ArticleCurrent protocols in bioinformatics2019
Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2.
Article in Current protocols in bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06981377 (Development of the PRIME Test for the Identification of Prostate Cancer Patients' Biomarkers Through Non-invasive Liquid Biopsies), which is not on this map. Cited by 12 papers.
What it found
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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.
Development of the PRIME Test for the Identification of Prostate Cancer Patients' Biomarkers Through Non-invasive Liquid Biopsies
Who cites it
12 citing papers in PubMed.
- Circulating tumor DNA profile recognizes transformation to castration-resistant neuroendocrine prostate cancer.The Journal of clinical investigation · 2020Trial
- Combined ctDNA and serum PSA for dynamic monitoring of metastatic prostate cancer starting first-line treatment: a prospective national cohort study.Nature cancer · 2026Article
- High BRAF variant allele frequency predicts poor outcomes in metastatic melanoma patients treated with BRAF/MEK inhibitors.Journal of translational medicine · 2025Article
- Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.Genome biology · 2025Article
- Validation of a Combined Prognostic Score Using Plasma Tumor DNA and Clinical Features in Metastatic Castration-Resistant Prostate Cancer Patients Treated with Taxanes.OncoTargets and therapy · 2025Article
- Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation.Cancer discovery · 2024Article
- Bladder cancer organoids as a functional system to model different disease stages and therapy response.Nature communications · 2023Article
- Allele-informed copy number evaluation of plasma DNA samples from metastatic prostate cancer patients: the PCF_SELECT consortium assay.NAR cancer · 2022Article
- Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.Cell systems · 2022Article
- Tumor subtype defines distinct pathways of molecular and clinical progression in primary prostate cancer.The Journal of clinical investigation · 2021Article
- Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.Computational and structural biotechnology journal · 2021Article
- Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2.Current protocols in bioinformatics · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
High-throughput DNA sequencing technology provides base-level and statistically rich information about the genomic content of a sample. In the contexts of cancer research and precision oncology, thousands of genomes from paired tumor and matched normal samples are profiled and processed to determine somatic copy-number changes and single-nucleotide variations. Higher-order informative analyses, in the form of allele-specific copy-number assessments or subclonality quantification, require reliable estimates of tumor DNA ploidy and tumor cellularity. CLONETv2 provides a complete set of functions to process matched normal and tumor pairs using patient-specific genotype data, is independent of low-level tools (e.g., aligner, segmentation algorithm, mutation caller) and offers high-level functions to compute allele-specific copy number from segmented data and to identify subclonal population in the input sample. CLONETv2 is applicable to whole-genome, whole-exome and targeted sequencing data generated either from tissue or from liquid biopsy samples. © 2019 The Authors.
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