modalities. Genetic factors affecting multiple modalities of pain perception, in contrast, may represent common mechanisms in primary afferent neurons or central pain pathways. In addition to experimentally induced pain, several studies have investigated the contribution of genetic variability to differences in severity of and susceptibility to chronic pain conditions. For example, a recent study, using 15,950 pairs of twins, found a genetic contribution of about 50% to the likelihood of developing fibromyalgia, a relatively prevalent chronic pain condition [44]. The importance of genetic contributions to chronic pain has also been illustrated using rodent models of inflammatory and neuropathic pain [45,46]. Mechanisms of Genetic Control of Pain Sensitivity While these studies have been useful in defining the importance of genetic variation in differences in pain perception, they do not provide mechanistic explanations of these differences. Analysis of clinically presenting, congenital disorders of pain sensation can define genes central to the ability to detect noxious stimuli, but rely on the resulting phenotype being relatively conspicuous. Quantita- tive trait locus (QTL) mapping (discussed in [47]), which identifies regions of the genome associated with variation in a particular trait, is one way in which genetic factors responsible for smaller variations in pain sensitivity can be detected. This technique has been used extensively by Mogil and others to define areas of the murine genome contributing to pain sensitivity (e.g., [48,49]). Using fine mapping, areas of ,1–5 centiMorgans can be defined [47]. In addition, a number of papers analysing QTL contributions to analgesia have been published [50]. Following identification of loci associated with variability in pain sensitivity, the analysis of single nucleotide polymorphisms (SNPs) can be used to determine more precisely the genetic location underlying this variability. SNPs are traditionally defined as having an allele frequency of .1% or .0.5% in the population, although this is no longer a strict requirement. They may occur within any part of the genome: coding and noncoding sections of genes, and in intergenic regulatory or undefined regions. Coding region SNPs which do not alter the resulting amino acid are termed synonymous. Although synonymous SNPs do not alter the sequence of protein produced, they may still result in major changes in function. For example, they may affect levels of transcription, splicing, mRNA stability, or regulatory RNA expression. One mechanism by which this may occur is through effects of synonymous SNPs on cotranslational folding [51]. Sodium channels are known to be regulated by splicing and microRNAs with important functional consequences for pain thresholds. Nonsynonymous SNPs result in an altered amino acid sequence, with functional consequences that can be more directly assessed. Since genetic loci are not randomly segregated during meiosis, sets of SNPs have a tendency to be inherited together. Particular combinations of linked SNPs are described as haplotypes (from haploid genotype). This means that an identified SNP may function as a marker of another linked genetic region affecting pain processes, rather than as a mechanistic factor. Additionally, several linked SNPs may affect pain perception, meaning that haplotype analysis may be more useful than that of single SNPs for the prediction of pain sensitivity. Pain-Related SNPs The study of pain-related SNPs in the human has proved problematic, due to the tendency of different data sets to yield conflicting conclusions; in many cases, a finding from one has been contradicted by those from others. Here, we present a selection of the positive associations that have been reported, with the caveat that a number of these findings have not been replicated in other investigations. SNPs in several genes have been found to have substantial impacts on pain sensitivity. These are summarised in Table 1. Perhaps the most studied of SNPs are those in the gene COMT, which are discussed in Box 2. Polymorphisms in the m-opioid receptor gene OPRM1 (A80G, A118G), which mediates the physiological anti-pain effects of endorphins, have been linked to variations in experimental pain sensitivity [52,53]. Interestingly, the A118G SNP in OPRM1 (frequency ,10%) affected both subjective pain reporting [52] and objective pain-related cortical activity [53]. Opioid analgesic requirements (representing either pain intensity or opioid efficacy) in chronic [54] pain are also affected by this polymorphism, which appears to act by down- regulating receptor mRNA [55]. The melanocortin-1-receptor gene MC1R contains polymor- phisms associated with both pain sensitivity and m-opioid analgesia in humans and mice [39], which also result in red hair and altered k-opioid analgesia in females. The mechanisms behind these effects are unclear, but may involve altered m-opioid action. In a study going from initial pathway identification to human pain variation, Tegeder et al. [35] recently described the involvement of tetrahydrobiopterin (BH4, a cofactor in nitric oxide, serotonin, and catecholamine production) and its synthesising enzyme GTP cyclohydrolase (GCH-1) in pain sensitivity. Excess BH4 is thought to increase pain due to increased nitric oxide synthesis. A pain- protective haplotype (probably consisting of five SNPs in a regulatory region of the gene) of GTP cyclohydrolase was identified in about 15% of the population studied, shown to decrease both persistent post-surgical and acute mechanical experimental pain. Subjects heterozygous or homozygous for the pain-protective haplotype were found to show reduced upregulation of the GCH1 transcript in response to cAMP, resulting in lower levels of BH4, suggesting that altered GCH1 transcriptional modulation underlies the decreased pain sensitivity observed in these individuals. Genetic variations in the TRPA1 gene encoding a channel activated by cold, mustard oil, and possibly mechanical stimula- tion in nociceptors [56,57], contribute to variations in cold pain sensitivity [58]. This effect was reported to be gender-dependent, in agreement with the effect of TRPA1 deletion on cold pain in the mouse [20]. SNPs in fatty acid amide hydrolase (FAAH), which inactivates the endocannabinoid anandamide, may also contribute to variation in pain sensitivity [58]. Genetic Polymorphisms Affecting Analgesia A range of genetic variations have been identified that alter the effectiveness of analgesic drugs. In particular, polymorphisms of the cytochrome P450 enzymes (CYP), which play a key role in the metabolism of many drugs, can affect the efficacy of opiates, and NSAIDs. Reduced activity of cytochromes can either reduce or enhance analgesic efficacy, depending on the activity of the metabolites compared to the original drug. For example, one metabolite of the opioid tramadol, O-desmethyltramadol, is a considerably more potent agonist of the m-opioid receptor than tramadol, meaning that low metabolisers of tramadol display reduced analgesia, despite an increased half-life of tramadol being observed [59]. Altered tramadol metabolism has been linked to polymorphisms in the gene coding for cytochrome P450 2D6 (CYP2D6), which also associate with reduced effectiveness of this analgesic [59,60]. Polymorphisms in other cytochrome P450 isoforms also appear to contribute to variations in analgesic efficacy, generally in a drug-specific manner. Additionally, PLoS Genetics | www.plosgenetics.org 7 July 2008 | Volume 4 | Issue 7 | e1000086