Single nucleotide polymorphisms (SNPs) are responsible for more than 80% of the variations between individuals, and are present throughout most genes and other important sequences in the human body, which makes them ideal for tracking down correlations between genotype and phenotype. As such, SNP analysis has become very important in the development of personalised medicines.

Compared with gene sequencing technology, SNP analysis offers a shortcut to genotyping analysis because SNPs are the most common mutations; if they are linked to a disease then you can predict the disease if you find the SNP. As you are searching for common base pair mutations instead of looking at everything in a sample, it should (in theory at least) make the process cheaper, more efficient and more relevant to linking sample to disease prediction. The process also becomes more cost-effective as more genomes are mapped. At the end of 2008, there were 910 completely sequenced genomes in the GOLD database (Genomes OnLine Database) — a huge increase from 2002 when the number was only in double digits. More genomes are also being mapped on an ongoing basis.

Many different techniques, such as polymerase chain reaction (PCR), have been developed to analyse SNPs, but these are typically made up of the same key components: amplification, allele discrimination/assay reaction mechanism, assay format, allele differentiation method and detection method. In recent years, the market for SNP analysis products has gone through a period of rapid change and growth in terms of product performance, revenue growth and scientific acceptance across numerous applications. In particular, the price and amount of content provided from SNP analysis has improved, with the cost per genotype dropping in the order of ten-fold every 2 years since 2000.

One of the main challenges over the next decade will be to make many of the development-stage products a reality. Will there be an array of products available on the market or only a few shining examples? What is desired is a wide range of test–drug combinations. Although there are tests in development, progress is not fast enough to meet expectations on new test–drug combinations. Some new specific tests will be successful and will be considered a 'personalised medicine', but the expectation that all care will become personalised is unlikely to be met.

There are also question marks over the future growth of the SNP analysis market. During 2009, the market hit a bump in the road. It had been anticipated that genome-wide association studies would result in the discovery of many disease associations for common diseases, but this has not happened. The scientific community had been relying on the assumption that common diseases were caused by common variants, which would be elucidated with SNP chips containing variants at 5% frequency. In reality, however, studies will need to look at rare variances at around 1% frequency or less. These are now being added to the newest chips and are expected to trigger a surge in research projects.

Although there is promise of stability in the long term with strong drivers boosting sales, there are also many shifting variables. Large genome-wide association studies will see growth, along with the need for follow-up studies, but beyond that questions remain.

Another key challenge is the role of SNP analysis versus sequencing technologies. Although SNP analysis can save time and money, sequencing still offers the most complete way of genome mapping. At the moment, SNP genotyping is combined with partial sequencing, but to catch all the results we may reach the point where sequencing replaces SNP analysis. Customers are showing some propensity to pay for more information, despite the greater cost, and we have predicted big growth in DNA sequencers.

Market predictions

The market for SNP analysis products has experienced rapid changes and a burst in growth, and we expect this to continue in the near term. According to our analysis, the global market for SNP analysis technologies is expected to be worth approximately $1.3 billion in 2014, with around 50% of sales coming from the US, and driven principally by whole genome SNP analysis products in the near term. In the longer term, however, lower multiplexing products used in clinical trials will begin to drive more growth. Prices are expected to drop continuously, offsetting the growth from increased adoption, and future analysers will be fitted with chips that have rarer variants and, thus, will offer improved predictability.

However, the market is also facing several complex challenges, such as regulatory requirements. Although regulatory agencies, such as the FDA, have been somewhat involved in personalised medicine, cases will vary from patient to patient and will be difficult to predict. Additionally, issues involving intellectual property and ethics will need to be addressed before personalised medicine can become a true reality.

Bruce Carlson is Publisher at Kalorama Information, publisher of the report SNP Geneotyping and Analysis Markets.