RT Journal Article
T1 Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases
A1 Pineda Sanjuan, Silvia
A1 Gómez Rubio, Paulina
A1 Picornell, Antonio
A1 Bessonov, Kyrylo
A1 Márquez, Mirari
A1 Kogevinas, Manolis
A1 Real, Francisco Xavier
A1 Van Steen, Kristel
A1 Malats, Nuria
AB 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.
SN 0001-5652
YR 2015
FD 2015
LK https://hdl.handle.net/20.500.14352/91946
UL https://hdl.handle.net/20.500.14352/91946
LA eng
NO Pineda, Silvia, et al. «Framework for the Integration of Genomics, Epigenomics and Transcriptomics in Complex Diseases». Human Heredity, vol. 79, n.o 3-4, 2015, pp. 124-36. https://doi.org/10.1159/000381184.
DS Docta Complutense
RD 14 dic 2025