Single nucleotide polymorphisms in clinics: Fantasy or reality for cancer?

Abstract

Single nucleotide polymorphisms (SNPs) have been classically used for dissecting various human complex disorders using candidate gene studies. During the last decade, large scale SNP analysis, i.e. genome-wide association studies (GWAS) have provided an agnostic approach to identify possible genetic loci associated with heterogeneous disease such as cancer susceptibility, prognosis of survival or drug response. Further, the advent of new technologies, including microarray-based genotyping as well as high throughput next generation sequencing has opened new avenues for SNPs to be used in clinical practice. It is speculated that the utility of SNPs to understand the mechanisms, biology of variable drug response and ultimately treatment individualization based on the individual’s genome composition will be indispensable in the near future. In the current review, we discuss the advantages and disadvantages of the clinical utility of genetic variants in disease risk-prediction, prognosis, clinical outcome and pharmacogenomics. The lessons and challenges for the utility of SNP-based biomarkers are also discussed, including the need for additional functional validation studies.

• SNP
• GWAS
• pharmacogenomics
• genome
• diagnostics
• cancer

Acknowledgements

The authors would like to thank John Lai for editorial corrections.

Declaration of interest

J. A. Clements is a National Health and Medical Research Council Principal Research Fellow. J. Batra is a National Health and Medical Research Council Career Development Fellow. S. Srinivasan is supported by the Queensland University of Technology Postgraduate Research Award.

Notes

* Referees: Dr Leisel Fitzgerald, Leisel, Cancer Council Victoria, Cancer Epidemiology Centre, Melbourne, Victoria 3004, Australia. Dr Johanna Schleutker, Medical Biochemistry and Genetics, University of Turku, Finland. Dr George Yousef, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada