ArticlePLoS computational biology2020
SuperFreq: Integrated mutation detection and clonal tracking in cancer.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 56 citations in OpenAlex.
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- A Phase II Study of Pembrolizumab in Combination with Capecitabine and Oxaliplatin with Molecular Profiling in Patients with Advanced Biliary Tract Carcinoma.The oncologist · 2022Trial
- Dual PD-L1 and TGF-b blockade in patients with recurrent respiratory papillomatosis.Journal for immunotherapy of cancer · 2021Trial
- Abundant CD8British journal of cancer · 2026Article
- Expanded GEP-NET organoid culture for personalized therapy evaluation.Science advances · 2026Article
- Mbd4 and MutSα protect cells from spontaneous deamination of 5-methylcytosine.Nucleic acids research · 2026Article
- Multiomic characterization, early detection, and therapeutic targeting of myeloid sarcoma.bioRxiv : the preprint server for biology · 2025Article
- RCANE: a deep learning algorithm for whole-genome pan-cancer somatic copy number aberration prediction using RNA-seq data.Communications biology · 2025Article
- Uridine-cytidine kinase 2 potentiates the mutagenic influence of the antiviral β-d-N4-hydroxycytidine.Nucleic acids research · 2023Article
- FGF/FGFR genomic amplification as a predictive biomarker for immune checkpoint blockade resistance: a short report.Journal for immunotherapy of cancer · 2023Article
- Overexpression of Lmo2 initiates T-lymphoblastic leukemia via impaired thymocyte competition.The Journal of experimental medicine · 2023Article
- Exome-Based Genomic Markers Could Improve Prediction of Checkpoint Inhibitor Efficacy Independently of Tumor Type.International journal of molecular sciences · 2023Article
- Evolution of synchronous female bilateral breast cancers and response to treatment.Nature medicine · 2023Article
- Integration of Genomic and Clinical Retrospective Data to Predict Endometrioid Endometrial Cancer Recurrence.International journal of molecular sciences · 2022Article
- Clonal relationship and alcohol consumption-associated mutational signature in synchronous hypopharyngeal tumours and oesophageal squamous cell carcinoma.British journal of cancer · 2022Article
- Using Genomic Variation to Distinguish Ovarian High-Grade Serous Carcinoma from Benign Fallopian Tubes.International journal of molecular sciences · 2022Article
- Patient-Derived Organoids from Colorectal Cancer with Paired Liver Metastasis Reveal Tumor Heterogeneity and Predict Response to Chemotherapy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Ganciclovir-induced mutations are present in a diverse spectrum of post-transplant malignancies.Genome medicine · 2022Article
- The telomere maintenance mechanism spectrum and its dynamics in gliomas.Genome medicine · 2022Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression. Existing approaches for clonal tracking from sequencing data typically require the user to combine multiple tools that are not purpose-built for this task. Furthermore, most methods require a matched normal (non-tumour) sample, which limits the scope of application. We developed SuperFreq, a cancer exome sequencing analysis pipeline that integrates identification of somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) and clonal tracking for both. SuperFreq does not require a matched normal and instead relies on unrelated controls. When analysing multiple samples from a single patient, SuperFreq cross checks variant calls to improve clonal tracking, which helps to separate somatic from germline variants, and to resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal exome samples across 33 cancer types in The Cancer Genome Atlas (TCGA) and evaluated the quality of the SNV and CNA calls. We simulated clonal evolution through in silico mixing of cancer and normal samples in known proportion. We found that SuperFreq identified 93% of clones with a cellular fraction of at least 50% and mutations were assigned to the correct clone with high recall and precision. In addition, SuperFreq maintained a similar level of performance for most aspects of the analysis when run without a matched normal. SuperFreq is highly versatile and can be applied in many different experimental settings for the analysis of exomes and other capture libraries. We demonstrate an application of SuperFreq to leukaemia patients with diagnosis and relapse samples.
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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.