The field of psychiatric genetics is undergoing a profound paradigm shift. For several decades, the prevailing model has held that psychiatric disorders arise in any individual due to the cumulative effects of a large number of common variants [
8-
10]. Each of these, by themselves, would have a very small effect on risk, but when the collective burden of such alleles passes a putative threshold, the system would be pushed into a pathogenic state. Though this model has little empirical support, it provided the theoretical foundation for genome-wide association studies (GWAS) [
11], which aim to detect such variants by comparing allele frequencies for millions of such variants between cases and controls [
12-
15]. For psychiatric disorders, these studies, now carried out on tens of thousands of people, have yielded a number of replicated common variants reaching the threshold for genome-wide significance [
16-
26]. These include eight loci for schizophrenia [
26,
27], two for bipolar disorder [
25] and one for schizophrenia and bipolar disorder together [
25]; three potential loci arising from individual GWAS for autism [
22-
24] have not yet been replicated on the same scale. These findings point to loci that may be involved in disease risk at a population level but do not identify or speak to the likely allelic frequency of causal variants [
28]. Each of the associated variants has a tiny statistical effect on risk at the population level and, collectively, the significant single nucleotide polymorphisms statistically account for only a few percent of the overall heritability of the disorder [
18,
25,
26].
The alternative model is that psychiatric disorders arise due to mutations in any of a very large number of genes [
11,
29-
33]. Under this model, psychiatric diagnostic categories are actually umbrella terms for large numbers of distinct genetic disorders that happen to result in similar spectra of symptoms. This is the sort of genetic heterogeneity that underlies categories such as congenital deafness, epilepsy, mental retardation, retinitis pigmentosa, many cancers and other conditions [
34,
35].
It has, of course, been known for some time that psychiatric illness could arise due to single mutations. Well-known examples include fragile × syndrome [
36], Rett syndrome [
37] and mutations in the
neuroligin genes
NLGN3 and
NLGN4 [
38], all of which are associated with autistic spectrum disorder, and velocardiofacial syndrome (22q11.2 deletion syndrome) [
39] and the Scottish DISC1 translocation [
40], which are associated with schizophrenia and other psychiatric diagnoses. The number of such identified mutations is now steadily and rapidly increasing, thanks to the application of new genomic microarray [
41,
42] and sequencing technologies [
43,
44], to the point where they collectively explain an appreciable fraction of psychiatric diagnoses.
Copy number variants (deletions or duplication of chromosomal segments, often affecting multiple genes) have been most readily identified and make up an important class of causal mutations in schizophrenia [
42,
45-
51], autism [
41,
52-
54], attention deficit-hyperactivity disorder [
55-
58], Tourette syndrome [
59], developmental delay and mental retardation [
60,
61], epilepsy [
62] and cortical malformations [
63]. Whole-exome and whole-genome sequencing approaches are now also identifying large numbers of point mutations individually responsible for psychiatric conditions [
64-
71].
A number of important principles have emerged from these studies. First, there is considerable overlap in the genetic etiology of what had previously been considered distinct disorders. Individual mutations that predispose to one class of psychiatric illness, such as schizophrenia, are also associated with other disorders, such as bipolar disorder, autism, mental retardation, epilepsy, attention deficit hyperactivity disorder and Tourette's syndrome (for example, [
31,
72-
77]), in agreement with recent epidemiological data indicating shared risk [
78-
83]. Traditional diagnostic categories, although still very useful in organizing daily practice in psychiatry, may therefore represent not natural kinds in terms of etiology, but more or less distinct phenotypic endpoints that may arise from common origins.
Second, the mutations so far discovered are characterized by incomplete penetrance and variable expressivity [
31,
77,
84]. As with the DISC1 translocation, such mutations may result in a range of phenotypes and many carriers may be unaffected by any psychiatric condition [
85]. Of course, the penetrance depends on which phenotype is being assessed - it will be lowest for specific diagnoses, higher for psychiatric illness generally and higher still for neurobiological endophenotypes, which may be apparent even in clinically unaffected carriers.
Third, many of the identified genes are involved in neural development [
42,
77,
86]. While certainly not exclusive, this is probably the largest category of susceptibility genes. Genes involved in activity-dependent synaptic plasticity, such as
FMR1, are also highly represented. With increasing numbers of genes being identified all the time, it is becoming possible to assign many of them to specific biochemical pathways or cellular processes, such as synapse formation and plasticity (for example, [
64,
66,
87-
89]).
Fourth, allelic specificity and dosage are extremely important. Different mutations in the same gene may result in very different phenotypic outcomes. As a classic example, Duchenne muscular dystrophy and Becker's muscular dystrophy are caused by different types of mutations in the
dystrophin gene: their clinical severity, manifestation, and age of onset are also different [
90]. Similar effects are seen for genes implicated in neurological and psychiatric disorders [
32,
35], as described later. In addition, some alleles may cause severe neurological disorders when homozygous but manifest as psychiatric illness in heterozygous form [
32,
35,
91].
Fifth, while these findings highlight the importance of rare single mutations, they do not necessarily imply a simple mode of inheritance. Many of the mutations found so far show a dominant effect, but recessive mutations are likely to also contribute a sizeable fraction of cases [
71,
92]. In addition, there is likely to be an important role for modifying mutations in the genetic background that can alter the phenotypic expression of the 'primary' mutation. This is the norm, even for the most classically 'Mendelian' disorders [
35,
77,
93]. One should thus expect a distribution of genetic mechanisms across cases - some will be caused by highly penetrant mutations, others by mutations with more variable outcome, which are modified to some extent by the genetic background, and yet others will involve the inheritance of two or more distinct mutations [
35,
77,
94-
96].
Sixth, the eventual phenotype will also be modified by non-genetic factors, including (i) intrinsic developmental variation, where the phenotypic outcome varies due to inherent noise in the molecular processes mediating neurodevelopment [
97], and (ii) environmental risk factors, which have been implicated by epidemiological studies. For schizophrenia, for example, these include maternal infection, urbanicity, migration and cannabis use [
98]. The impact of such factors in individuals may be highly uneven and dependent on genotype.
Despite these complexities, the major finding is clear: mutations with large effect on risk of psychiatric disorders exist and we now have the means to identify them. If we think of this as a genetic screen for mutations causing a specific phenotype, with demonstrated saturation mutagenesis of the human population [
32], then the most effective approach to follow up these discoveries is clear: find the mutations of largest effect and use these as entry points to elucidate the underlying biology.