ArticleThe Journal of molecular diagnostics : JMD2007
DNA degradation test predicts success in whole-genome amplification from diverse clinical samples.
Article in The Journal of molecular diagnostics : JMD, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- From collected stamps to hair locks: ethical and legal implications of testing DNA found on privately owned family artifacts.Human genetics · 2023Article
- Relative Risk of Bladder and Kidney Cancer in Lynch Syndrome: Systematic Review and Meta-Analysis.Cancers · 2023Review
- Enzymatic Methods for Mutation Detection in Cancer Samples and Liquid Biopsies.International journal of molecular sciences · 2023Review
- Artificial intelligence-augmented histopathologic review using image analysis to optimize DNA yield from formalin-fixed paraffin-embedded slides.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2022Article
- Review
- Mutation enrichment in human DNA samples via UV-mediated cross-linking.Nucleic acids research · 2022Article
- Article
- Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Do Tissues Fixed in a Non-crosslinking Fixative Require a Dedicated Formalin-free Processor?The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2021Article
- Sensitive detection of microsatellite instability in tissues and liquid biopsies: Recent developments and updates.Computational and structural biotechnology journal · 2021Review
- Digital microfluidic isolation of single cells for -Omics.Nature communications · 2020Article
- In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network.Journal of translational medicine · 2019Review
- Association between microRNA-125b expression in formalin-fixed paraffin-embedded tumor tissues and prognosis in patients with melanoma.Oncology letters · 2019Article
- Development of Novel Mutation-Specific Droplet Digital PCR Assays Detecting TERT Promoter Mutations in Tumor and Plasma Samples.The Journal of molecular diagnostics : JMD · 2019Article
- Nitrocellulose tissue prints: an innovative approach to preparing high quality DNA and RNA from prostate biopsies without compromising the cores for pathology diagnosis.Translational andrology and urology · 2018Article
- National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue.Biopreservation and biobanking · 2018Article
- Advancements in next-generation sequencing for diagnosis and treatment of non-small-cell lung cancer.Chronic diseases and translational medicine · 2017Article
- Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores.PloS one · 2017Article
- Assays for Qualification and Quality Stratification of Clinical Biospecimens Used in Research: A Technical Report from the ISBER Biospecimen Science Working Group.Biopreservation and biobanking · 2016Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
The need to apply modern technologies to analyze DNA from diverse clinical samples often stumbles on suboptimal sample quality. We developed a simple approach to assess DNA fragmentation in minute clinical samples of widely different origin and the likelihood of success of degradation-tolerant whole genome amplification (restriction and circularization-aided rolling circle amplification, RCA-RCA) and subsequent polymerase chain reaction (PCR). A multiplex PCR amplification of four glyceraldehyde-3-phosphate dehydrogenase amplicons of varying sizes was performed using genomic DNA from clinical samples, followed by size discrimination on agarose gel or fluorescent denaturing high-performance liquid chromatography (dHPLC). RCA-RCA followed by real-time PCR was also performed, for correlation. Even minimal quantities of longer PCR fragments ( approximately 300 to 400 bp), visible via high-sensitivity fluorescent dHPLC or agarose gel, were essential for the success of RCA-RCA and subsequent PCR-based assays. dHPLC gave a more accurate correlation between DNA fragmentation and sample quality than agarose gel electrophoresis. Multiplex-PCR-dHPLC predicted correctly the likelihood of assay success in formalin-fixed, paraffin-embedded samples fixed under controlled conditions and of different ages, in laser capture microdissection samples, in tissue print micropeels, and plasma-circulating DNA. Estimates of the percent information retained relative to snap-frozen DNA are derived for real-time PCR analysis. The assay is rapid and convenient and can be used widely to characterize DNA from any clinical sample of unknown quality.
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