ArticlePloS one2012
DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 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
- GelInsight: Open-source software for large-sample DNA fragmentation quality control in gel electrophoresis images.PloS one · 2026Article
- Distribution of copy number alterations and impact of chromosome arm call thresholds for meningioma.Nature communications · 2025Article
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- A critical spotlight on the paradigms of FFPE-DNA sequencing.Nucleic acids research · 2023Review
- Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability.International journal of molecular sciences · 2023Article
- Azalomycin FInternational journal of molecular sciences · 2020Article
- Immunogenetics of glioblastoma: the future of personalized patient management.NPJ precision oncology · 2018Review
- Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors.Neuro-oncology · 2017Article
- Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma.Neuro-oncology · 2017Article
- Germline and somatic BAP1 mutations in high-grade rhabdoid meningiomas.Neuro-oncology · 2017Article
- Oncogenic PI3K mutations are as common as AKT1 and SMO mutations in meningioma.Neuro-oncology · 2016Article
- A prognostic cytogenetic scoring system to guide the adjuvant management of patients with atypical meningioma.Neuro-oncology · 2016Article
- Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma.Neuro-oncology · 2015Article
- ARID1A and TERT promoter mutations in dedifferentiated meningioma.Cancer genetics · 2015Article
- Brain Malignancy Steering Committee clinical trials planning workshop: report from the Targeted Therapies Working Group.Neuro-oncology · 2015Review
- Angiomatous meningiomas have a distinct genetic profile with multiple chromosomal polysomies including polysomy of chromosome 5.Oncotarget · 2014Article
- Molecular pathologic diagnosis of epidermal growth factor receptor.Neuro-oncology · 2014Review
- Mitotic index, microvascular proliferation, and necrosis define 3 groups of 1p/19q codeleted anaplastic oligodendrogliomas associated with different genomic alterations.Neuro-oncology · 2014Article
- Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Whole-genome copy number analysis platforms, such as array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) arrays, are transformative research discovery tools. In cancer, the identification of genomic aberrations with these approaches has generated important diagnostic and prognostic markers, and critical therapeutic targets. While robust for basic research studies, reliable whole-genome copy number analysis has been unsuccessful in routine clinical practice due to a number of technical limitations. Most important, aCGH results have been suboptimal because of the poor integrity of DNA derived from formalin-fixed paraffin-embedded (FFPE) tissues. Using self-hybridizations of a single DNA sample we observed that aCGH performance is significantly improved by accurate DNA size determination and the matching of test and reference DNA samples so that both possess similar fragment sizes. Based on this observation, we developed a novel DNA fragmentation simulation method (FSM) that allows customized tailoring of the fragment sizes of test and reference samples, thereby lowering array failure rates. To validate our methods, we combined FSM with Universal Linkage System (ULS) labeling to study a cohort of 200 tumor samples using Agilent 1 M feature arrays. Results from FFPE samples were equivalent to results from fresh samples and those available through the glioblastoma Cancer Genome Atlas (TCGA). This study demonstrates that rigorous control of DNA fragment size improves aCGH performance. This methodological advance will permit the routine analysis of FFPE tumor samples for clinical trials and in daily clinical practice.
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