Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson’s disease
Open accessAbstract
We conducted a meta-analysis of Parkinson's disease genome-wide association studies using a common set of 7,893,274 variants across 13,708 cases and 95,282 controls. Twenty-six loci were identified as having genome-wide significant association; these and 6 additional previously reported loci were then tested in an independent set of 5,353 cases and 5,551 controls. Of the 32 tested SNPs, 24 replicated, including 6 newly identified loci. Conditional analyses within loci showed that four loci, including GBA, GAK-DGKQ, SNCA and the HLA region, contain a secondary independent risk variant. In total, we identified and replicated 28 independent risk variants for Parkinson's disease across 24 loci. Although the effect of each individual locus was small, risk profile analysis showed substantial cumulative risk in a comparison of the highest and lowest quintiles of genetic risk (odds ratio (OR) = 3.31, 95% confidence interval (CI) = 2.55-4.30; P = 2 × 10(-16)). We also show six risk loci associated with proximal gene expression or DNA methylation.
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Biallelic loss-of-function mutations in GRN cause juvenile-onset neuronal ceroid lipofuscinosis (NCL).
“Subsequently, rare families with biallelic loss of function mutations in GRN were identified, and affected individuals were found to have a juvenile-onset neuronal ceroid lipofuscinosis (NCL).114–116”
From The lysosome and proteostatic stress at the intersection of pediatric neurological disorders and adult neurodegenerative diseases (2025) · cites this paper as [114]
The Abstract and Expression and Methylation Methods passages describe Parkinson’s disease risk loci and gene-expression analyses, not GRN-related NCL. Searches for biallelic GRN loss of function and juvenile-onset neuronal ceroid lipofuscinosis returned no passage addressing the claim. (LLM, conf=0.75)
Experimental — accuracy not yet measuredOnly <10% of the heritability of PD has been explained by current genetic findings.
“While only <10% of the heritability of PD has been explained by current genetic findings (Darweesh et al., 2016; Nalls et al., 2014; Pihlstrom et al., 2016), and while the clinical utility of genetic testing for PD outside of early onset patient populations is limited (Klein & Westenberger, 2012), genetic risk models have been shown to predict PD status from healthy controls, or correlate with”
From Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson’s disease (2018) · cites this paper as Nalls et al., 2014
Less than 10% of the heritability of PD has been explained by current GWAS findings.
“First, a relatively small proportion (<10%) of the heritability of PD has been explained by current GWAS findings (Darweesh et al., 2016; Nalls et al., 2014; Pihlstrom et al., 2016)”
From Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson’s disease (2018) · cites this paper as Nalls et al., 2014
A PD polygenic risk score was calculated using a weighted allele-counting approach based on known common PD susceptibility loci from the largest and most recent PD GWAS meta-analysis.
“A PD polygenic risk score was calculated using a weighted allele-counting approach (Dudbridge, 2013) based on known, common PD susceptibility loci, derived from the largest and most recent PD genome-wide association study (GWAS) meta-analysis (Nalls et al., 2014).”
From Combined accelerometer and genetic analysis to differentiate essential tremor from Parkinson’s disease (2018) · cites this paper as Nalls et al., 2014
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- Authors
- International Parkinson's Disease Genomics Consortium (IPDGC), Nalls, M. A., Parkinson's Study Group (PSG) Parkinson's Research: The Organized GENetics Initiative (PROGENI), 23andMe, GenePD, NeuroGenetics Research Consortium (NGRC), Hussman Institute of Human Genomics (HIHG), Investigator, T. A. J. D., (CHARGE), C. F. H. A. A. R. I. G. E., North American Brain Expression Consortium (NABEC), United Kingdom Brain Expression Consortium (UKBEC), Greek Parkinson's Disease Consortium, Alzheimer Genetic Analysis Group, Pankratz, N., Lill, C. M., Do, C. B., Hernandez, D. G., Saad, M., DeStefano, A. L., Kara, E., Bras, J., Sharma, M., Schulte, C., Keller, M. F., Arepalli, S., Letson, C., Edsall, C., Stefansson, H., Liu, X., Pliner, H., Lee, J. H., Cheng, R., Ikram, M. A., Ioannidis, J. P. A., Hadjigeorgiou, G. M., Bis, J. C., Martinez, M., Perlmutter, J. S., Goate, A., Marder, K., Fiske, B., Sutherland, M., Xiromerisiou, G., Myers, R. H., Clark, L. N., Stefansson, K., Hardy, J. A., Heutink, P., Chen, H., Wood, N. W., Houlden, H., Payami, H., Brice, A., Scott, W. K., Gasser, T., Bertram, L., Eriksson, N., Foroud, T., & Singleton, A. B.
- Affiliations
- National Institutes of Health (US)
- University of Minnesota (US)
- University Medical Center of the Johannes Gutenberg University Mainz (DE)
- 23andMe (United States) (US)
- National Hospital for Neurology and Neurosurgery (GB)
- Boston University (US)
- National Institute on Aging (US)
- Université Toulouse III - Paul Sabatier (FR)
- Columbia University Irving Medical Center (US)
- University of Thessaly (GR)
- University of Washington (US)
- Washington University in St. Louis (US)
- deCODE Genetics (Iceland) (IS)
- New York State Department of Health (US)
- University of Miami (US)
- Hertie Institute for Clinical Brain Research (DE)
- Centre National de la Recherche Scientifique (FR)
- Max Planck Institute for Molecular Genetics (DE)
- Indiana University Indianapolis (US)
- Corresponding author
- Singleton, Andrew B
- ORCID
- Nalls, Mike A
- Pankratz, Nathan
- Lill, Christina M
- Hernandez, Dena G
- Saad, Mohamad
- DeStefano, Anita L
- Kara, Eleanna
- Sharma, Manu
- Schulte, Claudia
- Keller, Margaux F
- Letson, Christopher
- Edsall, Connor
- Liu, Xinmin
- Pliner, Hannah
- Lee, Joseph H
- Cheng, Rong
- Ikram, M Arfan
- Ioannidis, John P A
- Bis, Joshua C
- Martinez, Maria
- Perlmutter, Joel S
- Goate, Alison
- Marder, Karen
- Fiske, Brian
- Sutherland, Margaret
- Xiromerisiou, Georgia
- Myers, Richard H
- Clark, Lorraine N
- Hardy, John A
- Heutink, Peter
- Chen, Honglei
- Wood, Nicholas W
- Houlden, Henry
- Payami, Haydeh
- Brice, Alexis
- Scott, William K
- Gasser, Thomas
- Bertram, Lars
- Foroud, Tatiana
- Singleton, Andrew B
- Venue
- Nature Genetics
- Published
- 2014-09
- Volume
- 46
- Issue
- 9
- Pages
- 989-993
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4146673
- OpenAlex
- W2141459724
- Cited by
- 1,895
- References
- 40
- Citations by year
- 2026: 67 · 2025: 86 · 2024: 103 · 2023: 142 · 2022: 182 · 2021: 194 · 2020: 187 · 2019: 176 · 2018: 212 · 2017: 194 · 2016: 185 · 2015: 140 · 2014: 25
- FWCI
- 24.85
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Pure Amsterdam UMC (publishedVersion)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion)
- PubMed Central (acceptedVersion)
- Open Research Exeter (University of Exeter) (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- Leiden Repository (Leiden University) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- University of Thessaly Institutional Repository (University of Thessaly) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- DZNE Pub (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Radboud Repository (Radboud University) (submittedVersion)
- IUScholarWorks (Indiana University) (submittedVersion)
- Purdue University Indianapolis (Indiana University) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- Hirsla (Landspítali University Hospital) (submittedVersion)
- Funders
- Wellcome Trust (085475, 083948/Z/07/Z, 090355, 089698, 076113, WT089698/Z/09/Z)
- National Institute for Health and Care Research (ACF-2012-17-017)
- Parkinson's UK (F-1202, G-0907, G0909, J‐0804)
- National Institutes of Health (1r01hl120393-01a1, UL1TR001108, UL1TR000124, 5r44hg006981-03, Z01-AG000949)
- Medical Research Council (MC_G1000735, MR/J004758/1, MC_PC_09003, MR/L501554/1, MR/L010305/1, MR/L016400/1, MC_G0901330)
- National Institute on Aging (Z01AG000932, AG-16495, R01AG031287, AG031287, P30AG024826, AG08122, AG033193, AG025259, AG023629, R01AG041797, R01AG016495, P30AG013846, R01AG025259, R01AG033193, R01AG008122, U24AG056270, U24AG021886)
- National Heart, Lung, and Blood Institute (R01-HL120393)
- National Human Genome Research Institute (R44-HG006981)
- National Cancer Institute (R01CA141668)
- National Institute of Diabetes and Digestive and Kidney Diseases (DK063491, P30DK063491)
- National Institute of Neurological Disorders and Stroke (R01NS037167, R21NS050487, NS036630, R01NS036960, NS050487, K23NS070867, R01 NS 36960, NS17950, U01NS082151, R01NS088538, P50NS038377, R01NS076843, R01NS075321, R01NS060113, P50NS071674, K02NS073836, R01NS017950, NS060113)
- National Center for Research Resources (UL1RR024156, KL2RR024154)
- National Center for Advancing Translational Sciences
- Topics
- Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Nuclear Receptors and Signaling
- Keywords
- Parkinson's disease, genetic susceptibility loci, genome-wide association study, risk alleles, glucocerebrosidase, SNCA, HLA region, conditional analysis, cumulative genetic risk, gene expression, DNA methylation, replication
- MeSH terms
- Genotype, Humans, Parkinson Disease, Risk Factors, Case-Control Studies, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genetic Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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