RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions–particularly those expressed with low abundance– is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping pipeline within the LifeScope software. We introduced new features including filter and junction mapping, annotation-aided pairing rescue and accurate mapping quality values. We combined this pipeline with a Suffix Array Spliced Read (SASR) aligner to detect chimeric transcripts. Performing paired-end RNA-Seq of the breast cancer cell line MCF-7 using the SOLiD system, we called 40 gene fusions among over 120,000 splicing junctions. We validated 36 of these 40 fusions with TaqMan assays, of which 25 were expressed in MCF-7 but not the Human Brain Reference. An intra-chromosomal gene fusion involving the estrogen receptor alpha gene ESR1, and another involving the RPS6KB1 (Ribosomal protein S6 kinase beta-1) were recurrently expressed in a number of breast tumor cell lines and a clinical tumor sample

Human and mouse essentiality screens as a resource for disease gene discovery.

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery

Evaluation of temperature increase during in-office bleaching

ABSTRACT The use of light sources in the bleaching process reduces the time required and promotes satisfactory results. However, these light sources can cause an increase in the pulp temperature. Objective The purpose of the present study was to measure the increase in intrapulpal temperature induced by different light-activated bleaching procedures with and without the use of a bleaching gel. Material and Methods A human maxillary central incisor was sectioned 2 mm below the cementoenamel junction. A K-type thermocouple probe was introduced into the pulp chamber. A 35% hydrogen peroxide bleaching gel was applied to the vestibular tooth surface. The light units used were a conventional halogen, a hybrid light (only LED and LED/Laser), a high intensity LED, and a green LED light. Temperature increase values were compared by two-way ANOVA and Tukey´s tests (p<0.05). Results There were statistically significant differences in temperature increases between the different light sources used and between the same light sources with and without the use of a bleaching gel. The presence of a bleaching gel generated an increase in intra-pulpal temperature in groups activated with halogen light, hybrid light, and high intensity LED. Compared to the other light sources, the conventional halogen lamp applied over the bleaching gel induced a significant increase in temperature (3.83±0.41°C). The green LED unit with and without gel application did not produce any significant intrapulpal temperature variations. Conclusion In the present study, the conventional halogen lamp caused the highest increase in intrapulpal temperature, and the green LED caused the least. There was an increase in temperature with all lights tested and the maximum temperature remained below the critical level (5.5°C). The addition of a bleaching gel led to a higher increase in intrapulpal temperatures