Research article
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions
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* Corresponding author: Abdel Aouacheria a.aouacheria@ibcp.fr
- † Equal contributors
1 Laboratory of Biometry and Evolutionary Biology, CNRS UMR 5558, Claude Bernard University Lyon 1, 69622 Villeurbanne, France
2 Servicio de Hematología, Hospital Universitario de Salamanca, Centro de Investigación del Cáncer, Universidad de Salamanca-CISC, Spain
3 Department of Computer Science, Ben-Gurion University, 84105 Beer Sheva, Israel
4 Apoptosis and Oncogenesis Laboratory, Institute of Biology and Chemistry of Proteins, IBCP UMR 5086 CNRS-UCBL, IFR 128 Biosciences Lyon-Gerland; 7 passage du vercors, 69367 Lyon Cedex 07, France
BMC Genomics 2007, 8:2 doi:10.1186/1471-2164-8-2
Published: 3 January 2007Additional files
Additional File 1:
Complete list of cancer-associated UTR-SNPs. UTR-SNPs with significantly different allele frequency in normal versus tumoral tissues (exact Fisher's test; p < 0.01). Hits are ranked by decreasing p value (see Method section). Sequences for which no annotation is available are referred to as 'NULL'. Bias intensity is given for information. Candidate positive after the multiple testing corrections are underlined. Information concerning the SNPs present on SPARC appears in bold. References appear for validated SNPs from dbSNP (last column). Ambiguity code: R = G↔A; M = C↔A; K = G↔T; Y = C↔T; S = G↔C; W = A↔T. Nucleotide sequence of the reference RNA is shown within a 10-bp interval around each SNP site. Putative cis acting elements located in the regions containing cancer-associated SNPs were identified with UTRScan (see text for details). RNAMute was used to compute distances between variant and reference alleles. Gene symbols were from HGNC (HUGO Gene Nomenclature Committee). UTR-SNPs lying on transcripts for which non-synonymous SNPs were previously identified [7] are marked in light grey (first column).
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Additional File 2:
Polymerase chain reaction primers for detecting SPARC UTR-SNPs.
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Additional File 3:
Percentages of the different types of simple substitution SNPs.
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Additional File 4:
Distribution of the different types of simple substitution SNPs (graphical representation). (A) Substitutional patterns observed among UTR-SNPs. Transition rates were 67.2 % in the complete dataset of UTR-SNPs, 72.6 % in the total pool of cancer-associated UTR-SNPs, and 66.3 % in the subset of UTR-SNPs which were positive after the resampling procedure. Of the 358 cancer-associated UTR-SNPs, 260 were transition events while 298 were transversion events. When considering the 92 UTR-SNPs positive after the resampling procedure, 61 were transition events and 31 were transversion events. (B) The proportions for each pair of complementary substitutions are graphed next to each other for ease of comparison. Student t-test not significant (p > 0.05).
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