ArticleGigaScience2021
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations.
Article in GigaScience, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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
21 citing papers in PubMed, 28 citations in OpenAlex.
- Fluctuating environment causes neoplastic transition and epithelial-mesenchymal plasticity in human cells.Research square · 2026Article
- Molecular classification identifies aggressive gastrointestinal stromal tumor subtype targetable by PARP inhibitors.Cellular oncology (Dordrecht, Netherlands) · 2026Article
- Distinct mutation landscape with similar immune microenvironment in primary simultaneous operable squamous cell carcinoma and peripheral-type small-cell lung cancer.Translational lung cancer research · 2026Article
- Multimodal analysis of a rare BARD1 missense variant suggests its pathogenicity is conditional.NPJ breast cancer · 2026Article
- Decoding intertumoral heterogeneity in multifocal ground-glass nodule lung cancers: Clonal evolutionary insight for precision management.JTCVS open · 2025Article
- APC-related multiple salivary gland lesions: spatial transcriptomic analysis reveals progressive WNT activation.The Journal of pathology · 2025Article
- Clonal diversity shapes the tumour microenvironment leading to distinct immunotherapy responses in metastatic urothelial carcinoma.Nature communications · 2025Article
- Modelling Acral Melanoma in Admixed Brazilians Uncovers Genomic Drivers and Targetable Pathways.medRxiv : the preprint server for health sciences · 2025Article
- Whole exome sequencing of multi-regions reveals tumor heterogeneity in Opisthorchis viverrini-associated cholangiocarcinoma.Scientific reports · 2025Article
- Spatial-Temporal Diversity of Extrachromosomal DNA Shapes Urothelial Carcinoma Evolution and Tumor Immune Microenvironment.Cancer discovery · 2025Article
- CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations.Computational and structural biotechnology journal · 2025Article
- Multiregion WES of metastatic pancreatic neuroendocrine tumors revealed heterogeneity in genomic alterations, immune microenvironment and evolutionary patterns.Cell communication and signaling : CCS · 2024Article
- A functional personalised oncology approach against metastatic colorectal cancer in matched patient derived organoids.NPJ precision oncology · 2024Article
- Article
- Genetic analysis of low-grade adenosquamous carcinoma of the breast progressing to high-grade metaplastic carcinoma.Breast cancer research and treatment · 2023Article
- Strategic Approach to Heterogeneity Analysis of Cutaneous Adnexal Carcinomas Using Computational Pathology and Genomics.JID innovations : skin science from molecules to population health · 2023Article
- Article
- Genomic Patterns of Malignant Peripheral Nerve Sheath Tumor (MPNST) Evolution Correlate with Clinical Outcome and Are Detectable in Cell-Free DNA.Cancer discovery · 2023Article
- Induction immune-checkpoint inhibitors for resectable oncogene-mutant NSCLC: A multicenter pooled analysis.NPJ precision oncology · 2022Article
- Characterization of Genetic Heterogeneity in Recurrent Metastases of Renal Cell Carcinoma.Cancers · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMulti-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches.
findingsHere, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution.
conclusionsIn summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.
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.