Human whole blood genomic dna extraction kit

The details of the SNP selection were described previously [20 ,21 ]. Briefly, we previously developed a panel that included major genes in cancer-related pathways [21 ], among which there were seven microRNA processing genes. Tagging SNPs (±10 kb flanking each gene) and potential functional SNPs for each gene were included. MiRNA binding site SNPs were identified using the PolymiRTS v3.0 [22 (link)] for the genes included on the chip. Genomic DNA was extracted from the study patients’ peripheral blood using the Human Whole Blood Genomic DNA Extraction Kit (Qiagen, Valencia, CA). Genotyping was performed using Custom Illumina iSelect Infinium II Beadchips following the standard protocol (Illumina, San Diego, CA). Only SNPs with a sample call rate greater than 95% and samples with an SNP call rate greater than 95% were included in the final analysis.

Genotype data for SNPs of MDM4 gene were collected from two independent Chinese populations. We used the public HapMap SNP database (http://www.hapmap.org/) to identify the MDM4 tagging SNPs within 3′-UTR on chromosome 1q32 by using the tagger algorithm with a minor allele frequency (MAF) cutoff of 0.05 and a correlation coefficient (r²) threshold of 0.8. Genomic DNA was extracted from peripheral blood lymphocytes using the Human Whole Blood Genomic DNA Extraction Kit (Qiagen, Valencia, CA). For each SNP, genotyping was performed using the TaqMan Pre-Designed SNP Genotyping Assays (Applied Biosystems, Foster City, CA) following manufacturer's instructions. Approximately 15% of the samples were randomly selected for repeat genotyping by a different investigator, and the results were entirely concordant. SNPs were excluded from further analysis if they had call rates less than 95% or Hardy–Weinberg equilibrium p-values or MAFs less than 0.05.