Genetic association studies in cancer: good, bad or no longer ugly?

Biomarkers in cancer epidemiology: an integrative approach

There are different reasons for the increase in the use of biomarkers in cancer epidemiology which is as follows: (i) the fact that the identification of new carcinogens, characterized by complex exposure circumstances and weak effects, has become increasingly difficult with traditional epidemiological approaches; (ii) the increasing understanding of mechanisms of carcinogenesis and (iii) technical developments in molecular biology and genetics. While a distinction is made between biomarkers of exposure, intermediate events, disease, outcome and susceptibility, their integration in a unique conceptual model is needed. The use of exposure biomarkers in cancer epidemiology aims at measuring the biologically relevant exposure more validly and precisely. In some instances, there is an obvious improvement in using an exposure biomarker, as in the case of urinary markers of aflatoxin and tobacco-specific nitrosamines. Intermediate (effect) biomarkers measure early--in general non-persistent--biological events that take place in the continuum between exposure and cancer development. These include cellular or tissue toxicity, chromosomal alterations, changes in DNA, RNA and protein expression and alterations in functions relevant to carcinogenesis (e.g. DNA repair, immunological response, etc.). The analysis of acquired TP53 mutations is an example of the potentially important. Biomarkers should be validated and consideration of sources of bias and confounding in molecular epidemiology studies should be no less stringent than in other types of epidemiological studies. The overarching goal is the integration of different types of biomarkers to derive risk and outcome profiles for healthy individuals as well as patients.

Analysis of Genes Critical for Growth Regulation Identifies Insulin-like Growth Factor 2 Receptor Variations with Possible Functional Significance as Risk Factors for Osteosarcoma

BACKGROUND

Osteosarcoma, the most common malignant primary bone tumor, typically occurs during the adolescent growth spurt. Germ-line genetic variation in genes critical in growth regulation could confer altered risk of osteosarcoma.

METHODS

Fifty-two common single nucleotide polymorphisms (SNP) in 13 genes were genotyped in a prospective case-control study of osteosarcoma (104 osteosarcoma cases and 74 orthopedic controls). Genotype data analyzed with contingency tables suggested the strongest association with insulin-like growth factor 2 receptor (IGF2R) SNPs. Additional SNPs were genotyped to capture IGF2R common haplotypes and resequencing was done across the IGF2R block associated with osteosarcoma risk. Percentage methylation was determined by pyrosequencing of the IGF2R variant allele located in a CpG island.

RESULTS

IGF2R Ex16+88G>A (rs998075) and IVS16+15C>T (rs998074) SNPs were associated with increased risk for osteosarcoma compared with orthopedic controls (haplotype odds ratio, 2.04; 95% confidence interval, 1.29-3.24). Follow-up genotyping showed that IGF2R IVS15+213C>T was also associated with increased osteosarcoma risk. Resequence analysis identified two additional SNPs linked to the risk-associated SNPs; linkage disequilibrium was strongest in a 1-kb pair region around them. The Ex16+88G>A SNP is located within a CpG island and alters methylation at that site.

CONCLUSION

This pilot study of germ-line genetic variation in growth pathway genes and osteosarcoma identified a haplotype block in IGF2R associated with increased risk of osteosarcoma. The presence of a SNP in this block results in loss of methylation at a CpG island, providing corroborative evidence of a possible functional variant. Our analysis of the IGF2R haplotype structure will be applicable to future studies of IGF2R and disease risk.

Germ-line genetic variation of TP53 in osteosarcoma

BACKGROUND

Osteosarcoma (OS) has been well described in individuals with germ-line TP53 mutations (Li-Fraumeni Syndrome) but typically occurs sporadically in adolescents and young adults. Single nucleotide polymorphisms (SNPs), the most common germ-line genetic variation, have been associated with risk for other types of cancer. We hypothesized that genetic variation in TP53 could be associated with OS risk based on its critical role in cell growth and effect of somatic mutations in OS tumors.

PROCEDURE

Twelve common SNPs in TP53 were genotyped in a case-control study of sporadic OS. These SNPs spanned the TP53 locus and captured common haplotypes. Genotype data were analyzed using contingency tables for additive, dominant, and recessive genetic models. PHASEv2.1 and HaploStats were used to evaluate haplotypes.

RESULTS

The recessive model suggested an increased risk of OS when two copies of TP53-34 C>G variant (IVS2+38, rs1642785) were present, P = 0.041, odds ratio (OR) 6.70 (95% confidence interval [CI] 1.06-41.6). The TP53-01 variant C>G (Pro72Arg, rs1042522) may also be associated with increased risk for OS, P = 0.028, OR 7.5 (95% CI 1.20-46.3). Common TP53 haplotypes as well as the remaining 10 SNPs were not associated with risk for OS.

CONCLUSIONS

These data do not indicate a strong link between variation in TP53 and OS risk, although they provide preliminary evidence of an increased risk of OS associated with variants at IVS2+38 and Pro72Arg. The findings warrant replication in further studies.

The future of pediatric cancer and complex diseases: aren't they all?

Over the past decade, the investigation of human genetics and disease has pursued both common and uncommon germ-line variation and shown that both can be associated with altered risk for cancer and its outcomes. This line of investigation has not only begun to generate markers for disease but also insights into the biological pathways that are altered in cancer. Already, there is emerging evidence that germ-line genetic variation can alter susceptibility to different types of cancers, including pediatric cancers. It is evident that common genetic variation has emerged as a key component of a comprehensive understanding of pediatric cancer and its outcome. Future studies should unravel the complex interaction between genes and the environment.