ABSTRACT
The past few decades have seen medical science making rapid strides in the field of diagnostic technologies, thus making it possible to detect some conditions at a very early stage. An unwanted effect of these developments is overdiagnosis which occurs when a true abnormality is discovered, but detection of that abnormality and its treatment does not benefit the patient. Overdiagnosis is encountered as a result cancer screening, in genetic diseases and in some chronic conditions when disease definition is broadened. There is urgent need of development of evidence based decision-making tools for clinicians which will help patients understand the benefits and harms of different screening and treatment methods. And the treating physician has to play a important role to convince the patient that watchful waiting, for some of the lesions may be the best option available in some circumstances.
ABSTRACT
To determine annotations of the sequence elements on microarrays used for transcriptional profiling experiments in livestock species, currently researchers must either use the sparse direct annotations available for these species or create their own annotations. ANEXdb ( http://www.anexdb.org ) is an open-source web application that supports integrated access of two databases that house microarray expression (ExpressDB) and EST annotation (AnnotDB) data. The expression database currently supports storage and querying of Affymetrix-based expression data as well as retrieval of experiments in a form ready for NCBI-GEO submission; these services are available online. AnnotDB currently houses a novel assembly of approximately 1.6 million unique porcine-expressed sequence reads called the Iowa Porcine Assembly (IPA), which consists of 140,087 consensus sequences, the Iowa Tentative Consensus (ITC) sequences, and 103,888 singletons. The IPA has been annotated via transfer of information from homologs identified through sequence alignment to NCBI RefSeq. These annotated sequences have been mapped to the Affymetrix porcine array elements, providing annotation for 22,569 of the 23,937 (94%) porcine-specific probe sets, of which 19,253 (80%) are linked to an NCBI RefSeq entry. The ITC has also been mined for sequence variation, providing evidence for up to 202,383 SNPs, 62,048 deletions, and 958 insertions in porcine-expressed sequence. These results create a single location to obtain porcine annotation of and sequence variation in differently expressed genes in expression experiments, thus permitting possible identification of causal variants in such genes of interest. The ANEXdb application is open source and available from SourceForge.net.
