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
  • Parkinson's syndrome
  • Parkinson's disease
  • Parkinsons
  • Primary Parkinsonism
  • Parkinsons disease
  • Parkinson disease
  • Parkinson's disease (disorder)
  • Parkinson's disease NOS
  • Parkinson Disease, Idiopathic
  • PARKINSON DIS
  • Paralysis agitans
  • IDIOPATHIC PARKINSONS DIS
  • PARKINSON DIS IDIOPATHIC
  • Parkinsonism, Primary
  • IDIOPATHIC PARKINSON DIS
  • Parkinson's Disease, Lewy Body
  • Idiopathic PD
  • Lewy Body Parkinson's Disease
  • Idiopathic Parkinson Disease
  • Parkinsonian disorder
  • LEWY BODY PARKINSON DIS
  • Parkinson's
  • Idiopathic Parkinson's Disease
  • Parkinson's disease NOS (disorder)
  • paralysis agitans
  • Lewy Body Parkinson Disease
  • PARKINSONS DIS IDIOPATHIC
  • Parkinson's Disease, Idiopathic
  • PARKINSONS DIS
  • Parkinson syndrome
  • PARKINSONS DIS LEWY BODY
Mapped term(s) 19 mapped terms
  • COHD:381270
  • ICD10:G20
  • MESH:D010300
  • ICD9:332.0
  • MSH:D010300
  • NCIt:C26845
  • OMIM:616361
  • NCIT:C26845
  • SCTID:49049000
  • NIFSTD:birnlex_2098
  • OMIM:616710
  • OMIMPS:168600
  • KEGG:05012
  • SNOMEDCT:49049000
  • ICD9:332
  • DOID:14330
  • OMIM:168600
  • UMLS:C0030567
  • MONDO:0005180

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants 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

PGS 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 ID)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000395 PGS000123 (2017_PD16) PSS000225 PGP000059
Ibanez L et al. (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
PPM000397 PGS000123 (2017_PD16) PSS000226 PGP000059
Ibanez L et al. (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
PPM000396 PGS000123 (2017_PD16) PSS000225 PGP000059
Ibanez L et al. (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
PPM000398 PGS000123 (2017_PD16) PSS000226 PGP000059
Ibanez L et al. (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
PPM000648 PGS000211 (PD19) PSS000358 PGP000087
Pihlstrøm L et al. (2016)
Reported Trait: Motor decline (time to Hoehn & Yahr ≥ 3) HR: 1.29[1.06, 1.56] sex, age at diagnosis
PPM000143 PGS000056 (PD_PRS) PSS000088 PGP000041
Paul KC et al. (2018)
Reported Trait: Motor decline (time to H&Y Scale stage ≥ 3) HR: 1.34[1.0, 1.79] sex, age at diagnosis
PPM000142 PGS000056 (PD_PRS) PSS000088 PGP000041
Paul KC et al. (2018)
Reported Trait: Motor decline (time to UPDRS III 20-point increase HR: 1.42[1.0, 2.01] sex, age at diagnosis
PPM000141 PGS000056 (PD_PRS) PSS000088 PGP000041
Paul KC et al. (2018)
Reported Trait: Cognitive decline (time to MMSE 4-point decrease) HR: 1.44[1.0, 2.07] sex, age at diagnosis

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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)
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
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)
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)