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Schematic Overview of the Main  DNA  Extraction Steps From  FFPE  Tissue Sections by Five Different Methods

Journal: American Journal of Clinical Pathology

Article Title: Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA

doi: 10.1093/ajcp/aqw205

Figure Lengend Snippet: Schematic Overview of the Main DNA Extraction Steps From FFPE Tissue Sections by Five Different Methods

Article Snippet: The total duration of all five DNA extraction methods was comparable, except for the Zymo Research FFPE DNA miniprep kit, where several washes with ethanol contribute to a long handling time (approximately 3.5 hours) on day 1 of DNA extraction .

Techniques: DNA Extraction, Isolation, Lysis, Binding Assay, Incubation, Centrifugation, Purification

Comparison of Selected  DNA  Extraction Methods for  DNA  Extraction From  FFPE  Tissue Sections

Journal: American Journal of Clinical Pathology

Article Title: Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA

doi: 10.1093/ajcp/aqw205

Figure Lengend Snippet: Comparison of Selected DNA Extraction Methods for DNA Extraction From FFPE Tissue Sections

Article Snippet: The total duration of all five DNA extraction methods was comparable, except for the Zymo Research FFPE DNA miniprep kit, where several washes with ethanol contribute to a long handling time (approximately 3.5 hours) on day 1 of DNA extraction .

Techniques: DNA Extraction, Isolation, Incubation

The influence of five different DNA extraction methods on the multiplex ligation-dependent probe amplification (MLPA) probe’s copy number ratios. MLPA was performed on DNA extracted from eight various formalin-fixed, paraffin-embedded (FFPE) tissues with the P027 probe mix (50 probes). The y-axis represents the percentage of probes showing copy number ratios outside the 0.8 to 1.2 normal copy number range. The x-axis shows five different DNA extraction methods. Each bar represents a separate FFPE tissue-type block. For samples where DNA was extracted with the one-tube FFPE extraction method, results from crude (nonpurified) DNA lysate are presented for all tissues, except the lung. The crude lysate of the lung FFPE tissue was also purified. SEM (as indicated by error bars) was calculated by dividing the standard deviation of the mean of the number of probes with copy number ratios outside the normal range by the square root of the number of samples (triplicate) . colonSymb, tissue from Symbiant Pathology Expert Centre, Alkmaar; colonUMC, tissue from Department of Pathology, University Medical Centre Utrecht, Utrecht.

Journal: American Journal of Clinical Pathology

Article Title: Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA

doi: 10.1093/ajcp/aqw205

Figure Lengend Snippet: The influence of five different DNA extraction methods on the multiplex ligation-dependent probe amplification (MLPA) probe’s copy number ratios. MLPA was performed on DNA extracted from eight various formalin-fixed, paraffin-embedded (FFPE) tissues with the P027 probe mix (50 probes). The y-axis represents the percentage of probes showing copy number ratios outside the 0.8 to 1.2 normal copy number range. The x-axis shows five different DNA extraction methods. Each bar represents a separate FFPE tissue-type block. For samples where DNA was extracted with the one-tube FFPE extraction method, results from crude (nonpurified) DNA lysate are presented for all tissues, except the lung. The crude lysate of the lung FFPE tissue was also purified. SEM (as indicated by error bars) was calculated by dividing the standard deviation of the mean of the number of probes with copy number ratios outside the normal range by the square root of the number of samples (triplicate) . colonSymb, tissue from Symbiant Pathology Expert Centre, Alkmaar; colonUMC, tissue from Department of Pathology, University Medical Centre Utrecht, Utrecht.

Article Snippet: The total duration of all five DNA extraction methods was comparable, except for the Zymo Research FFPE DNA miniprep kit, where several washes with ethanol contribute to a long handling time (approximately 3.5 hours) on day 1 of DNA extraction .

Techniques: DNA Extraction, Multiplex Assay, Ligation, Amplification, Formalin-fixed Paraffin-Embedded, Blocking Assay, Purification, Standard Deviation

(cont) C , MLPA electropherogram of FFPE lung tissue crude lysate column purified with the DNA Clean & Concentrator-5 kit. RFU, residual fluorescence unit.

Journal: American Journal of Clinical Pathology

Article Title: Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA

doi: 10.1093/ajcp/aqw205

Figure Lengend Snippet: (cont) C , MLPA electropherogram of FFPE lung tissue crude lysate column purified with the DNA Clean & Concentrator-5 kit. RFU, residual fluorescence unit.

Article Snippet: The total duration of all five DNA extraction methods was comparable, except for the Zymo Research FFPE DNA miniprep kit, where several washes with ethanol contribute to a long handling time (approximately 3.5 hours) on day 1 of DNA extraction .

Techniques: Purification, Fluorescence