ArticleNucleic acids research2010
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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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.
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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.
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Who cites it
43 citing papers in PubMed.
- Whole-genome sequencing revealed an interstitial deletion encompassing OCRL and SMARCA1 gene in a patient with Lowe syndrome.Molecular genetics & genomic medicine · 2019Trial
- Clinical and genomic analysis of a randomised phase II study evaluating anastrozole and fulvestrant in postmenopausal patients treated for large operable or locally advanced hormone-receptor-positive breast cancer.British journal of cancer · 2015Trial
- Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.Journal of translational medicine · 2025Article
- Article
- Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network.Clinical cancer research : an official journal of the American Association for Cancer Research · 2021Article
- Prediction of tumour pathological subtype from genomic profile using sparse logistic regression with random effects.Journal of applied statistics · 2021Article
- Comparative analysis of somatic variant calling on matched FF and FFPE WGS samples.BMC medical genomics · 2020Article
- High-Resolution Copy Number Patterns From Clinically Relevant FFPE Material.Scientific reports · 2019Article
- Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies.BMC medical research methodology · 2018Article
- Evaluating the Feasibility of DNA Methylation Analyses Using Long-Term Archived Brain Formalin-Fixed Paraffin-Embedded Samples.Molecular neurobiology · 2018Article
- Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads.Molecular diagnosis & therapy · 2017Article
- The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples.Genome medicine · 2017Article
- Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA.Oncotarget · 2016Article
- Identification of hallmarks of lung adenocarcinoma prognosis using whole genome sequencing.Oncotarget · 2015Article
- A distinctive oral phenotype points to FAM20A mutations not identified by Sanger sequencing.Molecular genetics & genomic medicine · 2015Article
- Polycomb Repressor Complex 1 Member, BMI1 Contributes to Urothelial Tumorigenesis through p16-Independent Mechanisms.Translational oncology · 2015Article
- Targeted or whole genome sequencing of formalin fixed tissue samples: potential applications in cancer genomics.Oncotarget · 2015Article
- Isolating Viral and Host RNA Sequences from Archival Material and Production of cDNA Libraries for High-Throughput DNA Sequencing.Current protocols in microbiology · 2015Article
- CopywriteR: DNA copy number detection from off-target sequence data.Genome biology · 2015Article
- Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples.PloS one · 2015Article
Corrections and comments
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Authors and funding
19 authors.
Funding
Abstract
The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.
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Registered trials
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