Dataset Information

Ena-DATASET-Genentech-07-11-2014-17:09:43:626-885 - samples

ABSTRACT: RNA-seq from normal human tissues (2 x 75 bp)

PROVIDER: EGAD00001001057 | EGA |

REPOSITORIES: EGA

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Publications

Prediction and Quantification of Splice Events from RNA-Seq Data.

Goldstein Leonard D LD Cao Yi Y Pau Gregoire G Lawrence Michael M Wu Thomas D TD Seshagiri Somasekar S Gentleman Robert R

PloS one 20160524 5

Analysis of splice variants from short read RNA-seq data remains a challenging problem. Here we present a novel method for the genome-guided prediction and quantification of splice events from RNA-seq data, which enables the analysis of unannotated and complex splice events. Splice junctions and exons are predicted from reads mapped to a reference genome and are assembled into a genome-wide splice graph. Splice events are identified recursively from the graph and are quantified locally based on ...[more]

PMID: 27218464

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Project description:BackgroundNorovirus (NoV) is a major cause of gastroenteritis during the autumn and winter seasons in Japan as well as in other temperate climate regions. Most outbreaks are thought to occur by secondary attacks through person-to-person infection by fecal-oral route. Severe cases are found in young children or patients with chronic diseases. Clarifying the patterns of epidemic diffusion is important for considering effective monitoring and surveillance as well as possible prevention.MethodsWe considered the predominant viral genotype from the laboratory result obtained from Infectious Agents Surveillance Report (IASR) of National Institute of Infectious Diseases (NIID). We investigated the increase of NoV cases nationwide for the 2006-07 to 2008-09 seasons using sentinel gastroenteritis data collected from about 3000 pediatric clinics on National Epidemiological Surveillance of Infectious Diseases (NESID) acquired from the kriging method in the geographic information system (GIS).ResultsDuring these three seasons, the majority of the detected virus was GII.4, which ranged from 60.4 to 88.9%. The number of cases (per sentinel site) at the peak week was 22.81 in the 2006-07 season and it decreased in the following seasons. NoV cases began to increase earlier in the southern areas and gradually extended into the northern areas, similarly, over the seasons. The average period from when the increase of cases was detected in the southern area to when it reached the northern area was 12.7 weeks.ConclusionThe decrease of the number of sentinel cases at the peak week may suggest the development of herd immunity after a period of high prevalence. Although the NoV epidemic is thought to be associated with cold weather, its cases first increased in the southern area with relatively warm temperature, indicating there are other climate factors involved. Geographic study using the sentinel data could enhance the monitoring and surveillance of and preparedness against epidemics.

Dataset Information

Ena-DATASET-Genentech-07-11-2014-17:09:43:626-885 - samples

Publications

Prediction and Quantification of Splice Events from RNA-Seq Data.

Similar Datasets

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