ArticleNature methods2009
High-resolution mapping of copy-number alterations with massively parallel sequencing.
Article in Nature methods, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 282 papers, 1 of them a synthesis that pooled it.
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Who cites it
282 citing papers in PubMed, 1 synthesis or guideline pooled it.
- MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism.Nature genetics · 2016Pooled it
- Whole-genome re-sequencing for the identification of high contribution susceptibility gene variants in patients with type 2 diabetes.Molecular medicine reports · 2016Trial
- Comparative Genomic Hybridization (CGH) in Genotoxicology: From the Basics to Modern Approaches.Methods in molecular biology (Clifton, N.J.) · 2026Review
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- Transfer Learning for Error-Contaminated Poisson Regression Models.Statistics in medicine · 2025Article
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma.European thyroid journal · 2025Article
- LoRA-TV: read depth profile-based clustering of tumor cells in single-cell sequencing.Briefings in bioinformatics · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- The reckoning of chromosomal instability: past, present, future.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Review
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- The Production of Recombinant African Swine Fever Virus Lv17/WB/Rie1 Strains and Their In Vitro and In Vivo Characterizations.Vaccines · 2023Article
- Rapid gene content turnover on the germline-restricted chromosome in songbirds.Nature communications · 2023Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
- CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data.PLoS computational biology · 2022Article
- Whole genome sequencing-based copy number variations reveal novel pathways and targets in Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2022Article
- Improving the efficiency of single-cell genome sequencing based on overlapping pooling strategy and CNV analysis.Royal Society open science · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- High resolution copy number inference in cancer using short-molecule nanopore sequencing.Nucleic acids research · 2021Article
- Three different mutations in the DNA topoisomerase 1B in Leishmania infantum contribute to resistance to antitumor drug topotecan.Parasites & vectors · 2021Article
222 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Cancer results from somatic alterations in key genes, including point mutations, copy-number alterations and structural rearrangements. A powerful way to discover cancer-causing genes is to identify genomic regions that show recurrent copy-number alterations (gains and losses) in tumor genomes. Recent advances in sequencing technologies suggest that massively parallel sequencing may provide a feasible alternative to DNA microarrays for detecting copy-number alterations. Here we present: (i) a statistical analysis of the power to detect copy-number alterations of a given size; (ii) SegSeq, an algorithm to segment equal copy numbers from massively parallel sequence data; and (iii) analysis of experimental data from three matched pairs of tumor and normal cell lines. We show that a collection of approximately 14 million aligned sequence reads from human cell lines has comparable power to detect events as the current generation of DNA microarrays and has over twofold better precision for localizing breakpoints (typically, to within approximately 1 kilobase).
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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.