ArticleGenome biology2014
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- The impact of PCR duplication on RNAseq data generated using NovaSeq 6000, NovaSeq X, AVITI, and G4 sequencers.Genome biology · 2025Article
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- Quantifying allele-specific CRISPR editing activity with CRISPECTOR2.0.Nucleic acids research · 2024Article
- An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.BMC genomics · 2024Article
- Identifying high-confidence variants in human cytomegalovirus genomes sequenced from clinical samples.Virus evolution · 2022Article
- Streamlining data-intensive biology with workflow systems.GigaScience · 2021Article
- Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.Journal of virology · 2019Article
- Article
- Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity.Cell reports · 2018Article
- Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.BioTechniques · 2017Article
- Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer.Nature communications · 2017Article
- A population genetics perspective on the determinants of intra-tumor heterogeneity.Biochimica et biophysica acta. Reviews on cancer · 2017Review
- Wild-type Blocking PCR Combined with Direct Sequencing as a Highly Sensitive Method for Detection of Low-Frequency Somatic Mutations.Journal of visualized experiments : JoVE · 2017Article
- A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.BMC bioinformatics · 2017Article
- TumorNext: A comprehensive tumor profiling assay that incorporates high resolution copy number analysis and germline status to improve testing accuracy.Oncotarget · 2016Article
- Article
- Review
- Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development.Blood cancer journal · 2015Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Accurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth. Here we adapted the Illumina TruSeq Custom Amplicon kit to include single molecule tagging (SMT) and show that SMT-identified duplicates arise from PCR. We demonstrate that retention of PCR duplicate reads can imply clonal evolution when none exists, while their removal effectively controls the false positive rate. Additionally, PCR duplicates alter estimates of subclonal heterogeneity in tumor samples. Our method simplifies PCR duplicate identification and emphasizes their removal in studies of tumor heterogeneity and clonal evolution.
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