Influence of pre-analytical procedures on genomic DNA integrity in blood samples: The SPIDIA experience

Malentacchi, Francesca; Ciniselli, Chiara Maura; Pazzagli, Mario; Verderio, Paolo; Barraud, Luc; Hartmann, Christina; Pizzamiglio, Sara; Weisbuch, S.; Wyrich, Ralf; Gelmini, Stefania

doi:10.1016/j.cca.2014.12.004

Cited by 23 publications

(19 citation statements)

References 26 publications

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“…26 It is important that contamination and degradation of DNA and RNA samples are avoided, as the quality and integrity of nucleic acids are likely to directly influence the results of downstream research studies. 27,28 Hence, processing schemes for DNA and RNA are very important and informative as they assess the ability of laboratories to achieve the best yield, quality, and integrity of DNA and RNA, and will pinpoint suboptimal laboratory workflows or the need of training.…”

Section: Comparison Of Processing Methods: Nucleic Acid Extractionmentioning

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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Section: Comparison Of Processing Methods: Nucleic Acid Extractionmentioning

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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show abstract

“…At such long-read lengths, currently standard methods require modifications and gentle DNA extraction methods such as phenol-chloroform extraction (for reference the Rad003 protocol used by Loman lab to extract DNA for generating the megabase-length read is available at http://lab.loman.net/protocols/). The shearing of DNA caused by the extraction step itself is, at least in high-throughput laboratories such as biobanks, likely to generate fragments with a characteristic length of more than 50 kb, while turbulent forces during other parts of the process restrict the fragment length to 5-35 kb (Shao et al, 2012;Malentacchi et al, 2015). Among commonly used extraction methods, precipitation based DNA extraction generate the highest molecular weight of DNA but variations in fragment length (Shao et al, 2012) and other quality parameters mean that kit-by-kit comparisons will be necessary for the selection of suitable best practice procedures for DNA extraction depending on the intended usage of the samples.…”

Section: The Smear Ratio (Sr)mentioning

confidence: 99%

“…With the rising importance of long-read sequencing technologies and mapping technologies utilising linked reads (Schadt et al, 2010;Goodwin et al, 2016) shearing limits researchers from using the full capacity of emerging technologies where even megabase lengths can be sequenced in a single read (Jain et al, 2018). A better understanding of DNA structural integrity and fragmentation is therefore necessary to improve quality management practices for high-molecular-weight DNA (HMW-DNA) (English et al, 2012;Malentacchi et al, 2015;Goodwin et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA

Klingström

Bongcam‐Rudloff

2018

Preprint

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During DNA extraction the DNA molecule undergoes physical and chemical shearing, causing the DNA to fragment into shorter and shorter pieces. Under common laboratory conditions this fragmentation yields DNA fragments of 5-35 kilobases (kb) in length. This fragment length is more than sufficient for DNA sequencing using short-read technologies which generate reads 50-600 bp in length, but insufficient for long-read sequencing and linked reads where fragment lengths of more than 40 kb may be desirable.This study provides a theoretical framework for quality management to ensure access to high molecular weight DNA in samples. Shearing can be divided into physical and chemical shearing which generate different patterns of fragmentation. Exposure to physical shearing creates a characteristic fragment length where DNA fragments are cut in half by shear stress. This characteristic length can be measured using gel electrophoresis or instruments for DNA fragment analysis. Chemical shearing generates randomly distributed fragment lengths visible as a smear of DNA below the peak fragment length. By measuring the peak of DNA fragment length and the proportion of very short DNA fragments both sources of shearing can be measured using commonly used laboratory techniques, providing a suitable quantification of DNA integrity of DNA for sequencing with long-read technologies.

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“…Hence, the PB has been at ambient temperatures for up to three days before processing. Inadequate handling and storage of blood samples can have detrimental effects on quality and quantity of extracted DNA [17,18]. Also, the integrity of RNA and protein can be affected by storage temperature [19][20][21].…”

Section: High Quality Sequencing Data Generated From Time Points Up Tmentioning

confidence: 99%

The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

et al. 2017

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Abstract:Background: Epigenetic epidemiology has proven an important research discipline in the delineation of diseases of complex etiology. The approach, in such studies, is often to use bio-banked clinical material, however, many such samples were collected for purposes other than epigenetic studies and, thus, potentially not processed and stored appropriately. The Danish National Birth Cohort (DNBC) includes more than 100,000 peripheral and umbilical cord blood samples shipped from maternity wards by ordinary mail in EDTA tubes. While this and other similar cohorts hold great promises for DNA methylation studies the potential systematic changes prompted by storage at ambient temperatures have never been assessed on a genome-wide level. Methods and Results: In this study, matched EDTA whole blood samples were stored up to three days at room temperature prior to DNA extraction and methylated DNA immunoprecipitation coupled with deep sequencing (MeDIP-seq). We established that the quality of the MeDIP-seq libraries was high and comparable across samples; and that the methylation profiles did not change systematically during the short-time storage at room temperature. Conclusion: The global DNA methylation profile is stable in whole blood samples stored for up to three days at room temperature in EDTA tubes making genome-wide methylation studies on such material feasible.

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Influence of pre-analytical procedures on genomic DNA integrity in blood samples: The SPIDIA experience

Cited by 23 publications

References 26 publications

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

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

A comprehensive model of DNA fragmentation for the preservation of High Molecular Weight DNA

The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature

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