Software Systems for Clinical Research.
Year: 2011
Type: article
Abstract: By the end of 2011 we will likely know the DNA sequences for 30,000 human genomes. However, to truly understand how the variation between these genomes affect phenotype at a molecular level, future research projects need to analyze these genomes in conjunction with data from multiple ultra-high throughput assays obtained from large sample populations. In cancer research, for example, studies that examine 1000s of specific tumors in 1000s of patients are needed to fully characterize the more than 10,000 types and subtypes of cancer and develop diagnostic biomarkers. These studies will use high throughput DNA sequencing to characterize tumor genomes and their transcriptomes. Sequencing results will be validated with nonsequencing technologies and putative biomarkers will be examined in large populations using rapid targeted assay approaches. Geospiza is transforming the above scenario from vision into reality in several ways. The Company's GeneSifter platform utilizes scalable data management technologies based on open-source HDF5 and BioHDF technologies to capture, integrate, and mine raw data and analysis results from DNA, RNA, and other high-throughput assays. Analysis results are integrated and linked to multiple repositories of information that include variation, expression, pathway, and ontology databases to enable discovery process and support verification assays. Using this platform and RNA-Sequencing and Genomic DNA sequencing from matched tumor/normal samples, we were able to characterize differential gene expression, differential splicing, allele specific expression, RNA editing, somatic mutations and genomic rearrangements as well as validate these observations in a set of patients with oral and other cancers.
Source: Europe PMC (PubMed Central)
Institutions: Mayo Clinic, Cornell University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W2222333336