Braak staging diagram tail (Thal 2002 + CERAD), Imperial College Brain Bank (Parkinson’s UK contacts + sample request + section types + tissue collections + materials + Jaewon QA), ~400 genotyped PD cases table opener

Braak staging diagram (continued)

Subgroups (Stage I-VI) showing patterns of amyloid deposition.

In 2002, Thal and colleagues reported that while analysing 51 postmortem brains, a distinct pattern of involvement of brain regions with Aβ aggregates could be observed (29). The regional involvement was divided into 5 phases.

The Consortium to Establish a Registry for Alzheimer’s Disease standardized the neuropathologist assessment of Alzheimer’s disease (CERAD) (Mirra SS et al., 1991; Hyman, J D Mc Karl, S M Nasn).

Imperial College Brain Bank

Parkin	(Antha Japan) Imperial College of Sciences, supplier code STR0378
	www.parkinsonsvirtualbiotech.co.uk; the brain bank - parkinsons-uk-brain-bank

(Sample request)

1. Per Imperial Bank manager Dr George Givenc at d.givenc@imperial.ac.uk; Dr Djordje Gveric, Manager Multiple Sclerosis and Parkinson’s Tissue Bank, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, Tel: 020 7964 7204 (1.5%)
2. Email: d.givenc@imperial.ac.uk; cre.uk-brain-bank
3. I only need a completed request form by then. The rest of the documents (MTA, proof of ethics permission and customer form) can be submitted at the later date.

MTA	content
Ethics permission	1. Do you have an agreement in place with the brain bank? If so, please provide a copy. 2. List of clinical data you are requesting 3. Copy of your application and the approval from UK Brain Bank
Customer form	(we want to fully signed by an authorized representative)

Controls definition

• We don’t have significant confounding pathology which usually means Braak Tau of 2 or less and absence of neurodegenerative pathology or other types
• clinical criteria (eg memory impairment, dementia)

https://www.imperial.ac.uk/medicine/multiple-sciences-and-parkinsons-tissue-bank-research-projects/ +44 (0) 20 7963 3969 mobile: 07976986848

David Dexter (Associate Director-Research, Parkinson’s UK) ddexter@parkinsons.org.uk

Section types

• Standard tissue section - section dimensions 2x2 cm and up to 10µm thickness
• Large tissue section - section dimensions 2x2 cm and 6x4 cm and up to 15µm thickness
• Macro section - section encompassing one or both hemispheres (brain only) and up to 10µm thickness
• Standard tissue block - unfixed, frozen, formalin-fixed or paraffin embedded block, dimensions up to 2x2x1 cm
• Slice - whole brain slice of any dimensions, fresh or formalin-fixed
• FrCharafted tissue sample - tissue samples created using the FAST/AC/sequencer protocol (typically 2 mm in diameter)
• (Frozen and FFPE sections with section thickness over 10µm are available on request)

(cf. (Lobard 2018 #1992) when assessing brain tissue with neurons, some 1µm-thin section a 1 to 100 µm various cellular compartments composed of different proteins are localised in sections measuring 4 or 7 µm. Thus, what is seen in a 7 µm-thick section might be lacking in a 4 µm thick section. ST ranges from 7 to 15 µm when assessing PRm brain tissue.)

Tissue collections and access to data and images

• Snap-frozen brain and spinal cord tissue samples (blocks or sections)
• Formalin-fixed brain and spinal cord tissue samples (blocks or sections)
• Formalin-fixed and paraffin-embedded tissue samples (whole fixed brain and spinal cord, whole hemisphere, whole slices, large, medium and standard biopsies blocks, section on request)
• Snap-frozen and FFPE samples of pituitary and pineal glands
• Snap-frozen and FFPE samples of olfactory bulbs and tracts
• Snap-frozen and FFPE samples of muscle (limited number of cases)
• Snap-frozen and FFPE samples of colon and intestine (limited number of cases)
• Frozen cerebrospinal fluid samples

Materials included in the service charge

• Microtome slides (VWR 631-0108)
• Slide boxes 50- and 100-slide capacity (VWR 612-2708 and 631-1504)
• Small and large sample bags
• Cryotubes and 1.5ml tubes (VWR 479-6447 and Appletons Woolb KC124)
• Bijou bottles and 13ml centrifuge tubes (VWR 215-0123 and 525-0400)
• 60ml Sterilin pots and white specimen buckets (VWR 215-0220 and 216-4329)
• Small and large embedding cassettes with lids (VWR 720-0831 and 720-1671)
• 10% Formalin fixative (Sigma F1554-19)
• Phosphate buffered saline (VWR 41717K)

Shipment/Receipt	PO	customer setup form	ERB
		Postscript / IT charge

separately Jaewon only:

If you are asked to submit additional paperwork such as a proof of funding or ethics permission. If you have not already sent us a fully executed MTA and customer setup form please do so. 20220302 Biospecimen utilization review committee — 1) can you please confirm that the ID on the clinical pathology report is the coded research donor ID? 2) We would also like to know if it’s possible to remove the names of the Professors signing off on the report.

If you are based outside of the UK please include a proof of funding and a proof of ethical approval for your study. (Researchers from other countries must submit a copy of ethical approval or a proof of exemption.) You will also need to send us a fully signed and countersigned request form as that is a precondition for supplying tissue samples and data. Please note that request forms need to be signed by the principal investigator as well as an official representative of your institution, usually someone responsible for signing contracts or material transfer agreements.

We also have a number of Parkinson’s cases with confirmed genetic mutation as well as a small number of cases with other neurological conditions. Please check the MRC Brain Bank Network Database.

~400 genotyped PD cases (e ~60 + ~300)

	Name	Infinium Omni5-4 v1.2 Gene Annotation File	dbSNP	VEP	Hel ix
kgs8885 130	Mapinfo Markers / transcript(s) / e-/n / Mutation(s)	161770811 (1Tx) / NM_017981.NM_018768 / Linker Frags / PARK2,PARK2,PARK2 / EXON / Mast Mast	vs IRSnP / chr6:161770811 / r58026378_PARK2_intron / chr6:161780787 / chr6:161800787 / chr6:161800787 / IDENTOMM_C_4_PARK2_intron / chr6:161780787	(Varview) Functional Consequence: intron_variant Validated: by frequency, by clusterMAF: T=0.0002/1 (1000Genomes), T=0.0005/1 (Korea1K). HGVS:	Intron variant, clinical significance: NA
kgs8240 758	Missense_V352L, Missense_V231L, Missense_V380L