Biopreservation and Biobanking最新文献

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Homology Identification and Cross-Contamination Analysis: A Method for Evaluating the Quality of Biological Samples Stored in a Biobank Using the Advanta Sample ID Genotyping Panel. 同源性鉴定和交叉污染分析:一种使用Advanta样品ID基因分型面板评估生物库中储存的生物样品质量的方法。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-10-27 DOI: 10.1089/bio.2022.0187
Chao Wang, Zebin Hu, Xiaoyan Zhang, Midie Xu, Weixiang Shen, Lili Du, Menghong Sun, Hengjun Gao
{"title":"Homology Identification and Cross-Contamination Analysis: A Method for Evaluating the Quality of Biological Samples Stored in a Biobank Using the Advanta Sample ID Genotyping Panel.","authors":"Chao Wang, Zebin Hu, Xiaoyan Zhang, Midie Xu, Weixiang Shen, Lili Du, Menghong Sun, Hengjun Gao","doi":"10.1089/bio.2022.0187","DOIUrl":"10.1089/bio.2022.0187","url":null,"abstract":"<p><p>Biological samples are important resources for scientific research. These samples are stored in biobanks over years until needed, and some of them can never be retrieved if they are improperly stored, causing them to be wasted. Thus, they are priceless, and they should be used correctly and effectively. Sample quality substantially affects biomedical research results. However, sample misidentification or mix-up is common. It is necessary to establish quality standards for sample identification. In this study, we used the Advanta Sample ID genotyping panel to detect homology identification and cross-contamination. We compared the single-nucleotide polymorphism (SNP) typing results of two different samples and calculated the similarity score of homologous sample pairs and nonhomologous sample pairs. Through analysis, we obtained a similarity score cutoff point of 0.8620, which was an effective way to distinguish homology and nonhomology. Cross-contamination was detected in two sets of mixtures (STD8:STD6 and jj3:1-P) mixed at a series of special ratios. Sensitivity was dependent on the sample characteristics and mixing ratios. Finally, we assessed the effect of sample degradation degree on SNP genotyping and found that degraded samples with a minimal DNA integrity number of 1.9 had complete genotyping results. On the whole, this study shows that the Sample ID panel is reliable for homology identification and cross-contamination analysis. Moreover, this technology has promising further applications in biological sample quality control.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"115-122"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61566122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Achieving Procedural Parity in Managing Access to Genomic and Related Health Data: A Global Survey of Data Access Committee Members. 在管理基因组和相关健康数据的获取方面实现程序平等:数据获取委员会成员的全球调查。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-05-16 DOI: 10.1089/bio.2022.0205
Jonathan Lawson, Vasiliki Rahimzadeh, Jinyoung Baek, Edward S Dove
{"title":"Achieving Procedural Parity in Managing Access to Genomic and Related Health Data: A Global Survey of Data Access Committee Members.","authors":"Jonathan Lawson, Vasiliki Rahimzadeh, Jinyoung Baek, Edward S Dove","doi":"10.1089/bio.2022.0205","DOIUrl":"10.1089/bio.2022.0205","url":null,"abstract":"<p><p>Data access committees (DACs) are critical players in the data sharing ecosystem. DACs review requests for access to data held in one or more repositories and where specific constraints determine how the data may be used and by whom. Our team surveyed DAC members affiliated with genomic data repositories worldwide to understand standard processes and procedures, operational metrics, bottlenecks, and efficiencies, as well as their perspectives on possible improvements to quality review. We found that DAC operations and systemic issues were common across repositories globally. In general, DAC members endeavored to achieve an appropriate balance of review efficiency, quality, and compliance. Our results suggest a similarly proportionate path forward that helps DACs pursue mutual improvements to efficiency and compliance without sacrificing review quality.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"123-129"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11265613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9778503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Effect of Blood Clots on the Quality of RNA Extracted from PAXgene Blood RNA Tubes. 血块对从 PAXgene 血液 RNA 管中提取的 RNA 质量的影响。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-08-03 DOI: 10.1089/bio.2023.0001
Rong Tang, Ling Zhu, Ping Zhu, Ru Yin, Chunxia Zheng
{"title":"The Effect of Blood Clots on the Quality of RNA Extracted from PAXgene Blood RNA Tubes.","authors":"Rong Tang, Ling Zhu, Ping Zhu, Ru Yin, Chunxia Zheng","doi":"10.1089/bio.2023.0001","DOIUrl":"10.1089/bio.2023.0001","url":null,"abstract":"<p><p><b><i>Background:</i></b> PAXgene<sup>®</sup> Blood RNA tubes are routinely used in clinical research and molecular biology applications to preserve the stability of RNA in whole blood. However, in practice, blood clots are occasionally observed after blood collection and are often ignored. Currently, there are few studies on whether blood clots affect the quality of RNA extracted from these tubes. <b><i>Materials and Methods:</i></b> Fifteen pairs of non-clot and clot PAXgene Blood RNA tube samples (<i>n</i> = 30) were collected to form two matched groups from 15 patients. According to the maximum diameter (<i>d</i>) of the blood clot observed visually at the time of sample reception, the clot groups were divided into a small-clot group (0 cm < <i>d</i> < 0.5 cm) and a large-clot group (<i>d</i> ≥ 0.5 cm). RNA was extracted by the PAXgene Blood RNA Kit. To analyze the quality of RNA, its yield and purity were assessed by spectrophotometry, and integrity was measured by microfluidic electrophoresis. An A<sub>260/280</sub> ratio between 1.8 and 2.2 indicated purified RNA, and RNA integrity number (RIN) values ≥7.0 were considered to represent qualified integrity. <b><i>Results:</i></b> The median yields of RNA from the non-clot and clot groups were 3.84 (2.80-6.38) μg and 4.87 (2.77-8.30) μg, respectively. The median A<sub>260/280</sub> ratios were 2.08 (2.06-2.09) and 2.09 (2.07-2.11), whereas the median A<sub>260/230</sub> ratios were 1.77 (1.31-1.91) and 1.67 (1.21-1.94) in the two groups. In addition, the median RINs were 8.20 (8.00-8.40) and 7.20 (6.60-7.70), respectively. There were no significant differences in RNA yields, A<sub>260/280</sub>, or A<sub>260/230</sub> between the two groups. However, the RIN value of the clot group was significantly lower compared with the non-clot group (<i>p</i> < 0.05), with RIN ≥7.0 found in all non-clot samples and 60% of clot samples (<i>p</i> < 0.05). Furthermore, in the clot groups, the small-clot samples had higher RIN values than large-clot samples (8.25 [7.75-8.75] vs. 6.90 [6.60-7.30], <i>p</i> < 0.001). <b><i>Conclusions:</i></b> The formation of large blood clots in PAXgene Blood RNA tubes will reduce the integrity of extracted RNA.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"174-178"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9931501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward Professionalism of Biobanking in China: A Survey on Working Status, Career Development, Challenges, and Prospects of Biobankers. 中国生物银行职业化进程:中国生物库人员工作现状、职业发展、挑战与前景调查》。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-08-15 DOI: 10.1089/bio.2022.0038
Xuexun Zhou, Qian Li, Qian Zhao, Xiaoyan Zhang, Yanping Xu, Puyi Qian, Frank Liu Gao, Io Hong Cheong, Dan Guo, Shihui Ma, Huan Chen, Sijian Liu, Weiye Wang, Xiaonan Kang, Menghong Sun, Yajun Yang, Qubo Chen, Hengjun Gao
{"title":"Toward Professionalism of Biobanking in China: A Survey on Working Status, Career Development, Challenges, and Prospects of Biobankers.","authors":"Xuexun Zhou, Qian Li, Qian Zhao, Xiaoyan Zhang, Yanping Xu, Puyi Qian, Frank Liu Gao, Io Hong Cheong, Dan Guo, Shihui Ma, Huan Chen, Sijian Liu, Weiye Wang, Xiaonan Kang, Menghong Sun, Yajun Yang, Qubo Chen, Hengjun Gao","doi":"10.1089/bio.2022.0038","DOIUrl":"10.1089/bio.2022.0038","url":null,"abstract":"<p><p>Biobanking has become an increasingly important activity to provide resources for medical research support. In China, establishing and maintaining a biobank have been the latest trend in a research hospital. However, biobanking is still an emerging young field in terms of professionalization and professionalism. The development of professionalization in biobanking faces many challenges involving the development of skills, identities, norms, and values associated with becoming part of a professional group. Biobanking professionals (i.e., biobankers) are the most important factor and driving force toward professionalization in biobanking. To better understand biobankers' performance, needs, concerns, and career development, we conducted two comprehensive surveys among biobankers in China in 2019 and 2021, respectively. The questionnaires covered four major areas: (1) basic information and the status of biobankers; (2) job performance evaluation, salary, recognitions, rewards, and so on; (3) occupational training and career development; and (4) challenges and prospects and so on. The surveys revealed that most biobankers in China have positive working attitudes and a high desire for their future career development, but due to the uncertain evaluation mechanisms and promotion routes, etc., the participants were more optimistic about biobanking development compared to the biobanker's career development (77.0% and 57.4% respectively in 2021, <i>p</i> < 0.05). The biobankers expected more training opportunities and salary packages. Because biobankers are an integral factor and driving force to ensure the successful biobanking operation and advancement, the survey data analysis revealed interesting findings and references for the development of professionalism in biobanking. This survey will provide first-hand information to governments, biobank management teams, and the general public to further support, promote, or optimize (1) biobanking operation and sustainability, (2) biobankers' career development, (3) biobank management and quality control, and (4) strategic plans and approaches to establish a higher quality professional team of biobankers.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"139-145"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10009191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Insight into Increased Recovery and Simplification of Genomic DNA Extraction Methods from Dried Blood Spots. 从干血斑中提高基因组 DNA 提取率和简化提取方法的启示
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-07-07 DOI: 10.1089/bio.2022.0181
Kiara Lee, Anubhav Tripathi
{"title":"Insight into Increased Recovery and Simplification of Genomic DNA Extraction Methods from Dried Blood Spots.","authors":"Kiara Lee, Anubhav Tripathi","doi":"10.1089/bio.2022.0181","DOIUrl":"10.1089/bio.2022.0181","url":null,"abstract":"<p><p>There is no consensus on how to perform the manual extraction of nucleic acids from dried blood spots (DBSs). Current methods typically involve agitation of the DBSs in a solution for varying amounts of time with or without heat, and then purification of the eluted nucleic acids with a purification protocol. We explored several characteristics of genomic DNA (gDNA) DBS extraction such as extraction efficiency, the role of red blood cells (RBCs) in extraction and critical kinetic factors to understand if these protocols can be simplified while maintaining sufficient gDNA recovery. We found that agitation in a RBC lysis buffer before performing a DBS gDNA extraction protocol increases yield 1.5 to 5-fold, depending upon the anticoagulant used. The use of an alkaline lysing agent along with either heat or agitation was sufficient to elute quantitative polymerase chain reaction (qPCR) amplifiable gDNA in 5 minutes. This work adds insight into the extraction of gDNA from DBSs with the intention of informing a simple, standardized manual protocol for extraction.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"130-138"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10114918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Egg Yolk-Supplemented Tris-Citric Acid Extender Improves the Prefreezing and Post-Thaw Sperm Quality Indices of Guinea Pig (Cavia porcellus) Epididymal Spermatozoa. 添加蛋黄的三柠檬酸扩展剂可提高豚鼠附睾精子的冷冻前和解冻后质量指标
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-08-17 DOI: 10.1089/bio.2022.0214
Diego A Galarza, Wilson León-Machuca, Jorge X Samaniego, Rubén Carrera, Fernando P Perea, Mauricio Duma, Julián Santiago-Moreno
{"title":"Egg Yolk-Supplemented Tris-Citric Acid Extender Improves the Prefreezing and Post-Thaw Sperm Quality Indices of Guinea Pig (<i>Cavia porcellus</i>) Epididymal Spermatozoa.","authors":"Diego A Galarza, Wilson León-Machuca, Jorge X Samaniego, Rubén Carrera, Fernando P Perea, Mauricio Duma, Julián Santiago-Moreno","doi":"10.1089/bio.2022.0214","DOIUrl":"10.1089/bio.2022.0214","url":null,"abstract":"<p><p>This study aimed to assess the suitability of egg yolk (EY) supplementation to a tris-citric acid-based extender on cryosurvival of guinea pig (<i>Cavia porcellus</i>) epididymal spermatozoa. Two synthetic-based extenders, tris-citric acid-glucose plus 20% EY (TCG-EY) and tris-citric acid-fructose (TCF) both with 5% glycerol, were compared. Thirty-two epididymides were recovered from 16 adult guinea pig males by gonadectomy, and then the sperm samples were retrieved by retrograde flushing using TCG-EY and TCF extenders for left or right epididymis, respectively. TCG-EY and TCF sperm samples were frozen in static liquid nitrogen vapors through a two-step cooling procedure. Before freezing, the percentage of progressive sperm motility and sperm with intact plasma and acrosome membranes from TCG-EY sperm samples were higher (<i>p</i> < 0.05) than those diluted with TCF. Post-thaw sperm kinematic variables and membrane integrity were drastically reduced (<i>p</i> < 0.001) compared with prefreezing samples, regardless of extender type. The post-thaw plasmatic and acrosome membrane integrity from TCG-EY sperm samples was higher (<i>p</i> < 0.05) than those from TCF samples. Except for the length, the morphometric head dimensions of sperm diluted with TCG-EY or TCF did not vary (<i>p</i> > 0.05) after the freezing-thawing process compared with the prefreezing samples. In conclusion, despite greater cell cryoinjury with both extenders, the EY supplementation exerted greater cell membrane protection before and after the freezing-thawing process. This research shows an in-depth analysis of guinea pig sperm cryopreservation; however, more studies are recommended.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"157-165"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10020735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Researchers' Perspectives Regarding Ethical Issues of Biobank Research in the Arab Region. 研究人员对阿拉伯地区生物库研究伦理问题的看法。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-03-23 DOI: 10.1089/bio.2022.0112
Maha E Ibrahim, Latifa Adarmouch, Alya Elgamri, Samar Abd ElHafeez, Zeinab Mohammed, Fatma Abdelgawad, Eman H Elsebaie, Ahmed Samir Abdelhafiz, Ehsan Gamel, Karima El Rhazi, Asmaa Abdelnaby, Mamoun Ahram, Henry Silverman
{"title":"Researchers' Perspectives Regarding Ethical Issues of Biobank Research in the Arab Region.","authors":"Maha E Ibrahim, Latifa Adarmouch, Alya Elgamri, Samar Abd ElHafeez, Zeinab Mohammed, Fatma Abdelgawad, Eman H Elsebaie, Ahmed Samir Abdelhafiz, Ehsan Gamel, Karima El Rhazi, Asmaa Abdelnaby, Mamoun Ahram, Henry Silverman","doi":"10.1089/bio.2022.0112","DOIUrl":"10.1089/bio.2022.0112","url":null,"abstract":"<p><p><b><i>Background:</i></b> The recent expansion of genomic biobank research in the Arab region in the Middle East North Africa has raised complex ethical and regulatory issues. However, there is a lack of studies regarding the views of Arab researchers involved in such research. We aimed to assess the perceptions and attitudes of Arab researchers regarding these issues in biobank research. <b><i>Methods:</i></b> We developed a questionnaire to assess the perceptions and attitudes regarding genetic research of researchers from Egypt, Sudan, Morocco, and Jordan. The questionnaire requested demographic data, perceptions, and attitudes regarding the collection, storage, and use of biospecimens and data, the use of broad consent, data security, data sharing, and community engagement. We used multiple linear regressions to identify predictors of perceptions and attitudes. <b><i>Results:</i></b> We recruited 383 researchers. Researchers favored equally the use of broad and tiered consent (44.1% and 39.1%, respectively). Most respondents agreed with the importance of confidentiality protections to ensure data security (91.8%). However, lower percentages were seen regarding the importance of community engagement (64.5%), data sharing with national colleagues and international partners (60.9% and 41.1%, respectively), and biospecimen sharing with national colleagues and international partners (59.9% and 36.2%, respectively). Investigators were evenly split on whether the return of individual research results should depend on the availability or not of a medical intervention that can be offered to address the genetic anomaly (47.5% and 46.4%, respectively). Predictors of attitudes toward biospecimen research included serving on Research Ethics Committees, prior research ethics training, and affiliation with nonacademic institutions. <b><i>Conclusions:</i></b> We recommend further exploratory research with researchers regarding the importance of community engagement and to address their concerns about data sharing, with researchers within and outside their countries.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"98-109"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11044858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9513949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. 一种高效的提取方法,可从病毒运输介质中采集的病毒感染诊断样本中对宿主 DNA 进行遗传评估。
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-08-09 DOI: 10.1089/bio.2022.0188
Renan C Sbruzzi, Mariléa F Feira, Nathan A Cadore, Giovanna C Giudicelli, Thayne W Kowalski, Tatiana S Gregianini, José A B Chies, Fernanda S L Vianna
{"title":"An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium.","authors":"Renan C Sbruzzi, Mariléa F Feira, Nathan A Cadore, Giovanna C Giudicelli, Thayne W Kowalski, Tatiana S Gregianini, José A B Chies, Fernanda S L Vianna","doi":"10.1089/bio.2022.0188","DOIUrl":"10.1089/bio.2022.0188","url":null,"abstract":"<p><p><b><i>Introduction:</i></b> During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. <b><i>Objective:</i></b> To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. <b><i>Methods:</i></b> In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. <b><i>Results:</i></b> The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink<sup>®</sup> method (0.14 μg, <i>p</i> < 0.001), but not from the QIAamp<sup>®</sup> method (0.47 μg, <i>p</i> = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan<sup>®</sup> assay. <b><i>Conclusion:</i></b> The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"166-173"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10353122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA. 重复冻融循环对分离基因组 DNA 全基因组 DNA 甲基化特征的影响
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-04-18 DOI: 10.1089/bio.2022.0045
Verena Kopfnagel, Norman Klopp, Inga Bernemann, Nataliia Nizhegorodtseva, Rory Wilson, Raphael Gronauer, Martin Seifert, Thomas Illig
{"title":"Effects of Repeated Freeze and Thaw Cycles on the Genome-Wide DNA Methylation Profile of Isolated Genomic DNA.","authors":"Verena Kopfnagel, Norman Klopp, Inga Bernemann, Nataliia Nizhegorodtseva, Rory Wilson, Raphael Gronauer, Martin Seifert, Thomas Illig","doi":"10.1089/bio.2022.0045","DOIUrl":"10.1089/bio.2022.0045","url":null,"abstract":"<p><p>The characterization of DNA methylation patterns to identify epigenetic markers for complex human diseases is an important and rapidly evolving part in biomedical research. DNA samples collected and stored in clinical biobanks over the past years are an important source for future epigenetic studies. Isolated gDNA is considered stable when stored at low temperatures for several years. However, the effect of multiple use and the associated repeated thawing of long-term stored DNA samples on DNA methylation patterns has not yet been investigated. In this study, we examined the influence of up to 10 freeze and thaw cycles on global DNA methylation by comparing genome-wide methylation profiles. DNA samples from 19 healthy volunteers were either frozen at -80°C or subjected to up to 10 freeze and thaw cycles. Genome-wide DNA methylation was analyzed after 0, 1, 3, 5, or 10 thaw cycles using the Illumina Infinium MethylationEPIC BeadChip. Evaluation of the global DNA methylation profile by beta-value density plots and multidimensional scaling plots revealed an expected clear participant-dependent variability, but a very low variability depending on the freeze and thaw cycles. In accordance, no significant difference in any of the methylated cytosine/guanine sites studied could be detected in the performed statistical analyses. Our results suggest that long-term frozen DNA samples are still suitable for epigenetic studies after multiple thaw cycles.</p>","PeriodicalId":55358,"journal":{"name":"Biopreservation and Biobanking","volume":" ","pages":"110-114"},"PeriodicalIF":1.6,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9384590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Variable Control and Its Influence Before Urine Sample Analysis in a Field Environment. 现场环境下尿液样本分析前的变量控制及其影响
IF 1.6 4区 生物学
Biopreservation and Biobanking Pub Date : 2024-04-01 Epub Date: 2023-08-17 DOI: 10.1089/bio.2022.0219
Jingjing Jiang, Hanxuan Liu, Wenfeng Ni, Manli Zhang, Fangyan Gu, Jinlian Pei, Yan Wang, Yaping Tian
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