Chromosome 6p22 locus associated with clinically aggressive neuroblastoma

Abstract

Background: Neuroblastoma is a malignant condition of the developing sympathetic nervous system that most commonly affects young children and is often lethal. Its cause is not known.

Methods: We performed a genomewide association study by first genotyping blood DNA samples from 1032 patients with neuroblastoma and 2043 control subjects of European descent using the Illumina HumanHap550 BeadChip. Samples from three independent groups of patients with neuroblastoma (a total of 720 patients) and 2128 control subjects were then genotyped to replicate significant associations.

Results: We observed a significant association between neuroblastoma and the common minor alleles of three consecutive single-nucleotide polymorphisms (SNPs) at chromosome band 6p22 and containing the predicted genes FLJ22536 and FLJ44180 (P=1.71x10(-9) to 7.01x10(-10); allelic odds ratio, 1.39 to 1.40). Homozygosity for the at-risk G allele of the most significantly associated SNP, rs6939340, resulted in an increased likelihood of the development of neuroblastoma (odds ratio, 1.97; 95% confidence interval, 1.58 to 2.45). Subsequent genotyping of the three 6p22 SNPs in three independent case series confirmed our observation of an association (P=9.33x10(-15) at rs6939340 for joint analysis). Patients with neuroblastoma who were homozygous for the risk alleles at 6p22 were more likely to have metastatic (stage 4) disease (P=0.02), amplification of the MYCN oncogene in the tumor cells (P=0.006), and disease relapse (P=0.01).

Conclusions: A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.

Figure 1. Summary of the neuroblastoma GWAS results in the discovery set

The y-axis represents the level of significance for each SNP (log transformed P-values) at the relative genomic position on each chromosome along the x-axis from short arm terminus (left) to long arm terminus (right). The red line indicates the genome-wide significance threshold.

Figure 2. Pairwise linkage disequilibrium diagram of the 6p22 locus and association results for regional SNPs

A 290.98 Kb region from rs12207699 to rs9393266 is shown, with pairwise LD calculated from the discovery case and control data set combined (LD measured as D’ as indicated by scale). Individual SNP log transformed P-values are plotted in relation to the LD diagram, both created using Haploview. The three SNPs showing a genome-wide significant association signal (red horizontal line) are annotated (r²was 0.873 for SNPs rs4712653 and rs9295536; and 0.731 for SNPs rs9295536 and rs6939340) and map within a 94.2 Kb LD block, delimited by SNPs rs196051 and rs10498705 (dashed vertical lines). All SNPs are also annotated to their relative physical map positions (NCBI Build 36), with predicted genes in the region shown (exons/transcribed sequences indicated by dashed vertical lines).

Figure 3. Chromosome 6p22 risk alleles are associated with a more malignant neuroblastoma phenotype

Genotype frequency distributions (homozygous G, heterozygous AG, or homozygous A) of patients classified according to three clinical variables and controls are shown for SNP rs6939340, along with p-values of allelic tests between the clinical subgroups, and between each of them and the controls. Similar results are obtained for SNPs rs4712653 and rs9295536. Specifically, patients assigned to a high-risk group, with tumors that harbor MYCN amplification, and with Stage 4 disease were more likely to be homozygous for the risk allele C at rs4712653, A at rs9295536 and G at rs6939340 (see text and Supplementary Tables S4 and S5).