We find considerable evidence for several new MS susceptibility loci including KIF21B (rs12122721, combined P = 6.56 × 10−10, OR = 0.82), TMEM39A (rs1132200, combined P = 3.09 × 10−8, OR = 0.80) and PRM1 (rs243315, combined P = 1.07 × 10−7, OR = 0.83), all of which have demonstrated moderate-to-strong significance in each stage of our analyses and furthermore meet genome-wide significance using a stringent Bonferroni correction.
We have successfully identified novel loci for MS through more detailed examination of results from a large first-generation GWAS. Interestingly, in the original GWAS, the SNPs in KIF21B
, although relatively significant in the more powerful case/control analysis [Cochran–Mantel–Haenszel (CMH) P
-value ranks between 0.3 and 4.2%], failed to rise to the top of the more limited family-based analysis [the most significant SNP (rs12122721) had a transmission disequilibrium test (TDT) P
-value rank of 28.9%] (Tables and ). Furthermore, these SNPs were among the top P
-values (CMH P
-value ranks between 0.4 and 2.1%) in a recent meta-analysis of three GWASs (11
) (Table ). These overall results clearly demonstrate that additional true susceptibility loci are likely to be buried beneath the top association results from GWAS (and even meta-analyses of GWAS), and subsequently overlooked in the rush to follow up the top hits. Testing only the ‘top hits’ is often the result of the limited availability of resources after conducting such a massive initial screening experiment. Our data suggest that it is imperative to perform a more comprehensive follow-up study in the pursuit of identifying all loci contributing to the genetic load for a given complex disease.
MS susceptibility genes outside of the MHC
Furthermore, of the top Stage 1 results (P
≤ 0.001), the average original GWAS P
-value ranking of these SNPs is approximately 40 000 for the CMH test (most significant SNP ranking 177, least significant SNP ranking 319 841) and approximately 69 000 for the TDT test (most significant SNP ranking194, least significant SNP ranking 308 800). Approximately one-third (29/85) of the most significant non-MHC SNPs in Stage 1 (Table ) had original GWAS P
-values <0.10 in both the TDT and CMH tests, with only two of these SNPs further replicating in Stage 2 (rs11583328 and rs10469900) (Table ). We extended this examination by ranking the three SNPs meeting genome-wide significance (i.e. within or nearby KIF21B
1) along with the most significant SNPs from the original GWAS (or in the case of IL2RA
where rs2104286 has been indicated as the primary association (6
)) and from other subsequently identified MS susceptibility loci with varying levels of confidence. In addition, we examined the rank of these SNPs in a recent meta-analysis (Table ). The original P
-values of the three newly identified loci were similar to those P
-values seen in the other confirmed loci. Furthermore, each of these SNPs was mildly to moderately significant in the meta-analysis, but as in the initial GWAS follow-up, these loci fall far enough from the top that they are not initially selected for limited follow-up. It follows that there may be other yet-to-be-confirmed loci within this same range of the data. It is also noteworthy to highlight the robustness of the CMH test compared with the TDT in identifying all of these loci in the original screen. This may in part be related to the gain in power due to the additional samples used in the CMH analysis.
The new MS loci identified in this study are functionally interesting. KIF21B
is a plus end-directed kinesin-like protein (KLP) involved in neuronal (axonal) transport. Its uniqueness stems from its enrichment in dendrites compared with the typical cell body and from its contrast from other plus end-directed KLPs, which have axon enrichment (16
is also expressed in a variety of immune cells. Although KIF21B
has not been functionally associated with neurodegeneration or inflammation, given the nature and role of its protein in neurons, there is a plausible biologic role for this gene in MS. Recently, another kinesin superfamily member (KIF1B
) was reported as associated with MS (17
); however, efforts by the IMSGC have failed to confirm this association (IMSGC, unpublished data). KIF21B
is among the first genes identified via association studies, with the potential for a direct neurodegenerative role in MS pathology.
Very little has been known about TMEM39A (mRNA-transmembrane protein 39A). The associated SNP (rs1132200) within this gene causes a non-synonymous amino acid change (alanine–threonine) at position 487 in the protein. Although this SNP may hold some functional effect relevant to MS, almost nothing is known about this gene and what biologic role it might play with regard to disease susceptibility.
PRM1 (protamine 1) functions as a DNA-binding protein expressed in the nucleus of sperm. The strongest association in this region is with rs243315 and is 5′ of PRM1; however, there are several SNPs across this region of chromosome 16 showing mild-to-moderate levels of significance within the top hits (rs12922090, rs243315, rs1292773) (Table ). This region of chromosome 16 is >100 kb from CLEC16A and there is little-to-no LD between these SNPs and any SNP within CLEC16A. There is, however, a very nearby candidate gene, SOCS1 (suppressor of cytokine signaling 1), which is in strong LD with these SNPs and could possibly contain the true association. Additional work is needed to explore the exact location of this association, and is the focus of ongoing laboratory efforts.
Through this exhaustive follow-up approach, we have identified a number of additional MS susceptibility loci and highlighted even more loci that may yet prove to be involved in MS. Ultimately, fine mapping and functional studies will be required to understand the consequences of the associations detected in this experiment.