ALS GWAS 2016 meta-analysis

Publications

Genome-wide association analyses identify new risk variants and the genetic architecture of amyotrophic lateral sclerosis.
van Rheenen W, et al.
Nat Genet. 2016 Sep;48(9):1043-8. doi: 10.1038/ng.3622

Phenotypes

  • amyotrophic lateral sclerosis

Subjects

Cases Controls Cohort (Click to view selection criteria for cases and controls) Ancestry
444 438 Population based ALS registry, The Netherlands (NL1) European
305 331 University Hospital Gasthuisberg Leuven, Belgium (BE1) European
582 615 Population based ALS registry, The Netherlands (NL2) European
483 489 Umeå University ALS clinic, Sweden (SW1) European
0 5,951 Rotterdam Study, Erasmus University Medical Centre Rotterdam, The Netherlands (NL3) European
232 663 Hôpitaux de Paris, Hôpital de la Salpêtrière Paris, France (FR1) European
174 165 Institute of Psychiatry, King’s College London, UK (UK1) European
660 726 Massachusetts General Hospital Boston and Emory University Hospital Atlanta, USA (US1) European
217 211 Population based ALS registry, Ireland (IR1) European
103 126 Population based ALS registry, Ireland (IR2) European
647 0 UK Biobank for Motor Neuron Disease Research, UK (UK2) European
0 520 Coriell Institute for Medical Research, USA (US2) European
275 0 Coriell Institute for Medical Research, USA (US3) European
140 0 Population based registry (PARALS), Italy (IT1) European
259 245 Coriell Institute for Medical Research (IT2) European
0 2,500 Wellcome Trust Case Control Consortium UK National Blood Service, UK (UK3) European
0 2,688 Wellcome Trust Case Control Consortium 1958 Birth Cohort, United Kingdom (UK4) European
0 862 Coriell Institute for Medical Research, USA (US4) European
0 1985 The NeuroGenetics Research Consortium (NGRC), USA (US5) European
0 195 Population-based cohort, Finland (FIN1) European
393 185 Helsinki University Central Hospital, Finland (FIN2) European
0 97 Population-based cohort, Finland (FIN3) European
1,792 1,107 Italian Consortium for the Genetics of ALS (SLAGEN), Italy (IT3) European
0 1,030 3C study, Population-based French controls, France (FR2) European
0 655 PopGen, Population-based German controls, Germany (GER1) European
1,207 2,137 Population based ALS registry, The Netherlands (NL4) European
558 273 Hannover Medical School and University of Wuerzburg, Germany (GER2) European
309 96 Population based ALS registries (SLALOM and SLAP), Italy (IT4) European
39 45 University of Lisbon, Portugal (PU1) European
103 63 University of Madrid, University of Barcelona, Spain (SP1) European
219 231 Kantonsspital St. Gallen, Switzerland (SWISS1) European
215 245 University Hospital Gasthuisberg Leuven, Belgium (BE2) European
143 0 ALS clinics, Finland (via Umeå University, Sweden) (FIN4) European
268 470 Population based ALS registry, Ireland (IR3) European
279 269 ALS clinics, via Umeå University, Sweden (SW2) European
63 42 University of California Los Angeles, United States of America (US6) European
1,486 0 University of Ulm, Germany (GER3) European
360 0 Paris and Tours, France (FR3) European
550 0 Massachusetts General Hospital, Boston, Emory University, Atlanta and the Penn ALS Center, University of Pennsylvania, USA (US7) European
1,194 13 UK Biobank for Motor Neuron Disease Research, UK (UK5) European
679 615 Population based ALS registry, The Netherlands (NL5) European

Experiment summary

7,763 new ALS cases and 4,669 controls were genotyped and data were combined with those from previously published ALS GWAS studies. Cohorts were combined on the basis of genotyping platform and nationality to form 27 case–control strata. A custom reference panel for imputation was constructed based on high-coverage whole-genome sequencing data from 1,246 patients with ALS and 615 controls from the Netherlands. A merged reference panel consisting of the custom panel and the 100 Genomes reference panel was used for imputation. Association results were combined in an inverse-variance- weighted, fixed-effect meta-analysis using METAL to generate the ALS GWAS 2016 meta-analysis dataset. All strata were jointly analyzed in a linear mixed model to create the ALS GWAS 2016 LMM dataset.

Dataset ID
GWAS_ALS2016meta_eu