title: Methodology for single nucleotide polymorphism selection in promoter regions for clinical use. An example of its applicability.
abstract: Genetic variability in humans can explain many differences in disease risk factors. Polymorphism-related studies focus mainly on the single nucleotide polymorphisms (SNPs) of coding regions of the genes. SNPs on DNA binding motifs of the promoter region have been less explored. On a recent study of SNPs in patients with non-Hodgkin lymphomas we faced the problem of SNP selection from promoter regions and developed a practical methodology for clinical studies. The process consists in identifying SNPs in the coding and promoter regions of the antigen-processing system using the 'dbSNP' database. With the 'HapMap' program, we select SNPs with frequencies >20% in Caucasian populations. For coding regions, we sought biologically and clinically relevant SNPs described in the literature. For the promoter regions, we determined their chromosomal location on 'QiagenSABioscience' site database. The nucleotide sequence of ancestral and variant alleles is available in the 'dbSNP'. These sequences were used in 'Promoter TESS' to determine binding differences of transcription factors. Each sequence may have affinity to different TFs. Thus, SNP selection on the promoter regions was based in the differences on TF binding pattern between the old and the new allele. The potential clinical relevance of the new TFs was also evaluated before the final selection. With this approach, we found that almost half of the relevant SNP fall within the promoter region. In conclusion, we were able to develop a methodology of oriented selection of promoter regions of human genes, comparing the TF with affinity to the ancestral allele with the TF to a variant allele. We selected those SNPs that change the TF's affinity to a pattern with functional significance.
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate LaboratoryBraga/Guimarães, Portugal; Department of Oncology, Hospital de BragaBraga, Portugal.
authors.forename: Herlander
authors.initials: H
authors.lastname: Marques
authors.affiliation: Nova Medical School, New University of Lisbon Lisbon, Portugal.
authors.forename: José
authors.initials: J
authors.lastname: Freitas
authors.affiliation: Molecular Oncology Group & Virology LB-CI, Portuguese Institute of Oncology, Porto, Portugal; ICBAS, Abel Salazar Institute for the Biomedical Sciences, University of Porto, Porto, Portugal; CEBIMED, Faculty of Health Sciences of Fernando Pessoa University, Porto, Portugal; PCC, Research Department-Portuguese League Against Cancer (NRNorte) Porto, Portugal.
authors.forename: Rui
authors.initials: R
authors.lastname: Medeiros
authors.affiliation: Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate LaboratoryBraga/Guimarães, Portugal; Laboratory of Medical Investigation (LIM) 14, Faculty of Medicine, University of São PauloSão Paulo, Brazil.
authors.forename: Adhemar
authors.initials: A
authors.lastname: Longatto-Filho
keywords: DNA binding motifs; Genetic polymorphism; HapMap; Promoter TESS; SNP; coding region; dbSNP; promoter region