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Gridina MM, Vesna E, Minzhenkova ME, Shilova NV, Ryzhkova OP, Nazarenko LP, Belyaeva EO, Lebedev IN, Fishman VS. Influence of human peripheral blood samples preprocessing on the quality of Hi-C libraries. Vavilovskii Zhurnal Genet Selektsii 2023; 27:83-87. [PMID: 36923477 PMCID: PMC10009481 DOI: 10.18699/vjgb-23-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023] Open
Abstract
The genome-wide variant of the chromatin conformation capture technique (Hi-C) is a powerful tool for revealing patterns of genome spatial organization, as well as for understanding the effects of their disturbance on disease development. In addition, Hi-C can be used to detect chromosomal rearrangements, including balanced translocations and inversions. The use of the Hi-C method for the detection of chromosomal rearrangements is becoming more widespread. Modern high-throughput methods of genome analysis can effectively reveal point mutations and unbalanced chromosomal rearrangements. However, their sensitivity for determining translocations and inversions remains rather low. The storage of whole blood samples can affect the amount and integrity of genomic DNA, and it can distort the results of subsequent analyses if the storage was not under proper conditions. The Hi-C method is extremely demanding on the input material. The necessary condition for successfully applying Hi-C and obtaining high-quality data is the preservation of the spatial chromatin organization within the nucleus. The purpose of this study was to determine the optimal storage conditions of blood samples for subsequent Hi-C analysis. We selected 10 different conditions for blood storage and sample processing. For each condition, we prepared and sequenced Hi-C libraries. The quality of the obtained data was compared. As a result of the work, we formulated the requirements for the storage and processing of samples to obtain high-quality Hi-C data. We have established the minimum volume of blood sufficient for conducting Hi-C analysis. In addition, we have identified the most suitable methods for isolation of peripheral blood mononuclear cells and their long-term storage. The main requirement we have formulated is not to freeze whole blood.
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Affiliation(s)
- M M Gridina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E Vesna
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - N V Shilova
- Research Centre for Medical Genetics, Moscow, Russia
| | - O P Ryzhkova
- Research Centre for Medical Genetics, Moscow, Russia
| | - L P Nazarenko
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E O Belyaeva
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - I N Lebedev
- Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - V S Fishman
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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2
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The Implementation of Laboratory Information Management System in Multi-Site Genetics Study in Africa: The Challenges and Up-Scaling Opportunities. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3040022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
This study describes the roles of laboratory information management systems (LIMS) in multi-site genetics studies in Africa. We used the HiGeneS Africa project as a case study. The study participants were recruited in six African countries between 2019 to 2021. The Baobab LIMS, a server–client-based system (an African-led innovation) was used for the coordination of the biospecimen. The development phase of the LIMS showcased the team formation, data collection, biospecimen collection, and shipment strategies. The implementation phase showcased the biospecimen registration, processing, and quality control (QC) analytics. The sample QC was done using Nanodrop, Qubit, and PicoGreen/gDNATapestation assays. The results showed that a total of 3144 study participants were recruited from Cameroon, Ghana, Mali, Rwanda, Senegal, and South Africa. The biospecimen registration provided a comprehensive registry that included patient demographics, genetic information, and clinical and blood/saliva samples from the proband and family relatives. The QC analyzes identified 30 samples that failed QC, linked to overdue storage in the freezer before DNA extraction. The LIMS components implemented in this project formed a structure that can be upscaled to artificial intelligence-based LIMS. In conclusion, this study represents the largest and the most diverse collection of biospecimens for the genetic study of hearing impairment in Africa to date. A well-characterized LIMS should be recommended for multi-site molecular studies, particularly in Africa, to enhance African participation in global genomic medicine.
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Di Lecce I, Sudyka J, Westneat DF, Szulkin M. Preserving avian blood and DNA sampled in the wild: A survey of personal experiences. Ecol Evol 2022; 12:e9232. [PMID: 36052299 PMCID: PMC9424668 DOI: 10.1002/ece3.9232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/20/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Collecting and storing biological material from wild animals in a way that does not deteriorate DNA quality for subsequent analyses is instrumental for research in ecology and evolution. Our aims were to gather reports on the effectiveness of methods commonly used by researchers for the field collection and long-term storage of blood samples and DNA extracts from wild birds. Personal experiences were collected with an online survey targeted specifically at researchers sampling wild birds. Many researchers experienced problems with blood sample storage but not with DNA extract storage. Storage issues generated problems with obtaining adequate DNA quality and sufficient DNA quantity for the targeted molecular analyses but were not related to season of blood sampling, access to equipment, transporting samples, temperature, and method of blood storage. Final DNA quality and quantity were also not affected by storage time before DNA extraction or the methods used to extract DNA. We discuss practical aspects of field collection and storage and provide some general recommendations, with a list of pros and cons of different preservation methods of avian blood samples and DNA extracts.
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Affiliation(s)
- Irene Di Lecce
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
| | - Joanna Sudyka
- Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | | | - Marta Szulkin
- Centre of New TechnologiesUniversity of WarsawWarsawPoland
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4
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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Wang L, Guo S, Zeng B, Wang S, Chen Y, Cheng S, Liu B, Wang C, Wang Y, Meng Q. Draft Genome Assembly and Annotation for Cutaneotrichosporon dermatis NICC30027, an Oleaginous Yeast Capable of Simultaneous Glucose and Xylose Assimilation. MYCOBIOLOGY 2022; 50:69-81. [PMID: 35291590 PMCID: PMC8890563 DOI: 10.1080/12298093.2022.2038844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/10/2022] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
The identification of oleaginous yeast species capable of simultaneously utilizing xylose and glucose as substrates to generate value-added biological products is an area of key economic interest. We have previously demonstrated that the Cutaneotrichosporon dermatis NICC30027 yeast strain is capable of simultaneously assimilating both xylose and glucose, resulting in considerable lipid accumulation. However, as no high-quality genome sequencing data or associated annotations for this strain are available at present, it remains challenging to study the metabolic mechanisms underlying this phenotype. Herein, we report a 39,305,439 bp draft genome assembly for C. dermatis NICC30027 comprised of 37 scaffolds, with 60.15% GC content. Within this genome, we identified 524 tRNAs, 142 sRNAs, 53 miRNAs, 28 snRNAs, and eight rRNA clusters. Moreover, repeat sequences totaling 1,032,129 bp in length were identified (2.63% of the genome), as were 14,238 unigenes that were 1,789.35 bp in length on average (64.82% of the genome). The NCBI non-redundant protein sequences (NR) database was employed to successfully annotate 11,795 of these unigenes, while 3,621 and 11,902 were annotated with the Swiss-Prot and TrEMBL databases, respectively. Unigenes were additionally subjected to pathway enrichment analyses using the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cluster of Orthologous Groups of proteins (COG), Clusters of orthologous groups for eukaryotic complete genomes (KOG), and Non-supervised Orthologous Groups (eggNOG) databases. Together, these results provide a foundation for future studies aimed at clarifying the mechanistic basis for the ability of C. dermatis NICC30027 to simultaneously utilize glucose and xylose to synthesize lipids.
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Affiliation(s)
- Laiyou Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuxian Guo
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bo Zeng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shanshan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yan Chen
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Shuang Cheng
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Bingbing Liu
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Chunyan Wang
- School of Biological and Chemical Engineering, Nanyang Institute of Technology, Nanyang, China
- Henan Key Laboratory of Industrial Microbial Resources and Fermentation Technology, Nanyang Institute of Technology, Nanyang, China
| | - Yu Wang
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Qingshan Meng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Advancing Biomarker Development Through Convergent Engagement: Summary Report of the 2nd International Danube Symposium on Biomarker Development, Molecular Imaging and Applied Diagnostics; March 14-16, 2018; Vienna, Austria. Mol Imaging Biol 2021; 22:47-65. [PMID: 31049831 DOI: 10.1007/s11307-019-01361-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Here, we report on the outcome of the 2nd International Danube Symposium on advanced biomarker development that was held in Vienna, Austria, in early 2018. During the meeting, cross-speciality participants assessed critical aspects of non-invasive, quantitative biomarker development in view of the need to expand our understanding of disease mechanisms and the definition of appropriate strategies both for molecular diagnostics and personalised therapies. More specifically, panelists addressed the main topics, including the current status of disease characterisation by means of non-invasive imaging, histopathology and liquid biopsies as well as strategies of gaining new understanding of disease formation, modulation and plasticity to large-scale molecular imaging as well as integrative multi-platform approaches. Highlights of the 2018 meeting included dedicated sessions on non-invasive disease characterisation, development of disease and therapeutic tailored biomarkers, standardisation and quality measures in biospecimens, new therapeutic approaches and socio-economic challenges of biomarker developments. The scientific programme was accompanied by a roundtable discussion on identification and implementation of sustainable strategies to address the educational needs in the rapidly evolving field of molecular diagnostics. The central theme that emanated from the 2nd Donau Symposium was the importance of the conceptualisation and implementation of a convergent approach towards a disease characterisation beyond lesion-counting "lumpology" for a cost-effective and patient-centric diagnosis, therapy planning, guidance and monitoring. This involves a judicious choice of diagnostic means, the adoption of clinical decision support systems and, above all, a new way of communication involving all stakeholders across modalities and specialities. Moreover, complex diseases require a comprehensive diagnosis by converging parameters from different disciplines, which will finally yield to a precise therapeutic guidance and outcome prediction. While it is attractive to focus on technical advances alone, it is important to develop a patient-centric approach, thus asking "What can we do with our expertise to help patients?"
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7
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Sotoudeh Anvari M, Gharib A, Abolhasani M, Azari-Yam A, Hossieni Gharalari F, Safavi M, Zare Mirzaie A, Vasei M. Pre-analytical Practices in the Molecular Diagnostic Tests, A Concise Review. IRANIAN JOURNAL OF PATHOLOGY 2020; 16:1-19. [PMID: 33391375 PMCID: PMC7691716 DOI: 10.30699/ijp.2020.124315.2357] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/05/2020] [Indexed: 12/17/2022]
Abstract
Molecular assays for detection of nucleic acids in biologic specimens are valuable diagnostic tools supporting clinical diagnoses and therapeutic decisions. Pre-analytical errors, which occur before or during processing of nucleic acid extraction, contribute a significant role in common errors that take place in molecular laboratories. Certain practices in specimen collection, transportation, and storage can affect the integrity of nucleic acids before analysis. Applying best practices in these steps, helps to minimize those errors and leads to better decisions in patient diagnosis and treatment. Widely acceptable recommendations, which are for optimal molecular assays associated with pre-analytic variables, are limited. In this article, we have reviewed most of the important issues in sample handling from bed to bench before starting molecular tests, which can be used in diagnostic as well as research laboratories. We have addressed the most important pre-analytical points in performing molecular analysis in fixed and unfixed solid tissues, whole blood, serum, plasma, as well as most of the body fluids including urine, fecal and bronchial samples, as well as prenatal diagnosis samples.
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Affiliation(s)
- Maryam Sotoudeh Anvari
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Gharib
- Department of Pathology, Modarres Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Abolhasani
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran; Hasheminejad Kidney Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aileen Azari-Yam
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Moeinadin Safavi
- Molecular Pathology and Cytogenetics Division, Pathology Department, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Zare Mirzaie
- Department of Pathology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Vasei
- Cell-based Therapies Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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Palacios J, de la Hoya M, Bellosillo B, de Juan I, Matías-Guiu X, Lázaro C, Palanca S, Osorio A, Rojo F, Rosa-Rosa JM, Cigudosa JC. Mutational Screening of BRCA1/2 Genes as a Predictive Factor for Therapeutic Response in Epithelial Ovarian Cancer: A Consensus Guide from the Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH). Virchows Arch 2020; 476:195-207. [PMID: 31797087 PMCID: PMC7028830 DOI: 10.1007/s00428-019-02709-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/11/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022]
Abstract
Germline/somatic BRCA-mutated ovarian carcinomas (OC) are associated to have better response with platinum-based chemotherapy and long-term prognosis than non-BRCA-associated OCs. In addition, these mutations are predictive factors to response to Poly(ADP-ribose) polymerase (PARP) inhibitors. Different positioning papers have addressed the clinical recommendations for BRCA testing in OC. This consensus guide represents a collection of technical recommendations to address the detection of BRCA1/2 mutations in the molecular diagnostic testing strategy for OC. Under the coordination of Spanish Society of Pathology (SEAP-IAP) and the Spanish Society of Human Genetics (AEGH), these recommendations have been developed by pathologists and geneticists taking into account previously published recommendations and their experience in the molecular characterization of these genes. Since the implementation of BRCA testing as a predictive factor can initiate the workflow by testing germline mutations in the blood or by testing both germline and somatic mutations in tumor tissue, distinctive features of both strategies are discussed. Additionally, the recommendations included in this paper provide some references, quality parameters, and genomic tools aimed to standardize and facilitate the clinical genomic diagnosis of OC.
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Affiliation(s)
- J Palacios
- Servicio de Anatomía Patológica, Hospital Universitario Ramón y Cajal, 28034, Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034, Madrid, Spain.
- Universidad de Alcalá, 28801, Alcalá de Henares, Spain.
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - M de la Hoya
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Molecular Oncology Laboratory, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - B Bellosillo
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Laboratorio de Diagnóstico Molecular, Servicio de Patología, Hospital del Mar, 08003, Barcelona, Spain
| | - I de Juan
- Unidad de Biología Molecular, Servicio de Análisis Clínicos, Hospital Universitario y Politécnico La Fe, 46026, Valencia, Spain
| | - X Matías-Guiu
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Servicio de Anatomía Patológica, Hospital Universitario de Bellvitge, 08908, L'Hospitalet, Spain
| | - C Lázaro
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Unidad de Diagnóstico Molecular, Institut Català d'Oncologia, (ICO-IDIBELL-ONCOBELL), 08908, L'Hospitalet, Spain
| | - S Palanca
- Unidad de Biología Molecular, Servicio de Análisis Clínicos, Hospital Universitario y Politécnico La Fe, 46026, Valencia, Spain
| | - A Osorio
- Human Cancer Genetics Programme, Spanish National Cancer Centre (CNIO), 28029, Madrid, Spain
- CIBER-ER, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - F Rojo
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Departamento de Patología, Fundación Jímenez-Díaz, 28040, Madrid, Spain
| | - J M Rosa-Rosa
- Instituto Ramón y Cajal de Investigación Sanitaria, 28034, Madrid, Spain
- CIBER-ONC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - J C Cigudosa
- NIMGenetics, Parque Científico de Madrid, Campus Cantoblanco, 28049, Madrid, Spain
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9
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Fichou Y, Berlivet I, Richard G, Tournamille C, Castilho L, Férec C. Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the ACKR1 Gene Encoding the Duffy Antigens. Transfus Med Hemother 2019; 47:23-32. [PMID: 32110191 DOI: 10.1159/000504584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/01/2019] [Indexed: 01/31/2023] Open
Abstract
Background In the novel era of blood group genomics, (re-)defining reference gene/allele sequences of blood group genes has become an important goal to achieve, both for diagnostic and research purposes. As novel potent sequencing technologies are available, we thought to investigate the variability encountered in the three most common alleles of ACKR1, the gene encoding the clinically relevant Duffy antigens, at the haplotype level by a long-read sequencing approach. Materials and Methods After long-range PCR amplification spanning the whole ACKR1 gene locus (∼2.5 kilobases), amplicons generated from 81 samples with known genotypes were sequenced in a single read by using the Pacific Biosciences (PacBio) single molecule, real-time (SMRT) sequencing technology. Results High-quality sequencing reads were obtained for the 162 alleles (accuracy >0.999). Twenty-two nucleotide variations reported in databases were identified, defining 19 haplotypes: four, eight, and seven haplotypes in 46 ACKR1*01, 63 ACKR1*02, and 53 ACKR1*02N.01 alleles, respectively. Discussion Overall, we have defined a subset of reference alleles by third-generation (long-read) sequencing. This technology, which provides a "longitudinal" overview of the loci of interest (several thousand base pairs) and is complementary to the second-generation (short-read) next-generation sequencing technology, is of critical interest for resolving novel, rare, and null alleles.
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Affiliation(s)
- Yann Fichou
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | | | | | - Christophe Tournamille
- Laboratoire d'Excellence GR-Ex, Paris, France.,IMRB-Inserm U955 Equipe 2 Transfusion et Maladies du Globule Rouge, EFS Ile-de-France, Créteil, France
| | | | - Claude Férec
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France
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10
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Riegman PHJ, Becker KF, Zatloukal K, Pazzagli M, Schröder U, Oelmuller U. How standardization of the pre-analytical phase of both research and diagnostic biomaterials can increase reproducibility of biomedical research and diagnostics. N Biotechnol 2019; 53:35-40. [PMID: 31202859 DOI: 10.1016/j.nbt.2019.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/17/2019] [Accepted: 06/12/2019] [Indexed: 12/01/2022]
Abstract
Comparison of published biomedical studies shows that a large proportion are irreproducible, causing severe damage to society and creating an image of wasted investments. These observations are of course damaging to the biomedical research field, which is currently full of future promise. Precision medicine and disease prevention are successful, but are progressing slowly due to irreproducible study results. Although standardization is mentioned as a possible solution, it is not always clear how this could decrease or prevent irreproducible results in biomedical studies. In this article more insight is given into what quality, norms, standardization, certification, accreditation and optimized infrastructure can accomplish to reveal causes of irreproducibility and increase reproducibility when collecting biomaterials. CEN and ISO standards for the sample pre-analytical phase are currently being developed with the support of the SPIDIA4P project, and their role in increasing reproducibility in both biomedical research and diagnostics is demonstrated. In particular, it is described how standardized methods and quality assurance documentation can be exploited as tools for: 1) recognition and rejection of 'not fit for purpose' samples on the basis of detailed sample metadata, and 2) identification of methods that contribute to irreproducibility which can be adapted or replaced.
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Affiliation(s)
- P H J Riegman
- Erasmus MC Rotterdam, Pathology department, Wytemaweg 80, 3015 CN Rotterdam, the Netherlands.
| | - K F Becker
- Technical University of Munich, Institute of Pathology, Trogerstrasse 18, 81675 Munich, Germany
| | - K Zatloukal
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Pathology, Medical University of Graz, Austria
| | - M Pazzagli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Italy
| | - U Schröder
- DIN Deutsches Institut für Normung e.V., Saatwinkler Damm 42/43, 13627 Berlin, Germany
| | - U Oelmuller
- QIAGEN GmbH, MDx Development, QIAGEN Str. 1, 40724 Hilden, Germany
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11
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Schröder C, Steimer W. gDNA extraction yield and methylation status of blood samples are affected by long-term storage conditions. PLoS One 2018; 13:e0192414. [PMID: 29415017 PMCID: PMC5802893 DOI: 10.1371/journal.pone.0192414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is believed to provide great chances for a better understanding of the development and treatment of many diseases where the analysis of genomic DNA has so far failed to provide conclusive answers. Methylcytosine is a frequently used quantitative marker of epigenetic studies. Since immediate analysis of sampled material is in most cases not possible, storage time and conditions are critical aspects regarding the quality of genomic DNA and reliability of analysis. Blood is frequently used for such analyses. We, therefore, collected blood samples of ten volunteers and stored them under various conditions for ten months: -70°C, -20°C, 2-8°C and room temperature. An additional aliquot was frozen at -70°C and thawed once a week at room temperature. We then compared the DNA extraction yields and methylation status in relation to storage time and conditions. We found significantly lower DNA extraction yields (up to -97.45%; p ≤ 0.001) as well as significantly higher methylation levels after ten months of storage (up to +42.0%; p ≤ 0.001). These results suggest that storage time has an important influence on DNA analyses of blood samples for all storage conditions. This might be due to differences in stability of methylated and non-methylated DNA. Our study indicates that storage conditions and time may be a critical factor for epigenetic methylation studies and require rigorous validation. For reliable analyses we, therefore, recommend to perform epigenetic analysis directly after sample collection.
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Affiliation(s)
- Charlotte Schröder
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Werner Steimer
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
- * E-mail:
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12
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The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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13
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Jagielski T, Gawor J, Bakuła Z, Zuchniewicz K, Żak I, Gromadka R. An optimized method for high quality DNA extraction from microalga Prototheca wickerhamii for genome sequencing. PLANT METHODS 2017; 13:77. [PMID: 29026433 PMCID: PMC5627410 DOI: 10.1186/s13007-017-0228-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 09/19/2017] [Indexed: 05/25/2023]
Abstract
BACKGROUND The complex cell wall structure of algae often precludes efficient extraction of their genetic material. The purpose of this study was to design a next-generation sequencing-suitable DNA isolation method for unicellular, achlorophyllous, yeast-like microalgae of the genus Prototheca, the only known plant pathogens of both humans and animals. The effectiveness of the newly proposed scheme was compared with five other, previously described methods, commonly used for DNA isolation from plants and/or yeasts, available either as laboratory-developed, in-house assays, based on liquid nitrogen grinding or different enzymatic digestion, or as commercially manufactured kits. RESULTS All five, previously described, isolation assays yielded DNA concentrations lower than those obtained with the new method, averaging 16.15 ± 25.39 vs 74.2 ± 0.56 ng/µL, respectively. The new method was also superior in terms of DNA purity, as measured by A260/A280 (-0.41 ± 4.26 vs 2.02 ± 0.03), and A260/A230 (1.20 ± 1.12 vs 1.97 ± 0.07) ratios. Only the liquid nitrogen-based method yielded DNA of comparable quantity (60.96 ± 0.16 ng/µL) and quality (A260/A280 = 2.08 ± 0.02; A260/A230 = 2.23 ± 0.26). Still, the new method showed higher integrity, which was best illustrated upon electrophoretic analysis. Genomic DNA of Prototheca wickerhamii POL-1 strain isolated with the protocol herein proposed was successfully sequenced on the Illumina MiSeq platform. CONCLUSIONS A new method for DNA isolation from Prototheca algae is described. The method, whose protocol involves glass beads pulverization and cesium chloride (CsCl) density gradient centrifugation, was demonstrated superior over the other common assays in terms of DNA quantity and quality. The method is also the first to offer the possibility of preparation of DNA template suitable for whole genome sequencing of Prototheca spp.
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Affiliation(s)
- Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Jan Gawor
- DNA Sequencing and Oligonucleotides Synthesis Laboratory at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, 02-096 Warsaw, Poland
| | - Karolina Zuchniewicz
- DNA Sequencing and Oligonucleotides Synthesis Laboratory at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Iwona Żak
- Department of Clinical Microbiology, Children’s University Hospital of Cracow, Kraków, Poland
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotides Synthesis Laboratory at the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, A. Pawińskiego 5a, 02-106 Warsaw, Poland
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14
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McMahon TC, Blais BW, Wong A, Carrillo CD. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures. Front Microbiol 2017; 8:332. [PMID: 28303131 PMCID: PMC5332415 DOI: 10.3389/fmicb.2017.00332] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of current methods for EHEC detection in foods.
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Affiliation(s)
- Tanis C McMahon
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, OttawaON, Canada; Department of Biology, Carleton University, OttawaON, Canada
| | - Burton W Blais
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa ON, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa ON, Canada
| | - Catherine D Carrillo
- Research and Development, Ottawa Laboratory (Carling), Ontario Laboratory Network, Canadian Food Inspection Agency, Ottawa ON, Canada
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15
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Wheelock ÅM, Paulson L, Litton JE. The EuPA Biobank Initiative: Meeting the future challenges of biobanking in proteomics & systems medicine. J Proteomics 2016. [PMID: 26216594 DOI: 10.1016/j.jprot.2015.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
UNLABELLED In this News & Reviews Discussion, the recently launched EuPA (European Proteomics Association) Biobank Initiative is introduced in the context of current and future challenges in biobanking. The purpose of the initiative is to provide a forumand knowledge platform for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forum and easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, as well as the output and productivity from existing biobanks. The underutilization of biobanks has recently been identified as an emerging issue of biobankingworldwide. Measures to improve our ability to locate and access appropriate sample collections for a wide range of research purposes may enhance both the scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. BIOLOGICAL SIGNIFICANCE This manuscript is intended as a Discussion piece, and represents a recollection of the presentation under the “EuPA Initiative” session at HUPO/EuPA 2014 in Madrid. The launch of the EuPA (European Proteomics Association) Biobank Initiative in the context of current and future challenges in biobanking is discussed. The purpose of the initiative is to provide a forum and knowledge base for integrating the extensive experiences collected by the EuPA community, and link it to the European and international biobanking communities at large. The specific impact of providing a forumand easy access to this type of information to the EuPA community is the potential of improving the quality of future sample collections and biobanks, the quality of the research produced from these sample collections, aswell as the output and productivity fromexisting biobanks. The underutilization of biobanks has recently been identified as a challenge to the well-being and economic sustainability of biobanking worldwide. Measures to improve our ability to localize and access appropriate sample collections for validation studies and other research purposes is thus of benefit bothto scientific quality and biobank sustainability, thereby contributing to the important task of moving our research beyond basic findings and mere publications, into clinical practice. This article is part of a Special Issue entitled: HUPO 2014.
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Gaignaux A, Ashton G, Coppola D, De Souza Y, De Wilde A, Eliason J, Grizzle W, Guadagni F, Gunter E, Koppandi I, Shea K, Shi T, Stein JA, Sobel ME, Tybring G, Van den Eynden G, Betsou F. A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience. Biopreserv Biobank 2016; 14:429-439. [PMID: 27195612 DOI: 10.1089/bio.2015.0108] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
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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Affiliation(s)
| | - Garry Ashton
- 2 Cancer Research UK Manchester Institute , Manchester, United Kingdom
| | | | - Yvonne De Souza
- 4 AIDS Specimen Bank, University of California , San Francisco, San Francisco, California
| | | | - James Eliason
- 6 Great Lakes Stem Cell Innovation Center , Detroit, Michigan
| | - William Grizzle
- 7 Tissue Collection and Banking Facility, University of Alabama , Birmingham, Birmingham, Alabama
| | - Fiorella Guadagni
- 8 BioBIM (Multidisciplinary Interinstitutional Biobank) IRCCS San Raffaele , Rome, Italy
| | | | - Iren Koppandi
- 10 Cellular Technology Limited , Shaker Heights, Ohio
| | | | - Tim Shi
- 12 GlobalMD Network Corporation , Catonsville, Maryland
| | - Julie A Stein
- 13 PPD Vaccines and Biologics Lab , Wayne, Pennsylvania
| | - Mark E Sobel
- 14 American Society for Investigative Pathology , Bethesda, Maryland
| | | | - Gert Van den Eynden
- 16 Molecular Immunology Unit, Institut Jules Bordet , Brussels, Belgium .,17 Pathobiology Group , EORTC, Brussels, Belgium
| | - Fay Betsou
- 1 Integrated Biobank of Luxembourg , Luxembourg, Luxembourg
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17
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Malentacchi F, Pizzamiglio S, Ibrahim-Gawel H, Pazzagli M, Verderio P, Ciniselli CM, Wyrich R, Gelmini S. Data and performances evaluation of the SPIDIA-DNA Pan-European External Quality Assessment: 2nd SPIDIA-DNA laboratory report. Data Brief 2016; 6:980-4. [PMID: 26949730 PMCID: PMC4760182 DOI: 10.1016/j.dib.2016.01.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/22/2016] [Accepted: 01/27/2016] [Indexed: 11/30/2022] Open
Abstract
Within the EU-SPIDIA project (www.spidia.eu), the quality parameters of blood genomic DNA were defined [SPIDIA-DNA: an External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses - [1]; Influence of pre-analytical procedures on genomic DNA integrity in blood samples: the SPIDIA experience - [2]; Combining qualitative and quantitative imaging evaluation for the assessment of genomic DNA integrity: the SPIDIA experience - [3]. DNA quality parameters were used to evaluate the laboratory performance within an External Quality Assessment (EQA) [Second SPIDIA-DNA External Quality Assessment (EQA): Influence of pre-analytical phase of blood samples on genomic DNA quality - [4]. These parameters included DNA purity and yield by UV spectrophotometric measurements, the presence of PCR interferences by Kineret software and genomic DNA integrity analysis by Pulsed Field Gel Electrophoresis. Here we present the specific laboratory report of the 2nd SPIDIA-DNA EQA as an example of data and performances evaluation.
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Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | | | | | - Mario Pazzagli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | - Paolo Verderio
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Stefania Gelmini
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
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18
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Bulla A, De Witt B, Ammerlaan W, Betsou F, Lescuyer P. Blood DNA Yield but Not Integrity or Methylation Is Impacted After Long-Term Storage. Biopreserv Biobank 2016; 14:29-38. [PMID: 26812548 DOI: 10.1089/bio.2015.0045] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Collection of human whole blood for genomic DNA extraction is part of numerous clinical studies. Since DNA extraction cannot always be performed at the time of sample collection, whole blood samples may be stored for years before being processed. The use of appropriate storage conditions is then critical to obtain DNA in sufficient quantity and of adequate quality in order to obtain reliable results from the subsequent molecular biological analyses. In this study, EDTA whole blood samples were collected from 8 healthy volunteers, and different durations (up to 1 year) and temperatures (room temperature, 4°C, -20°C, and -80°C) of storage were compared. The effect of the addition of a DNA preservative agent was also assessed before and after storage. DNA concentrations measured by UV spectrophotometry and spectrofluorometry were used to calculate DNA extraction yields and double-strand DNA ratios. DNA integrity was controlled by agarose gel electrophoresis and long-range polymerase chain reaction. The impact of storage conditions on DNA methylation was also evaluated. Results showed that certain storage conditions have a significant impact on the DNA extraction yield but little or no effect on DNA integrity and methylation. Storage of EDTA blood at -80°C guarantees high-quality DNA with a good yield. Higher DNA extraction yields were obtained with the addition of a DNA preservative agent before thawing EDTA blood stored at -20°C or -80°C. Long-term storage at room temperature in the presence of a DNA preservative agent also appeared to be a reliable procedure.
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Affiliation(s)
- Alexandre Bulla
- 1 Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Genève , Geneva, Switzerland
| | | | | | - Fay Betsou
- 2 Integrated Biobank of Luxembourg , Luxembourg
| | - Pierre Lescuyer
- 1 Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Genève , Geneva, Switzerland
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Malentacchi F, Pizzamiglio S, Ibrahim-Gawel H, Pazzagli M, Verderio P, Ciniselli CM, Wyrich R, Gelmini S. Second SPIDIA-DNA External Quality Assessment (EQA): Influence of pre-analytical phase of blood samples on genomic DNA quality. Clin Chim Acta 2015; 454:10-4. [PMID: 26721315 DOI: 10.1016/j.cca.2015.12.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND In order to develop evidence-based quality guidelines for the pre-analytical phase of blood samples used for DNA molecular testing, two pan-European External Quality Assessments (EQAs) were implemented within the European Commission funded project SPIDIA. Here we report the results of the 2nd SPIDIA EQA that has been implemented on the basis of the 1st DNA EQA with the inclusion of some stringent conditions related to blood storage temperature and time. METHODS SPIDIA facility sent to all the participants the same blood sample to be processed by their own procedure following SPIDIA suggestion for time and temperature storage. Evaluated genomic DNA (gDNA) quality parameters were: purity and yield by UV spectrophotometric analysis, PCR interferences by Kineret software and integrity by a dedicated algorithm. RESULTS/CONCLUSIONS 188 applications have been collected from 26 European countries. A high variability of gDNA integrity was observed whereas purity, yield and PCR interferences had a narrow distribution within laboratories. A dedicated analysis on pre-analytical variables and the evaluated gDNA quality parameters showed that blood storage and DNA extraction procedures influence gDNA integrity. The performances of the participants were improved in comparison with the 1st SPIDIA-DNA EQA, probably due to adopted more stringent pre-analytical conditions.
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Affiliation(s)
- Francesca Malentacchi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.
| | | | | | - Mario Pazzagli
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
| | - Paolo Verderio
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Stefania Gelmini
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy
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20
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Ciniselli CM, Pizzamiglio S, Malentacchi F, Gelmini S, Pazzagli M, Hartmann CC, Ibrahim-Gawel H, Verderio P. Combining qualitative and quantitative imaging evaluation for the assessment of genomic DNA integrity: The SPIDIA experience. Anal Biochem 2015; 479:60-2. [DOI: 10.1016/j.ab.2015.03.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/12/2015] [Accepted: 03/20/2015] [Indexed: 11/25/2022]
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