A Simple Variable Number of Tandem Repeat-Based Genotyping Strategy for the Detection of Handling Errors and Validation of Sample Identity in Biobanks.

Abstract:

:Biobanking biological samples involve multiple handling, processing, and labeling steps. Each step may be a source of error, which if unnoticed or uncorrected may have consequences for research. We aimed to develop a simple and inexpensive genotyping method that would be valuable to detect such errors and confirm sample identity. For this purpose, seven variable number of tandem repeat (VNTR) loci were selected, analyzed by polymerase chain reaction (PCR) amplification, and organized in a PCR-based DNA profiling algorithm that proved useful to minimize the number of steps required for the procedure. Match probability calculations suggest that this method/algorithm has the potential to discriminate every participant of a biobank. As a proof of concept, the algorithm was applied on samples taken from the PROCURE Prostate Cancer Biobank. It was applied on 403 DNA samples from 101 randomly chosen patients who provided prostate tissues at surgery and blood at two to three different time points over a period of up to 7 years. A unique DNA profile requiring the analysis of no more than four VNTR loci (D16S83, D17S5, D1S80, D19S20) was successfully obtained for each of the 101 cases studied and led to the identification of two mismatches among the 403 samples evaluated (0.5% error rate). Further investigations using the same genotyping method revealed that one of the errors was due to tissue mishandling and that the other was due to tissue mislabeling. These errors, typical to the complex biobanking process, highlight the importance to implement a routine genotyping method as part of quality assurance in biobanking.

journal_name

Biopreserv Biobank

authors

Pellerin C,McKercher G,Aprikian AG,Saad F,Lacombe L,Carmel M,Chevalier S

doi

10.1089/bio.2015.0113

subject

Has Abstract

pub_date

2016-10-01 00:00:00

pages

383-389

issue

5

eissn

1947-5535

issn

1947-5543

journal_volume

14

pub_type

杂志文章
  • Consensus-Driven Development of a Terminology for Biobanking, the Duke Experience.

    abstract::Biobanking at Duke University has existed for decades and has grown over time in silos and based on specialized needs, as is true with most biomedical research centers. These silos developed informatics systems to support their own individual requirements, with no regard for semantic or syntactic interoperability. Duk...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2016.0092

    authors: Ellis H,Joshi MB,Lynn AJ,Walden A

    更新日期:2017-04-01 00:00:00

  • Don't Take It Personal: European Union Legal Aspects of Procuring and Protecting Environmental Exposure Data in Population Biobanks Through the Use of a Geo-Information-Systems Toolkit.

    abstract::Under European Union (EU) law, population-based cohort studies have the right to collect environmental data and to access geospatial data, at street level, on the web, from a host of public sources. As to geospatial information, they should be able to avail themselves of Member States' networks of services for geospat...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2016.0007

    authors: Bovenberg JA,de Hoogh K,Knoppers BM,Hveem K,Hansell AL

    更新日期:2016-06-01 00:00:00

  • Effects of L-Carnitine on Equine Semen Quality During Liquid Storage.

    abstract::l-Carnitine (LC) plays a key role in sperm metabolism, easily providing energy through β-oxidation, which positively affects motility. The objective of this study was to investigate the association between blood plasma and seminal plasma LC levels, as well as the effect of LC as an additive in a skimmed milk-based ext...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2020.0025

    authors: Nery IHAV,Araújo Silva RAJ,Souza HM,Arruda LCP,Monteiro MM,Seal DCM,Silva GR,Silva TMS,Carneiro GF,Batista AM,Câmara DR,Guerra MMP

    更新日期:2020-10-01 00:00:00

  • Cryopreservation and Culture of Testicular Tissues: An Essential Tool for Biodiversity Preservation.

    abstract::Systematic cryo-banking of reproductive tissues could enhance reproductive management and ensure sustainability of rare mammalian genotypes. Testicular tissues contain a vast number of germ cells, including at early stages (spermatogonia and spermatocytes), that can potentially develop into viable spermatozoa after gr...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2020.0010

    authors: Silva AMD,Pereira AF,Comizzoli P,Silva AR

    更新日期:2020-06-01 00:00:00

  • Consent to a Postmortem Tissue Procurement Study: Distinguishing Family Decision Makers' Knowledge of the Genotype-Tissue Expression Project.

    abstract::Tissues from postmortem transplantation donors are a viable and productive option for genomic research. This entails obtaining authorization from the family decision makers (FDMs) of deceased donors. This study examined best practices for making such requests within the context of the Genotype-Tissue Expression (GTEx)...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2017.0115

    authors: Siminoff LA,Wilson-Genderson M,Gardiner HM,Mosavel M,Barker KL

    更新日期:2018-06-01 00:00:00

  • Practical electronic information system and printed recording promote management accuracy in an early-stage small-scale non-automatic biobank.

    abstract::It is particularly necessary for biomedical researchers to obtain applicable biosamples accurately and efficiently, especially from a biobank with multiple-disease catalogs. To optimize the retrieval procedure, especially in the early stages of a non-automatic biobank, we developed a procedure that combined the electr...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2014.0102

    authors: Gao Z,Gu Y,Lv Z,Yu G,Zhou J

    更新日期:2015-02-01 00:00:00

  • Sample Confirmation Testing: A Short Tandem Repeat-Based Quality Assurance and Quality Control Procedure for the eyeGENE Biorepository.

    abstract::Quality assurance and quality control (QA/QC) procedures are vital to good biorepository management. The National Eye Institute (NEI) core CLIA-certified laboratory of the eyeGENE(®) Network receives blood from individuals with inherited eye conditions and isolates DNA for clinical genetic diagnostic testing and resea...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2015.0098

    authors: Parrish RS,Garafalo AV,Ndifor V,Goetz KE,Reeves MJ,Yim A,Cooper RC,Iano-Fletcher J,Wang X,Tumminia SJ

    更新日期:2016-04-01 00:00:00

  • The Montpellier Leishmania Collection, from a Laboratory Collection to a Biological Resource Center: A 39-Year-Long Story.

    abstract::We report the development of a laboratory collection of Leishmania that was initiated in 1975 and, after 39 years, has become an international Biological Resource Center (BRC-Leish, Montpellier, France, BioBank No. BB-0033-00052), which includes 6353 strains belonging to 36 Leishmania taxa. This is a retrospective ana...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2015.0101

    authors: Pratlong F,Balard Y,Lami P,Talignani L,Ravel C,Dereure J,Lefebvre M,Serres G,Bastien P,Dedet JP

    更新日期:2016-12-01 00:00:00

  • The challenge of sustaining a hospital-based biobank and core molecular laboratory: the Beaumont experience.

    abstract::The Beaumont Health System BioBank was established in 2008, not only to leverage the potential to collect biospecimens for translational research, but to undertake such research in a seamless facility that combined high quality biobanking with state-of-the-art laboratory platforms geared towards biospecimen-based rese...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2014.0049

    authors: Wilson GD,D'Angelo K,Pruetz BL,Geddes TJ,Larson DM,Akervall J

    更新日期:2014-10-01 00:00:00

  • Development of pancreas storage solutions: Initial screening of cytoprotective supplements for β-cell survival and metabolic status after hypothermic storage.

    abstract::Insulin-dependent diabetes mellitus is one of the leading causes of death world-wide. Donor-derived pancreas and Islet of Langerhans transplantation are potential cures; however, postmortem ischemia impacts islet quality. The murine βt3 cell line was employed as a model to study cell viability and proliferation after ...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2012.0023

    authors: Campbell LH,Taylor MJ,Brockbank KG

    更新日期:2013-02-01 00:00:00

  • Processing of diagnostic blood specimens: is it really necessary to mix primary blood tubes after collection with evacuated tube system?

    abstract:BACKGROUND:The preanalytical phase is considered the most vulnerable phase in biopreservation, biobanking, and laboratory diagnostics. Accurate mixing after blood collection is claimed to be important and recommended by the manufacturers. OBJECTIVE:To evaluate whether it is really necessary to mix the primary blood tu...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2013.0043

    authors: Lima-Oliveira G,Lippi G,Salvagno GL,Brocco G,Gaino S,Dima F,Volaski W,Rego FG,Picheth G,Guidi GC

    更新日期:2014-02-01 00:00:00

  • Advancing Professionalization of Biobank Business Operations: Performance and Utilization.

    abstract::Biobanks are now in the spotlight as key enablers supporting preclinical, clinical, and environmental research. Awareness of their value has increased along with the need for these infrastructures to be sustained through business-focused practices. Following our 2017 pilot survey on biobank business planning, we initi...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2019.0005

    authors: Henderson MK,Goldring K,Simeon-Dubach D

    更新日期:2019-06-01 00:00:00

  • Inactivation of Influenza A virus, Adenovirus, and Cytomegalovirus with PAXgene tissue fixative and formalin.

    abstract::Formalin fixation is known to inactivate most viruses in a vaccine production context, but nothing is published about virus activity in tissues treated with alternative, non-crosslinking fixatives. We used a model assay based on cell culture to test formalin and PAXgene Tissue fixative for their virus-inactivating abi...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2013.0010

    authors: Kap M,Arron GI,Loibner M,Hausleitner A,Siaulyte G,Zatloukal K,Murk JL,Riegman P

    更新日期:2013-08-01 00:00:00

  • International Data Sharing in Practice: New Technologies Meet Old Governance.

    abstract::The social structures that govern data/sample release aim to safeguard the confidentiality and privacy of cohort research participants (without whom there would be no data or samples) and enable the realization of societal benefit through optimizing the scientific use of those cohorts. Within collaborations involving ...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2016.0002

    authors: Murtagh MJ,Turner A,Minion JT,Fay M,Burton PR

    更新日期:2016-06-01 00:00:00

  • Phase Change Behavior of NaCl-H2O Binary Solution Under the Control of AC Electric Field.

    abstract::Cryopreservation, which refers to preservation of cells or tissues at subzero temperatures, inevitably involves the problem of cryoinjury caused by ice crystals. The application of an external electric field during the freezing process has been shown to be a promising approach to produce miniature ice grains and decre...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2020.0045

    authors: Ma Y,Fan X,Cai J,Tao J

    更新日期:2020-10-16 00:00:00

  • The use of biospecimens in population-based research: a review of the National Cancer Institute's Division of Cancer Control and Population Sciences grant portfolio.

    abstract::Over the past two decades, researchers have increasingly used human biospecimens to evaluate hypotheses related to disease risk, outcomes and treatment. We conducted an analysis of population-science cancer research grants funded by the National Cancer Institute (NCI) to gain a more comprehensive understanding of bios...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章,评审

    doi:10.1089/bio.2014.0009

    authors: Carrick DM,Mette E,Hoyle B,Rogers SD,Gillanders EM,Schully SD,Mechanic LE

    更新日期:2014-08-01 00:00:00

  • Short-term stability study of RNA at room temperature.

    abstract::The quality of RNA preserved in different stabilization matrices was investigated after 2 weeks of storage at room temperature. RNA samples in RNAstable (Biomatrica), GenTegra (IntegenX), and RNAshell (Imagene) were compared to RNA stored at -80°C (the current gold standard for RNA preservation) and with liquid or dri...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章,多中心研究

    doi:10.1089/bio.2012.0030

    authors: Mathay C,Yan W,Chuaqui R,Skubitz AP,Jeon JP,Fall N,Betsou F,Barnes M,ISBER Biospecimen Science Working Group.

    更新日期:2012-12-01 00:00:00

  • The influence of tissue procurement procedures on RNA integrity, gene expression, and morphology in porcine and human liver tissue.

    abstract::The advent of molecular characterization of tissues has brought an increasing emphasis on the quality of biospecimens, starting with the tissue procurement process. RNA levels are particularly affected by factors in the collection process, but the influence of different pre-analytical factors is not well understood. H...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2014.0076

    authors: Kap M,Sieuwerts AM,Kubista M,Oomen M,Arshad S,Riegman P

    更新日期:2015-06-01 00:00:00

  • Organization of BBMRI.pl: The Polish Biobanking Network.

    abstract::In Poland storage of human biological samples takes place at most universities and scientific institutions conducting research projects in the field of biomedicine. The First International Biobanking Conference organized by the Ministry of Science and Higher Education in 2014 shed a light on the situation of Polish bi...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2016.0091

    authors: Witoń M,Strapagiel D,Gleńska-Olender J,Chróścicka A,Ferdyn K,Skokowski J,Kalinowski L,Pawlikowski J,Marciniak B,Pasterk M,Matera-Witkiewicz A,Kozera Ł

    更新日期:2017-06-01 00:00:00

  • Integrating Molecular Control to Improve Cryopreservation Outcome.

    abstract::Cryopreservation (CP) is a critical component in enabling on-demand access to biological material (macromolecules, cells, and tissues), yet CP has evolved little over the last several decades. Today's CP processes often yield a suboptimal "product," which has slowed progression in areas such as cell therapy and stem c...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章,评审

    doi:10.1089/bio.2016.0119

    authors: Baust JG,Snyder KK,Van Buskirk R,Baust JM

    更新日期:2017-04-01 00:00:00

  • Enhanced Cryoprotective Effect of Melatonin and Resveratrol by Coencapsulation: Improved In Vitro Development of Vitrified-Warmed Mouse Germinal Vesicle Oocytes.

    abstract::Oocyte vitrification, as a vital step in reproductive medicine, is strongly associated with lower development caused by cryodamaging factors, such as oxidative stress. In this study, we evaluated the antioxidative synergistic effects of Melatonin (Mel) and Resveratrol (RES) coencapsulated by solid lipid nanocarriers (...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2020.0102

    authors: Aghaz F,Vaisi-Raygani A,Khazaei M,Arkan E

    更新日期:2020-12-22 00:00:00

  • Mesenchymal stem cell isolation from human umbilical cord tissue: understanding and minimizing variability in cell yield for process optimization.

    abstract::Human tissue banks are a potential source of cellular material for the nascent cell-based therapy industry; umbilical cord (UC) tissue is increasingly privately banked in such facilities as a source of mesenchymal stem cells for future therapeutic use. However, early handling of UC tissue is relatively uncontrolled du...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2013.0027

    authors: Iftimia-Mander A,Hourd P,Dainty R,Thomas RJ

    更新日期:2013-10-01 00:00:00

  • Construction of a business model to assure financial sustainability of biobanks.

    abstract::Biobank-suisse (BBS) is a collaborative network of biobanks in Switzerland. Since 2005, the network has worked with biobank managers towards a Swiss biobanking platform that harmonizes structures and procedures. The work with biobank managers has shown that long-term, sustainable financing is difficult to obtain. In t...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2014.0057

    authors: Warth R,Perren A

    更新日期:2014-12-01 00:00:00

  • Repository Planning, Design, and Engineering: Part I--Infrastructure.

    abstract::This is a two-part review describing the planning, engineering, and design considerations for building a new repository for biological and environmental samples. Part I addresses the physical infrastructure requirements for a repository; Part II will cover equipment and costing. Planning for construction of a new repo...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章,评审

    doi:10.1089/bio.2015.0084

    authors: Baird PM,Gunter EW

    更新日期:2016-04-01 00:00:00

  • Reconsidering Anonymization-Related Concepts and the Term "Identification" Against the Backdrop of the European Legal Framework.

    abstract::Sharing data in biomedical contexts has become increasingly relevant, but privacy concerns set constraints for free sharing of individual-level data. Data protection law protects only data relating to an identifiable individual, whereas "anonymous" data are free to be used by everybody. Usage of many terms related to ...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2015.0100

    authors: Sariyar M,Schlünder I

    更新日期:2016-10-01 00:00:00

  • Targeting Future Customers: An Introductory Biobanking Course for Undergraduate Students of Life Sciences.

    abstract:INTRODUCTION:Biobanking is a relatively new concept in the Arab region. Targeting different stakeholders to introduce the concept of biobanking and develop an acceptance of it among them is important for the growth of biobanking in the region. Undergraduate students of life sciences represent an important segment of st...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2016.0111

    authors: Abdelhafiz AS,Fouda MA,El-Jaafary SI,Farghly MI,Salem M,Tammam A,Gabr H

    更新日期:2017-08-01 00:00:00

  • Sustainability in Biobanking: Model of Biobank Graz.

    abstract::Research infrastructures remain the key for state-of-the-art and successful research. In the last few decades, biobanks have become increasingly important in this field through standardization of biospecimen processing, sample storage, and standardized data management. Research infrastructure in cohort studies and oth...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2015.0087

    authors: Sargsyan K,Macheiner T,Story P,Strahlhofer-Augsten M,Plattner K,Riegler S,Granitz G,Bayer M,Huppertz B

    更新日期:2015-12-01 00:00:00

  • Oocyte Cryopreservation Based in Sheep: The Current Status and Future Perspective.

    abstract::The establishment of a cryopreservation procedure for sheep oocytes will enhance the development of long-term conservation of sheep female genetic resources and the advancement of sheep embryonic biotechnology. However, higher cytoplasmic lipid content and complex subcellular structures affect the relatively higher se...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章,评审

    doi:10.1089/bio.2017.0074

    authors: Quan G,Wu G,Hong Q

    更新日期:2017-12-01 00:00:00

  • Comparison Between an Animal-Derived Product Medium and a Chemically Defined Medium for Ram Sperm Cryopreservation.

    abstract::Animal-derived products are widely used in sperm cryopreservation for their cryoprotective properties. These components, however, tend to be replaced because of sanitary risks. STEMALPHA.CRYO3 (Ref. 5617; Stem Alpha, Saint-Genis-l'Argentière, France), called "CRYO3," is a chemically defined preservation medium current...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2018.0067

    authors: Gavin-Plagne L,Commin L,Bruyère P,Buff S,Joly T

    更新日期:2019-01-01 00:00:00

  • Standardized Serum-Free Cryomedia Maintain Peripheral Blood Mononuclear Cell Viability, Recovery, and Antigen-Specific T-Cell Response Compared to Fetal Calf Serum-Based Medium.

    abstract::The ability to analyze cryopreserved peripheral blood mononuclear cells (PBMCs) from biobanks for antigen-specific T-cell immunity is necessary to evaluate responses to immune-based therapies. Comprehensive studies have demonstrated that the quality of frozen PBMCs is critical and the maintenance of cell viability and...

    journal_title:Biopreservation and biobanking

    pub_type: 杂志文章

    doi:10.1089/bio.2010.0033

    authors: Germann A,Schulz JC,Kemp-Kamke B,Zimmermann H,von Briesen H

    更新日期:2011-09-01 00:00:00