Common variation in COL 4 A 1 / COL 4 A 2 is associated with sporadic cerebral small vessel disease

Objectives: We hypothesized that common variants in the collagen genes COL4A1/COL4A2 are associated with sporadic forms of cerebral small vessel disease. Methods: We conducted meta-analyses of existing genotype data among individuals of European ancestry to determine associations of 1,070 common single nucleotide polymorphisms (SNPs) in the COL4A1/COL4A2 genomic region with the following: intracerebral hemorrhage and its subtypes (deep, lobar) (1,545 cases, 1,485 controls); ischemic stroke and its subtypes (cardioembolic, large vessel disease, lacunar) (12,389 cases, 62,004 controls); and white matter hyperintensities (2,733 individuals with ischemic stroke and 9,361 from population-based cohorts with brain MRI data). We calculated a statistical significance threshold that accounted for multiple testing and linkage disequilibrium between SNPs (p , 0.000084). Results: Three intronic SNPs in COL4A2 were significantly associated with deep intracerebral hemorrhage (lead SNP odds ratio [OR] 1.29, 95% confidence interval [CI] 1.14–1.46, p 5 0.00003; r2 . 0.9 between SNPs). Although SNPs associated with deep intracerebral hemorrhage did not reach our significance threshold for association with lacunar ischemic stroke (lead SNP OR 1.10, 95% CI 1.03–1.18, p 5 0.0073), and with white matter hyperintensity volume in symptomatic ischemic stroke patients (lead SNP OR 1.07, 95% CI 1.01–1.13, p 5 0.016), the direction of association was the same. There was no convincing evidence of association with white matter hyperintensities in population-based studies or with non–small vessel disease cerebrovascular phenotypes. Conclusions: Our results indicate an association between common variation in the COL4A2 gene and symptomatic small vessel disease, particularly deep intracerebral hemorrhage. These findings merit replication studies, including in ethnic groups of non-European ancestry. Neurology® 2015;84:918–926 GLOSSARY CE 5 cardioembolic; CHARGE 5 Cohorts for Heart and Aging Research in Genomic Epidemiology; CI 5 confidence interval; eQTL 5 expression quantitative trait locus; GTEx 5 Genotype-Tissue Expression; ICH 5 intracerebral hemorrhage; ISGC 5 International Stroke Genetics Consortium; LD 5 linkage disequilibrium; LVD 5 large vessel disease; OR 5 odds ratio; SNAP 5 SNP Annotation and Proxy Search; SNP 5 single nucleotide polymorphism; SVD 5 small vessel disease; WMH 5 white matter hyperintensity. Small vessel diseases of the brain include a distinct subtype (hereafter referred to in this report as “cerebral SVD”) that affects the small, deep, penetrating arteries and arterioles of the brain, and is thought to be responsible for most symptomatic lacunar ischemic strokes and deep intracerebral hemorrhages (ICHs), as well as for “clinically silent” brain MRI features, such as white matter hyperintensities (WMH). This cerebral SVD also contributes to cognitive impairment and dementia in older people, both through clinically symptomatic strokes and clinically silent ischemia. Despite increasing evidence supporting a distinct vascular pathology for cerebral SVD compared with other subtypes of cerebrovascular disease, our knowledge of the underlying genes and pathophysiologic mechanisms is limited, with a lack of specific treatment strategies. Common polymorphisms studied in genome-wide association studies (GWAS) of ICH, ischemic stroke, andWMH to date appear to contribute little to the risk of cerebral SVD, despite its established heritability. Kristiina Rannikmäe, MD Gail Davies, PhD Pippa A. Thomson, PhD Steve Bevan, BSc, PhD William J. Devan, BSc Guido J. Falcone, MD, ScD, MPH Matthew Traylor, MSc Christopher D. Anderson, MD, MMSc Thomas W.K. Battey, BS Farid Radmanesh, MD, MPH Ranjan Deka, PhD Jessica G. Woo, PhD Lisa J. Martin, MD Jordi Jimenez-Conde, MD, PhD Magdy Selim, MD, PhD Devin L. Brown, MD, MS Scott L. Silliman, MD Chelsea S. Kidwell, MD Joan Montaner, MD, PhD Carl D. Langefeld, PhD Agnieszka Slowik, MD Björn M. Hansen, MD Arne G. Lindgren, MD, PhD James F. Meschia, MD Myriam Fornage, PhD Joshua C. Bis, PhD Stéphanie Debette, MD, PhD Mohammad A. Ikram, MD Will T. Longstreth, MD Reinhold Schmidt, MD Cathy R. Zhang, MA Qiong Yang, PhD Pankaj Sharma, MD, PhD, FRCP Author list continued on next page Authors’ affiliations are listed at the end of the article. Go to Neurology.org for full disclosures. Funding information and disclosures deemed relevant by the authors, if any, are provided at the end of the article. 918 © 2015 American Academy of Neurology a 2015 American Academy of Neurology. Unauthorized reproduction of this article is prohibited. COL4A1 and COL4A2 genes are located in tandem on chromosome 13q34 and have a shared communal bidirectional promoter. They encode the collagen chains a1(IV) and a2(IV), which constitute a major component of the vascular basement membrane. Dominant missense mutations in COL4A1/COL4A2 cause rare familial forms of cerebral SVD, manifesting as deep ICHs, lacunar ischemic strokes, and WMH. Genes causing rare familial forms of cerebral SVD may also contain variants conferring risk for common forms of cerebral SVD. We therefore hypothesized that variants in the COL4A1 and COL4A2 genes may confer risk for common cerebral SVD. METHODS Identification of participating studies. Through an established network of collaborations with relevant groups and consortia (International Stroke Genetics Consortium [ISGC, http://www.strokegenetics.org/], the METASTROKE Collaboration, the WMH in Ischemic Stroke GWAS Collaboration, and the CHARGE [Cohorts for Heart and Aging Research in Genomic Epidemiology] WMH Group [http://web.chargeconsortium.com/]), we identified and included data from the majority of currently available large GWAS of relevant cerebrovascular phenotypes in individuals of European ancestry. The entire dataset consisted of the following: 3 cohorts of 1,545 patients with ICH and 1,485 controls, including information on the main ICH subtypes (deep and lobar); 15 cohorts of 12,389 patients with ischemic stroke, including information on the main determined TOAST (Trial of Org 10172 in Acute Stroke Treatment) subtypes (large vessel disease [LVD], cardioembolic [CE], and small vessel disease/lacunar ischemic stroke) and 62,004 controls; 9 cohorts of 2,733 ischemic stroke patients; and 7 cohorts of 9,361 individuals from population-based studies with brain MRI-based measures of WMH volume (table 1). Table e-1 on the Neurology® Web site at Neurology.org includes detailed descriptions of the design and characteristics of the participating studies. Data collection from participating studies. We collected existing genotype data from participating studies for the COL4A1 and COL4A2 genomic region of approximately 464 kilo base pairs (kbp), which includes .1,000 single nucleotide polymorphisms (SNPs) covering the bidirectional communal promoter, introns, exons, and a 50-kbp upstream and downstream flanking region (Human Genome reference build 19 [hg19] coordinates 110.751.310–111.215.373). For each phenotype (deep ICH, lobar ICH, all ICH, lacunar ischemic stroke, CE ischemic stroke, LVD ischemic stroke, all ischemic stroke, WMH volume in ischemic stroke and in population-based studies), we collected the following cohort-level summary genotypephenotype association data for all directly genotyped and imputed SNPs in the region: SNP reference (rs) number and position; effect allele/noneffect allele and their frequencies; association effect size estimate (b coefficient); standard error of the b coefficient; p value for the association; and, for imputed SNPs, the imputation quality measure used and its value. In addition, we collected data on study design and characteristics from relevant publications, as well as by direct communication with group/consortium leads, individual study principal investigators, and other study team members. Data analysis. Meta-analyses of COL4A1/COL4A2 SNPs for each phenotype. We performed meta-analyses of the genotype summary data, from each contributing cohort, assessing associations of COL4A1 and COL4A2 SNPs with each of the cerebrovascular phenotypes available, both those assumed to represent cerebral SVD specifically (deep ICH, lacunar ischemic stroke, WMH volume in ischemic stroke and in population-based studies) and others (lobar ICH, all ICH, CE ischemic stroke, LVD ischemic stroke, all ischemic stroke). We hypothesized that associations would be specific to, or at least strongest with, cerebral SVD phenotypes. We used a fixed-effects inverse variance–based model in METAL genetic meta-analysis software, which weights the b coefficients by their estimated standard errors. We used a casecontrol approach for ICH, ischemic stroke, and their subtypes, generating for each SNP odds ratios (ORs) per additional minor allele for being a case vs control. We used a quantitative trait approach for WMH analysis, assessing for each SNP the effect per additional minor allele on the natural log-transformed WMH volume. Details of WMH volume measurements are provided in table e-1. Quality-control measures had been applied to all individual studies before provision of data (table e-1). Data from the included studies had been imputed to different reference datasets (HapMap II, HapMap III, or 1000 Genomes) using a range of imputation software (IMPUTE, MACH, and BimBam) and Steven J. Kittner, MD Braxton D. Mitchell, PhD Elizabeth G. Holliday, PhD Christopher R. Levi, MD John Attia, MD Peter M. Rothwell, FMedSci Deborah L. Poole, BSc Giorgio B. Boncoraglio, MD Bruce M. Psaty, MD, PhD Rainer Malik, PhD Natalia Rost, MD Bradford B. Worrall, MD, MSc Martin Dichgans, MD Tom Van Agtmael, PhD Daniel Woo, MD Hugh S. Markus, DM Sudha Seshadri, MD Jonathan Rosand, MD Cathie L.M. Sudlow, MD, PhD On behalf of the METASTROKE Consortium, the CHARGE WMH Group, the ISGC ICH GWAS Study Collaboration, the WMH in Ischemic Stroke GWAS Study Collaboration, and the International Stroke Genetics Consortium Corres