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Reports from University of British Columbia Advance Knowledge in Cancer Gene Therapy (On the identification of potential regulatory variants within...

August 25, 2014



Reports from University of British Columbia Advance Knowledge in Cancer Gene Therapy (On the identification of potential regulatory variants within genome wide association candidate SNP sets)

By a News Reporter-Staff News Editor at Cancer Gene Therapy Week -- Current study results on Biotechnology have been published. According to news reporting originating in Vancouver, Canada, by NewsRx journalists, research stated, "Genome wide association studies (GWAS) are a population-scale approach to the identification of segments of the genome in which genetic variations may contribute to disease risk. Current methods focus on the discovery of single nucleotide polymorphisms (SNPs) associated with disease traits."

The news reporters obtained a quote from the research from the University of British Columbia, "As there are many SNPs within identified risk loci, and the majority of these are situated within non-coding regions, a key challenge is to identify and prioritize variants affecting regulatory sequences that are likely to contribute to the phenotype assessed. We focused investigation on SNPs within lung and breast cancer GWAS loci that reached genome-wide significance for potential roles in gene regulation with a specific focus on SNPs likely to disrupt transcription factor binding sites. Within risk loci, the regulatory potential of sub-regions was classified using relevant open chromatin and epigenetic high throughput sequencing data sets from the ENCODE project in available cancer and normal cell lines. Furthermore, transcription factor affinity altering variants were predicted by comparison of position weight matrix scores between disease and reference alleles. Lastly, ChIP-seq data of transcription associated factors and topological domains were included as binding evidence and potential gene target inference. The sets of SNPs, including both the disease-associated markers and those in high linkage disequilibrium with them, were significantly over-represented in regulatory sequences of cancer and/or normal cells; however, over-representation was generally not restricted to disease-relevant tissue specific regions. The calculated regulatory potential, allelic binding affinity scores and ChIP-seq binding evidence were the three criteria used to prioritize candidates. Fitting all three criteria, we highlighted breast cancer susceptibility SNPs and a borderline lung cancer relevant SNP located in cancer-specific enhancers overlapping multiple distinct transcription associated factor ChIP-seq binding sites."

According to the news reporters, the research concluded: "Incorporating high throughput sequencing epigenetic and transcription factor data sets from both cancer and normal cells into cancer genetic studies reveals potential functional SNPs and informs subsequent characterization efforts."

For more information on this research see: On the identification of potential regulatory variants within genome wide association candidate SNP sets. Bmc Medical Genomics, 2014;7():34. (BioMed Central - www.biomedcentral.com/; Bmc Medical Genomics - www.biomedcentral.com/bmcmedgenomics/)

Our news correspondents report that additional information may be obtained by contacting C.Y. Chen, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada. Additional authors for this research include I.S. Chang, C.A. Hsiung and W.W Wasserman (see also Biotechnology).

Keywords for this news article include: Biotechnology, Canada, Genetics, Oncology, Vancouver, British Columbia, Cancer Gene Therapy, Transcription Factors, North and Central America.

Our reports deliver fact-based news of research and discoveries from around the world. Copyright 2014, NewsRx LLC


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Source: Cancer Gene Therapy Week


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