Mendelian proof that low vitamin D (due to 3 genes) increase risk of MS by 20 percent – Nov 2016

Mendelian randomization shows a causal effect of low vitamin D on multiple sclerosis risk

Neurol Genet 2016;2:e97; doi: 10.1212/ NXG.0000000000000097
Brooke Rhead, BS Barcellos: lbarcellos@ berkeley.edu ;Maria Baarnhielm, MD* Milena Gianfrancesco, MPH; Amanda Mok, MPH Xiaorong Shao, MA Hong Quach, BA Ling Shen, PhD Catherine Schaefer, PhD Jenny Link, PhD Alexandra Gyllenberg, PhD; Anna Karin Hedstrom, MD; Tomas Olsson, PhD Jan Hillert, PhD Ingrid Kockum, PhD M. Maria Glymour, ScD Lars Alfredsson, PhD* Lisa F. Barcellos, PhD*

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Objective: We sought to estimate the causal effect of low serum 25(OH)D on multiple sclerosis (MS) susceptibility that is not confounded by environmental or lifestyle factors or subject to reverse causality.

Methods: We conducted mendelian randomization (MR) analyses using an instrumental variable (IV) comprising 3 single nucleotide polymorphisms found to be associated with serum 25(OH)D levels at genome-wide significance. We analyzed the effect of the IV on MS risk and both age at onset and disease severity in 2 separate populations using logistic regression models that controlled for sex, year of birth, smoking, education, genetic ancestry, body mass index at age 18-20 years or in 20s, a weighted genetic risk score for 110 known MS-associated variants, and the presence of one or more HLA-DRB1*15:01 alleles.

Results: Findings from MR analyses using the IV showed increasing levels of 25(OH)D are associated with a decreased risk of MS in both populations. In white, non-Hispanic members of Kaiser Per- manente Northern California (1,056 MS cases and 9,015 controls), the odds ratio (OR) was 0.79 (p = 0.04, 95% confidence interval (CI): 0.64-0.99). In members of a Swedish population from the Epidemiological Investigation of Multiple Sclerosis and Genes and Environment in Multiple Sclerosis MS case-control studies (6,335 cases and 5,762 controls), the OR was 0.86 (p = 0.03, 95% CI: 0.76-0.98). A meta-analysis of the 2 populations gave a combined OR of 0.85 (p = 0.003, 95% CI: 0.76-0.94). No association was observed for age at onset or disease severity.

Conclusions: These results provide strong evidence that low serum 25(OH)D concentration is a cause of MS, independent of established risk factors.

GLOSSARY
CI = confidence interval; EHR = electronic health record; EIMS = Epidemiological Investigation of Multiple Sclerosis; GERA = Genetic Epidemiology Research on Adult Health and Aging; GEMS = Genes and Environment in Multiple Sclerosis; GWAS = genome-wide association study; HWE = Hardy-Weinberg equilibrium; ICD-9 = International Classification of Diseases, 9th Revision; IV = instrumental variable; KPNC = Kaiser Permanente in Northern California; LD = linkage disequilibrium; MAF = minor allele frequency; MDS = multidimensional scaling; MR = mendelian randomization; MS = multiple sclerosis; MSSS = Multiple Sclerosis Severity Scores; SNP = single nucleotide polymorphism; VDRE = vitamin D response element; wGRS = weighted genetic risk score.

Multiple sclerosis (MS) is an immune-mediated, demyelinating disease that leads to a wide variety of symptoms and disability. Both genetic and environmental factors have been implicated in its etiology, including vitamin D deficiency. Observational studies have consistently shown an association of low serum 25(OH)D and increased risk of MS, but it has not been shown that low 25(OH)D is actually a cause of MS.1 The apparent beneficial effects of 25(OH)D on MS might alternately be explained by reverse causation (i.e., MS could be leading to low 25(OH)D) or by confounding by sun exposure, obesity, or some other unknown factors.

Mendelian randomization (MR), equivalently, instrumental variable (IV) analysis using a genetic instrument, is a technique that can overcome the problems of both reverse causation and confounding when assessing the causal relationship between an exposure and an outcome.2 Single nucleotide polymorphisms (SNPs) known to be associated with 25(OH)D levels, rather than measured 25 (OH)D, can be used as an IV to estimate the effect of low 25(OH)D on MS. Because SNP genotypes are determined at birth and are not likely to be influenced by potential confounding variables, the effect estimate from MR analysis should not be confounded, and reverse causation is unlikely because MS does not determine which 25(OH)D-associated SNPs are inherited (figure). We used MR analysis to estimate the causal relationship between serum 25(OH)D levels and MS susceptibility in 2 large case-control studies. We also investigated 2 clinical phenotypes for MS: age at onset and disease severity.

METHODS KPNC participants. Data were collected from members of Kaiser Permanente Medical Care Plan, Northern California Region (KPNC). KPNC is an integrated health service delivery system with a membership of 3.2 million that comprises about 25—30% of the population of a 22-county service area and is the largest health care provider in northern California. Membership is largely representative of the general population in the service area; however, persons in impoverished neighborhoods are underrepresented.3
Eligible KPNC cases were defined as individuals with a diagnosis of MS by a neurologist (ICD-9 code 340.xx), age 18—69 years, and membership in KPNC at initial contact. The study was restricted to self-identified white (non-Hispanic) race/ethnicity, the population with the highest prevalence of MS. The treating neurologist was contacted for approval to contact each case as a potential MS study participant. A total of 3,293 potential MS cases were reviewed by KPNC neurologists, who approved contact with 2,823 (86%) at the time of the data freeze (August 2014). Diagnoses were validated using electronic health record (EHR) review and according to published diagnostic criteria.4 Multiple Sclerosis Severity Scores (MSSS) were calculated for each case at the time of study entry (mean disease duration = 17.7 years), as described,5 and participants were asked to recall the age of first MS symptom onset which was validated using EHR data when possible.
Controls were white (non-Hispanic) current KPNC members without a diagnosis of MS or related condition (optic neuritis, transverse myelitis, or demyelinating disease; ICD-9 codes: 340, 341.0, 341.1, 341.2, 341.20, 341.21, 341.22, 341.8, 341.9, 377.3, 377.30, 377.39, and 328.82) confirmed through EHR data. Potential study participants were contacted by email with a follow-up phone call. The participation rate was 80% for cases and 66% for controls. Genetic data were available for approximately 80% of study participants.

Additional controls were individuals of the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort participating in the KPNC Research Program on Genes, Environment, and Health, which is described elsewhere (dbGaP phs000674.v2. p2) ,6,7 Respondents completed a written consent form and provided a saliva sample for DNA extraction. A total of110,266 participant samples were initially collected. Approximately 103,000 samples were successfully genotyped, and 77% of participants subsequently returned new consent forms for placement in dbGaP (NIH), resulting in a final sample size of 78,486 participants.

The rest is in the PDF