EST analysis online: WWW tools for detection of SNPs and alternative splice forms

ANEXdb: an integrated animal ANnotation and microarray EXpression database

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.

DISC1 splice variants are upregulated in schizophrenia and associated with risk polymorphisms

Disrupted-In-Schizophrenia-1 (DISC1) is a promising susceptibility gene for major mental illness, but the mechanism of the clinical association is unknown. We searched for DISC1 transcripts in adult and fetal human brain and tested whether their expression is altered in patients with schizophrenia and is associated with genetic variation in DISC1. Many alternatively spliced transcripts were identified, including groups lacking exon 3 (Delta3), exons 7 and 8 (Delta7Delta8), an exon 3 insertion variant (extra short variant-1, Esv1), and intergenic splicing between TSNAX and DISC1. Isoforms Delta7Delta8, Esv1, and Delta3, which encode truncated DISC1 proteins, were expressed more abundantly during fetal development than during postnatal ages, and their expression was higher in the hippocampus of patients with schizophrenia. Schizophrenia risk-associated polymorphisms [non-synonymous SNPs rs821616 (Cys704Ser) and rs6675281 (Leu607Phe), and rs821597] were associated with the expression of Delta3 and Delta7Delta8. Moreover, the same allele at rs6675281, which predicted higher expression of these transcripts in the hippocampus, was associated with higher expression of DISC1Delta7Delta8 in lymphoblasts in an independent sample. Our results implicate a molecular mechanism of genetic risk associated with DISC1 involving specific alterations in gene processing.

Alternative splicing in cancer: Noise, functional, or systematic?

Pre-messenger RNA splicing is a fine-tuned process that generates multiple functional variants from individual genes. Various cell types and developmental stages regulate alternative splicing patterns differently in their generation of specific gene functions. In cancers, splicing is significantly altered, and understanding the underlying mechanisms and patterns in cancer will shed new light onto cancer biology. Cancer-specific transcript variants are promising biomarkers and targets for diagnostic, prognostic, and treatment purposes. In this review, we explore how alternative splicing cannot simply be considered as noise or an innocent bystander, but is actively regulated or deregulated in cancers. A special focus will be on aspects of cell biology and biochemistry of alternative splicing in cancer cells, addressing differences in splicing mechanisms between normal and malignant cells. The systems biology of splicing is only now applied to the field of cancer research. We explore functional annotations for some of the most intensely spliced gene classes, and provide a literature mining and clustering that reflects the most intensely investigated genes. A few well-established cancer-specific splice events, such as the CD44 antigen, are used to illustrate the potential behind the exploration of the mechanisms of their regulation. Accordingly, we describe the functional connection between the regulatory machinery (i.e., the spliceosome and its accessory proteins) and their global impact on qualitative transcript variation that are only now emerging from the use of genomic technologies such as microarrays. These studies are expected to open an entirely new level of genetic information that is currently still poorly understood.

Bioinformatics and cancer target discovery

The convergence of genomic technologies and the development of drugs designed against specific molecular targets provides many opportunities for using bioinformatics to bridge the gap between biological knowledge and clinical therapy. Identifying genes that have properties similar to known targets is conceptually straightforward. Additionally, genes can be linked to cancer via recurrent genomic or genetic abnormalities. Finally, by integrating large and disparate datasets, gene-level distinctions can be made between the different biological states that the data represents. These bioinformatics approaches and their associated methodologies, which can be applied across a range of technologies, facilitate the rapid identification of new target leads for further experimental validation.

Single nucleotide polymorphisms associated with rat expressed sequences

Single nucleotide polymorphisms (SNPs) are the most common source of genetic variation in populations and are thus most likely to account for the majority of phenotypic and behavioral differences between individuals or strains. Although the rat is extensively studied for the latter, data on naturally occurring polymorphisms are mostly lacking. We have used publicly available sequences consisting of whole-genome shotgun (WGS), expressed sequence tag (EST), and mRNA data as a source for the in silico identification of SNPs in gene-coding regions and have identified a large collection of 33,305 high-quality candidate SNPs. Experimental verification of 471 candidate SNPs using a limited set of rat isolates revealed a confirmation rate of approximately 50%. Although the majority of SNPs were identified between Sprague-Dawley (EST data) and Brown Norway (WGS data) strains, we found that 66% of the verified variations are common among different rat strains. All SNPs were extensively annotated, including chromosomal and genetic map information, and nonsynonymous SNPs were analyzed by SIFT and PolyPhen prediction programs for their potential deleterious effect on protein function. Interestingly, we retrieved three SNPs from the database that result in the introduction of a premature stop codon and that could be confirmed experimentally. Two of these "in silico-identified knockouts" reside in interesting QTL regions. Data are publicly available via a Web interface (http://cascad.niob.knaw.nl), allowing simple and advanced search queries.

Database and analyses of known alternatively spliced genes in plants

Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The number of alternatively spliced genes reported so far in plants is much smaller than that in mammals, but is increasing as a result of the explosive growth of available EST and genomic sequences. We have searched for all alternatively spliced genes reported in GenBank and PubMed in all plant species under Viridiplantae. After careful merging and manual review of the search results, we obtained a comprehensive, high-quality collection of 168 genes reported to be alternatively spliced in plants, spanning 44 plant species (March 22, 2003 update). We developed a relational database with Web-based user interface to store and present the data, named the Plant Alternative Splicing Database (PASDB), freely available at http://pasdb.genomics.org.cn. We analyzed the functional categories that these genes belong to using the Gene Ontology. We also analyzed in detail the biological roles and gene structures of the four genes that are known to be alternatively spliced in more than one plant species. Finally, we studied the structural features of the splice sites in the alternatively spliced genes.

Identification of polymorphisms in the human Reprimo gene using public EST data

The human Reprimo gene is a recently identified cytoplasmic protein, which plays an important role in the regulation of p53-dependent G2 arrest of the cell cycle. Genetic variations in the Reprimo gene that may influence enzyme activity can be of both biological and epidemiological significance. The human expressed sequence tag (EST) database is a wealth of resources, which can be used to rapidly screen for potential polymorphisms in proteins of physiological interest. On the basis of the alignment of human EST sequences, we identified two candidate polymorphisms at nucleotides 824 and 839 in the 3'-untranslated region of the Reprimo gene. The presence of these polymorphisms was confirmed in a Caucasian population (n=82) by the use of the allele specific polymerase chain reaction (PCR). The rare allele frequency at position 824 (38.4%) is much higher than rare allele frequency at position 839 (3.7%). Our results suggest that the human EST data may serve as a valuable source for the rapid identification of genetic variation.

Information technology tools for efficient SNP studies

We are currently facing a new era of studies involving single nucleotide polymorphisms (SNPs). This increased attention is stimulated by interest in individual differences in disease susceptibility as well as individual responses to drug treatment and the falling cost of genotyping. This review is a guide to the numerous public data repositories and Information Technology (IT) tools that may aid planning, preparation, running and analysis of studies involving SNPs. I will also highlight areas where researchers will have to resort to home-made IT solutions. Unfortunately, both information and IT tools are scattered throughout the internet and a lack of data exchange conventions can hamper the efficient use of these existing resources. This can lead to situations where the planning, preparation and analysis of a SNP study can actually cost more than the actual genotyping. We propose that only a customizable backbone IT infrastructure for SNP studies can help reduce costs associated with SNP data handling and tool launching.

Online genomics facilities in the new millennium

The review begins by providing a brief typology of biological databases on the Internet, illustrated by examples of the most influential resources of each kind. We then take an insider look at one typical on-line genomic resource -- the yeast genome database hosted at the Munich Information Center for Protein Sequences (MIPS) -- and explain how and why it has evolved from a basic sequence repository to a multidomain knowledge base. The role of community efforts in curating and annotating genome data is discussed. The crucial role of data integration and interoperability in developing next-generation genomic facilities is underscored.

The contribution of exon-skipping events on chromosome 22 to protein coding diversity

Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000-40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have revealed that alternate transcription, including alternative splicing, polyadenylation and transcription start sites, occurs within at least 30-40% of human genes. Transcript form surveys have yet to integrate the genomic context, expression, frequency, and contribution to protein diversity of isoform variation. We determine here the degree to which protein coding diversity may be influenced by alternate expression of transcripts by exhaustive manual confirmation of genome sequence annotation, and comparison to available transcript data to accurately associate skipped exon isoforms with genomic sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22. Combining manual assessment with software screening of exon boundaries provides a highly accurate and internally consistent indication of skipping frequency. 57 of 62 exon skipping events occur in the protein coding regions of 52 genes. A single gene, (FBXO7) expresses an exon repetition. 59% of highly represented multi-exon genes are likely to express exon-skipped isoforms in ratios that vary from 1:1 to 1:>100. The proportion of all transcripts corresponding to multi-exon genes that exhibit an exon skip is estimated to be 5%.

Alternative splicing and expressivity of the Axin(Fu) allele in mice

Variable expressivity and incomplete penetrance are common for numerous mutations. In most cases the reasons behind these phenomena remain obscure. Caused by the insertion of a murine retrotransposon into intron 6 of the Axin locus, the Axin(Fu) mutation induces alternative splicing and ultimately leads to abnormal tail development in mice. In this investigation RNase protection assay was used to investigate the potential connection between alternative splicing with the expressivity and penetrance of the mutant allele. The results reported here confirm previous observations that alternative splicing occurs in mRNA transcribed from the mutant Axin(Fu) allele. However this investigation also shows that lower levels of alternative splicing commonly take place in the wild type transcript. Correlation analysis reveals a significant connection between tail abnormalities and the ratio of correct to alternatively spliced mRNAs. Overall this paper demonstrates that higher levels of alternatively spliced mRNAs correlate with stronger expression of the mutant trait.