17 research outputs found
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Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays
Background
Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples.
Results
We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2% of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log2 units ( 6% of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators.
Conclusions
This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells
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A Psychosocial Assessment of Patients before and after Autologous Stem Cell Transplantation
Abstract
There are relatively few reports in the medical literature describing psychosocial assessment of bone marrow transplant patients; what data exists primarily focuses on allogeneic transplant recipients. We have begun to prospectively assess psychosocial parameters of patients undergoing autologous transplantation using the Functional Assessment of Cancer Therapy-BMT (FACT-BMT) tool. The general questions consist of four subscales developed and normed in cancer patients that measure; physical well-being; social/family well-being; emotional well-being; functional well-being; and a specific module to address BMT-specific concerns. Each subscale is positively scored, with higher scores indicating better functioning. A baseline survey is collected by the social worker pre-transplant and a follow-up survey is administered and collected approximately 6 weeks post-transplant by the Transplant Coordinator. 56 consecutive patients undergoing autologous stem cell transplant have FACT-BMT data both pre-transplant and approximately one month post-discharge. Median age was 50. 52% are male; underlying diagnoses include NHL (45%), Hodgkin’s disease (32%), myeloma (16%), AML (5%), testicular cancer (2%). 93% had chemosensitive disease at the time of transplant. All patients received peripheral blood progenitor cells (PBPCs), and all received a chemotherapy-only preparative regimen. All patients were hospitalized for approximately three weeks for the transplant. For most of the variables measured by the FACT-BMT tool, there was no significant difference in pre-transplant and post-transplant scores. The one variable that did change was emotional well-being: patients scored statistically significantly higher post-transplant as compared to the pre-transplant score (p<0.001). We also have collected baseline FACT-BMT data on 42 consecutive allogeneic BMT recipients, as well as 12 recipients of non-myeloablative allogeneic BMT transplants. There is no significant difference in any pre-transplant variables measured by the FACT-BMT score between autologous recipients, ablative allogeneic recipients, and non-myeloablative allogeneic recipients. We conclude that patients undergoing an autologous stem cell transplant have a higher sense of emotional well-being after engraftment and hospital discharge. Presumably this reflects positive feelings about accomplishing this intensive treatment for their underlying malignancy, and suggests that emotional and physical recovery after auto-BMT is reasonably rapid. A larger dataset will hopefully allow a more detailed comparison of allo and auto BMT recipients
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Psychosocial Factors in Decision-Making of Patient Eligibility for Allogeneic Bone Marrow Transplantation
Abstract
Oncologists specializing in bone marrow transplants (BMT) make daily decisions about appropriate medical candidates for allogeneic BMT based on clinical criteria. It is not clear how, and if, patient eligibility decisions are made based on psychosocial criteria. Although setting limits of patient eligibility based on psychosocial criteria has been researched in solid organ transplantation, data is sparse in BMT. This report focuses on physician responses to a psychosocial survey. An IRB approved survey was mailed to members of the ASBMT (North America) mailing list. Of 704 members, 663 were deemed viable respondents: excluded were non-physician members and physicians specializing in research or not working with allogeneic BMT patients. These surveys were mailed in April 2004. As of 7/6/04, 253 surveys were returned, representing a 38% response rate. Average age of responders was 47 years. Average number of years experience in BMT was 14, with a range of 2–39 years. 17 case vignettes were presented. These vignettes asked whether or not it was appropriate to proceed with allo BMT (assuming an appropriate donor was available) based on a specific psychosocial problem. In virtually every case vignette, at least 10% of respondents stated they would not proceed with allogeneic BMT based on the issues raised in the vignette. In seven case vignettes, the majority of respondents stated that they would recommend not proceeding with BMT. The general theme/construct of these 7 vignettes appears to be ability to comply with treatment plans. Specifically, the following were case vignettes in which the majority of respondents recommended not to proceed with transplant: no caregiver available to assist with the patient post-transplant (do not proceed = 70%); the patient is actively alcoholic (do not proceed = 62%); the patient is non-compliant (do not proceed = 75%); the patient is currently suicidal (do not proceed = 84%); the patient is currently using addictive illicit drugs (do not proceed = 73%); the patient has mild dementia (do not proceed = 55%); the patient cannot pay for the transplant (do not proceed = 52%). Conversely, the following case vignettes were less worrisome to the survey respondents, and in general represented surmountable psychosocial and/or clinical issues. These vignettes included; a history of prior suicidal attempts although not currently suicidal (proceed with transplant = 86%); controlled schizophrenia (proceed with transplant = 83%); daily marijuana use (proceed with transplant = 82%); smokes tobacco (proceed with transplant = 79%); morbid obesity (proceed with transplant = 71%); major depression (proceed with transplant = 84%). These findings underline the importance of post-transplant longitudinal care in determining the ultimate success of an allogeneic BMT, and underscore their importance in patient eligibility decision-making. These findings also illustrate that psychosocial variables play a significant role in determining patient eligibility for allogeneic BMT and that there is no clear-cut consensus on this topic, highlighting the need for ongoing clinical research
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A Quality of Life Assessment of Ablative Allogeneic Bone Marrow Transplant (BMT) Recipients One and Twelve Months after Transplant
Abstract
Quality of life (QOL) data concerning allogeneic BMT recipients is relatively sparse. We surveyed allogeneic BMT recipients at baseline, one month post-transplant, and one year from transplant attempting to determine fluctuations in QOL over time. We used the FACT-BMT tool, which consists of five component scores, including physical well-being (PWB), social well-being (SWB), emotional well-being (EWB), functional well-being (FWB), and additional concerns (AC). PWB, SWB, and FWB uses a 0–28 point scale while EWB ranges from 0–24. Fifty-three patients were initially entered into this analysis, all of whom received ablative allogeneic transplants from 6/2003 to 6/2005. Median age was 46 years; the majority (57%) were female; underlying diagnoses included AML (42%), ALL (23%), MDS (13%), and other (22%). Median time from diagnosis to transplant was rapid, at 5.2 months. Fifty-one percent had a matched related donor, and 49% had a matched unrelated donor. As of August 2005, 70% of these 53 patients are alive. This analysis compares scores obtained one month from transplant and one year from transplant to baseline values. The average hospital length of stay for this ablative transplant was 29 days. One month after transplant, 21% of patients had grade 2–4 acute GVHD. The median WBC was 4.4 K/μL and the median platelet count was 51 K/μL. When surveyed one month post-transplant, not surprisingly, patients had a significant deterioration of physical well-being and functional well-being scores as shown in the table below. However, this was coupled by a significant increase in emotional well-being:
FACT-BMT SCORES: median (range) Component Baseline (n = 53) 1-month post-transplant BMT (n = 53) 1-month p-value compared to baseline 12-months post-BMT (n = 23) 12-month p-value compared to baseline PWB 21 (6–28) 18 (2–26) p < 0.001 21 (3–28) 0.82 FWB 17 (0–27) 13 (4–23) p = 0.006 17 (6–27) 0.46 EWB 17 (3–24) 19 (1–24) p < 0.001 19 (5–24) 0.015
The decrease in PWB and FWB was expected given the rigors of an ablative allogeneic transplant, but the significant rise in EWB was surprising. This may reflect a sense of accomplishment, relief, and optimism among patients concerning their underlying diagnosis and treatment. Twenty-three patients were available to complete the survey tool 12 months after transplant. This was a favorable cohort of patients with continued remissions. Fifty-two percent of these 23 patients, however, did have some degree of chronic graft-versus-host disease. The PWB and SWB scores returned to baseline, and the enhanced EWB scores persisted. Thus, the negative impact of the BMT on PWB and SWB was self-limited. The underlying mechanisms of the sustained EWB improvement one year post-transplant may reflect the fact that these patients were doing well clinically. Further analysis of the early rise in emotional well-being after ablative allogeneic BMT would be of interest
A patient and family data domain collection framework for identifying disparities in pediatrics: results from the pediatric health equity collaborative
Abstract Background By 2020, the child population is projected to have more racial and ethnic minorities make up the majority of the populations and health care organizations will need to have a system in place that collects accurate and reliable demographic data in order to monitor disparities. The goals of this group were to establish sample practices, approaches and lessons learned with regard to race, ethnicity, language, and other demographic data collection in pediatric care setting. Methods A panel of 16 research and clinical professional experts working in 10 pediatric care delivery systems in the US and Canada convened twice in person for 3-day consensus development meetings and met multiple times via conference calls over a two year period. Current evidence on adult demographic data collection was systematically reviewed and unique aspects of data collection in the pediatric setting were outlined. Human centered design methods were utilized to facilitate theme development, facilitate constructive and innovative discussion, and generate consensus. Results Group consensus determined six final data collection domains: 1) caregivers, 2) race and ethnicity, 3) language, 4) sexual orientation and gender identity, 5) disability, and 6) social determinants of health. For each domain, the group defined the domain, established a rational for collection, identified the unique challenges for data collection in a pediatric setting, and developed sample practices which are based on the experience of the members as a starting point to allow for customization unique to each health care organization. Several unique challenges in the pediatric setting across all domains include: data collection on caregivers, determining an age at which it is appropriate to collect data from the patient, collecting and updating data at multiple points across the lifespan, the limits of the electronic health record, and determining the purpose of the data collection before implementation. Conclusions There is no single approach that will work for all organizations when collecting race, ethnicity, language and other social determinants of health data. Each organization will need to tailor their data collection based on the population they serve, the financial resources available, and the capacity of the electronic health record