ArticleBMC medical genomics2009
High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays.
Article in BMC medical genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 0 citations in OpenAlex.
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- A Comparative Study on Copy Number Variation in Subtypes of Breast Phyllodes Tumors.Breast cancer : basic and clinical research · 2025Article
- Diagnosis of melanoma by imaging mass spectrometry: Development and validation of a melanoma prediction model.Journal of cutaneous pathology · 2021Article
- Percentage genome change and chromosome 7q amplification predict sorafenib response in advanced hepatocellular carcinoma.Biomedical journal · 2021Article
- Polymorphous Low-Grade Neuroepithelial Tumor of the Young (PLNTY): Molecular Profiling Confirms Frequent MAPK Pathway Activation.Journal of neuropathology and experimental neurology · 2021Article
- Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer.Scientific reports · 2021Article
- Cell-free DNA From Pleural Effusion Samples: Is It Right for Molecular Testing in Lung Adenocarcinoma?Pathology oncology research : POR · 2021Article
- Through the looking glass and what you find there: making sense of comparative genomic hybridization and fluorescence in situ hybridization for melanoma diagnosis.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2020Review
- Association Between Spatial Heterogeneity Within Nonmetastatic Gastroesophageal Adenocarcinomas and Survival.JAMA network open · 2020Article
- Characterization of Copy Number Variations in Oral Cavity Squamous Cell Carcinoma Reveals a Novel Role for MLLT3 in Cell Invasiveness.The oncologist · 2019Article
- Quality and concordance of genotyping array data of 12,064 samples from 5840 cancer patients.Genomics · 2019Article
- Genome-wide copy number analyses of samples from LACE-Bio project identify novel prognostic and predictive markers in early stage non-small cell lung cancer.Translational lung cancer research · 2018Article
- Prediction of early-stage hepatocellular carcinoma using OncoScan chromosomal copy number aberration data.World journal of gastroenterology · 2017Article
- Genetic evaluation of juvenile xanthogranuloma: genomic abnormalities are uncommon in solitary lesions, advanced cases may show more complexity.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2017Article
- Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study.BMC genomics · 2017Article
- Genomic characteristics of trastuzumab-resistant Her2-positive metastatic breast cancer.Journal of cancer research and clinical oncology · 2017Article
- Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy.The Prostate · 2017Article
- Loss of maternal chromosome 11 is a signature event in SDHAF2, SDHD, and VHL-related paragangliomas, but less significant in SDHB-related paragangliomas.Oncotarget · 2017Article
- Genome-wide copy number aberrations and HER2 and FGFR1 alterations in primary breast cancer by molecular inversion probe microarray.Oncotarget · 2017Article
Corrections and comments
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Authors and funding
19 authors at 7 institutions in 2 countries.
Funding
Abstract
backgroundA major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from cell line and frozen tumor DNA. Since the MIP probes require only a small (approximately 40 bp) target binding site, we reasoned they may be well suited to assess degraded FFPE DNA. We assessed CN with a MIP panel of 50,000 markers in 93 FFPE tumor samples from 7 diverse collections. For 38 FFPE samples from three collections we were also able to asses CN in matched fresh frozen tumor tissue.
resultsUsing an input of 37 ng genomic DNA, we generated high quality CN data with MIP technology in 88% of FFPE samples from seven diverse collections. When matched fresh frozen tissue was available, the performance of FFPE DNA was comparable to that of DNA obtained from matched frozen tumor (genotype concordance averaged 99.9%), with only a modest loss in performance in FFPE.
conclusionMIP technology can be used to generate high quality CN and genotype data in FFPE as well as fresh frozen samples.
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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.