular determinants of recurrence.<\/jats:p>\n               <jats:p>Results:\u2003To address cellular subpopulation dynamics within human tumors, we developed a bioinformatic method, EXPANDS. It estimates the proportion of cells harboring specific mutations in a tumor. By modeling cellular frequencies as probability distributions, EXPANDS predicts mutations that accumulate in a cell before its clonal expansion. We assessed the performance of EXPANDS on one whole genome sequenced breast cancer and performed SP analyses on 118 glioblastoma multiforme samples obtained from TCGA. Our results inform about the extent of subclonal diversity in primary glioblastoma, subpopulation dynamics during recurrence and provide a set of candidate genes mutated in the most well-adapted subpopulations. In summary, EXPANDS predicts tumor purity and subclonal composition from sequencing data.<\/jats:p>\n               <jats:p>Availability and implementation:\u2003EXPANDS is available for download at http:\/\/code.google.com\/p\/expands (matlab version - used in this manuscript) and http:\/\/cran.r-project.org\/web\/packages\/expands (R version).<\/jats:p>\n               <jats:p>Contact:\u2003claudia.petritsch@ucsf.edu<\/jats:p>\n               <jats:p>Supplementary information:\u2003Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt622","type":"journal-article","created":{"date-parts":[[2013,11,1]],"date-time":"2013-11-01T06:53:15Z","timestamp":1383288795000},"page":"50-60","source":"Crossref","is-referenced-by-count":127,"title":["EXPANDS: expanding ploidy and allele frequency on nested subpopulations"],"prefix":"10.1093","volume":"30","author":[{"given":"Noemi","family":"Andor","sequence":"first","affiliation":[{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julie V.","family":"Harness","sequence":"additional","affiliation":[{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabine","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, 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Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudia","family":"Petritsch","sequence":"additional","affiliation":[{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 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94143, USA, 5Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA, 6Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Freising-Weihenstephan, Technische Universit\u00e4t M\u00fcnchen, 80333, Munich, Germany, 7Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158 and 8Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA"},{"name":"1 Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94143, USA, 2Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen, German Research Center for Environmental Health, 85764 Neuherberg, Germany, 3Brain Tumor Research Center, University of California San Francisco, San Francisco, CA 94158, USA, 4Department of Neurology, University of California San Francisco, San Francisco, CA 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