Comparison of Two Available Platforms for Determination of RNA Quality

Riedmaier, Irmgard; Bergmaier, M.; Pfaffl, Michael W.

doi:10.2478/v10133-010-0074-7

Cited by 20 publications

(14 citation statements)

References 6 publications

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“…An alternative platform (Experion) is reported to show superior reproducibility and quantity assessment. 9,39,40 The storage and release of quality samples are the sine qua non of a modern biobank, and biobank personnel assume this responsibility on behalf of patient donors, funders, and researchers, including those who ultimately develop new patient interventions. Biospecimen science focuses on improving the quality of a biobank's unique human sample resource, and will henceforth ensure that fewer research studies are discredited because of substandard samples.…”

Section: Discussionmentioning

confidence: 99%

Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

Mee

Carroll

Donatello

et al. 2011

Biopreservation and Biobanking

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The Saint James's Hospital Biobank was established in 2008, to develop a high-quality breast tissue BioResource, as a part of the breast cancer clinical care pathway. The aims of this work were: (1) to ascertain the quality of RNA, DNA, and protein in biobanked carcinomas and normal breast tissues, (2) to assess the efficacy of AllPrep(®) (Qiagen) in isolating RNA, DNA, and protein simultaneously, (3) to compare AllPrep with RNEasy(®) and QIAamp(®) (both Qiagen), and (4) to examine the effectiveness of Allprotect(®) (Qiagen), a new tissue stabilization medium in preserving DNA, RNA, and proteins. One hundred eleven frozen samples of carcinoma and normal breast tissue were analyzed. Tumor and normal tissue morphology were confirmed by frozen sections. Tissue type, tissue treatment (Allprotect vs. no Allprotect), extraction kit, and nucleic acid quantification were analyzed by utilizing a 4 factorial design (SPSS PASW 18 Statistics Software(®)). QIAamp (DNA isolation), AllPrep (DNA, RNA, and Protein isolation), and RNeasy (RNA isolation) kits were assessed and compared. Mean DNA yield and A(260/280) values using QIAamp were 33.2 ng/μL and 1.86, respectively, and using AllPrep were 23.2 ng/μL and 1.94. Mean RNA yield and RNA Integrity Number (RIN) values with RNeasy were 73.4 ng/μL and 8.16, respectively, and with AllPrep were 74.8 ng/μL and 7.92. Allprotect-treated tissues produced higher RIN values of borderline significance (P=0.055). No discernible loss of RNA stability was detected after 6 h incubation of stabilized or nonstabilized tissues at room temperature or 4°C or in 9 freeze-thaw cycles. Allprotect requires further detailed evaluation, but we consider AllPrep to be an excellent option for the simultaneous extraction of RNA, DNA, and protein from tumor and normal breast tissues. The essential presampling procedures that maintain the diagnostic integrity of pathology specimens do not appear to compromise the quality of molecular isolates.

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Section: Discussionmentioning

confidence: 99%

Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

Mee

Carroll

Donatello

et al. 2011

Biopreservation and Biobanking

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“…It has been suggested that the Experion returns more reproducible results with a higher sensitivity than the Bioanalyzer due to its more automated sample preparation and chip loading procedure. 18,19 However, due to the low number of participating laboratories using the Experion and other alternative methods, a platform comparison becomes problematic. A comparison between the Agilent and Qiaxcel technologies has shown that Qiaxcel is more precise for certain types of RNA samples.…”

Section: Comparison Of Testing Methodsmentioning

confidence: 99%

A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience

Gaignaux

Ashton

Coppola

et al. 2016

Biopreservation and Biobanking

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Biobanks produce and distribute biospecimens, ensuring their fitness for purpose and accurately qualifying them before distribution. In their efforts toward professionalization, biobanks can nowadays seek certification or accreditation. One of the requirements of these standards is regular participation in Proficiency Testing (PT) programs. An international PT program has been developed and provided to biobanks and other laboratories that perform specific tests to qualify different types of biospecimens. This PT program includes biospecimen testing schemes, as well as biospecimen processing interlaboratory exercises. This PT program supports the development of biobank quality assurance by providing the possibility to assess biobank laboratory performance and useful insights into biobank laboratory method performance characteristics and thus fulfill the demands from accreditation authorities.

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“…Briefly, the algorithm compares three regions of the electrophoretic profile: 28S region, 18S region and pre‐18S regions. The highest score is 10 . Despite the DNAse I digestion integrated in the QIAcube extraction program, gDNA contamination occurred.…”

Section: Resultsmentioning

confidence: 99%

“…The highest score is 10. [28][29][30] Despite the DNAse I digestion integrated in the QIAcube extraction program, gDNA contamination occurred. The gDNA was clearly visible on the red curve at the end of the electrophoresis as a large peak between 55 s and 60 s. However, the additional step of both DNAse I digestion and filtration on a 100 kDa MWCO filter removed the contamination with high efficiency.…”

Section: Resultsmentioning

confidence: 99%

RNA sample preparation applied to gene expression profiling for the horse biological passport

Bailly-Chouriberry¹,

Baudoin²,

Cormant³

et al. 2017

Drug Testing and Analysis

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The improvement of doping control is an ongoing race. Techniques to fight doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA), or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the horse biological passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques.

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Comparison of Two Available Platforms for Determination of RNA Quality

Cited by 20 publications

References 6 publications

Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

Maintaining Breast Cancer Specimen Integrity and Individual or Simultaneous Extraction of Quality DNA, RNA, and Proteins from Allprotect-Stabilized and Nonstabilized Tissue Samples

A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience

RNA sample preparation applied to gene expression profiling for the horse biological passport

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