Computational protocol: Potential contribution of SIM2 and ETS2 functional polymorphisms in Down syndrome associated malignancies

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Protocol publication

[…] We used different web based tools namely SIFT (http://sift.jcvi.org), PolyPhen (http://coot.embl.de/PolyPhen/), SNPs3D (http://www.snps3d.org/), Pupasuite 2 (http://pupasuite.bioinfo.cipf.es), GlobPlot, FastSNP (http://fastsnp.ibms.sinica.edu.tw), [email protected] (http://variome.kobic.re.kr/SNPatPromoter), and dbSMR (http://miracle.igib.res.in/dbSMR) to identify fSNPs in the genomic regions of SIM2 and ETS2 as reported earlier []. fSNPs selected for genotyping in the present study are listed in Table . [...] Difference in allelic and genotypic frequency of the studied fSNPs in different study groups as compared to control was calculated by simple r x c contingency table (http://www.physics.csbsju.edu/stats/contingency_NROW_NCOLUMN_form.html). Minor allele frequency (MAF) of eleven fSNPs of Indian control individuals was also compared with four major populations studied in the HapMap project [Caucasians from Utah with ancestry from western and northern Europe (CEU), Han Chinese from Beijing, China (HCB) and Japanese from Tokyo, Japan (JPT) and Yoruba from Ibadan, Nigeria (YRI)]. Allelic odds ratios were calculated by Odds ratio calculator (http://www.hutchon.net/ConfidORnulhypo.htm). All P values obtained by allelic and genotypic association test were corrected for multiple testing by PLINK [] and R program http://www.r-project.org/. Linkage Disequilibrium (LD) between the SNPs was measured by Haploview 4.1 using default settings. Haplotype frequency of fSNPs was inspected by Unphased program (Version 2.404) []. Interaction among the genotypes of SIM2 and ETS2 was analyzed by multifactor dimensionality reduction (MDR) software (version 2.0 beta 8.1) [] and values were expressed as information gain (IG). Power of all chi square tests was calculated by Piface program []. Genotype data of four fSNPs (rs461155, rs1051425 in ETS2 and rs2073601, rs2073416 in SIM2) were also included for LD, haplotype and SNP-SNP interaction analysis. For convenience, triplicate homozygous genotypes were considered as diploid homozygous genotypes in DS probands while the triplicate heterozygous genotypes were considered as the diploid heterozygous genotype for all the calculations to compare with respective reference diploid groups [,]. […]

Pipeline specifications

Software tools PolyPhen, SNPs3D, PupaSuite, GlobPlot, FastSNP, PLINK, Haploview
Databases [email protected]
Organisms Homo sapiens
Diseases Breast Neoplasms, Disease, Erythroblastosis, Fetal, Neoplasms, Precursor Cell Lymphoblastic Leukemia-Lymphoma