ArticleBioinformatics (Oxford, England)2012
PurityEst: estimating purity of human tumor samples using next-generation sequencing data.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 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
40 citing papers in PubMed.
- DNA methylation marker to estimate the breast cancer cell fraction in DNA samples.Medical oncology (Northwood, London, England) · 2018Trial
- 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
- Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.Briefings in bioinformatics · 2024Article
- Article
- A systematic assessment of cell type deconvolution algorithms for DNA methylation data.Briefings in bioinformatics · 2022Article
- Tumor Purity in Preclinical Mouse Tumor Models.Cancer research communications · 2022Article
- Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study.Patterns (New York, N.Y.) · 2022Article
- Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.Briefings in bioinformatics · 2021Article
- A BAYESIAN NONPARAMETRIC MODEL FOR INFERRING SUBCLONAL POPULATIONS FROM STRUCTURED DNA SEQUENCING DATA.The annals of applied statistics · 2021Article
- Prediction of prognosis of patients with lung cancer in combination with the immune score.Bioscience reports · 2021Article
- Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data.BMC bioinformatics · 2021Article
- Identification of Immune-Related Prognostic Biomarkers Based on the Tumor Microenvironment in 20 Malignant Tumor Types With Poor Prognosis.Frontiers in oncology · 2020Article
- Accurate Inference of Tumor Purity and Absolute Copy Numbers From High-Throughput Sequencing Data.Frontiers in genetics · 2020Article
- TPES: tumor purity estimation from SNVs.Bioinformatics (Oxford, England) · 2019Article
- CeL-ID: cell line identification using RNA-seq data.BMC genomics · 2019Article
- Power and sample size calculations for high-throughput sequencing-based experiments.Briefings in bioinformatics · 2018Article
- A new method for constructing tumor specific gene co-expression networks based on samples with tumor purity heterogeneity.Bioinformatics (Oxford, England) · 2018Article
- Detecting Somatic Mutations in Normal Cells.Trends in genetics : TIG · 2018Review
- Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.Bioinformatics (Oxford, England) · 2018Article
- Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach.PeerJ · 2018Article
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
unlabelledWe developed a novel algorithm, PurityEst, to infer the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data. We applied our tool to a whole cancer genome sequencing datasets and demonstrated the accuracy of PurityEst compared with DNA copy number-based estimation. AVAILABILITY: PurityEst has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/PurityEst.html.
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.