ArticleBioinformatics (Oxford, England)2014
EXPANDS: expanding ploidy and allele frequency on nested subpopulations.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
91 citing papers in PubMed.
- Improved Tumor Purity Metrics in Next-generation Sequencing for Clinical Practice: The Integrated Interpretation of Neoplastic Cellularity and Sequencing Results (IINCaSe) Approach.Applied immunohistochemistry & molecular morphology : AIMMTrial
- ITHindex: An integrated web-based platform for intratumor heterogeneity evaluation.PLOS digital health · 2026Article
- Integration of omics data in the diagnosis and therapy of glioblastoma.Brain pathology (Zurich, Switzerland) · 2026Review
- Quantitative profiling of intratumor immune heterogeneity identifies loss of immune diversity as a hallmark of cancer progression.NPJ precision oncology · 2025Article
- Cell lineage tracing: Methods, applications, and challenges.Quantitative biology (Beijing, China) · 2025Review
- DEPTH2 score was associated with cell proliferation and immune cell infiltrations but not with systemic treatment response in breast cancer.Scientific reports · 2025Article
- Advances in tumor subclone formation and mechanisms of growth and invasion.Journal of translational medicine · 2025Review
- Impact of ITH on PRAD patients and feasibility analysis of the positive correlation gene MYLK2 applied to PRAD treatment.Frontiers in genetics · 2025Article
- A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors.PLoS computational biology · 2024Article
- Mutant-allele dispersion correlates with prognosis risk in patients with advanced non-small cell lung cancer.Journal of cancer research and clinical oncology · 2023Article
- Molecular characterization of sub-frontal recurrent medulloblastomas reveals potential clinical relevance.Frontiers in neurology · 2023Article
- Multi-region sequencing with spatial information enables accurate heterogeneity estimation and risk stratification in liver cancer.Genome medicine · 2022Article
- Exploratory genomic analysis of high-grade neuroendocrine neoplasms across diverse primary sites.Endocrine-related cancer · 2022Article
- Relapse patterns and radiation dose exposure in IDH wild-type glioblastoma at first radiographic recurrence following chemoradiation.Journal of neuro-oncology · 2022Article
- Concerted Regulation of Glycosylation Factors Sustains Tissue Identity and Function.Biomedicines · 2022Article
- Intratumor Heterogeneity and Antitumor Immunity Shape One Another Bidirectionally.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Review
- Accurate Identification of Subclones in Tumor Genomes.Molecular biology and evolution · 2022Article
- DEPTH2: an mRNA-based algorithm to evaluate intratumor heterogeneity without reference to normal controls.Journal of translational medicine · 2022Article
- A deep learning model for molecular label transfer that enables cancer cell identification from histopathology images.NPJ precision oncology · 2022Article
- Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study.Patterns (New York, N.Y.) · 2022Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
motivationSeveral 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.
resultsTo 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. AVAILABILITY AND IMPLEMENTATION: EXPANDS 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).
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.