Evaluation of five DNA extraction methods for detection of H. pylori in formalin-fixed paraffin-embedded (FFPE) liver tissue from patients with hepatocellular carcinoma

Rabelo-Gonçalves, Elizabeth Maria Afonso; Röesler, Bruna Maria; Guardia, A.C.; Milan, Arlete; Hara, Natalícia Hifumi; Escanhoela, C.A.F.; Almeida, João; Boin, I.F.S.F.; Zeitune, José Murilo Robilotta

doi:10.1016/j.prp.2013.11.003

Cited by 30 publications

(19 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Introducing RAPD-PCR into our aCGH workflow reduced the rate of failed amplifications. [7][8][9][10]18]We also examined the DNA yield per section (Figure 2). This controlled for the number of slides used in each extraction as well as the elution volumes used for each method.…”

Section: Discussionmentioning

confidence: 99%

“…They found that the Qiagen columns performed best, and that DNA yield became especially low in samples more than 50 years old. There is some controversy between laboratories, however, as other studies have compared the Qiagen kit with phenol-chloroform and found either the columns [7] or the phenol method [8]to be superior in yield and amplifiability. Other methods less frequently usednot measured in our study include the Maxwell 16 method by Promega (Mannheim, Germany), which was shown to perform well against other automated Qiagen kits [9], and the Chelex bead method (Bio-Rad, Berkeley, California) which has been used with some success in manual or automated extractions from FFPE tissues [10].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

Potluri

Mahas

Kent

et al. 2015

Analytical Biochemistry

View full text Add to dashboard Cite

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

Potluri

Mahas

Kent

et al. 2015

Analytical Biochemistry

View full text Add to dashboard Cite

“…Retrospective analysis of archival samples with modern laboratory techniques is a growing area of research [1][2][3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

“…Quantitative PCR, microarray, DNA methylation, and proteomic analysis of archived maternal blood, placental, or fetal tissues have shed light on various fetal-maternal complications [7][8][9][10] and other human diseases [6,11,12]. In humans, the growth hormone (GH) protein is translated from one of two genes (GH1, GH2) that predominate in postnatal and prenatal life, respectively [13,14].…”

Section: Introductionmentioning

confidence: 99%

Rapid method for growth hormone receptor exon 3 delete (GHRd3) SNP genotyping from archival human placental samples

et al. 2015

View full text Add to dashboard Cite

Analysis of archival samples from cohorts of pregnant women may be key to discovering prognosticators of stillbirth and pregnancy/perinatal complications. Growth hormone (GH) and its receptor (GHR) are pivotal in feto-placental development and pregnancy maintenance. We report a rapid, optimized method for genotyping the GHR full-length versus exon 3-deleted isoform (GHRd3). TaqMan single nucleotide polymorphism (SNP) genotyping proved superior to standard multiplex polymerase chain reaction (PCR) in allele detection and GHR genotyping from archived samples, including those with poor genomic deoxyribonucleic acid quality/quantity such as formalin fixed, paraffin embedded, blood, and serum. Furthermore, this assay is suitable for high through put 96 or 384-well plate quantitative PCR machines with automated genotype calling software. The TaqMan genotyping assay can increase the data obtained from precious archival human samples.

show abstract

“…Thus, an automated DNA extraction system that gives the highest DNA quantity and quality as possible, without inhibiting the downstream applications, is needed. Many studies have evaluated and improved DNA extraction methods from FFPE samples [7]–[9], however most studies compared manual extraction methods with each other or only one automated extraction system with manual DNA extraction [10]. This is the first study comparing different automated DNA extraction systems with FFPE material.…”

Section: Introductionmentioning

confidence: 99%

Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

et al. 2014

View full text Add to dashboard Cite

Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3–24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.

show abstract

Evaluation of five DNA extraction methods for detection of H. pylori in formalin-fixed paraffin-embedded (FFPE) liver tissue from patients with hepatocellular carcinoma

Cited by 30 publications

References 26 publications

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

Rapid method for growth hormone receptor exon 3 delete (GHRd3) SNP genotyping from archival human placental samples

Comparison of Pre-Analytical FFPE Sample Preparation Methods and Their Impact on Massively Parallel Sequencing in Routine Diagnostics

Contact Info

Product

Resources

About