CHAPTER 10 222 10 effect of genetic modifiers. Furthermore, a Finnish GWAS demonstrated that hemiplegic migraine patients without a high-penetrant disease-causing mutation carry an excess of common (frequency > 1%) variants compared to patients suffering from common (complex) migraine subtypes.143 In addition, in Chapter 8 it has become clear that CACNA1A plays a role in monogenic as well as in complex forms of migraine. Thus there are multiple lines of evidence provided that show that common genetic variants contributes to the aetiology of hemiplegic migraine. Something that is also seen in developmental and epileptic encephalopathies (DEEs), where the aetiology of the DEEs is now regarded as complex, rather than monogenic.144 This data suggests that the heritability of hemiplegic migraine can also be more complex. It is likely that the combination of both rare and common variants influence disease rick of complex disorders, however, the relative contribution of rare and common variants to disease risk is unknown. The difficulty in identifying these variants involved lies in the analysis method, where the GWA-approach (used in Chapters 6 - 8) is ideal in identifying common variants, next-generation sequencing is best in identifying rare variants. The inheritance of hemiplegic migraine might lie in a combination of both rare and common variants and/or an accumulation of variants in essential genes. It has already become clear that both common and rare variants can contribute to the same disease locus in other diseases.145 Even though some analysis methods have been developed to look at both common and rare variants at once, the all require individual level data.146 In Chapter 9 we have adapted a method for summary level data to look at all missense variants, both rare and common, and there association with hemiplegic migraine. In other words we looked at the accumulation of variants or burden in a predefined number of genes, in order to have enough power. Therefore in Chapter 9 the variant burden was investigated in next-generation sequencing data of mutation-negative hemiplegic migraine patients in genes of the CACNA1x family. From this study it can be concluded that a burden of likely not per se pathogenic missense variants in CACNA1H and CACNA1I is implicated as modifier and hence confers susceptibility to hemiplegic migraine. Burden in this case can be regarded as both the total number of variants as well as the amount of variants each subjects carried. The allele frequencies of the variants included, differed from 0.00003 – 0.59, thus including both common and rare variants. These results substantiate the hypothesis that all forms of migraine including hemiplegic migraine are explained by a spectrum of genetic variants ranging from rare high-risk mutations to common low-risk variants. However, these result still needs to be replicated in an independent cohort preferably based on individual level data. The GWAS-era has left us with “missing heritability”,where we know that the contribution of genetics is larger than thus far found with GWAS. Part of this “missing heritability” might be explained by the contribution of rare variants to common risk loci. Another way of looking at the contribution of both rare and common variants to disease risk is by combining data types. This approach is shown in a recent Danish study in extended migraine pedigrees (consisting of 1,040 individuals from 155 families) where they combined whole-genome sequencing (WGS) data with GWAS data.147 Their aim was to fine-map the migraine risk loci with WGS data. It was found that there is an excess of rare segregating variants in regulatory regions (one CpG island and three polycomb group response
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