Article (Scientific journals)
Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases.
Pineda, Silvia; Gomez-Rubio, Paulina; Picornell, Antonio et al.
2015In Human Heredity, 79 (3-4), p. 124-36
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Keywords :
Adult; Aged; Aged, 80 and over; CpG Islands/genetics; DNA Methylation/genetics; Disease/genetics; Epigenomics; Female; Gene Expression Profiling; Gene Expression Regulation; Gene Frequency/genetics; Genome-Wide Association Study; Genotyping Techniques; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide/genetics; Quantitative Trait Loci/genetics; Statistics as Topic
Abstract :
[en] OBJECTIVES: Different types of '-omics' data are becoming available in the post-genome era; still a single -omics assessment provides limited insights to understand the biological mechanism of complex diseases. Genomics, epigenomics and transcriptomics data provide insight into the molecular dysregulation of neoplastic diseases, among them urothelial bladder cancer (UBC). Here, we propose a detailed analytical framework necessary to achieve an adequate integration of the three sets of -omics data to ultimately identify previously hidden genetic mechanisms in UBC. METHODS: We built a multi-staged framework to study possible pair-wise combinations and integrated the data in three-way relationships. SNP genotypes, CpG methylation levels and gene expression levels were determined for a total of 70 individuals with UBC and with fresh tumour tissue available. RESULTS: We suggest two main hypothesis-based scenarios for gene regulation based on the -omics integration analysis, where DNA methylation affects gene expression and genetic variants co-regulate gene expression and DNA methylation. We identified several three-way trans-association 'hotspots' that are found at the molecular level and that deserve further studies. CONCLUSIONS: The proposed integrative framework allowed us to identify relationships at the whole-genome level providing some new biological insights and highlighting the importance of integrating -omics data.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Pineda, Silvia
Gomez-Rubio, Paulina
Picornell, Antonio
Bessonov, Kyrylo ;  Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Marquez, Mirari
Kogevinas, Manolis
Real, Francisco X.
Van Steen, Kristel  ;  Université de Liège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Malats, Nuria
Language :
English
Title :
Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases.
Publication date :
2015
Journal title :
Human Heredity
ISSN :
0001-5652
eISSN :
1423-0062
Publisher :
Karger, Basel, Switzerland
Volume :
79
Issue :
3-4
Pages :
124-36
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
2015 S. Karger AG, Basel.
Available on ORBi :
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