ArticleGenome research2014
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 307 papers.
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Who cites it
307 citing papers in PubMed, 568 citations in OpenAlex.
- CfDNA-based copy-number dynamics during anti-PD1 treatment in metastatic triple negative breast cancer.Cell reports. Medicine · 2025Trial
- Predictive value of chromosome 18q11.2-q12.1 loss for benefit from bevacizumab in metastatic colorectal cancer: A post hoc analysis of the randomized phase III-trial AGITG-MAX.International journal of cancer · 2022Trial
- Accumulation of copy number alterations and clinical progression across advanced prostate cancer.Genome medicine · 2022Trial
- Trial
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- 4D nucleome landscape reveals dissolution of bipartite active X chromosome in liver cancer development.Nature cell biology · 2026Article
- Human inflammatory bowel disease-on-a-chip for modelling disease progression, cancer initiation and sex-specific effects.Nature biomedical engineering · 2026Article
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Wavelet-based whole genome doubling aware single-cell copy number calling.Nucleic acids research · 2026Article
- Dual plasmepsin IX and X inhibitors are refractory to development of resistance.PLoS pathogens · 2026Article
- Nano-RAPID: Integrated Diagnosis for Sarcoma Using a Nanopore Sequencer.Genes, chromosomes & cancer · 2026Article
- Inflammatory Rhabdomyoblastic Tumor with Malignant Progression of the Neck: Unique Copy Number Profile Identified by Nanopore Sequencing.Head and neck pathology · 2026Article
- An integrative epigenomic and single-cell framework identifies a prognostic DNA methylation risk score and ZNF638 silencing in urothelial carcinoma.Journal of translational medicine · 2026Article
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Systematic evaluation of long-read and short-read sequencing in neurological disorders diagnosis: a direct comparison study of 310 patients.NPJ genomic medicine · 2026Article
- Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes.NAR genomics and bioinformatics · 2026Article
- Rapid prenatal CNV detection using nanopore technology.BMC research notes · 2026Article
- Copy number alteration fingerprint predicts the clinical response of oxaliplatin-based chemotherapy in metastatic colorectal cancer.NPJ precision oncology · 2026Article
- Epstein-Barr virus status drives morphological and molecular intra-tumour heterogeneity in gastric cancer: insights from a case report and literature review.Virchows Archiv : an international journal of pathology · 2026Review
247 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors at 6 institutions in 3 countries.
Funding
Abstract
Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ∼0.1× genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.
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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.