Dataset Information

Translational Genomics Research Institute

ABSTRACT: Organisation EGAO00000000618

PROVIDER: EGAO00000000618 | EGA |

REPOSITORIES: EGA

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Publications

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

Murtaza Muhammed M Dawson Sarah-Jane SJ Pogrebniak Katherine K Rueda Oscar M OM Provenzano Elena E Grant John J Chin Suet-Feung SF Tsui Dana W Y DWY Marass Francesco F Gale Davina D Ali H Raza HR Shah Pankti P Contente-Cuomo Tania T Farahani Hossein H Shumansky Karey K Kingsbury Zoya Z Humphray Sean S Bentley David D Shah Sohrab P SP Wallis Matthew M Rosenfeld Nitzan N Caldas Carlos C

Nature communications 20151104

Circulating tumour DNA analysis can be used to track tumour burden and analyse cancer genomes non-invasively but the extent to which it represents metastatic heterogeneity is unknown. Here we follow a patient with metastatic ER-positive and HER2-positive breast cancer receiving two lines of targeted therapy over 3 years. We characterize genomic architecture and infer clonal evolution in eight tumour biopsies and nine plasma samples collected over 1,193 days of clinical follow-up using exome and ...[more]

PMID: 26530965

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Project description:BackgroundThe use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.ResultsThe process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.ConclusionsThis database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

Dataset Information

Translational Genomics Research Institute

Publications

Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.

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