UK Brain Bank Network (NBB), BDR / NeuroChip / Camp dataset access table, NIH NeuroBiBank, NCRAD + EUFortuv MICAgou, PrecisionMed, BIOIVT hemoglobin, fibroblast vendors (NINOS / Cell Applications / Lonza / Lifeline / promogen / Sanjusbo / LEDBO / Cellbio / pmgenel), Biochain catalog, BioSEND, Novus Biologicals NB820-59177
(Note: this page is a dense vendor/cohort contact register that runs across many small rows; the full text is preserved in format_notes and key entries are reproduced below.)
UK Brain Bank Network (NBB)
Established in 2017 collaboration among 4 Japanese academia including Niigata U Tokyo Geriatric Centers — and Niigata U have the other biobanks PD brain bank list 269 specimens; Niigata Medical University.
Contact: 020 7848 0290; Christopher Lee, Consultant Neuropathologist, Neuropathology Resource Centre, 020 7848 0290.
Search with: Parkinson’s disease — 184 cases (27 with genomics that can’t see genomics data, no requests); Dementia search with Multiple Sclerosis and Parkinson’s Tissue Bank (Imperial); 9 Cases.
Genome sequencing data is available from BDR. Contact richard.cox@bristol.ac.uk for the data. The genome sequencing data in UKBBN is providing be condemnating studies. UKBBN does not validate the data, so researchers using this data should contact the original authors of the research studies for further information.
BDR access table
| Publications | N | Case ID | Application process | Access method | |
|---|---|---|---|---|---|
| BDR-BX | (Drinkenburg et al, 2018, Neuropsychology and Applied Neurobiology e.pdf #1646 BiopainAccessJournals) | 281 | Case ID | The BDR genomic data (collected by ‘DNA ID’ or hosted by DPUK). Access to the data has to go through the BDR DAC. You need to fill in an application (https://portal.dementiasplatform.uk/Apply). Once approved an Application Submission Plan is required to comply with the BBR DAC’s data DUC. The request will be reviewed by BDR and access will be granted by Chris Orton at DPUK | DPUK uses a ‘virtual desktop’ infrastructure. You log in remotely to their servers and can’t take data out |
| BDR-NCN-MND | (Dr Massibakannet 2017 #2127 neuroscience 2 #2127) The NeuroChip HOMS content includes 1.337 variants (1.4M of which can be common to PD-related neurodegenerative diseases) | 197 | Case ID | As above | As above |
| CAH | (Bourgh 2017 #2628) Camp paper #2 1.4M GLNS rs8048-NA1 | 1846 | EGA | Contact Rich Cox (richard.cox@bristol.ac.uk) for an EGA account. Researchers with access to UKBBN have already been approved for access although accounts are only created on request | EGA hosts this data under accession Number EGA50000010195. You’ll need to download a Python client and use it from the command line to download the individual VCF files. |
The Cambridge (University of California) data is stored on individual VCF files one per case, totalling 155GB. The BDR and UKBBN are held in 2 big VCF files (or via a PLINK file if you prefer).
NIH NeuroBiBank
NIH NeuroBiBank Brain Bank Network for Neurological Disorders, an open Source largely from neurodevelopmental and psychiatric disorders and neurodegenerative disease other than Alzheimer’s disease https://neurobiobank.nih.gov
Contact links together six repositories through a common Webportal: These comprise the Harvard Brain Tissue Resource Center at McLean Hospital, Belmont, Massachusetts; the Human Brain and Spinal Fluid Resource Center at the University of California, Los Angeles; the National Disease Research Interchange at Philadelphia; the Brain and Tissue Repository in New York City; the University of Maryland Brain and Tissue Bank, Baltimore; and the Brain Tissue Donation Program at the University of Pittsburgh.
| content | |
|---|---|
| Database | https://neurobiobank.nih.gov/search/ |
| Inquire / orders | Contact: 1-2778 prototype data 4-2K9 |
| Internal request | https://neurobiobank.nih.gov/learn/research/projects |
| Federalwide Assurance (FWA) | 1271-(R-IL Takeda’s RWA # in FWA00031723 |
| https://incad.iu.edu/internal_login/index.html | |
| nlz5tudy@iu.edu | |
| Phone | 800-526-2839 |
NCRAD (National Centralized Repository for Alzheimer’s Disease and Related Dementias)
Disease Number Type / Brain bank for Europe; Established in 2001 18 brain banks in 11 European countries. Website has been discontinued (Netherlands brain bank). Netherlands genetic testing available Center for Aging Brain Brain.
EUFortuv MICAgou
| content | |
|---|---|
| URL | https://www.umnpfortuv-mickagou.org/ |
| Movement Disorder Society Genetic mutation database MDC.gen / Individual clinical information for genetic information / IO is only reported for a fraction of cases (n ~ 1, 9%) | |
| Anatomic Pathology | Genetic Epidemiology of Parkinson’s Disease consortium - https://gicep5.gov.gr |
PrecisionMed
| content | |
|---|---|
| Tek (818) 847-4517; tnf@protocomprod.com | |
| Established Princess Inca Development Associates, 137 N Avzaza Ave, Solano Beach, CA 92075, Phone 858-847-9117, ed: 110 dwerely PO Sd 1009 (the number of Patient with CSF either visit 1 or 5 ≤ 0.05 the number patient with longitudinal CSF samples 4) and control: 5d 1009 4500 |
The first step for purchase is to highlight the samples we want in the spreadsheet (from the slack visit we want) and submit to them just like we do with NBB. And then they need a quote and then we generate purchase order. Then they ship the samples (any day to all but only Mon-Fri in Japan). So I think it would compare the samples to follow this process. We will use the new ATPS budget. (To Tabe-finance system, what defines FY13 budget is product reception by 5 m Mar 31 2022. I am not sure the new ATPS Finance system).
I will try to purchase POI of (and HC) this way within this month. Do you think this is worthwhile with AD or you want to do it together with me?
| Note below is the exact prices: HC PD ND HC PD | CSF | Plasma |
|---|---|---|
| a/c | 540 | 540 |
| 5500 / 5550 / 5500 | 5790 / 5780 / 5790 | |
| 5500 / 5750 / 5790 | 5500 / 5750 / 5790 | |
| 5500 / 5750 / 5790 | 5500 / 5750 / 5790 | |
| Total cost |
BIOIVT
| content | |
|---|---|
| CSF / hemoglobin level (mg/ml) | mouse 0-10, rat 20-50, human 200-400. Using hemoglobin as a surrogate marker for blood cell protein contamination, you can see that any pooled mouse CSF (and I have really clear-looking CNF from BIOIVT) is highly contaminated compared to human and rat. |
| Dr Bossymples (SAN DIEGO) | fibroblast vendor |
| NINOS | https://www.ninds.nih.gov/Funding/Apply-Funding/Application-Support/NINDS-Bioguide |
| Cell Applications GmbH | https://www.cellapplications.com/human-dermal-fibroblasts-hdf |
| Lonza | https://www.lonza.com/lonza_bv/SP/en/Primary-and-Stem-Cells-iv/0000000000000018491/4/NHDF-Ad |
| Lifeline | Human-Dermal-Fibroblasts-FC-Adult |
| promogen / Sanjusbo / LEDBO | Lifeline.com / CSF panel from (Howard Hwang, promogen) |
| MT Group | medbio.com (CSF panel from PRELN, MT, Sandhanam, postmortem) |
| Biochain | (HC - 10 donors in 1-2 weeks. For 50 donors, we will have to procure more tissues and that will take 2-8 weeks) |
| AC | (We can do only couple of donors immediately. For 10 or 30 donors, we will have to procure) |
| PD https://www.biochan.com/total-protein-parkinson-s-disease-brain-occipital-lobe-p1236002 / Total Protein - Parkinson’s Disease Brain Occipital Lobe CATALOG # P1236002Par PD; OF # B12110 |
BioSEND
Indiana University is the home of Biospecimen Exchange for Neurological Disorders or Diseases (BioSEND); NINDS biomarker repository, collected through studies supported by or conducted in collaboration with…
(Dear Jaewon)
Thank you for contacting Novus Biologicals regarding NB820-59177. We only offer 1 lot at a time but multiple donors can be available with a custom request. You would want to submit a separate custom request by emailing nb-custom@bio-techne.com with what you are requesting so they can see what is feasible and the cost associated. The current donor is from lot CF11134 with the following donor information.