Trait: Parkinson's disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0002508
Description A progressive degenerative disorder of the central nervous system characterized by loss of dopamine producing neurons in the substantia nigra and the presence of Lewy bodies in the substantia nigra and locus coeruleus. Signs and symptoms include tremor which is most pronounced during rest, muscle rigidity, slowing of the voluntary movements, a tendency to fall back, and a mask-like facial expression. [NCIT: P378]
Trait category
Neurological disorder
Synonyms 31 synonyms
  • IDIOPATHIC PARKINSON DIS
  • IDIOPATHIC PARKINSONS DIS
  • Idiopathic PD
  • Idiopathic Parkinson Disease
  • Idiopathic Parkinson's Disease
  • LEWY BODY PARKINSON DIS
  • Lewy Body Parkinson Disease
  • Lewy Body Parkinson's Disease
  • PARKINSON DIS
  • PARKINSON DIS IDIOPATHIC
  • PARKINSONS DIS
  • PARKINSONS DIS IDIOPATHIC
  • PARKINSONS DIS LEWY BODY
  • Paralysis agitans
  • Parkinson Disease, Idiopathic
  • Parkinson disease
  • Parkinson syndrome
  • Parkinson's
  • Parkinson's Disease, Idiopathic
  • Parkinson's Disease, Lewy Body
  • Parkinson's disease
  • Parkinson's disease (disorder)
  • Parkinson's disease NOS
  • Parkinson's disease NOS (disorder)
  • Parkinson's syndrome
  • Parkinsonian disorder
  • Parkinsonism, Primary
  • Parkinsons
  • Parkinsons disease
  • Primary Parkinsonism
  • paralysis agitans
Mapped term(s) 19 mapped terms
  • COHD:381270
  • DOID:14330
  • ICD10:G20
  • ICD9:332
  • ICD9:332.0
  • KEGG:05012
  • MESH:D010300
  • MONDO:0005180
  • MeSH:D010300
  • NCIT:C26845
  • NCIt:C26845
  • NIFSTD:birnlex_2098
  • OMIM:168600
  • OMIM:616361
  • OMIM:616710
  • OMIMPS:168600
  • SCTID:49049000
  • SNOMEDCT:49049000
  • UMLS:C0030567

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000056
(PD_PRS)
PGP000041 |
Paul KC et al. JAMA Neurol (2018)
Parkinson Disease Parkinson's disease 23
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000056/ScoringFiles/PGS000056.txt.gz
PGS000123
(2017_PD16)
PGP000059 |
Ibanez L et al. BMC Neurol (2017)
Parkinson disease Parkinson's disease 16
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000123/ScoringFiles/PGS000123.txt.gz
PGS000211
(PD19)
PGP000087 |
Pihlstrøm L et al. Mov Disord (2016)
Parkinson's disease Parkinson's disease 19
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000211/ScoringFiles/PGS000211.txt.gz
PGS000750
(PRS_43)
PGP000155 |
Bobbili DR et al. J Med Genet (2020)
Parkinson's disease Parkinson's disease 43
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000750/ScoringFiles/PGS000750.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM000141 PGS000056
(PD_PRS)
PSS000088|
European Ancestry|
285 individuals
PGP000041 |
Paul KC et al. JAMA Neurol (2018)
Reported Trait: Cognitive decline (time to MMSE 4-point decrease) HR: 1.44 [1.0, 2.07] sex, age at diagnosis
PPM000142 PGS000056
(PD_PRS)
PSS000088|
European Ancestry|
285 individuals
PGP000041 |
Paul KC et al. JAMA Neurol (2018)
Reported Trait: Motor decline (time to UPDRS III 20-point increase HR: 1.42 [1.0, 2.01] sex, age at diagnosis
PPM000143 PGS000056
(PD_PRS)
PSS000088|
European Ancestry|
285 individuals
PGP000041 |
Paul KC et al. JAMA Neurol (2018)
Reported Trait: Motor decline (time to H&Y Scale stage ≥ 3) HR: 1.34 [1.0, 1.79] sex, age at diagnosis
PPM000398 PGS000123
(2017_PD16)
PSS000226|
European Ancestry|
786 individuals
PGP000059 |
Ibanez L et al. BMC Neurol (2017)
Reported Trait: Age at Onset (Survival) β: 9.3 [3.59, 15.0] Association (p-value): 0.00141 age at last assessment, sex, 2 PCs of ancestry Cox regression
PPM000396 PGS000123
(2017_PD16)
PSS000225|
European Ancestry|
469 individuals
PGP000059 |
Ibanez L et al. BMC Neurol (2017)
Reported Trait: Age at Onset (Survival) β: 16.62 [9.63, 23.61] Association (p-value): 3.19e-06 age at last assessment, sex, 2 PCs of ancestry Cox regression
PPM000397 PGS000123
(2017_PD16)
PSS000226|
European Ancestry|
786 individuals
PGP000059 |
Ibanez L et al. BMC Neurol (2017)
Reported Trait: Parkinson disease β: 4.85 [2.32, 7.39] Association (p-value): 0.00018 age at last assessment, sex, 2 PCs of ancestry
PPM000395 PGS000123
(2017_PD16)
PSS000225|
European Ancestry|
469 individuals
PGP000059 |
Ibanez L et al. BMC Neurol (2017)
Reported Trait: Parkinson disease β: 5.84 [3.1, 8.59] Association (p-value): 3e-05 age at last assessment, sex, 2 PCs of ancestry
PPM000648 PGS000211
(PD19)
PSS000358|
European Ancestry|
336 individuals
PGP000087 |
Pihlstrøm L et al. Mov Disord (2016)
Reported Trait: Motor decline (time to Hoehn & Yahr ≥ 3) HR: 1.29 [1.06, 1.56] sex, age at diagnosis
PPM001904 PGS000750
(PRS_43)
PSS000952|
Multi-ancestry (including European)|
486 individuals
PGP000155 |
Bobbili DR et al. J Med Genet (2020)
Reported Trait: Parkinson's disease AUROC: 0.703 [0.698, 0.708] Sex, singleton loss of function variant count, Parkinson's disease family history. Mean AUROC over 1000 repetitions on test sets randomly drawn with a 0.9 training-test pslit
PPM001905 PGS000750
(PRS_43)
PSS000952|
Multi-ancestry (including European)|
486 individuals
PGP000155 |
Bobbili DR et al. J Med Genet (2020)
Reported Trait: Parkinson's disease AUROC: 0.653 [0.647, 0.659] Sex, singleton loss of function variant count. Mean AUROC over 1000 repetitions on test sets randomly drawn with a 0.9 training-test pslit
PPM001906 PGS000750
(PRS_43)
PSS000952|
Multi-ancestry (including European)|
486 individuals
PGP000155 |
Bobbili DR et al. J Med Genet (2020)
Reported Trait: Parkinson's disease AUROC: 0.616 [0.611, 0.621] Sex Mean AUROC over 1000 repetitions on test sets randomly drawn with a 0.9 training-test pslit

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000226
[
  • 493 cases
  • , 293 controls
]
,
58.27 % Male samples
European WUSTL Both the PPMI and WUSTL datasets are available by request from the PPMI website (www.ppmi-info.org)
PSS000358 UPDRS motor severity was estimated as a mean value acrosseach patient’s recordings, relative to the rest of the data Mean = 5946.0 days
Sd = 2299.0 days
Range = [1574.0, 13992.0] days
[
  • 336 cases
  • , 0 controls
]
,
66.0 % Male samples
Range = [35.0, 85.0] years European Testing dataset genotyped as part of a larger study of a total of 1380 patients with idiopathic PD and 1295 control subjects by 5 collaborating groups in Norway and Sweden. (https://www.sciencedirect.com/science/article/abs/pii/S0197458012005301?showall%3Dtrue%26via%3Dihub)
PSS000952 Cases are individuals with sporadic Parkinson's disease.
[
  • 340 cases
  • , 146 controls
]
European, NR European, Not reported PPMI
PSS000088 Parkinson Disease symptom progression was assessed during 1 to 3 follow-up examinations by a movement disorder team (June 1, 2007, to August 31, 2013; mean [SD] time from disease onset, 7.3 [2.8] years) using the following methods: - Cognitive decline was determined with the Mini-Mental State Examination (MMSE; range, 0-30, with lower scores indicating worse cognitive function). Cognitive decline was defined as a 4-point decrease from baseline MMSE score and time to event as the time from the baseline to follow-up examinations in which a 4-point decrease was first measured - Motor decline was defined as a 20-point increase in Unified Parkinson’s Disease Rating Scale part III (UPDRS-III) score, and time to event as the time from the baseline to follow-up examinations in which a 20-point increase was first measured. - Motor decline was also measured by assessing conversion to stage 3 or higher of the Hoehn & Yahr (H&Y) scale. Time to conversion to H&Y stage 3 was defined as the time from the baseline to first follow-up examinations in which the patient scored at least stage 3. Mean = 5.3 years
Sd = 2.1 years
[
  • 285 cases
  • , 0 controls
]
,
56.14 % Male samples
Mean = 69.1 years
Sd = 10.4 years
European PEG Patients with idiopathic PD diagnosed less than 3 years previously were recruited from June 1, 2001, through November 31, 2007. Patients were confirmed as having clinically probable or possible Parkinson Disease by a team of movement disorder specialists
PSS000225
[
  • 334 cases
  • , 135 controls
]
,
55.22 % Male samples
European PPMI Both the PPMI and WUSTL datasets are available by request from the PPMI website (www.ppmi-info.org)