GenoMEL: second Nature Genetics report

In 2005 ServiceXS joined the GenoMEL consortium to study genetic and environmental determinants of melanoma. ServiceXS contributed to this study by performing genotype analyses using the Illumina 317K array (a total of 5986 samples) and the Illumina 610K array (a total of 2635 samples). This week, the Consortium published its second Nature Genetics paper (Barrett et al., Nat Genet. 2011 Oct 9. doi: 10.1038/ng.959). Bart Janssen, Innovation and Quality Manager at ServiceXS, is co-author on this publication

The Nature Genetics publication contains the results of the second phase of the GenoMEL genome-wide association study (GWAS). The data from the GWAS verified some of the risk loci found for melanoma in the past. These relate to genes involved in known melanoma-related processes or traits such as skin pigmentation, eye color, or hair color. Scientifically exciting is the fact that the study also revealed three previously unknown melanoma-associated regions including two genes that have so far not been implicated in melanoma-related processes.

Melanoma-associated sequence variants were found in and around three genes: MX2, a gene previously implicated in narcolepsy, ATM, a gene involved in DNA repair, and CASP8, a gene from a family of protease protein-coding genes that help to control apoptosis and cell proliferation. Another locus near the chromosome 1 proto-oncogene CCND1 seemed to somewhat influence melanoma risk, but was not conclusively associated with the disease in the validation stage of the study.

 

Tabel 1: Summary of results

SNP Chromosome  Position Allele MAF          OR            P-value Gene
rs13016963  2 2018521.73   A 0.37 1.18    5.68 x 10-7       CASP8   
rs1485993 11 69071595 A 0.37 1.19    4.15 x 10-7     CCND1   
rs1801516 11 107680672 A 0.13 0.79    4.80 x 10-7     ATM    
rs45430 21 41667951 G 0.39 0.85    5.60 x 10-7    MX2   

 

 

 

 

Wilbert van Workum, Business Development Director and cofounder of ServiceXS stated that “Thanks to our participation in GenoMEL, ServiceXS had the opportunity to obtain experience with large-scale genotype analyses such as GWAS studies”.  Today, the company is involved in multiple large genotyping studies each year. Five years ago, when ServiceXS joined GenoMEL and obtained its first Illumina platform, things were very different:  Illumina was a rather unknown company and large association studies involving more than half a million SNPs per sample were not yet feasible.  “Our first melanoma Nature Genetics publication in 2009 was a milestone for ServiceXS and the GenoMEL Consortium. This second Nature Genetics paper is the icing on the cake”.