39 research outputs found
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation
No full textAbstract Background The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies via public repositories. However, although the MAGE object model is flexible enough to support different annotation strategies, the annotation of array descriptions can be complex. Results We have developed a graphical Java-based application (Adamant) to assist with submission of Microarray designs to public repositories. Output of the application is fully compliant with the standards prescribed by the various public data repositories. Conclusion Adamant will allow researchers to annotate and submit their own array designs to public repositories without requiring programming expertise, knowledge of the MAGE-OM or XML. The application has been used to submit a number of ArrayDesigns to the Array Express database.</p
Security-oriented data grids for microarray expression profiles
No full textMicroarray experiments are one of the key ways in which gene activity can be identified and measured thereby shedding light and understanding for example on biological processes. The BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project has developed an infrastructure which allows post-genomic life science researchers to ask and answer the following questions: who has undertaken microarray experiments that are in some way similar or relevant to mine; and how similar were these relevant experiments? Given that microarray experiments are expensive to undertake and may possess crucial information for future exploitation (both academically and commercially), scientists are wary of allowing unrestricted access to their data by the wider community until fully exploited locally. A key requirement is thus to have fine grained security that is easy to establish and simple (or ideally transparent) to use across inter-institutional virtual organisations. In this paper we present an enhanced security-oriented data Grid infrastructure that supports the definition of these kinds of queries and the analysis and comparison of microarray experiment results
Cancer incidence in people with AIDS in Italy
No full textLo studio è stato condotto in collaborazione con medici, epidemiologi e ricercatori in tutta Italia che sono entrati a far parte del Cancer and AIDS Registries Linkage Study. Tale stuudio ha prodotto una pubblicazione a stampa in cui compare tra gli autori la dr Rosa Maria Limina, di questa Università, che ha inserito questo prodotto con il codice 31053 nella tipologia Articolo su Rivista
Estimates of cancer burden in Italy
No full textThis paper presents updated estimates of the incidence, prevalence and mortality of stomach, colorectal, lung, breast, uterine cervix and prostate cancer and skin melanoma in the Italian population. In particular, point estimates for 2012 and time trends from 1970 to 2015 will be provided
[Population ageing effect on number of cancer cases: Italian cancer registries data].
No full textOBJECTIVE:
To describe causes of cancer incidence increase. We identified and quantified a population ageing factor, a factor due to incidence trend of cancer sites with early-diagnosis interventions and a remainder factor (concerning all other cancer sites).
METHODS:
We calculated incidence rates for two calendar period (1993-95 and 2003-05).We used data from Cancer Registries with at least one incidence year available for each period (jointly for males and female). We compared crude and age-adjusted rates by the direct method for prostate cancer, breast cancer, colorectal cancer, melanoma of the skin cancer, thyroid cancer, group of other cancer sites and for all cancer sites (but non-melanoma skin cancer).
RESULTS:
Since 1993-95 to 2003-05 all cancer crude incidence rates have been increasing 17.9% (from 555.4 cases for 100,000 inhabitants/years to 654.8). If population age structure had remained the same, rates would have increased only 6.6% (from 555.4 to 592.0): almost 2/3 of observed increasing are due to population ageing. The remainder part of the increasing is due to incidence trend of cancer sites with early-diagnosis interventions (that anticipates the diagnosis).
CONCLUSIONS:
This study helps to quantify the incidence increase due to population ageing and the raise due to trend of cancer sites with early-diagnosis interventions
CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes
No full textBackground: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research community. The CATMA initiative offers the power and
flexibility to regularly update the GST collection according to evolving knowledge about the gene
repertoire. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies. This ongoing initiative has already produced approximately 24,000 GSTs that have been made publicly available for spotted microarray printing and RNA interference.
Results: GSTs from the CATMA version 2 repertoire (CATMAv2, created in 2002) were mapped onto the gene models from two independent Arabidopsis nuclear genome annotation efforts,
TIGR5 and PSB-EuGène, to consolidate a list of genes that were targeted by previously designed CATMA tags. A total of 9,027 gene models were not tagged by any amplified CATMAv2 GST, and 2,533 amplified GSTs were no longer predicted to tag an updated gene model. To validate the efficacy of GST mapping criteria and design rules, the predicted and experimentally observed hybridization characteristics associated to GST features were correlated in transcript profiling datasets obtained with the CATMAv2 microarray, confirming the reliability of this platform. To
complete the CATMA repertoire, all 9,027 gene models for which no GST had yet been designed were processed with an adjusted version of the Specific Primer and Amplicon Design Software (SPADS). A total of 5,756 novel GSTs were designed and amplified by PCR from genomic DNA.Together with the pre-existing GST collection, this new addition constitutes the CATMAv3 repertoire. It comprises 30,343 unique amplified sequences that tag 24,202 and 23,009 proteinencoding
nuclear gene models in the TAIR6 and EuGène genome annotations, respectively. To cover the remaining untagged genes, we identified 543 additional GSTs using less stringent design criteria and designed 990 sequence tags matching multiple members of gene families (Gene Family
Tags or GFTs) to cover any remaining untagged genes. These latter 1,533 features constitute the CATMAv4 addition.
Conclusion: To update the CATMA GST repertoire, we designed 7,289 additional sequence tags, bringing the total number of tagged TAIR6-annotated Arabidopsis nuclear protein-coding genes to 26,173. This resource is used both for the production of spotted microarrays and the large-scale
cloning of hairpin RNA silencing vectors. All information about the resulting updated CATMA
repertoire is available through the CATMA database http://www.catma.org
Survival after cancer in Italian persons with AIDS, 1986-2005: A population-based estimation.
No full textBACKGROUND:
Cancer survival in persons with AIDS (PWA) after introduction of antiretroviral therapies remains poorly characterized. The aim is to provide population-based estimates of cancer survival, overall and for the most important cancer types in PWA, and a comparison with persons without AIDS (non-PWA) affected by the same cancers.
METHODS:
PWA with cancer at AIDS or thereafter were individually matched with non-PWA by type of cancer, sex, age, year of diagnosis, area of living and, for lymphomas, histological subtype. Five-year observed survival and hazard ratios (HRs) of death in PWA versus non-PWA with 95% confidence intervals (CI) were estimated.
RESULTS:
We included 2262 Italian PWA and 4602 non-PWA with cancer diagnosed during 1986-2005. Between 1986-1995 and 1996-2005, 5-year survival for all cancers in PWA improved from 12% to 41% and the corresponding HR versus non-PWA decreased from 5.1 (95% CI: 4.3-6.1) to 2.9 (95% CI: 2.6-3.3). In 1996-2005, HRs were 2.0 (95% CI: 1.4-2.9) for Kaposi sarcoma; 3.4 (2.9-4.1) for non-Hodgkin lymphoma; 2.4 (1.4-4.0) for cervical cancer. HRs were 2.5 (2.1-3.1) for all non-AIDS-defining cancers; 5.9 (3.1-11.2) for Hodgkin lymphoma; and 7.3 (2.8-19.2) for non-melanoma skin. A ≤3-fold survival difference was found for cancer of the stomach, liver, anus, lung, brain and the most aggressive lymphoma subtypes.
CONCLUSION(S):
The persisting, although narrowing, gap in cancer survival between PWA and non-PWA indicates the necessity of enhancing therapeutic approaches, so that PWA will be provided the same chances of survival observed in the general population, and improving cancer prevention and screening
Incidence of stomach cancer is decreasing faster in the Centre-North of Italy
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Survival for all cancers is increasing, especially in men, but only thanks to PSA.
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