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Brain Banks, Biobanks, and Postmortem Sample Landscape

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Brain Banks, Biobanks, and Postmortem Sample Landscape

Synthesis layer over the canonical by-photo corpus. This page does not replace data/processed/markdown/by-photo/. Every substantive statement links back to a source note or canonical transcription. Where the source carries Uncertain Spans, that uncertainty is preserved here rather than smoothed out.

Bounded synthesis. This page covers the 12 source pages that map Takeda’s brain-bank / biobank / postmortem sample landscape inside gba-pd-asyn. Ten pages sit on the Page 407 / 423 / 440 capture-time band under the `Pipeline of GD & GBA-PD > Supplement > … > Biobank > MJF > Netherlands Brain Bank > Imperial College Brain Bank > Other Biobanks

Biobanks in Japan > BIOMARKERchain; two are the standaloneBrain Bank nav-root pages (_184200, _184203) on Page 925. The downstream BioOrchestra biomarker catalog (_182708–_183115`) is owned by bioorchestra-biomarker-catalog (Cluster C) and is not included here.

Authoring Rules

  • No domain-knowledge corrections. The page reflects what the sources record, not what the field is “supposed” to say.
  • Uncertain Spans on the source page are preserved as uncertainty; cohort sizes, sample counts, vendor catalog numbers, MTA / cost figures, and Korean inline annotations are not paraphrased.
  • The body of data/processed/markdown/by-photo/ is not modified.
  • No raw photos are staged; no new figure assets added; figure-bearing pages are linked rather than re-embedded (docs/decisions/2026-04-29-body-purity-and-figure-only-embeds.md).
  • Tables on canonical pages (Available-Subjects matrices, BM Tracking KPI matrix, BIOMARKER tracker, biobank vendor catalogs, HORC-MSA / MSAR cohort tables) are not re-quoted verbatim; the canonical link carries the table.
  • Out-of-scope sources (BioOrchestra biomarker catalog, α-synuclein Tier 1 + aSyn program entities, GBA-PD biology, GBA / GCase modalities, supplement anatomy chain, MSA section pages, samples-collaborations operations / logistics pages) are linked, not re-narrated, per § Source Boundary / Delegation.

Source Boundary / Delegation

This topic is bounded against several sibling owners. Sources outside the 12-page set are linked from this section, not re-narrated in the axis sections.

neighbour clusterstemsowner
BioOrchestra biomarker catalog (downstream BIOMARKER chain)20240722_182708–20240722_183115 (74 stems; _183050 excluded as α-synuclein Tier 1)bioorchestra-biomarker-catalog (Cluster C)
α-synuclein Tier 1 and aSyn program entitiesper alpha-synuclein-source-boundaryalpha-synuclein, tak-341, snca-aso-wave, snca-btv-hdo, asyn-propagation-suppressor
GBA / GD / GBA-PD biology block20240722_181813, _182123–_182146, _182153–_182323 (36 pages)gba-pd-biology
GBA / GCase therapeutic-modality cluster20240722_182326–_182419 (16 pages)gba-gcase-modalities
GBA-PD pilot range20240722_181748–20240722_181809 (6 pages)gba-pd, gba-therapeutics, biomarkers, eliglustat, ambroxol, venglustat, pr001
Supplement anatomy chain20240722_182422–_182447section-only (see gba-pd-asyn)
MSA section pages (cohort / Dx / Pathology / Pipeline MSA)per msamsa, msa
samples-collaborations operations / logistics-only pages (P2P, NDU, Neurogenomics Partnership, Pittsburgh University, SECONDMENT, Liquid Nitrogen)per samples-collaborationssection-only (samples-collaborations) — operations / logistics, not part of the brain-bank / postmortem sample landscape
PARKN GT cross-filed page20240722_182103parkn-gt

Per the program-routing map and the gba-pd-biology / gba-gcase-modalities boundary notes, this page is the residual Cluster D synthesis — the brain-bank / biobank / postmortem sample-landscape band that those siblings explicitly delegated. It is not a cross-section topic in the strict sense: all 12 sources sit inside gba-pd-asyn, including the two standalone Brain Bank nav-root pages (_184200, _184203); the section assignment for those two pages was already heuristically set to gba-pd-asyn in the source-catalog and source-note frontmatter. The samples-collaborations section name overlaps semantically with this cluster, but its 9 sources are operations / logistics-only (P2P platform-trial scaffolding, NDU / DDU subteam scaffolding, Liquid Nitrogen logistics, SECONDMENT, Burton-Lab / Pittsburgh visit, Neurogenomics Partnership) rather than direct brain-bank / postmortem sample-landscape pages, and they are deferred here.

alpha-synuclein-source-boundary delegates the entire _182617 → _183115 capture range plus the two standalone Brain Bank pages (_184200, _184203) under its “Brain Bank / BioOrchestra biomarker-catalog cluster” rule (“treat as an external evidence catalog … link the Postmortem / Braak Staging / DLB-vs-PDD-vs-MSA / Cholinergic / NBB / Mesenex aSyn immunotx rows by stem reference, not table re-quote”). Inside that range, five of the twelve stems in this topic (_182617, _182630, _182644, _184200, _184203) are also individually listed in the boundary map’s Tier 2 candidate table with the label “Brain bank / postmortem aSyn-adjacent”. All twelve are owned by this Cluster D topic and remain delegated from alpha-synuclein § Tier 1; the BioOrchestra continuation of the same boundary range (_182708–_183115) is owned by bioorchestra-biomarker-catalog (Cluster C) and is not included here.

No new entity pages are created in this pass; biobank, brain-bank, vendor, and cohort entries listed on these 12 source pages remain catalog rows on the canonical by-photo files. The Brain Bank nav-root standalone pages already have a generated index at brain-bank (2 sources); this synthesis adds the 10 chain pages from Pipeline of GD & GBA-PD > Supplement to that picture without modifying the by-nav index.

Source Coverage

The 12 sources split across two nav_path first-entry roots inside gba-pd-asyn:

nav root (first nav_path entry)sourcescovered axis
Pipeline of GD & GBA-PD10Biobank / brain-bank landscape (7) · BIOMARKER tracker bridge — Biobanks in Japan tail and BM-Tracking KPI matrix on Page 423 / 440 (3)
Brain Bank2Standalone Brain Bank — MSA postmortem / cohort axis (2)
total12

Across these 12 sources, the source-note frontmatter records 10 uncertain_span_count entries and 0 body-embedded figure assets — review surface area, not resolutions. The 10 uncertain spans are concentrated on the two standalone Brain Bank nav-root pages (_184200 6 + _184203 4); the 10 supplement-chain pages record 0 uncertain spans each in their source-note frontmatter, which matches their nature as page-after-page catalog / contact / process matrix continuations rather than free-text claim pages. The zero-figure-embed count reflects the 2026-04-29 body-purity decision: figure-bearing crops on these pages (Braak-staging diagram, NBB tissue request flow visuals, BM-tracking KPI matrix) are kept as evidence at the canonical level rather than re-embedded here.

Biobank / Brain-Bank Landscape — MJF, NBB, ICBB, Other Biobanks, Biobanks in Japan

Seven pages walk the corpus’s biobank-and-brain-bank inventory under `Pipeline of GD & GBA-PD > Supplement > … > Biobank > MJF > Netherlands Brain Bank > Imperial College Brain Bank > Other Biobanks

Biobanks in Japan` on the Page 407 / 423 capture-time band. They form one continuous reading-order chain, each page picking up the prior page’s tail and opening the next page’s anchor. Cell values (cohort sizes, contact names, sample-type columns, cost / shipment fields, MTA terms) remain on the canonical pages.

  • MJF — PPMI, BioFiND, LCC, S4, Nilo-PD opener. PPMI Subjects / Available Data / Biospecimens, the Shahn Rahmadhan + 20240228 Samantha-notes block, BioFiND, the LRRK2 Cohort Consortium (LCC) cross-sectional / longitudinal / 23&Me studies, the S4 Systemic Syn Sampling Study (Chahine 2020 #1605), the Cf SC12 antibody note, and the Nilo-PD opener (md, 0 uncertain spans).
  • MJF biobank tail and Netherlands Brain Bank opener. Nilo-PD Cohort 1 / 2 + Available Data / Biospecimens continuation, MJFF PPMI iPSC LINES, MJFF biobank contacts, the 14 Types of Samples Available list, the Cohort Consortium ETBNRPP and tranSMART panel, and the Netherlands Brain Bank opener (autopsy procedures, paraffin-embedded samples) (md, 0 uncertain spans).
  • NBB tissue request flow. Netherlands Brain Bank tissue request continued — sample transfer process, MTA, transportation, cost per sample, IHC paraffin vs frozen, molecular analysis, the Location / Region / Analysis / Brain-Amount table, the Tony Wolinsky purchasing flow, NBB blood-cells correction, genetic testing, segregation in the family, pathogen testing, the NLRP3 plan note, AD co-pathologies reverse-translation, and the Braak-stage classification opener (md, 0 uncertain spans).
  • NBB → Imperial College Brain Bank handoff. Braak staging diagram tail (Thal 2002 + CERAD), the Imperial College Brain Bank block — Parkinson’s UK contacts, sample request flow, Controls definition, Section types, Tissue collections and access to data and images, Materials included in the service charge, Jaewon QA — and the ~400 genotyped PD cases (e ~60 + ~300) table opener (md, 0 uncertain spans).
  • ICBB sample availability and Other Biobanks opener. ICBB PD genotyping table tail, sample availability + USDA statement, the Imperial College Brain Bank Ariba PO process, and the Other Biobanks block opener (NCNP J-PPMI, Niigata univ — Postmortem brain PD aSyn fibril, TMM Cohort Study) (md, 0 uncertain spans).
  • Other Biobanks register — UK BBN, NIH NeuroBiBank, NCRAD, vendors. UK Brain Bank Network (NBB), the BDR / NeuroChip / Camp dataset access table, NIH NeuroBiBank, NCRAD + EUFortuv MICAgou, PrecisionMed, BIOIVT hemoglobin, the fibroblast-vendor list (NINOS, Cell Applications, Lonza, Lifeline, promogen, Sanjusbo, LEDBO, Cellbio, pmgenel), Biochain, BioSEND, and the Novus Biologicals NB820-59177 row (md, 0 uncertain spans).
  • Other Biobanks → Biobanks in Japan opener. Other Biobanks register continued (BIOIVT, vendors, Biochain, BioSEND, Novus Biologicals, ACCEGEN, Genomics England Banner Brain, NJ Brain Endowment Bank in Miami / Aging Center, NDRI, Neurobiobank Munich (NBM)), the Korean Open Government License KOGL Type 4 block, the J-PPMI (NCNP) row, and the Biobanks in Japan table opener (md, 0 uncertain spans).

BIOMARKER Tracker Bridge — Biobanks-in-Japan Tail and BM Tracking KPI Matrix

Three pages bridge the Biobanks-in-Japan tail into the BIOMARKER tracker matrix on the Page 423 / 440 capture-time band. They sit on the boundary between the brain-bank / biobank inventory above and the BioOrchestra biomarker catalog that opens on the next page (_182708, owned by bioorchestra-biomarker-catalog (Cluster C)). All three pages still list biobank-side BIOMARKER tracker rows (lysosomal markers, aSyn / GlcSph / pSer65-Ub assay status against MJ / NBB / J-PPMI / NDE samples) rather than crossing into the BioOrchestra catalog itself, so they are kept here.

  • Biobanks in Japan tail and BM-Tracking KPI opener. Biobanks in Japan tail (Tsukuba1 + Kyoto-U Nagahama phase0), the 20231009 Hooki Tsmurni Niigata-univ row, the BWMVRINER NSTM BM Tracking (KPI) matrix, the GBA Activity / GBM / GACer assay rows, the CSF Sample (Sato) prototype, the CSF & NDE row, and the ARM lysosomal-marker discussion (md, 0 uncertain spans). Page bridges Biobanks in Japan into the BIOMARKER axis.
  • BIOMARKER tracker — lysosomal markers + aSyn / GlcSph / CSF rows. BIOMARKER tracker matrix continuation — lysosomal markers + aSyn / GlcSph / SCSF assay rows, the GlcSph (Sato) and GlcSph & GalSph (Sato) assay-status block, the C8H CSF LCMS row, the CSF (LCMS) Annapurna SOMA / Juntendo-collaboration note, the Dr Margreith UMCS oligo-aSyn discussion (Steve / USPS wide cluster row), the cGAMP / Parkin / Substantia / pSer65-Ub MID/ELISA assay rows, the CSF Buffer 125 pg/mL row, and the Migdalisa Richards Ciegg patient-sample notes (md, 0 uncertain spans). Cross-link to parkin / pSer65-Ub assay evidence and to gba-pd-biology is intentional but is not re-narrated here.
  • BIOMARKER tracker continued — pSer65-Ub MJ assay, MITOKININ NBB CSF, BoMM 240 NBB samples. BIOMARKER tracker continued — pSer65-Ub MJ assay updates (Atalee + SMC4Ps + Boston Bioscience LSBio antibody), pSer65-Ub assay sensitivity / quantitation, MITOKININ NBB CSF, BoMM 240 NBB samples, the NLM newsletter PhanoSwitch saliva-EV proteomics note, the Korean RDDDU/OCT decision note, and the Survey of available external options / partnerships → Vendor or internal SCM12 8 row (md, 0 uncertain spans). This is the last page in the brain-bank / biobank chain before the BioOrchestra catalog opens on _182708; the next page is owned by bioorchestra-biomarker-catalog (Cluster C).

Standalone Brain Bank — MSA Postmortem Assays and Cohort Examples

Two pages sit under the standalone Brain Bank nav root on Page 925. They are catalog-flavoured pages that anchor MSA-side postmortem aSyn assays and an MSA cohort / clinical-trial example. Per the α-synuclein boundary map, these pages are categorised “Brain bank / postmortem aSyn-adjacent” (Tier 2) and remain delegated from alpha-synuclein § Tier 1 to this synthesis. MSA-side biology / Dx / Pipeline-MSA detail is owned by msa / msa and is not re-narrated here.

  • Brain Bank — MSA postmortem aSyn assays. The page lists Oligomeric aSyn in MSA, RT-QuIC in MSA, RBC aSyn in MSA, Skin aSyn in MSA, Autonomic Failure, and a Brain Bank section header — all as postmortem-assay catalog rows tied to brain-bank source materials (md, 6 uncertain spans). The 6 uncertain spans are the densest hot spot in this topic; cell values, identifier abbreviations, and assay-status columns are flagged uncertain on the canonical page.
  • Brain Bank > Clinical Progression > Clinical Trial example > Cohort. The page carries the Brain Bank / Clinical Progression / Clinical Trial example / Cohort hierarchy headers, the HORC-MSA cohort row, and the MSAR study (Hospital Clinic de Barcelona, Spain) / BIOMUSE row (md, 4 uncertain spans). MSA cohort detail is delegated to msa; the row is kept here as the brain-bank-side cohort-table linkage. The page also lists _184219 as a related-photo continuation (the MSA cohort table tail), which is owned by msa and is not included in this Source Table.

Source Table

Provenance ground-truth for the 12 sources, in capture-time order.

stemnav path / headingsource notecanonicaluncertain spansembedded images
20240722_182617Pipeline of GD & GBA-PD > Supplement > Process > BeyondBio > Biobank > MJFnotemd00
20240722_182620Pipeline of GD & GBA-PD > Supplement > BeyondBio > Biobank > MJF > Netherlands Brain Banknotemd00
20240722_182624Pipeline of GD & GBA-PD > Supplement > BeyondBio > Biobank > MJF > Netherlands Brain Banknotemd00
20240722_182627Pipeline of GD & GBA-PD > Supplement > Biobank > MJF > Netherlands Brain Bank > Imperial College Brain Banknotemd00
20240722_182630Pipeline of GD & GBA-PD > Supplement > MJF > Netherlands Brain Bank > Imperial College Brain Bank > Other Biobanksnotemd00
20240722_182634Pipeline of GD & GBA-PD > Supplement > MJF > Netherlands Brain Bank > Imperial College Brain Bank > Other Biobanksnotemd00
20240722_182637Pipeline of GD & GBA-PD > Supplement > Netherlands Brain Bank > Imperial College Brain Bank > Other Biobanks > Biobanks in Japannotemd00
20240722_182641Pipeline of GD & GBA-PD > Supplement > Imperial College Brain Bank > Other Biobanks > Biobanks in Japan > BIOMARKERnotemd00
20240722_182644Pipeline of GD & GBA-PD > Supplement > Imperial College Brain Bank > Other Biobanks > Biobanks in Japan > BIOMARKERnotemd00
20240722_182704Pipeline of GD & GBA-PD > Supplement > Imperial College Brain Bank > Other Biobanks > Biobanks in Japan > BIOMARKERnotemd00
20240722_184200Brain Banknotemd60
20240722_184203Brain Bank > Clinical Progression > Clinical Trial example > Cohortnotemd40

Totals across the 12 sources: uncertain_span_count = 10; embedded_image_count = 0. Per-axis subtotals:

  • Biobank / brain-bank landscape (7 pages): 0 uncertain spans, 0 embedded images.
  • BIOMARKER tracker bridge (3 pages): 0 uncertain spans, 0 embedded images.
  • Standalone Brain Bank — MSA postmortem / cohort axis (2 pages): 10 uncertain spans (6 + 4), 0 embedded images.

Numbers are review surface area, not resolutions. The biobank-landscape pages record 0 uncertain spans because they are catalog / process-flow / contact-list continuations whose cell-level detail is on the canonical page; the standalone Brain-Bank pages carry the topic’s uncertainty load.

Uncertainties Carried Forward

Uncertainty hot spots worth checking before downstream extraction. The page does not paraphrase uncertain content; open the canonical page for cell values.

  • Standalone Brain Bank — MSA postmortem assays (_184200, 6 uncertain spans). Oligomeric / RT-QuIC / RBC / Skin aSyn rows, Autonomic Failure row, and the Brain Bank header carry the page’s uncertainty load. Identifier abbreviations and assay-status columns should be re-checked on the canonical page rather than inferred from the topic.
  • Standalone Brain Bank — Clinical Progression / Cohort (_184203, 4 uncertain spans). HORC-MSA cohort and MSAR / BIOMUSE rows on the page; the related-photo continuation _184219 (owned by msa) holds the MSA cohort table tail and is not part of this topic.
  • Biobank / brain-bank landscape pages (_182617–_182637, reported 0 uncertain spans each). Despite the 0 count, these pages carry dense vendor / cohort / contact / process-flow tables (PPMI Available-Data matrix, NBB tissue request flow with cost/MTA fields, ~400 genotyped PD cases at ICBB, BDR / NeuroChip / Camp dataset table, fibroblast-vendor list, Biobanks-in-Japan catalog) where downstream extractors should treat the canonical cell values as the source of truth rather than the topic page.
  • BIOMARKER tracker bridge pages (_182641, _182644, _182704, reported 0 uncertain spans each). The BM-Tracking KPI matrix, lysosomal-marker / aSyn / GlcSph / pSer65-Ub assay columns, MITOKININ NBB CSF row, BoMM 240 NBB samples row, and Korean RDDDU/OCT decision note are dense matrix cells whose numerics, vendor names, and Korean inline annotations should be re-verified on the canonical page before any downstream extraction.
  • BIOMARKER → BioOrchestra boundary (_182704 → _182708). The chain transitions on the next page from biobank-side BIOMARKER tracker into the BioOrchestra biomarker catalog. Downstream readers should be aware that the BIOMARKER axis spans both this Cluster D topic (sample-side bridge) and the BioOrchestra catalog body owned by bioorchestra-biomarker-catalog (Cluster C); cell values on the BIOMARKER tracker matrix that overlap both pages are preserved verbatim on the canonical pages.

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