- Analysis Name and Accession
Note: This analysis was released as part of the study entitled Genome-Wide Association Study of NeuroblastomaName: NBL-GWAS version 2
- Analysis Description
- Genome-wide genotyping data was generated on the Illumina HumanHap550 Beadchip for 1,627 neuroblastoma patients and 3,254 genetically matched disease-free controls. All samples passed our pre-specified quality control measures, and 1,529 neuroblastoma cases have complete clinical phenotype data, as provided by the COG. To correct for potential effects of population structure, genome-wide IBS estimates for all pair-wise comparisons among all case subjects and control subjects were analyzed to identify two matched controls for each case. SNPs were excluded from further analysis if they showed: 1) deviation from Hardy Weinberg equilibrium with P < 0.001; 2) individual SNP genotype yield < 95%; 3) minor allele frequency (MAF) < 5%; or 4) were not present on both version 1 (V1) and version 3 (V3). This resulted in 480,279 SNPs being utilized in the subsequent analyses.
- Analysis Methods
- We performed a genome-wide association study by first genotyping 1,627 neuroblastoma patients and 3,254 controls of European descent using the Illumina HumanHap550 BeadChip. The primary statistical analyses for association were carried out using PLINK. Allelic odds ratios and the corresponding 95% confidence intervals were calculated for the association analyses. Detailed methods can be found in nature09609-s1.pdf (PMID 21124317) document included with this submission.
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