Download Week 14 - CTMM TraIT

Biobank literature update week 14 (2015)
1. Stevenson HS, Wang Y, Muller R, Edelman DC: Long-term Stability of Total RNA in RNAstable as Evaluated by Expression Microarray. Biopreserv.Biobank. 2015.
Abstract: Storage of labile RNA in laboratories is accomplished through ultra-low freezing of the nucleic acids. This however requires expensive freezers, convenient
storage, reliable electrical power, and increased shipping costs, thereby making it a less viable option. Biomatrica (San Diego, CA) has created RNAstable(R), a
stabilization reagent that is used to store RNA in a dehydrated state at room temperature (RT) and protects the RNA from degradation. Our objective was to
investigate the sequence integrity and suitability of RNA when stored in RNAstable at extended time periods and at varying temperatures through use of Illumina
and Agilent RNA expression microarrays. We observed in Bioanalyzer electropherograms that total RNA extracted from 293 cells stored at RT in RNAstable for 4.5
and 11.5 months is similar in quality to RNA stored at -80 degrees C. Illumina mRNA expression array QC metrics and gene expression patterns from
RNAstable-protected RNA, in contrast to RNA stored without RNAstable, correlated well with those of freezer controls. Significantly, when RNA was stored in
RNAstable at 45 degrees C for 4.5 months, equivalent to 22 months RT storage, RNA quality, microarray probe signal intensities, probe detection rates, and
expression profiles remained similar between RNAstable-protected RNA at RT and the -80 degrees C controls. At 10.5 months, miRNA levels were compared among
the storage conditions using miRNA expression arrays. Here too we found strong concordance between miRNA expression patterns when total RNA was stored in
RNAstable or at -80 degrees C. Further, Bioanalyzer electrophoresis of RNAstable-protected samples stored at RT for a relative total of 33 months or 50.5 months
showed comparable integrity scores to those of -80 degrees C controls. We conclude that use of RNAstable holds promise as an effective stabilization reagent for
total RNA and should be useful in situations where shipping and storage options are limited resources
2. Hong YH, Martin LA, Mulvaney JM, Burhans MS, Blaxall BC, Hinton RB: RNA Extraction from Healthy and Failing Human Myocardium: A Comparative Evaluation.
Biopreserv.Biobank. 2015.
Abstract: BACKGROUND: Isolation of high-quality RNA from tissue is mandatory for producing reliable data for downstream applications. In heart tissue, the relative
strengths and weaknesses of different approaches to isolate total RNA are unknown. The objective of this study was to compare different RNA isolation methods in
healthy and diseased human myocardium. METHODS: Frozen left ventricular myocardium was obtained from individuals with heart failure and individuals who died
from non-cardiac causes with normal heart function (control). Three extraction methods, including guanidine isothiocyanate (TRIzol), silica-gel column (RNeasy),
and the combination method (TRIzol/RNeasy), were assessed for their effect on the yield, integrity, and gene expression levels of RNA using quantitative real-time
PCR. RESULTS: In the control group (n=5), the highest RNA yield per tissue mass was obtained with TRIzol, and a significantly higher RNA integrity was obtained
from the RNeasy method. The quantification cycle (Cq) values for both the reference gene GAPDH and two target genes were lower with TRIzol. Normalization by
GAPDH showed the highest gene expression levels with RNeasy. Similar patterns were observed in the heart failure group (n=5), suggesting assays were not
negatively impacted by myocardial disease processes. CONCLUSION: In both healthy and diseased heart tissue, the TRIzol method provides the highest RNA yield,
while the RNeasy method shows superior RNA integrity, demonstrating comparable RNA quality in studies examining myocardial disease. A balanced approach to
RNA quality is necessary for the successful downstream applications of RNA
3. Ewing AT, Erby LA, Bollinger J, Tetteyfio E, Ricks-Santi LJ, Kaufman D: Demographic Differences in Willingness to Provide Broad and Narrow Consent for Biobank
Research. Biopreserv.Biobank. 2015.
Abstract: PURPOSE: This study examined acceptability of two biobank consent models and evaluated the impact of beliefs about privacy and genetic safeguards on
acceptance. METHODS: U.S. adults surveyed online in English and Spanish were randomly assigned to one of two scenarios examining acceptance of broad consent
(n=1528), or narrow consent (n=1533). RESULTS: Overall, willingness to provide broad (76%) and narrow (74%) consents were similar. African Americans were as
likely as white non-Hispanics to accept narrow consent (72% vs. 77%, p=0.35) but significantly less likely to accept broad consent (69% vs. 81%, p=0.004).
Education, insurance, and blood donation history were also related to acceptance. Adjusting for beliefs about privacy and policy protections (Genetic Information
Nondiscrimination Act, GINA), the effects of the variables were reduced. Respondents who drew comfort from GINA were more likely to support both consent
(both p<0.001); those who believed it is impossible to maintain privacy were less likely to find both broad (p=0.04) and narrow models acceptable (p=0.02).
CONCLUSIONS: Choice of consent model matters when engaging diverse populations in biobank research. Beliefs underlying concerns about privacy and genetic
protections should be considered when constructing biobank protocols
4. Hamot G, Ammerlaan W, Mathay C, Kofanova O, Betsou F: Method Validation for Automated Isolation of Viable Peripheral Blood Mononuclear Cells.
Biopreserv.Biobank. 2015.
Abstract: BACKGROUND: This article is part of a series of publications providing formal method validation for biospecimen processing in the context of accreditation
in laboratories and biobanks. We report the optimization and validation for fitness-for-purpose of automated and manual protocols for isolating peripheral blood
mononuclear cells (PBMCs) from whole blood, and compare the two methods. METHODS: The manual method was optimized for whole blood centrifugation
speed, gradient type (Ficoll, Leucosep, CPT), and freezing method (Mr Frosty, Controlled Rate Freezing). Various parameters of the automated protocol using a CPT
gradient on a Tecan liquid handler were optimized. Optimal protocols were validated in parallel for reproducibility and robustness. Optimization and validation
were assessed in terms of cell yield, viability, recovery, white blood cell (WBC) subpopulation distribution, gene expression, and lymphoblastoid cell line (LCL)
transformation. RESULTS: An initial centrifugation of whole blood at 2000 g was considered optimal for further processing, allowing isolation of plasma and PBMCs
from a single sample. The three gradients gave similar outcomes in terms of cell yield, viability, and WBC subpopulation distribution. Ficoll showed some
advantages and was selected for further evaluations. Optimization of the automated protocol script using a CPT gradient gave 61% cell recovery. No significant
differences in quality, quantity, and WBC subpopulation distribution were seen between the two freezing methods, and Mr. Frosty was selected. The manual and
automated protocols were reproducible in terms of quantity, recovery, viability, WBC subpopulation distribution, gene expression, and LCL transformation. Most
(75%-100%) of the 13 robustness parameters were accepted for both methods with an 8 h pre-centrifugation delay versus 38%-85% after 24 h. Differences
identified between the automated and manual methods were not considered consequential. CONCLUSIONS: We validated the first fully automated method for
isolating viable PBMCs, including RNA analysis and generation of LCLs. We recommend processing within 8 h of blood collection
5. Greytak SR, Engel KB, Bass BP, Moore HM: Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res. 2015.
Abstract: Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained
from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of
the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic
accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in
case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database
(http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among
analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters
that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however,
discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or
frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters
with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens. Cancer
Res; 75(8); 1-7. (c)2015 AACR
6. Haverkamp L, Parry K, van Berge Henegouwen MI, van Laarhoven HW, Bonenkamp JJ, Bisseling TM, Siersema PD, Sosef MN, Stoot JH, Beets GL, de Steur WO,
Hartgrink HH, Verspaget HW, van der Peet DL, Plukker JT, van EB, Wijnhoven BP, van Lanschot JJ, van HR, Ruurda JP: Esophageal and Gastric Cancer Pearl: a
nationwide clinical biobanking project in the Netherlands. Dis.Esophagus. 2015.
Abstract: Esophageal and gastric cancer is associated with a poor prognosis since many patients develop recurrent disease. Treatment requires specific expertise
and a structured multidisciplinary approach. In the Netherlands, this type of expertise is mainly found at the University Medical Centers (UMCs) and a few
specialized nonacademic centers. Aim of this study is to implement a national infrastructure for research to gain more insight in the etiology and prognosis of
esophageal and gastric cancer and to evaluate and improve the response on (neoadjuvant) treatment. Clinical data are collected in a prospective database, which is
linked to the patients' biomaterial. The collection and storage of biomaterial is performed according to standard operating procedures in all participating UMCs as
established within the Parelsnoer Institute. The collected biomaterial consists of tumor biopsies, blood samples, samples of malignant and healthy tissue of the
resected specimen and biopsies of recurrence. The collected material is stored in the local biobanks and is encoded to respect the privacy of the donors. After
approval of the study was obtained from the Institutional Review Board, the first patient was included in October 2014. The target aim is to include 300 patients
annually. In conclusion, the eight UMCs of the Netherlands collaborated to establish a nationwide database of clinical information and biomaterial of patients with
esophageal and gastric cancer. Due to the national coverage, a high number of patients are expected to be included. This will provide opportunity for future studies
to gain more insight in the etiology, treatment and prognosis of esophageal and gastric cancer
7. Simon CM, Klein DW, Schartz HA: Interactive multimedia consent for biobanking: a randomized trial. Genet.Med. 2015.
Abstract: PURPOSE: The potential of interactive multimedia to improve biobank informed consent has yet to be investigated. The aim of this study was to test the
separate effectiveness of interactivity and multimedia at improving participant understanding and confidence in understanding of informed consent compared with
a standard, face-to-face (F2F) biobank consent process. METHODS: A 2 (face-to-face versus multimedia) x 2 (standard versus enhanced interactivity) experimental
design was used with 200 patients randomly assigned to receive informed consent. All patients received the same information provided in the biobank's nine-page
consent document. RESULTS: Interactivity (F(1,196) = 7.56, P = 0.007, partial eta2 = 0.037) and media (F(1,196) = 4.27, P = 0.04, partial eta2 = 0.021) independently
improved participants' understanding of the biobank consent. Interactivity (F(1,196) = 6.793, P = 0.01, partial eta2 = 0.033), but not media (F(1,196) = 0.455, not
significant), resulted in increased participant confidence in their understanding of the biobank's consent materials. Patients took more time to complete the
multimedia condition (mean = 18.2 min) than the face-to-face condition (mean = 12.6 min). CONCLUSION: This study demonstrated that interactivity and
multimedia each can be effective at promoting an individual's understanding and confidence in their understanding of a biobank consent, albeit with additional
time investment. Researchers should not assume that multimedia is inherently interactive, but rather should separate the two constructs when studying electronic
consent.Genet Med advance online publication 02 April 2015Genetics in Medicine (2015); doi:10.1038/gim.2015.33
8. Sudlow C, Gallacher J, Allen N, Beral V, Burton P, Danesh J, Downey P, Elliott P, Green J, Landray M, Liu B, Matthews P, Ong G, Pell J, Silman A, Young A, Sprosen T,
Peakman T, Collins R: UK Biobank: An Open Access Resource for Identifying the Causes of a Wide Range of Complex Diseases of Middle and Old Age. PLoS.Med. 2015,
12:e1001779.
Abstract: Cathie Sudlow and colleagues describe the UK Biobank, a large population-based prospective study, established to allow investigation of the genetic and
non-genetic determinants of the diseases of middle and old age
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