Table A1.

Summary of the main clinical and promising omics-based tests for PD diagnostics.

Technique	Summary
Clinical Tests
Pharmacological test using levodopa and/or dopamine agonists for the dopaminergic treatment.	Performed for confirmation of the diagnosis of PD and differentiating PD from the other parkinsonian syndromes [22,23,24].
Imaging techniques:
1. Transcranial sonography (TCS) for investigation of the morphology of substantia nigra (SN) and assessing of substantia nigra hyperechogenicity (SNH) due to its increased iron content.	Used for the diagnosis of PD at any stage and establishing a predisposition to the development of PD in individuals before the onset of motor symptoms of the disease; also can be used for differential diagnosis with essential tremor (ET) and atypical parkinsonism [25,26,27,28,35,36].
2. Positron emission tomography (PET) for measuring the activity of DOPA decarboxylase and thus assessing the metabolism and accumulation of levodopa during the scanning period.	Used for the differential diagnosis of PD, ET, and vascular parkinsonism, but not able to reliably differentiate PD from progressive supranuclear palsy (PSP), multiple system atrophy (MSA), or corticobasal degeneration (CBD) [37,38,39,40,41,42,43,44].
3. Single-photon emission computed tomography (SPECT) for brain imaging of the dopamine transporter (DAT) with specific radioligands.	Used for distinguishing patients with PD from the control group or patients with ET, but it is not possible to reliably differentiate typical and atypical variants of parkinsonism [47,48,49,50].
4. Magnetic resonance imaging (MRI) for visualization of nigrosome-1 and neuromelanin for SN assessment.	Used for differentiating PD patients from healthy subjects, but not able to differentiate from some cases of atypical parkinsonism (MSA, PSP, and CBD) [51,52,53,54,55,56,57,58,59,60,61,62].
Olfactometry for hyposmia assessment.	Despite the good prognostic significance of the marker, the specificity of hyposmia is not high, since it can precede not only PD and dementia with Lewy bodies (DLB) but also Alzheimer’s disease [63,64,65].
Color visual evoked potentials (VEP) for diagnosing and clarifying the nature of visual dysfunction and color perception disorders.	The marker is related to age characteristics, the form of the PD, and the therapy [66,67].
Polysomnography for rapid eye movement (REM) sleep behavior disorder (RBD) assessment.	Performed for diagnostics various variants of synucleinopathy: PD, DLB, MSA, but not so sensitive for the prodromal stage of PD [68,69].
Electromyography (EMG) for the examination of clinically intact limbs in patients using skin electrodes.	EMG changes have been revealed in 71% of cases in the upper extremities and 58% of cases in the lower extremities in patients with early-stage PD and can facilitate early diagnosis of PD [70,71].
Omics-Based Tests
Genomics:
1. Identification of mutations in the alpha-synuclein (SNCA) gene (PARK1).	Duplications, triplications, or point mutation in SNCA cause autosomal dominant forms of PD and are the basis of the risk of developing sporadic PD [73,74,75].
2. Identification of mutations in the E3-ubiquitin ligase (PRKN) gene (PARK2).	The most common cause of autosomal recessive early-onset PD with frequency estimations ranging from 4.6% to 10.5%, depending on the population [73,74,75].
3. Identification of mutations in the phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1) gene (PARK6).	The second most common cause of autosomal recessive early-onset PD with frequency in the range of 1–9%, depending on the population [73,74,75].
4. Identification of mutations in the DJ-1 gene (PARK7).	The third most common cause of autosomal recessive early-onset PD with frequency in the range of 1–2% of cases [73,74,75].
5. Identification of mutations in the LRRK2 gene (PARK8).	The most frequent known cause of late-onset autosomal-dominant and sporadic PD, with a mutation frequency ranging from 2% to 40% in different populations [73,74,75].
6. Identification of mutations in the glucocerebrosidase (GBA) gene.	The heterozygous carrier of mutations in the GBA gene is associated with the development of PD with frequency in the range of 7–12% depending on the population [76].
Transcriptomics:
1. Quantitative PCR assays analysis of previously identified RNA biomarkers—PTPN1, COPZ1, FAXDC2, SLC14A1s, and NAMPT in the blood.	Linear discriminant analysis showed that COPZ1 and PTPN1 distinguished PD from PSP patients with 62.5% accuracy. Five biomarkers, PTPN1, COPZ1, FAXDC2, SLC14A1s, and NAMPT were useful for distinguishing PSP from controls with 69% accuracy [85].
2. Quantitative PCR analysis of expression levels of the CFS- microRNAs: Mir-7-5p, miR-331-5p, miR-145-5p, miR-9-3p, and miR-106b-5p.	Level of the set of mir-7-5p, miR-331-5p, and miR-145-5p discriminated PD from controls with accuracy of 88%; level of the set of miR-9-3p and miR-106b-5p distinguished PD from MSA with accuracy of 73%; and level of miR-106b-5p provided the best discrimination between PD and PSP with accuracy of 85% [88].
3. Analysis of the mRNA levels of ATP13A2, PARK2, PARK7, PINK1, LRRK2, SNCA, ALDH1A1, PDHB, PPARGC1A, and ZNF746 genes in the peripheral blood.	A statistically significant increase in the mRNA levels of ATP13A2, PARK7, and ZNF746 genes was observed in the group of untreated patients with PD but not in the neurological disease control group [89].
Proteomics:
1. Immunoassay analysis of alpha-synuclein and phosphorylated alpha-synuclein (PS-129) in CFS and blood plasma.	A combination of PS-129 and total alpha-synuclein in CFS performed better than PS-129 alone in detection of PD, MSA, and PSP patients versus healthy controls with sensitivities of 61%, 75%, and 67%, respectively. The sensitivities among the three different parkinsonian disease groups were: PD versus MSA patients, 40%; PD versus PSP patients, 72%; and MSA versus PSP patients, 63%. The diagnostic values (specificity) were PD versus controls, 64%; MSA versus controls, 73%; PSP versus controls, 55%; PD versus MSA, 63%; PD versus PSP, 63%; and MSA versus PSP, 67% [92,93].
2. Immunoassay or enzyme-linked immunosorbent assay measuring of total and phosphorylated tau protein, beta-amyloid peptide l-42, and alpha-synuclein in CFS.	Slightly, but significantly lower levels of these proteins were seen in subjects with PD compared with healthy controls [94].
3. Measuring using Luminex assays of alpha-synuclein, DJ-1 protein, total and phosphorylated tau protein, beta-amyloid peptide l-42, Fit3 ligand, and microglial inflammatory mediator fractalkine in CFS.	A combination of DJ-1 plus Flt3 ligand differentiates PD from control with sensitivity 94% and specificity 60%. With CSF Flt3 ligand, MSA patients were differentiated from PD patients with sensitivity 99% and specificity 95%, and high sensitivity (90%) and a reasonable specificity (71%) could also be achieved using a combination of alpha-synuclein and ratio of p-tau and t-tau [96].
4. Analysis of expression of potential biomarker autoantibodies in the blood serum using human protein microarrays, each containing 9486 native antigens.	10 selected autoantibodies with a different expression, including antibodies to intercellular adhesion molecule 4 (ICAM4), pentatricopeptide with repeated domain 2 (PTCD2), myotilin (MYOT), and fibronectin 1 (FN1), effectively differentiated PD from control with a sensitivity of 93.1% and specificity of 100% and also distinguished PD from Alzheimer’s disease with accuracy of 86% [99].
5. Identification of distinct blood protein autoantibody biomarkers of early-stage PD by using the Gene Expression Omnibus database.	Two biomarkers, mitochondrial ribosome recycling factor (MRRF) and ribosomal protein S18 (RPS18), distinguished the early-stage PD samples from the control samples and can be regarded as high-confidence distinct protein autoantibody biomarkers of early-stage PD [100].
Metabolomics:
1. Quantification of plasmatic TAs, and the catecholamines and indolamines pertaining to the same biochemical pathways using an ultra-performance chromatography mass spectrometry (UPLC-MS/MS) method.	Tyramine has been suggested as a promising marker for assessing the disease at an early stage of PD (AUC = 0.90). Tyramine, norepinephrine, and tyrosine showed the possibility that these compounds behave as promising markers for the progression of the disease (AUC > 0.75) [107].
2. Measuring of CSF and plasma levels of catechols including dopamine, norepinephrine, and their main respective neuronal metabolites dihydroxyphenylacetic acid and dihydroxyphenylglycol.	CSF level of dihydroxyphenylacetic acid was 100% sensitive at 89% specificity in separating patients with recent onset of PD from controls but was of no value in differentiating PD from MSA [106].
3. Metabolomic profiling of blood plasma samples using high-performance liquid chromatography coupled with electrochemical coulometric array detection (LCECA).	Obtained blood plasma samples metabolomics profiles made it possible to clearly differentiate patients with PD from healthy donors. In particular, uric acid was significantly reduced while glutathione was significantly increased in PD patients [108].
4. Metabolomic profiling of blood plasma samples by direct injection mass spectrometry.	The metabolome signature of 21 metabolite ions, including lysine, phospholipids, hydroxyisovalerylcarnitine, histamine, putrescine, and asymmetric dimethylarginine, with high PD’s diagnostic significance (accuracy—94%, sensitivity—94%, specificity—95%), was detected [118].