The possibilities of using biological knowledge for filtering pairs of SNPs in GWAS studies: an exploratory study on public protein-interaction and pathway data.

LEXA, Matej a Stanislav ŠTEFANIČ. The possibilities of using biological knowledge for filtering pairs of SNPs in GWAS studies: an exploratory study on public protein-interaction and pathway data. In Oscar Pastor, Christine Sinoquet, Guy Plantier, Tanja Schultz, Ana L. N. Fred, Hugo Gamboa. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms. Angers, France: SciTePress, 2014, s. 259-264. ISBN 978-989-758-012-3. Dostupné z: https://dx.doi.org/10.5220/0004915002590264.

Základní údaje

• Originální název: The possibilities of using biological knowledge for filtering pairs of SNPs in GWAS studies: an exploratory study on public protein-interaction and pathway data.
• Autoři: LEXA, Matej (703 Slovensko, garant, domácí) a Stanislav ŠTEFANIČ (703 Slovensko, domácí).
• Vydání: Angers, France, Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, od s. 259-264, 6 s. 2014.
• Nakladatel: SciTePress

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Stať ve sborníku
• Obor: 10201 Computer sciences, information science, bioinformatics
• Stát vydavatele: Francie
• Utajení: není předmětem státního či obchodního tajemství
• Forma vydání: tištěná verze "print"
• WWW: URL
• Kód RIV: RIV/00216224:14330/14:00074889
• Organizační jednotka: Fakulta informatiky
• ISBN: 978-989-758-012-3
• Doi: http://dx.doi.org/10.5220/0004915002590264
• Klíčová slova anglicky: GWAS; SNPs; biological knowledge; databases; genotyping; filtering
• Příznaky: Mezinárodní význam, Recenzováno

Anotace

Genome-wide association studies have become a standard way of discovering novel causative alleles by loooking for statisticaly significant associations in patient genotyping data. The present challenge for these methods is to discover associations involving multiple interacting loci, a common phenomenon in diseases often related to epistasis. The main problem is the exponential increase in necessary computational power for every additional interacting locus considered in association tests. Several approaches have been proposed to manage this problem, including limiting analysis to interacting pairs and filtering SNPs according to external biological knowledge. Here we explore the possibilities of using public protein interaction data and pathway maps to filter out only pairs of SNPs that are likely to interact, perhaps because of epistatic mechanisms working at the protein level. After filtering all possible pairs of SNPs by their presence in a common protein-protein interaction or proteins sharing a metabolic or signalling pathway, we calculate the possible reduction in computational requirements under different scenarios. We discuss these exploratory results in the context of the so-called "lost heredity" and the usefulness of similar approach for similar scenarios.

Návaznosti

• 7E13011, projekt VaV: Název: THALAssaemia MOdular Stratification System for personalized therapy of beta-thalassemia (Akronym: THALAMOSS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, THALAssaemia MOdular Stratification System for personalized therapy of beta-thalassemia