Shipped Samples Research Articles

Profound impact of sample processing delay on gene expression of multiple myeloma plasma cells

BackgroundGene expression profiling (GEP) has significantly contributed to the elucidation of the molecular heterogeneity of multiple myeloma plasma cells (MMPC) and only recently it has been recommended for risk stratification. Prior to GEP MMPC need to be enriched resulting in an inability to immediately freeze bone marrow aspirates or use RNA stabilization reagents. As a result in multi-center MM trials sample processing delay due to shipping may be an important confounder of molecular analyses and risk stratification based on GEP data.ResultsWe compared GEP data of 145 in-house and 246 shipped samples and detected 3301 down-regulated and 3501 up-regulated genes in shipped samples. For 3994 genes we confirmed differential expression in an independent set of 85 in-house and 97 shipped samples. Differentially expressed genes were enriched in processes like ribosome biogenesis, cell cycle, and apoptosis. Among GEP based risk predictors the IFM-15 seemed to underestimate high risk in shipped samples, whereas the GEP70 and the EMC-92 gene signatures were more robust. In order to provide a tool to assess the “shipping effect” in public repositories, we generated a 17-gene predictor for shipped samples with a 10-fold cross validation error rate of 0.06 for the training set and an error rate of 0.15 for the validation set.ConclusionSample processing delay significantly influences GEP of MMPC, implying it should be avoided if samples were used for risk stratification.Electronic supplementary materialThe online version of this article (doi:10.1186/s12920-015-0161-6) contains supplementary material, which is available to authorized users.

Surface Cleaning of SiGe(100) and Passivation of Ge(100) with Aqeuous Ammonium Sulfide

As scaling of microelectronic devices continues, germanium and silicon-germanium are promising materials for integration into silicon-based technology. Germanium and silicon-germanium based field-effect transistors can reduce leakage current and consume less power by means of improved carrier mobility and a narrower band gap, as opposed to traditional electronics. However, silicon-germanium surfaces are more challenging to work with because the topmost surface layer is comprised of germanium oxides that complicate cleaning and passivation processes. Here we seek to obtain a smooth, oxide free SiGe surface and hope to garner an understanding of the best conditions to effectively remove surface oxides. Additionally, we hope to further our understanding of aqueous ammonium sulfide passivation processes on Ge surfaces that will prevent re-oxidation of the surface for applications towards modern field-effect transistors (FETs). The first portion of this work focuses on the removal of oxides from the SiGe surface with 50 and 75% Ge molar ratios using a variety of aqueous processes. These processes include SC-1, HCl, HF, and HCl/HF mixtures. The SiGe surface was characterized using X-ray photoelectron Spectroscopy (XPS) after each chemical treatment. Film thicknesses were measured using spectroscopic ellipsometry. Immersion in HCl showed similar results to as shipped samples and was ineffective in removing surface oxides. Aqueous HF, however, removed both surface oxides and carbon contamination. SC-1 treatments selectively reduced the Ge in the SiGe film and left the surface enriched in Si, which oxidized as confirmed by XPS. If the Ge could be completely removed from the top-most layer, the SiO2 layer that forms could be used to passivate the SiGe surface and avoid problematic Ge oxides. Ellipsometry results showed that SC-1 solutions (NH4OH:H2O2:H2O, 1:1:100 v/v) etched 1 nm of the SiGe film, which was then oxidized. Ge 2p to Si 2p XPS peak ratios confirmed that increasing concentrations of SC-1 depleted the Ge content on the surface from 0.8 to 0.4, confirming the enrichment of the surface in Si. Ge to Si peak area ratios as a function of the SC-1 dilution factor showed a non-linear trend for SiGe 50% surfaces. Passivation of Ge with aqueous (NH4)2S was also studied. Because Ge oxides are unstable and water soluble, it is advantageous to remove them and deposit a sulfur layer to prevent further oxidation when exposed to air. Surface passivation was studied as a function of deposition time, solution concentration and the addition of H2O2. Passivation of the surface was ineffective at times below 20 min. Changing the concentration of (NH4)2S also had no noticeable effect on the surface based on XPS. Furthermore, at high ammonium sulfide concentrations the addition of H2O2 did not affect the passivation process. The addition of H2O2 to dilute (NH4)2S showed poor passivation due to oxidation of the surface by H2O2.

Prevalencia de los patrones electroforéticos de hemoglobina analizados en el CIHATA durante el período 2011-2013

<span>Las hemoglobinopatías son alteraciones de las cadenas de globina que componen la hemoglobina, dentro de las alteraciones más comunes destacan las talasemias y la drepanocitosis. En el CIHATA se realizó un estudio retrospectivo de las muestras analizadas por electroforesis de hemoglobina durante el período 2011-2013, en donde se obtuvo un total de 2345 muestras analizadas, de las cuáles el patrón electroforético más frecuente fue el de Hb AA2, con un valor A2 promedio de (4.8±0.8%), compatible con el diagnóstico de β talasemia menor; seguido por el patrón asociado a portadores Hb S. En menor cantidad se observaron resultados de Hb AC, AF, AA2F, entre otros. Los patrones se distribuyeron a lo largo del país, pero localizados mayormente en la región central (sesgo relacionado a mayor área de atracción). Es importante la detección de los patrones anormales, pues aunque no se asocien con un cuadro clínico, en condiciones de hipoxia o estrés fisiológico si se pueden presentar complicaciones graves y sobre para brindar consejo genético. Esta actualización brinda un panorama de la frecuencia de hemoglobinopatías circulantes en Costa Rica durante los últimos años. Se debe procurar la recopilación de información clínica, y demográfica completa de todos los pacientes, con el fin de hacer reportes de caso completos que puedan ayudar en el óptimo abordaje diagnóstico de los pacientes y familiares.</span>

Description and utilization of the United States department of defense serum repository: a review of published studies, 1985-2012.

Specimens in the United States Department of Defense (DoD) Serum Repository have accumulated in frozen storage since 1985 when the DoD began universal screening for human immunodeficiency virus. Use of the stored serum for health research has been carefully controlled, but the resulting publications have never been systematically identified or described. The Armed Forces Health Surveillance Center (AFHSC) information systems and open (online) sites were used as data sources. Through 2012, the repository contained 54,542,658 serum specimens, of which 228,610 (0.42%) have been accessed for any purpose. Between 2001 (the first year that comprehensive, digital records were available) and 2012, 65.2% of all approved requests for serum were for healthcare or public health investigations, but greater than 99% of all shipped samples were for research. Using two different methods – a structure search of PubMed and an exhaustive online search based on records from AFHSC – we identified 76 articles published between October 1988 and March 2013 that covered a multitude of infectious diseases, injuries, environmental exposures and mental health conditions through analysis of antibodies, biological metabolic, signaling and regulatory substances, Vitamin D, organochlorines, dioxin, omega-3-fatty acid, and portions of human deoxyribonucleic acid. Despite its operational and scientific value, it appears that the DoD Serum Repository has been underutilized. Changes to policy and increased capacity for specimen processing could increase use of the repository without risking privacy or the availability of specimens for the healthcare of individual service members in the future.

Abstract 302: Novel implementation of cloud computing and mobile technology to transform data collection and management in cancer epidemiology

Abstract Cancer epidemiology cohorts (CECs) make vital contributions to molecular epidemiology and translational research. Large, well-annotated CECs require many years and substantial resources to build, mature, and maintain, but many CECs use inefficient legacy methods to collect and manage data. CECs must become more cost-efficient and find better ways to gather, store, and share data, and declining response rates suggest CEC participants increasingly require more personal and engaging methods. The California Teachers Study (CTS) is a CEC that has followed 133,479 female public school professionals since 1995-1996. We implemented a cloud-based customer relationship management (CRM) solution from Salesforce.com for a 4-year project (2012-2016), funded by the NCI and NIEHS, that is collecting 21,722 blood or saliva samples from CTS participants for use in future biomarker discovery and validation research. Phlebotomists at 3 sites (COH, CPIC, & UCI) visit participants in-person, conduct interviews, collect blood, and ship samples overnight to Fisher BioServices in Maryland for processing and storage. Our cloud-based system uses the web, smartphones, and tablets to recruit participants; schedule appointments; aggregate questionnaire data; and automate specimen collection, shipping, and tracking. Phlebotomists use a custom-built mobile app to scan consent forms, blood tubes, and FedEx shipping labels. The app includes a smart e-questionnaire that is customized for each person based on her answers to previous CTS questionnaires. Each night, the system automatically assembles and transmits a detailed shipping manifest directly to Fisher BioServices. All data are available for immediate access via a secure, CTS-specific Salesforce.com instance, in which we can track multiple progress and performance metrics on demand. Extensive security and validations protect data privacy and confidentiality. By using mobile technology to automate the study protocol across all sites, eliminating manual data entry during collection appointments, and removing data silos, our innovative approach increases productivity, ensures protocol compliance across study sites, and reduces data management costs. The Salesforce.com system is easily scalable for additional types of data collection and is an excellent tool for improving CEC infrastructure. Citation Format: Jennifer L. Benbow, Christina A. Clarke, Hannah L. Park, Christine N. Duffy, Nadia T. Chung, Amy E. Brankin, Karen Angell-Mendez, Argyrios Ziogas, Rich Pinder, Dennis Deapen, Hoda Anton-Culver, Susan L. Neuhausen, Leslie Bernstein, Sophia S. Wang, James V. Lacey. Novel implementation of cloud computing and mobile technology to transform data collection and management in cancer epidemiology. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 302. doi:10.1158/1538-7445.AM2014-302

Effects of holding time and measurement error on culturing Legionella in environmental water samples

Outbreaks of Legionnaires' disease require environmental testing of water samples from potentially implicated building water systems to identify the source of exposure. A previous study reports a large impact on Legionella sample results due to shipping and delays in sample processing. Specifically, this same study, without accounting for measurement error, reports more than half of shipped samples tested had Legionella levels that arbitrarily changed up or down by one or more logs, and the authors attribute this result to shipping time. Accordingly, we conducted a study to determine the effects of sample holding/shipping time on Legionella sample results while taking into account measurement error, which has previously not been addressed. We analyzed 159 samples, each split into 16 aliquots, of which one-half (8) were processed promptly after collection. The remaining half (8) were processed the following day to assess impact of holding/shipping time. A total of 2544 samples were analyzed including replicates. After accounting for inherent measurement error, we found that the effect of holding time on observed Legionella counts was small and should have no practical impact on interpretation of results. Holding samples increased the root mean squared error by only about 3–8%. Notably, for only one of 159 samples, did the average of the 8 replicate counts change by 1 log. Thus, our findings do not support the hypothesis of frequent, significant (≥= 1 log10 unit) Legionella colony count changes due to holding.

Relating the metatranscriptome and metagenome of the human gut.

Although the composition of the human microbiome is now well-studied, the microbiota's >8 million genes and their regulation remain largely uncharacterized. This knowledge gap is in part because of the difficulty of acquiring large numbers of samples amenable to functional studies of the microbiota. We conducted what is, to our knowledge, one of the first human microbiome studies in a well-phenotyped prospective cohort incorporating taxonomic, metagenomic, and metatranscriptomic profiling at multiple body sites using self-collected samples. Stool and saliva were provided by eight healthy subjects, with the former preserved by three different methods (freezing, ethanol, and RNAlater) to validate self-collection. Within-subject microbial species, gene, and transcript abundances were highly concordant across sampling methods, with only a small fraction of transcripts (<5%) displaying between-method variation. Next, we investigated relationships between the oral and gut microbial communities, identifying a subset of abundant oral microbes that routinely survive transit to the gut, but with minimal transcriptional activity there. Finally, systematic comparison of the gut metagenome and metatranscriptome revealed that a substantial fraction (41%) of microbial transcripts were not differentially regulated relative to their genomic abundances. Of the remainder, consistently underexpressed pathways included sporulation and amino acid biosynthesis, whereas up-regulated pathways included ribosome biogenesis and methanogenesis. Across subjects, metatranscriptional profiles were significantly more individualized than DNA-level functional profiles, but less variable than microbial composition, indicative of subject-specific whole-community regulation. The results thus detail relationships between community genomic potential and gene expression in the gut, and establish the feasibility of metatranscriptomic investigations in subject-collected and shipped samples.

SEMI-AUTOMATIC SHIP DETECTION USING PI-SAR-L2 DATA BASED ON RAPID FEATURE DETECTION APPROACH

Synthetic Aperture Radar (SAR) satellite an active sensor offering unique high spatial resolution regardless of weather conditions can operate both day and night time with wide area coverage. Therefore, SAR satellite can be used for monitoring ship on sea surface. This study showed on an alternative method for ship detection of SAR data using Pi-SAR-L2 (L-band, JAXA-Airborne SAR) data. The ship detection method is this study was consisted of eight main stages. After the Pi-SAR data was registered and speckle was filtered, then the land was masked using SRTM-DEM (Shuttle Radar Topography Mission-Digital Elevation Model) data since most ship detectors produced false detections when it applied to land areas. A ship sample image was then selected (cropped). The next step was to detect some unique keypoints of ship sample image using Speeded Up Robust Features (SURF) detector. The maximum distance (‘MaxDist’) of keypoints was also calculated. The same detector was then applied to whole Pi-SAR imagery to detect all possible keypoints. Then, for each detected keypoint, we calculated distance to other keypoint (‘Dist’). If ‘Dist’ was smaller than ‘MaxDist’, then we marked these two (or more) keypoints as neighboring keypoints. If the number of neighbor keypoints was equal or greater than two, finally we marked these keypoints as ‘Detected Ship’ (draw rectangle and show its geographic position). Results showed that our method can detect successfully 32 ‘possible ships’ from Pi-SAR-L2 data acquired on the area of North Sulawesi, Indonesia (August 8, 2012).

Sample submissions to a diagnostic laboratory

The quality and appropriateness of samples submitted to a veterinary diagnostic laboratory have a significant effect on the quality of the test results obtained. A veterinary technician can be of valuable assistance with veterinary diagnostic sample submission. Specimens that are properly collected and preserved are beneficial in helping to establish a diagnosis. Prior to collecting samples, it is important to know what type of sample is needed for the suspected diagnostic differentials, size or quantity of sample needed, type of storage container, shipping requirements, and any special handling recommendations. The technician may assist the veterinarian in collecting specimens, consult with animal owners on sample collection, contact the diagnostic laboratory if needed, complete submission forms, and pack and ship samples.

Cross-Validation of IFN-γ Elispot Assay for Measuring Alloreactive Memory/Effector T Cell Responses in Renal Transplant Recipients

Assessment of donor-specific alloreactive memory/effector T cell responses using an IFN-γ Elispot assay has been suggested to be a novel immune-monitoring tool for evaluating the cellular immune risk in renal transplantation. Here, we report the cross-validation data of the IFN-γ Elispot assay performed within different European laboratories taking part of the EU RISET consortium. For this purpose, development of a standard operating procedure (SOP), comparisons of lectures of IFN-γ plates assessing intra- and interlaboratory assay variability of allogeneic or peptide stimuli in both healthy and kidney transplant individuals have been the main objectives. We show that the use of a same SOP and count-settings of the Elispot bioreader allow low coefficient variation between laboratories. Frozen and shipped samples display slightly lower detectable IFN-γ frequencies than fresh samples. Importantly, a close correlation between different laboratories is obtained when measuring high frequencies of antigen-specific primed/memory T cell alloresponses. Interestingly, significant high donor-specific alloreactive T cell responses can be similarly detected among different laboratories in kidney transplant patients displaying histological patterns of acute T cell mediated rejection. In conclusion, assessment of circulating alloreactive memory/effector T cells using an INF-γ Elispot assay can be accurately achieved using the same SOP, Elispot bioreader and experienced technicians in kidney transplantation.

Measurement of Testosterone in Human Sexuality Research: Methodological Considerations

Testosterone (T) and other androgens are incorporated into an increasingly wide array of human sexuality research, but there are a number of issues that can affect or confound research outcomes. This review addresses various methodological issues relevant to research design in human studies with T; unaddressed, these issues may introduce unwanted noise, error, or conceptual barriers to interpreting results. Topics covered are (1) social and demographic factors (gender and sex; sexual orientations and sexual diversity; social/familial connections and processes; social location variables), (2) biological rhythms (diurnal variation; seasonality; menstrual cycles; aging and menopause), (3) sample collection, handling, and storage (saliva vs. blood; sialogogues, saliva, and tubes; sampling frequency, timing, and context; shipping samples), (4) health, medical issues, and the body (hormonal contraceptives; medications and nicotine; health conditions and stress; body composition, weight, and exercise), and (5) incorporating multiple hormones. Detailing a comprehensive set of important issues and relevant empirical evidence, this review provides a starting point for best practices in human sexuality research with T and other androgens that may be especially useful for those new to hormone research.

The Malaspina Dragon: A newly-discovered pattern of the early spring bloom in the Strait of Georgia, British Columbia, Canada

MERIS and MODIS ocean colour satellite imagery of the Strait of Georgia, British Columbia, Canada shows a recurring pattern which suggests seeding of the early spring bloom from deep, glacial inlets to the north. We call the pattern the “Malaspina Dragon” after its shape in satellite imagery in 2005, 2008 and 2009 shortly after it enters the Strait. It appears to have been active in five of the nine years, 2003–2011. We use the satellite imagery to determine a start date for the main spring bloom in the Strait of Georgia in each year, and show that in the five “Dragon” years the spring bloom occurred nearly 4weeks earlier than in the remaining four, suggesting that seeding from inlets may be a significant factor controlling timing. In 2009 and 2010, the presence and evolution of the bloom was confirmed using an ocean glider, and in 2010 and 2011, recording fluorometers provided surface data. Ship samples in 2009 showed that the bloom forming the Dragon pattern consisted of diatoms (Thalassiosira spp.) similar to those that form the main spring bloom in the Strait.

A Two-Band Algorithm for Total Suspended Solid Concentration Mapping Using THEOS Data

Lim, H.S.; MatJafri, M.Z.; Abdullah, K., and Asadpour, R., 2013. A two-band algorithm for total suspended solid concentration mapping using THEOS data. Environmental monitoring through the method of traditional ship sampling is time consuming and requires a high survey cost. This study was carried out to investigate the relationship between total suspended solids (TSS) and satellite THEOS data by using a calibrated algorithm. The study area is the seawater region around Penang Island, Malaysia. Water-quality TSS values were collected simultaneously during the acquisition of the satellite imagery and later analyzed in the laboratory. The digital numbers of the corresponding TSS measurements were extracted and converted into reflectance values for algorithm regression. The two-band algorithm used here is based on the reflectance model, which is a function of the inherent optical properties of water, and this in turn can be related to the concentration of its constituents. The developed algorithm was used to correlate the digital signal and the TSS values. The generated algorithm was developed for two visible wavelengths, red and blue for this study. The digital numbers corresponding to the sea truth locations were extracted for algorithm calibration. Based on the values of the correlation coefficient squares (R2) and root-mean-square deviation (RMS), the proposed algorithm is considered superior. A water-quality image was generated using the multispectral data set and the proposed calibrated TSS algorithm. Finally, the generated TSS map was geometrically corrected to produce a geocoded map. Filtering was performed to the generated map to remove random noise, and it was color-coded for visual interpretation. This study indicates that the TSS algorithm developed from optical properties is a promising TSS model for high-accuracy TSS mapping using satellite data.

Storage and shipping of tissue samples for DNA analyses: A case study on earthworms

Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources or remote field sites. Moreover, shipping samples over long distances can cause loss of DNA quality e.g. by thawing or leaking of preservation liquid. In this study we use earthworms, a key organism in soil research, to compare three different DNA preservation methods – freezing at −20 °C, storing in 75% ethanol, and freeze drying. Samples were shipped from the United States of America to Austria. The DNA of the samples was extracted using two different extraction methods, peqGOLD™ and Chelex® 100. The DNA amplification success was determined by amplifying four DNA fragments of different length. The PCR amplification success is significantly influenced by preservation method and extraction method and differed significantly depending on the length of the DNA fragment. Freeze drying samples was the best preservation method when samples were extracted using the silica based extraction method peqGOLD™. For samples that were extracted with Chelex® 100, storage in ethanol was the best preservation method. However, the overall amplification success was significantly lower for the extraction procedure based on Chelex® 100. The detection of the small DNA fragments was higher and independent from the extraction method, while the amplification success was significantly reduced for the longer DNA fragments.We recommend freeze drying of DNA samples, especially when they have to be shipped for longer distances. No special packaging or declaration is needed for freeze dried samples, and the risk of thawing is excluded. Storage of freeze dried samples also reduces costs because samples can be kept at room temperature in a desiccator. It should be noted, that the extraction methods showed significant differences in DNA amplification success. Thus, the extraction method should be taken into account when choosing the preservation method.

HLA-DR expression as a biomarker of inflammation for multicenter clinical trials of ocular surface disease

There are currently no validated minimally invasive objective metrics for the classification and evaluation of ocular surface diseases and/or for evaluating treatment efficacy. We thus sought to establish a standardized methodology for determining the relative amount of the inflammatory biomarker HLA-DR on the ocular surface and to evaluate the precision, reliability and repeatability of its use for large multicenter clinical trials and translational research studies of ocular surface disease. Multiple studies were conducted to establish a Standard Operating Procedure (SOP) for utilizing HLA-DR expression as a minimally invasive, objective, ocular surface inflammatory biomarker. The established SOPs provide specific guidelines for HLA-DR collection and analysis, in order to incorporate it reliably into multicenter clinical trials and/or translational research. Duplicate cell samples from impression cytology (IC) samples of both normal and dry eye individuals were collected and split to assess repeatability (between the splits and between the duplicate samples). To determine storage capability, one duplicate was stained immediately and the other after 30 days cold storage. To demonstrate the feasibility of the use of the SOP for a multicenter clinical trial, clinicians out-of-state were trained to collect IC samples, and the samples shipped to our Biomarker Laboratory, logged, processed and analyzed. Demonstration of the ability to incorporate of IC into a randomized double masked clinical trial of dry eye disease (DED) was performed. In all cases, processing and analyses were performed by a masked independent observer. The validity/viability of the SOPs was established by demonstrating that: 1) sufficient numbers of cells can be collected via IC; 2) the precision/repeatability of the relative biomarker expression quantified in samples; 3) personnel at distant sites can be taught to collect, store and ship samples successfully; 4) samples can be stored for up to 30 days (refrigeration) before processing without affecting results; 5) IC can be incorporated into a double blind randomized clinical trial (RCT) of DED; and 6) the Biomarker Laboratory can track a large number of masked samples reliably. In conclusion, our standard operating procedure for impression cytology analysis of HLA-DR expression appears to be repeatable and reproducible for use in multicenter clinical trials, providing a minimally invasive objective biomarker of inflammation of the ocular surface.

Northern fur seals augment ship-derived ocean temperatures with higher temporal and spatial resolution data in the eastern Bering Sea

Oceanographic data collected by marine vertebrates are increasingly being used in biological and physical studies under the assumption that data recorded by free-ranging animals are comparable to those from traditional vertical sampling. We tested this premise by comparing the water temperatures measured during a 2009 oceanographic cruise with those measured during 82 foraging trips by instrumented northern fur seals (Callorhinus ursinus) in the eastern Bering Sea. The animal-borne data loggers were equipped with a fast-response temperature sensor and recorded 6492 vertical profiles to depths ≥50m during long distance (up to 600km) foraging trips. Concurrent sampling during the oceanographic cruise collected 247 CTD casts in the same 5-week period. Average temperature differences between ship casts and seal dives (0.60±0.61°C), when the two were within 1 day and 10km of each other (n=32 stations), were comparable to mean differences between adjacent 10km ship casts (0.46±0.44°C). Isosurfaces were evaluated at region wide scales at depths of 1m and 50m while the entire upper 100m of the water column was analyzed at finer-scales in highly sampled areas. Similar patterns were noted in the temperature fields produced by ships or seals despite the differences in sampling frequency and distribution. However, the fur seal dataset was of higher temporal and spatial resolution and could therefore be used to visualize finer detail with less estimated error than ship-derived data, particularly in dynamic areas. Integrating the ship and seal datasets provided temperature maps with an unprecedented combination of resolution and coverage allowing fine-scale processes on-shelf and over the basin to be described simultaneously. Fur seals (n=65 trips) also collected 4700 additional profiles post-cruise which allowed ≥1°C warming of the upper 100m to be documented through mid-September, including regions where ship sampling has traditionally been sparse. Our data show that hydrographic information collected by wide-ranging, diving animals such as fur seals can contribute physical data comparable to, or exceeding those, of traditional sampling methods at regional or finer scales when the questions of interest coincide with the ecology of the species.

73-P

Aim The Cylex ImmuKnow (ICF) is a biologic assay that has a great deal of inherent variability. Our lab performs both internal (IPT) and external (EPT) proficiency testing to show assay proficiency. This abstract demonstrates our use of data from PT to improve performance of the assay. Methods Duplicate specimens were collected from 5 subjects each time. Aging studies were tested on the draw day and 24 hours later. IPT was performed by multiple techs in our own lab on these samples. For the EPT, the duplicate specimens were shipped to the external lab. The other lab also drew 5 duplicate samples and shipped them to us for testing. Both labs tested the 10 samples at 24 hours. Results were evaluated qualitatively (QL) and quantitatively (QN). Results Assay results were reproducible in a quantitative and a qualitative manner (QN results within +/−10% of the QL cutoff were considered a QL match) but there was a significant amount of variability. Shipped samples from either lab had an avg deviation of −20 (avg %CV 18.6% & SD 111). 60% of shipped samples showed a negative shift between the sending and receiving lab. 24 hour old unshipped samples showed an avg deviation of −19.5, (avg %CV 15.5 & SD 77). 54% of all unshipped samples showed a negative shift of result relative to the fresh sample. Using the results of IPT, we were able to reduce variability among technologists by insuring careful adherence to the procedure. Improvement was measured by looking at assay variability among techs on the same sample. From a baseline of 15.5% avg %CV and 67.3 avg SD from 2006 – 2008, we reduced our test variation by 33% to 10.3% avg CV and 42.3 avg SD. Conclusions The best ICF results are obtained by serial monitoring of a patient in a single lab. Testing fresh samples gives more reproducible results than shipped/aged samples. When it is necessary to use shipped or 24 hour old samples, it should be noted in the test report. We used our PT data to reduce the variation of ICF assay results.

Influence of Temperature during Transportation on Cell-Free DNA Analysis

Objective: To determine the effect of shipping blood in Streck blood collection tubes (BCT) prior to processing on cell-free DNA (cf-DNA) levels. Methods: Blood was collected in ethylenediaminetetraacetic acid (EDTA) and BCT tubes from 10 pregnant women carrying male fetuses. One set of each tube for each subject was processed to plasma immediately (standard cf-DNA protocol), whereas the other set was shipped by air courier and then processed. DNA was extracted and total and fetal DNA concentrations were measured by TaqMan multiplexed quantitative real-time PCR. Results: No significant difference was observed in total cf-DNA in plasma between immediately processed EDTA (control) and immediately processed BCT samples. Moreover, no significant change in total cf-DNA was detected in plasma of BCT samples shipped at room temperature. Significant differences in total cf-DNA leading to a significantly decreased fetal fraction were found in shipped EDTA samples and BCT samples shipped at 4°C. Discussion: BCT tubes are suitable for shipping whole blood prior to processing with respect to cf-DNA levels. However, care should be taken to ensure that samples are not exposed to extreme temperatures during shipment. This finding will benefit the development and clinical application of noninvasive methods of fetal diagnosis that utilize cf-DNA.

Innovative technology for DNA blood stabilization at room temperature

Long term storage, shipping and biobanking of patient blood DNA for future analyses are on the rise. Conventional storage and shipment of blood poses space, cost and energy problems. Biomatrica, Inc. has developed a novel technology to store, ship and archive blood samples at room temperature based on the natural principles of anhydrobiosis (“life without water”), a biological mechanism employed by some multicellular organisms that enables their survival in a dry state for extended periods. QIAsafe DNA Blood (QSB), a product developed in collaboration with QIAGEN, allows the dry storage and shipment of whole blood at room temperature for long periods until isolation of DNA is necessary. Adding water to the QSB‐stored blood DNA releases the matrix shell protection, which can then be followed by DNA isolation/extraction. DNA yields and integrity from QSB‐stored blood are comparable to frozen controls (−20°C or −80°C). Our data demonstrates that blood stored for 9 months at room temperature or 45°C (equivalent to approx. 3 years of room temperature storage) allows recovery of high molecular DNA that is in quality and amount of recovery equivalent to freezer stored material. The isolated DNA can be used in a broad range of downstream applications including PCR, qPCR, genotyping, and DNA sequencing experiments. QBS eliminates the need of blood storage in freezers reducing cost and eliminating freeze/thaw degradation.

Evaluation of the Effects of Radiation from an X-ray Baggage Inspection System on Microbial Agents

During shipping, microbial cultures and clinical samples are subjected to irradiation by x-ray baggage inspection systems and most high-containment laboratories use similar equipment to screen mate...