Abstract
Lung nodule segmentation allows for automatic measurement of the nodule's size or volume which is of utmost importance in lung cancer diagnosis. It is a challenging task since there are many different types of nodules (solid or non-solid, solitary or multiple, etc). A supervised lung nodule segmentation method uses a shape-based, contrast-based and intensity-based feature set to produce three preliminary segmentations and an artificial neural network to obtain a more accurate segmentation. This method was applied to 20 computer tomography studies, all containing nodules. The data has 10 images of solid nodules and 10 images of ground glass opacity nodules, all with ground-truth. The segmentation uses a region growing approach and the volumetric shape index is used for nodule detection and providing a seed point. In the first and second segmentation the probability of each neighbor belonging to the nodule is estimated using the volumetric shape index and the convergence index filter, respectively. The third segmentation is obtained using a feature set region regression method where for each neighbor the probability of belonging to the nodule or not is obtained using k nearest neighbor regression. Then, using a leave-one out method, an artificial neural network uses the three preliminary segmentations as input and is trained to obtain a more accurate segmentation. Results obtained a 12% relative volume error, 88% and 93% Jaccard and Dice coefficient respectively. © 2014, Springer International Publishing Switzerland.

Abstract
The cis-regulatory effects responsible for cancer development have not been as extensively studied as the perturbations of the protein coding genome in tumorigenesis. To better characterize colorectal cancer (CRC) development we conducted an RNA-sequencing experiment of 103 matched tumour and normal colon mucosa samples from Danish CRC patients, 90 of which were germline-genotyped. By investigating allele-specific expression (ASE) we show that the germline genotypes remain important determinants of allelic gene expression in tumours. Using the changes in ASE in matched pairs of samples we discover 71 genes with excess of somatic cis-regulatory effects in CRC, suggesting a cancer driver role. We correlate genotypes and gene expression to identify expression quantitative trait loci (eQTLs) and find 1,693 and 948 eQTLs in normal samples and tumours, respectively. We estimate that 36% of the tumour eQTLs are exclusive to CRC and show that this specificity is partially driven by increased expression of specific transcription factors and changes in methylation patterns. We show that tumour-specific eQTLs are more enriched for low CRC genome-wide association study (GWAS) P values than shared eQTLs, which suggests that some of the GWAS variants are tumour specific regulatory variants. Importantly, tumour-specific eQTL genes also accumulate more somatic mutations when compared to the shared eQTL genes, raising the possibility that they constitute germline-derived cancer regulatory drivers. Collectively the integration of genome and the transcriptome reveals a substantial number of putative somatic and germline cis-regulatory cancer changes that may have a role in tumorigenesis.

Abstract
Chimeric RNAs originating from two or more different genes are known to exist not only in cancer, but also in normal tissues, where they can play a role in human evolution. However, the exact mechanism of their formation is unknown. Here, we use RNA sequencing data from 462 healthy individuals representing 5 human populations to systematically identify and in depth characterize 81 RNA tandem chimeric transcripts, 13 of which are novel. We observe that 6 out of these 81 chimeras have been regarded as cancer-specific. Moreover, we show that a prevalence of long introns at the fusion breakpoint is associated with the chimeric transcripts formation. We also find that tandem RNA chimeras have lower abundances as compared to their partner genes. Finally, by combining our results with genomic data from the same individuals we uncover intronic genetic variants associated with the chimeric RNA formation. Taken together our findings provide an important insight into the chimeric transcripts formation and open new avenues of research into the role of intronic genetic variants in post-transcriptional processing events. © 2014 Greger et al.

Abstract
Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype to be recapitulated completely. Here we represent the splicing pattern of a gene as the distribution of the relative abundances of a geneâ(tm) s alternative transcript isoforms. We develop a statistical framework that uses a distance-based approach to compute the variability of splicing ratios across observations, and a non-parametric analogue to multivariate analysis of variance. We implement this approach in the R package sQTLseekeR and use it to analyze RNA-Seq data from the Geuvadis project in 465 individuals. We identify hundreds of single nucleotide polymorphisms (SNPs) as splicing QTLs (sQTLs), including some falling in genome-wide association study SNPs. By developing the appropriate metrics, we show that sQTLseekeR compares favorably with existing methods that rely on univariate approaches, predicting variants that behave as expected from mutations affecting splicing. © 2014 Macmillan Publishers Limited.

Abstract
Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying transcriptional profile is still poorly understood. We have performed deep RNA sequencing in different subpopulations of normal B-lymphocytes and CLL cells from a cohort of 98 patients, and characterized the CLL transcriptional landscape with unprecedented resolution. We detected thousands of transcriptional elements differentially expressed between the CLL and normal B cells, including protein-coding genes, noncoding RNAs, and pseudogenes. Transposable elements are globally derepressed in CLL cells. In addition, two thousand genes-most of which are not differentially expressed-exhibit CLL-specific splicing patterns. Genes involved in metabolic pathways showed higher expression in CLL, while genes related to spliceosome, proteasome, and ribosome were among the most down-regulated in CLL. Clustering of the CLL samples according to RNA-seq derived gene expression levels unveiled two robust molecular subgroups, C1 and C2. C1/C2 subgroups and the mutational status of the immunoglobulin heavy variable (IGHV ) region were the only independent variables in predicting time to treatment in a multivariate analysis with main clinico-biological features. This subdivision was validated in an independent cohort of patients monitored through DNA microarrays. Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences. © 2014 Hansen et al.

Abstract
In a lung nodule detection task, parenchyma segmentation is crucial to obtain the region of interest containing all the nodules. Thus, the challenge is to devise a methodology that includes all the lung nodules, particularly those close to the walls, as the juxtapleural nodules. In this paper, different region growing approaches are proposed for the automatic segmentation of the lung parenchyma. The methodology is organized in five different steps: first, the image intensity is corrected to improve the contrast of the lungs. With that, the fat area is obtained, automatically deriving the interior of the lung region. Then, the traquea is extracted by a 3D region growing, being subtracted from the lung region results. The next step is the division of the two lungs to guarantee that both are separated. And finally, the lung contours are refined to provide appropriate final results. The methodology was tested in 50 images taken from the LIDC image database, with a large variability and, specially, including different types of lung nodules. In particular, this dataset contains 158 nodules, from which 40 are juxtapleural nodules. Experimental results demonstrate that the method provides accurate lung regions, specially including the centers of 36 of the juxtapleural nodules. For the other 4, although the centers are not included, parts of their areas are retained in the segmentation, which is useful for lung nodule detection.