The Bioconductor channel in F1000Research.

Bioconductor ( bioconductor.org) is a rich source of software and know-how for the integrative analysis of genomic data. The Bioconductor channel in F1000Research provides a forum for task-oriented workflows that cover a solution to a current, important problem in genome-scale data analysis. It also hosts manuscripts describing software packages, package-based vignettes, teaching labs, benchmark studies, methodological reviews and bioinformatics software oriented perspective papers.

Increased methylation variation in epigenetic domains across cancer types.

Tumor heterogeneity is a major barrier to effective cancer diagnosis and treatment. We recently identified cancer-specific differentially DNA-methylated regions (cDMRs) in colon cancer, which also distinguish normal tissue types from each other, suggesting that these cDMRs might be generalized across cancer types. Here we show stochastic methylation variation of the same cDMRs, distinguishing cancer from normal tissue, in colon, lung, breast, thyroid and Wilms' tumors, with intermediate variation in adenomas. Whole-genome bisulfite sequencing shows these variable cDMRs are related to loss of sharply delimited methylation boundaries at CpG islands. Furthermore, we find hypomethylation of discrete blocks encompassing half the genome, with extreme gene expression variability. Genes associated with the cDMRs and large blocks are involved in mitosis and matrix remodeling, respectively. We suggest a model for cancer involving loss of epigenetic stability of well-defined genomic domains that underlies increased methylation variability in cancer that may contribute to tumor heterogeneity.

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.

Alternative mRNA splicing adds a layer of regulation to the expression of thousands of genes in Drosophila melanogaster. Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are degraded by the nonsense-mediated mRNA decay (NMD) pathway. This coupling of alternative splicing and NMD provides a mechanism for gene regulation that is highly conserved in mammals. NMD is also active in Drosophila, but its effect on the repertoire of alternative splice forms has been unknown, as has the mechanism by which it recognizes targets. Here, we have employed a custom splicing-sensitive microarray to globally measure the effect of alternative mRNA processing and NMD on Drosophila gene expression. We have developed a new algorithm to infer the expression change of each mRNA isoform of a gene based on the microarray measurements. This method is of general utility for interpreting splicing-sensitive microarrays and high-throughput sequence data. Using this approach, we have identified a high-confidence set of 45 genes where NMD has a differential effect on distinct alternative isoforms, including numerous RNA-binding and ribosomal proteins. Coupled alternative splicing and NMD decrease expression of these genes, which may in turn have a downstream effect on expression of other genes. The NMD-affected genes are enriched for roles in translation and mitosis, perhaps underlying the previously observed role of NMD factors in cell cycle progression. Our results have general implications for understanding the NMD mechanism in fly. Most notably, we found that the NMD-target mRNAs had significantly longer 3' untranslated regions (UTRs) than the nontarget isoforms of the same genes, supporting a role for 3' UTR length in the recognition of NMD targets in fly.

Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

A complete description of the transcriptome of an organism is crucial for a comprehensive understanding of how it functions and how its transcriptional networks are controlled, and may provide insights into the organism's evolution. Despite the status of Saccharomyces cerevisiae as arguably the most well-studied model eukaryote, we still do not have a full catalog or understanding of all its genes. In order to interrogate the transcriptome of S. cerevisiae for low abundance or rapidly turned over transcripts, we deleted elements of the RNA degradation machinery with the goal of preferentially increasing the relative abundance of such transcripts. We then used high-resolution tiling microarrays and ultra high-throughput sequencing (UHTS) to identify, map, and validate unannotated transcripts that are more abundant in the RNA degradation mutants relative to wild-type cells. We identified 365 currently unannotated transcripts, the majority presumably representing low abundance or short-lived RNAs, of which 185 are previously unknown and unique to this study. It is likely that many of these are cryptic unstable transcripts (CUTs), which are rapidly degraded and whose function(s) within the cell are still unclear, while others may be novel functional transcripts. Of the 185 transcripts we identified as novel to our study, greater than 80 percent come from regions of the genome that have lower conservation scores amongst closely related yeast species than 85 percent of the verified ORFs in S. cerevisiae. Such regions of the genome have typically been less well-studied, and by definition transcripts from these regions will distinguish S. cerevisiae from these closely related species.

Advanced paternal age and risk of fetal death: a cohort study.

A possible detrimental paternal age effect on offspring health due to mutations of paternal origin should be reflected in an association between paternal age and fetal loss. The authors used data from a prospective study of 23,821 pregnant women recruited consecutively to the Danish National Birth Cohort from 1997 to 1999 to assess the association between paternal age and fetal death. Fathers of the pregnancies were identified by record linkage to population registers. The paternal age-related risks of fetal death and its components, early and late fetal loss, were estimated using survival analysis. Pregnancies fathered by a man aged 50 or more years (n = 124) had almost twice the risk of ending in a fetal loss compared with pregnancies with younger fathers (hazard ratio = 1.88, 95% confidence interval: 0.93, 3.82), after adjustment for maternal age, reproductive history, and maternal lifestyle during pregnancy. Various approaches to adjustment for potential residual confounding of the relation by maternal age did not affect the relative risk estimates. The paternal age-related risk of late fetal death was higher than the risk of early fetal death and started to increase from the age of 45 years. It should, however, be interpreted cautiously because of the restricted number of fetal deaths.

Fertility pattern does not explain social gradient in breast cancer in denmark.

The present study was undertaken to assess the impact of reproductive behavior on the social class gradient in breast cancer occurrence in Denmark. Objectives were to study whether the gradient across socioeconomic groups could be explained by fertility differences, whether the gradient across educational groups could be explained by fertility differences and whether the effect of socioeconomic group on breast cancer incidence and mortality could be explained by education and vice versa. We studied 674,084 women aged 20-39 at the census on 9 November 1970 for whom we had complete data on fertility history. The cohort was followed up for breast cancer incidence and mortality until 8 November 1998. Fertility history varied considerably across socioeconomic group, where 38% of the academics were childless at the age of 30, in contrast to only 8% of women in agriculture. The academics had the highest risk of breast cancer and women in agriculture had the lowest risk. For incidence, the gradient in the relative risks was 1.74, which changed to 1.49 when fertility history was incorporated and to 1.29 when school education was also taken into account. For school education, women with > or = 12 years of schooling had the highest risk and women with < or = 7 years of schooling had the lowest risk. For incidence, the gradient in the relative risk was 1.38, which changed to 1.26 when fertility history was incorporated and to 1.22 when socioeconomic group was also taken into account.

Use of census data for construction of fertility history for Danish women.

BACKGROUND: Modern epidemiology increasingly uses data on families. The authors constructed an extended fertility database for women born in Denmark from 1930 onwards by supplementing the existing Fertility Database with household data from the 1970 census. METHODS: A fertility history was constructed for all women participating in the 1970 census, but aiming for complete data only for women aged 20-39. The fertility history of these women prior to the 1970 census was constructed from the census data including 1,648,813 persons coded as children. An algorithm was used transforming household information into fertility history data by matching women and children according to family position. Children for whom the algorithm gave no match were searched for in the Fertility Database; children not found in the Fertility Database either were searched for manually. The fertility history after the 1970 census was retrieved from the Fertility Database. RESULTS: Using data from the census 1970, 98.5% of the children were linked to a mother, and 99.6% of these links were estimated to be correct, corresponding to 98.1% of the children being linked correctly. In total, 964,720 children of women aged 20-39 in 1970 were identified, which was equivalent to 96.6% of the expected live-born children, and to 99.1% of the expected surviving children. CONCLUSION: Census household data proved to be an excellent data source for construction of fertility histories.