PPMI Subjects/Available Data/Biospecimens, Shahn Rahmadhan + Por 20240228 Samantha notes, BioFiND, LRRK2 Cohort Consortium (LCC) Cross-sectional + Longitudinal + 23&Me Studies, S4 Systemic Syn Sampling Study (Chahine 2020 #1605), Cf SC12 antibody note, Nilo-PD opener
PPMI
| content | |
|---|---|
| Study Subjects (PPMI 1.0) | 425 individuals with idiopathic PD; 196 healthy controls; 64 SWEDD; 65 prodromal; 217 individuals with PD and 419 unaffected mutation carriers in the Genetic Cohort; 201 individuals with PD and 295 unaffected mutation carriers in the Genetic Registry |
| Available Data | Clinical data including motor, non-motor, neuropsychological, autonomic, olfaction, sleep; imaging (fMRI, DaTSCAN, SPECT, DTI, AV-133); biological (spinal fluid α-syn, amyloid β, tau, phosphorylated tau levels); and genetic (CNP genotyping, whole exome sequencing, whole genome sequencing) data; All data are de-identified to protect patient privacy. The study protocol, case report forms and operations manuals are available through the PPMI study website. |
| Available Biospecimens | DNA, RNA, CSF, plasma, serum, stem cells, urine, whole blood, and buffy coat |
| 20220318 Shahn Rahmadhan | the lab list 5’-3’ CTA AT4 5’-CT- CSF on the GTNS to apply for accessing PPMI samples; we would need to evaluate readiness of your assay for the cohort, and this includes a full review of the proposal data which contains relatively independent of all the cohorts that include changes longitudinally. Access to PPMI samples is in 2 stages: a short LOI, followed by a full proposal. If the committee thinks your assay is not ready, they will tell you so at the LOI stage and may even provide feedback. |
| Study site / Download | Download our data and Data Cuts |
| Request | Request Biospecimens / Explore Biospecimens Inventory |
| Por 20240228 Samantha | suggest the most robust assay in PPMI pending: i) evaluation of preliminary data ii) comparison of which analytes are on each platform iii) and how they perform in the relevant matrices |
BioFiND
https://www.michaeljfox.org/biofind
an observational clinical study designed to discover and verify biomarkers of Parkinson’s disease. This cross-sectional study, 119 well-defined moderately advanced PD and 96 healthy controls.
Available Biospecimens and Data
| Clinical Data | RBC-WBC | Plasma | Urine | Saliva | DNA | RNA | Cerebrospinal Fluid | |
|---|---|---|---|---|---|---|---|---|
| Parkinson's disease | 126 | 117 | 117 | 21 | 234 | 122 | 116 | 168 |
| Control | 106 | 93 | 95 | 28 | 212 | 27 | 101 | 91 / 83 |
20220322 acoust: [email protected] (yes! Annaheule0942) The inventory and associated clinical information, please visit the Data Repository at LONI here: https://biofind.loni.usc.edu/
(Confidentiality)
- 3.1 Confidential Information
- ARC: information will be used by MJFF staff or third-party reviewers under a duty to maintain and not use or disclose Confidential information except as set forth in this Agreement only for the purpose of reviews and assessments
[publication obligation]
- 4.0 Public Data Sharing Policy: You will cooperate with MJFF to deposit its results created by you during the course of the Project into a third party repository accessible to the public and designated by MJFF and BioFiND to make such results available
- 7.0 Publication
- 7.1 MJFF expects that you shall use all reasonable efforts to publish the research findings of the Project regardless of positive or negative outcomes in a forum that is widely available to scientific researchers within one year from the date
- 8.1 will prepare lay abstracts to be posted on the BioFiND website of analyses that I am performing with BioFiND data
LRRK2 Cohort Consortium (LCC)
The LRRK2 Cohort Consortium (LCC) is comprised of three closed studies: The LRRK2 Cross-sectional Study, the LRRK2 Longitudinal Study, and the 23 And Me Blood Collection Study. The LCC will an international multi-cohort to study individuals with idiopathic, LRRK2-, healthy controls, LRRK2 mutation-positive PD patients, and LRRK2 mutation-positive controls. The LCC was intended to provide a resource for the study of novel PD biomarkers determining the therapeutic relevance of the LRRK2 genetic pathway.
LRRK2 Cross-sectional Study
Clinical data, including demographics, neurological history, medication history, MoCA, ADL, MDS-UPDRS, Hoehn and Yahr Stage, and sleep/REM Sleep Behavior Disorder questionnaires are available from over 1,600 PD patients and 1,200 controls. Of these subjects, 822 of the PD patients and 722 of the controls carry a mutation in the LRRK2 gene. RNA, CSF, plasma, serum, whole blood, and urine are available from a subset of these subjects, are available from these studies.
Available Subject Summary Table
| Diagnosis | Total Subjects | DNA | PLASMA | CSF | RNA | SERUM | URINE | Whole Blood |
|---|---|---|---|---|---|---|---|---|
| LRRK2- PD | ||||||||
| LRRK2+ PD | ||||||||
| LRRK2- Healthy | ||||||||
| LRRK2+ Healthy | ||||||||
LRRK2 Longitudinal Study
Clinical data, including demographics, neurological history, medication history, MoCA, ADL, MDS-UPDRS, Hoehn and Yahr Stage, and sleep/REM Sleep Behavior Disorder questionnaires are available from 76 PD patients and 230 controls of Ashkenazi Jewish descent. Of these subjects, 100 of the PD patients carry a mutation in the LRRK2 gene. RNA, CSF, plasma, serum, whole blood, and urine are available from a subset of these subjects, are available from these studies.
23&Me Blood Collection Study
Limited clinical data, including demographics, family history, MDS-UPDRS, H&Y Stage and UPSIT scores are available from 94 PD patients and 258 controls. Of these subjects, 63 of the PD patients and 227 of the controls carry a mutation in the LRRK2 gene. RNA, plasma, serum, whole blood, and urine are available from these subjects.
S4 — The Systemic Syn Sampling (S4) Study
- is an observational clinical study to better understand the progression of PD by identifying the best biofluids and tissues for measuring the protein alpha-syn outside of the brain as a potential biomarker in people with PD.
- Study Subjects: 19 Early PD, 20 Moderate PD, 21 Advanced PD, 21 Healthy Controls
- (Chahine, 2020 #1605) below (all total)
| Tissue (from same patients) | Change in PD? | Sensitivity | Specificity |
|---|---|---|---|
| CSF a-LBSAA | = | 87% | 63.2% |
| SUBMandibular gland (SCI 2 antibody pt positive slides) | ↑ (36%) | 56.1% | 92.9% |
| Submandibular gland (Sn-22) | ↑ (56% vs 7%) and was related to DAT signal | 74-100% | |
| Skin (SCI 2 antibody pt positive slides) | ↑ (24% vs 0%) | 24.1% | 100% |
| Sigmoid (Sn-22) | 80% | ||
| Skin (2sn 22) | >90% | ||
| Skin (2nd p-aSyn1) | (47%) | ||
| SALIVA | = | ||
| WHOLE BLOOD | = | ||
| PLASMA | = | ||
| SERUM | ↓ (Hir-13 0r AA-S/sym-1 antibody) advanced PD | ||
| COLOn (CT positive slides) | ↑ (14% vs 0%) | 36-100% | |
| Colon (2) |
Cf SC12 antibody: the paper says this is for unmodified aSyn, but not sure if this is for p-aSyn, rather it seems this is for total aSyn. The paper says they used Roche’s method that removes non-pathological aSyn by using proteases.
These findings suggest that in periphery, a-syn distribution is patchy rather than diffuse.
Available Biospecimens: DNA, RNA, CSF, plasma, serum, whole blood, saliva, skin, colon tissue, and submandibular gland tissue.
Nilo-PD
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| Nilo-PD | A Randomized, double-blind, placebo-controlled, Phase IIa parallel group, two-cohort study to define the safety, tolerability, clinical and exploratory |