For the complete documentation index, see llms.txt. This page is also available as Markdown.

Supplement: Orphan-Disease, Rare-Tumor & Cutting-Edge IHC

Addendum to the National Reference Laboratory IHC Menu — Dako Omnis context

Slots into the base document's section numbering. Status flags: T2 = add to the standing reference menu now; LDT = emerging/validated-in-literature, run as in-house validated laboratory-developed test (usually RUO reagent); R = research-only, never for clinical treatment selection.


S0. Why this layer exists — and how to run it

This supplement covers three things the base menu deliberately deferred: (1) fusion/mutation-surrogate IHC that substitutes for molecular testing (SS18-SSX, H3 G34R/V, p65, AFF2, DDIT3, EZHIP), (2) orphan-disease panels that only a national reference center will ever run at volume (neuromuscular, EB antigen mapping, PFIC, amyloid typing, novel MN antigens, prion), and (3) molecular-subtype surrogates entering trials and tumor boards (GATA6/CK17 in PDAC, ASCL1/NEUROD1/POU2F3/YAP1 in SCLC, GPNMB in renal tumors).

Operational rules specific to this layer:

  • EQA mostly does not exist for these markers (NordiQC/UK NEQAS coverage is sparse). Substitute: genotyped index cases and cell-line FFPE blocks as controls, split-sample exchange with 1–2 peer reference labs, and molecular concordance audits (every surrogate-IHC result vs NGS/FISH for the first 20+ cases, then periodic).

  • Regulatory framing: most reagents here are RUO. Under EU IVDR logic (Art. 5(5) health-institution exemption) and ISO 15189, each becomes an in-house LDT with a validation dossier (analytical sensitivity/specificity vs genotype, precision, lot-to-lot). In Turkey, align the dossier with TÜRKAK ISO 15189 scope and TİTCK device rules.

  • Omnis practicalities: most of these are rabbit polyclonals or low-abundance rabbit mAbs → plan TRS High pH HIER + 3-step (linker) detection by default, then de-escalate if signal allows. Batch ultra-low-volume markers (weekly/monthly runs).

  • Digital pathology hook: QuPath-assisted scoring is already published for GATA6 H-score in PDAC and is the obvious route for Ki-67-like quantitative surrogates — a natural fit for your image-analysis pipeline.


S3-bis. GI, pancreatobiliary & liver (extends base §3)

Marker
Clone / format
Use
Status

GATA6

No consensus dx clone; published IHC (COMPASS ancillary work) with pathologist + QuPath-assisted H-score; RNA-ISH alternative

PDAC transcriptional subtype surrogate: GATA6-high = classical (ORR 33% and better mFOLFIRINOX outcomes in COMPASS); GATA6-low = basal-like (ORR 10%, mFFX progression 60% vs 15%)

LDT

CK17 (E3)

Dako/std E3

Dual role: (a) basal-like PDAC marker (with CK5/6+, p63+, GATA6/HNF4α-low); (b) PDAC-vs-reactive panel with IMP3, maspin, S100P

T2

HNF4α

rabbit mAb/polyclonal

Classical-subtype partner; 4-marker panel CK5/6+p63 vs GATA6+HNF4α defines classical/transitional/basal IHC patterns with independent prognostic value

LDT

ATRX + DAXX

ATRX polyclonal/BSB-108 (on menu); DAXX rabbit polyclonal

Loss in ~40% PanNET → ALT phenotype, worse prognosis; distinguishes PanNET from PanNEC (RB/p53 route)

T2

Menin (MEN1)

rabbit mAb/polyclonal

Nuclear loss in MEN1-mutant PanNET; syndromic flag

LDT

BSEP (ABCB11)

rabbit polyclonal

Canalicular loss → PFIC2; orphan pediatric cholestasis service

T2

MDR3 (ABCB4)

P3II-26

Canalicular loss/reduction → PFIC3

T2

Alpha-1-antitrypsin

polyclonal (Dako)

PiZZ globules (PAS-D+ correlate); A1ATD liver

T2

Pitfall note

GATA6 also stains many upper-GI/pancreatobiliary lineages — subtype use requires quantitative scoring, not binary read

S7-bis. Thoracic (extends base §7)

Marker
Clone / format
Use
Status

ASCL1

24B72D11 (BD)

SCLC-A (ASCL1-dominant ≈69% of SCLC); NE-high/DLL3-high

LDT

NEUROD1

EPR20766

SCLC-N (≈17%); NE-high

LDT

POU2F3

rabbit polyclonal (e.g., NBP1-83966)

SCLC-P tuft-cell-like (≈7%); mutually exclusive with ASCL1/NEUROD1; NE-low/DLL3-low — explains "NE-marker-negative SCLC"

LDT

YAP1

63.7

SCLC-Y/inflamed (low-level, mostly combined SCLC; contested as pure subtype); also Hippo-pathway work in mesothelioma; also ST-EPN-YAP1

LDT

NF2/Merlin

rabbit mAb/polyclonal

Loss in mesothelioma (Hippo axis) — adjunct to BAP1/MTAP

R→LDT

Rationale

Subtype correlates with DLL3 (tarlatamab), chemo-IO response patterns; expect trial-driven requests. Report as dominant-TF pattern, not single-marker binary

S5-bis. Genitourinary (extends base §5)

Marker
Clone / format
Use
Status

GPNMB

rabbit mAb (automated assays published)

Sensitive screen for TFE3/TFEB tRCC AND TSC1/2/mTOR-altered tumors (ESC RCC, EVT, LOT, AML/PEComa) — shared MiT-pathway output. Caveats: does not separate those two groups; ~13% equivocal/false-negative vs FISH; confirm with TFE3/TFEB IHC-FISH. TRIM63 RNA-ISH is the emerging alternative

LDT

HOXB13

rabbit mAb (e.g., D7N8O)

Prostate lineage in NKX3.1-dim/PSA-negative metastases

LDT

Prostein (P501S)

10E3

Prostatic lineage (with NKX3.1)

T2

PBRM1

rabbit polyclonal

ccRCC prognostic (with BAP1); research reporting only

R

S6-bis. Gynecologic (extends base §6)

Marker
Clone / format
Use
Status

FOXL2

rabbit polyclonal

Sex cord-stromal lineage (adult granulosa); C402G/C134W confirmation stays molecular

T2

BCOR

C-10 (mouse)

High-grade endometrial stromal sarcoma (BCOR-ITD/ZC3H7B::BCOR) — pairs with diffuse cyclin D1; also see sarcoma/CNS entries

LDT

SMARCA4 (BRG1) + SMARCA2 (BRM)

EPNCIR111A (on menu) + BRM polyclonal

SCCOHT: BRG1 loss with BRM co-loss is near-pathognomonic — reflex both in young-female undifferentiated ovarian tumors

T2

Pattern note

Mesonephric-like adenocarcinoma: GATA3+/TTF-1+/luminal CD10+ with ER/PR-low, wild-type p53 — panel logic, no new reagent

S8-bis. Head & neck, endocrine (extends base §8)

Marker
Clone / format
Use
Status

AFF2 (C-terminus)

rabbit anti-AFF2 C-term

Nuclear AFF2 = sensitive & specific surrogate for DEK::AFF2 sinonasal/skull-base carcinoma (papilloma-like, deceptively bland, aggressive); replaces FISH triage

LDT

IDH2 R172 (multi-specific)

MsMab-1 / 11C8B1

IDH2-mutant SNUC (and rare gliomas); imperfect sensitivity — NGS confirms negatives

LDT

NRAS Q61R

SP174

RAS-like thyroid neoplasms; melanoma adjunct

LDT

p27/CDKN1B

SX53G8

MEN4 workup; pituitary/parathyroid context

LDT

NUT scope note

C52B1 (on menu)

Extend NUT IHC beyond NUT carcinoma: NUTM1-rearranged porocarcinoma/adnexal and sarcomas

S9-bis. Hematopathology (extends base §9)

Marker
Clone / format
Use
Status

BOB1 / OCT2

SP92 (or TG14) / Oct-207

B-cell program integrity: CHL (dim/lost) vs NLPHL/PMBL/LBCL

T2

CD200

e.g., UMAB223

CLL (+) vs MCL (−); HCL (+)

T2

MNDA / IRTA1

253A / rabbit mAb

Marginal-zone vs follicular lymphoma

T2

HGAL (GCET1) / LMO2

MRQ-49 / SP51

Germinal-center program (Hans-plus algorithms)

T2

CXCL13 / ICOS

polyclonal / SP98

TFH phenotype — AITL/nodal TFH lymphoma (with PD-1, CD10, BCL6)

T2

TCF4 (E2-2)

rabbit mAb

BPDCN (with CD123, TCL1)

LDT

TBX21 (T-bet) + GATA3

4B10 + L50-823

PTCL-NOS TBX21 vs GATA3 subtyping (prognostic; entering trials)

LDT

NPM1 (cytoplasmic)

clone 376

Cytoplasmic dislocation = NPM1-mutant AML surrogate on trephines

LDT

CD19

e.g., BT51E

Antigen-escape assessment post-CAR-T/blinatumomab (report presence/loss)

LDT

CD79b / CD22

mAbs

Polatuzumab / inotuzumab target documentation on request

R→LDT

BCMA

mAbs

Myeloma CAR-T/bispecific target — no validated clinical IHC selection assay yet

R

S10-bis. Soft tissue & bone (extends base §10)

Marker
Clone / format
Use
Status

SS18-SSX (fusion junction)

E9X9V

Synovial sarcoma: ~100% specific, ~95% sensitive; diffuse strong nuclear

T2

SSX (C-terminus)

E5A2C

~100% sensitive, ~96% specific; run as a pair — concordant staining can replace FISH/NGS in most cases; false negatives in decalcified/poorly fixed small biopsies

T2

CCNB3

rabbit polyclonal

BCOR::CCNB3 sarcoma (with BCOR C-10)

LDT

ETV4

mAb/polyclonal (per Hung et al.)

CIC-rearranged sarcoma (diffuse nuclear; with strong WT1); DUX4 C-terminal Abs remain RUO

LDT

FOSB

5G4

Pseudomyogenic hemangioendothelioma; epithelioid hemangioma

LDT

FOS (c-FOS)

rabbit mAb

FOS-rearranged osteoblastoma/osteoid osteoma vs osteosarcoma

LDT

DDIT3 (CHOP)

e.g., 9C8

Nuclear DDIT3 = FUS/EWSR1::DDIT3 myxoid liposarcoma surrogate

LDT

GLI1

RUO mAb/polyclonal

GLI1-amplified/rearranged mesenchymal tumors ("gastroblastoma-like", plexiform fibromyxoma spectrum)

LDT

SMARCA2 (BRM)

polyclonal

Co-loss with SMARCA4 in thoracic/undifferentiated tumors, SCCOHT

LDT

Pitfall

NKX3.1 (EP356) is positive in mesenchymal chondrosarcoma — do not read as prostatic in small-round-cell context

S11-bis. Neuropathology (extends base §11)

Marker
Clone / format
Use
Status

H3 G34R

RM240 (RevMAb)

Diffuse hemispheric glioma, H3 G34-mutant (~90% of G34 cases); context: OLIG2-negative, ATRX loss, p53+

T2

H3 G34V

RM307 (RevMAb)

The rarer G34V DHG (run both on suspicion; G34M escapes both → sequence)

LDT

p65 (RelA)

e.g., D14E12; nuclear

ZFTA::RELA ST-ependymoma surrogate: ~100% sensitive / ~92% specific for RELA fusion; combine with L1CAM (more sensitive for non-RELA ZFTA partners) ± cyclin D1; double-negative virtually excludes fusion

T2

EZHIP (CXorf67)

rabbit polyclonal (runs on Omnis per RENOCLIP data)

PFA ependymoma: ~93% EZHIP+, remainder H3K27M+ — pairs with H3K27me3 loss; also H3-WT DMG with EZHIP overexpression; germinoma cross-positivity caveat

LDT

BCOR

C-10

CNS tumor with BCOR-ITD (also sarcoma/HG-ESS uses)

LDT

YAP1

63.7

ST-EPN-YAP1 (infant); see also thoracic uses

LDT

MB surrogate panel: GAB1, YAP1, filamin A, OTX2

polyclonal / 63.7 / PM6/317 / rabbit mAb

Provisional medulloblastoma grouping when methylation is unavailable: β-catenin-nuclear=WNT; GAB1/YAP1/filamin A+=SHH; all-neg=group 3/4

LDT

CRX

rabbit polyclonal

Retinoblastoma/pineoblastoma photoreceptor lineage

LDT

PrP (prion)

3F4, KG9, 12F10

CJD surveillance IHC (PrP^Sc deposition patterns). Formic-acid pretreatment, dedicated processing/instrument decontamination, national-surveillance linkage — a defining reference-lab obligation

T2

S12-bis. Dermatopathology (extends base §12)

Marker
Clone / format
Use
Status

MCPyV large T

CM2B4

Merkel cell carcinoma: virus-positive vs virus-negative (UV-driven, TTF-1-independent CK20-dot context); etiologic + prognostic

T2

5hmC

rabbit polyclonal

Global loss favors melanoma over nevus; nevoid melanoma adjunct

LDT

MxA

mAb/polyclonal

Type-I interferon signature — dermatomyositis skin (and muscle, see S-NM)

LDT

S13-bis. Nephropathology (extends base §13)

Marker
Clone / format
Use
Status

NELL1

rabbit polyclonal

2nd most common MN antigen after PLA2R (~13–16% of PLA2R-negative MN); segmental GBM pattern, IgG1-dominant; associations: malignancy, bucillamine, lipoic acid

T2

EXT1 + EXT2

rabbit polyclonals

~12% of PLA2R-negative MN; autoimmune/membranous-lupus association; bright granular GBM

T2

Sema3B / PCDH7 / NCAM1 / HTRA1

polyclonals

Minor MN antigens (Sema3B pediatric) — batch on request

LDT

IgG subclasses (IgG1–4)

HP600x-series mAbs or sheep polyclonals

MN primary-vs-secondary logic (IgG4-dominant=PLA2R type), PGNMID (monotypic IgG3κ), fibrillary GN

T2

Amyloid typing panel: AA, ATTR, AFib (fibrinogen Aα), ALECT2, κ, λ

mc1 (AA) + polyclonals

IHC pre-typing of amyloid; explicit caveat: IHC mistyping risk is real — laser-microdissection mass spectrometry remains gold standard; DNAJB9 (base menu) covers fibrillary GN

T2

S-NM. Neuromuscular orphan-disease panel (NEW section)

The single largest orphan-disease IHC block a national reference lab should own. Classic clones are Leica/Novocastra heritage; many now validated on FFPE, but keep a frozen-section IF track for dystroglycan and service continuity.

Marker
Clone(s)
Use

Dystrophin rod / C-term / N-term

DYS1 (Dy4/6D3) / DYS2 (Dy8/6C5) / DYS3 (Dy10/12B2)

DMD (absent) vs BMD (reduced/patchy); all three domains mandatory

α/β/γ/δ-sarcoglycan

Ad1/20A6, βSarc/5B1, 35DAG/21B5, δSarc3/12C1

Sarcoglycanopathies (LGMD R3–R6); secondary reductions cross-panel

Dysferlin

NCL-Hamlet

LGMD R2 / Miyoshi

Merosin (laminin-α2)

Mer3/22B2

MDC1A congenital dystrophy

Emerin

4G5

X-linked Emery-Dreifuss (nuclear rim loss)

Caveolin-3

mAb/polyclonal

LGMD 1C / rippling muscle

Spectrin

RBC2/3D5

Sarcolemmal integrity control for every run

α-dystroglycan

IIH6C4 / VIA4-1

Dystroglycanopathies (glyco-epitope; frozen/WB support)

Utrophin

DRP3/20C5

Compensatory sarcolemmal upregulation in DMD

Fast / slow / neonatal myosin

WB-MHCf / WB-MHCs / WB-MHCn

Fiber typing, grouping, regeneration

MHC class I / II

W6/32 / CR3/43

Sarcolemmal upregulation — inflammatory myopathy screen

C5b-9 (MAC)

aE11

DM capillary deposits; IMNM sarcolemmal deposits

MxA

mAb/polyclonal

Sarcoplasmic MxA = sensitive/specific DM interferon signature

p62 + TDP-43

3/P62-lck + phospho/std

IBM rimmed-vacuole pathology (with COX/SDH histochemistry)

CD56/NCAM (reuse)

123C3

Regenerating fibers

S-EB. Epidermolysis bullosa antigen mapping (NEW section)

IF mapping (frozen preferred) localizes the split and the deficient protein — genotype-guiding orphan service.

Target
Clone
Disease level

Keratin 5 / 14

XM26 / LL002

EB simplex (basal keratinocyte)

Plectin

mAb (e.g., 10F6)

EBS with muscular dystrophy

Integrin α6/β4

mAbs

JEB with pyloric atresia

Laminin-332

GB3

Junctional EB (lamina lucida)

Collagen XVII (BP180)

NC16A-domain mAbs

Junctional EB

Collagen VII

LH7.2

Dystrophic EB (sublamina densa)

Collagen IV

CIV22 (base menu)

Floor/roof reference of the split

S14-bis. Infectious (extends base §14)

Tropheryma whipplei IHC exists but availability is limited — PAS-D morphology + PCR remains the practical reference pathway; list as send-out/LDT-on-demand only.

S18-bis. Pediatric (extends base §18)

ALK IHC (D5F3/5A4, already on menu) gains a neuroblastoma use: ALK-aberrant NB flagging for lorlatinib-era protocols (report intensity/extent; molecular confirms). PHOX2B, INI1, LIN28A already cover the rest.

S-R. Research-only horizon (never for clinical selection)

Marker
Note

LAG-3 (17B4 / D2G4O)

Relatlimab context; no CDx requirement

β2-microglobulin / HLA-I (EMR8-5)

Immune-evasion phenotyping

STK11/LKB1

IHC unreliable — molecular only

CLDN6, B7-H3 (CD276), CD70

ADC/CAR-T targets in trials

PLCG2 (SCLC stem-like), TRIM63 RNA-ISH (renal)

Emerging adjuncts


Updated menu arithmetic

Block
New antibodies (approx.)

GI/pancreatobiliary/liver

+8

Thoracic (SCLC subtyping, NF2)

+5

GU

+4

Gyn (net of cross-listed)

+2

H&N/endocrine

+4

Hematopathology

+13

Soft tissue & bone

+9

Neuropathology

+11

Dermatopathology

+3

Nephropathology (incl. amyloid panel)

+11

Neuromuscular panel

+19

EB mapping (net new)

+6

Research-only shelf

(+5 flagged R)

Supplement total

≈ +95

Combined menu: ~430–460 distinct antibodies — the top of the 300–500 reference-lab envelope, which is exactly where a national center serving all subspecialties should sit. Suggested sequencing: (1) fusion-surrogate sarcoma/CNS block (SS18-SSX pair, H3 G34R/V, p65+L1CAM, BCOR, DDIT3) — highest referral value per antibody; (2) neuromuscular + EB orphan panels — service-defining, low reagent risk (legacy clones); (3) nephropathology antigens + amyloid; (4) subtype-surrogate trio (GATA6/CK17-PDAC, SCLC-TF panel, GPNMB) as trial demand materializes; keep the S-R shelf strictly research-labeled.

Caveats specific to this supplement

  • Surrogate-IHC ≠ genotype: maintain a standing molecular-concordance log; sequence discordant and antibody-negative-but-suspicious cases (e.g., G34M, variant SS18::SSX, non-RELA ZFTA).

  • Decalcification and small poorly-fixed biopsies are the dominant false-negative mode for fusion-junction antibodies (documented for E9X9V/E5A2C) — repeat on better material before excluding.

  • Polyclonal lot drift is the chief analytic risk (EZHIP, NELL1, EXT1/2, CCNB3, GAB1, amyloid panel): re-verify each lot against index-case controls.

  • GPNMB and other MiT-target markers cannot distinguish translocation-driven from TSC/mTOR-driven tumors — report as pathway-level screen.

  • Amyloid IHC pre-typing must carry a mandatory LMD-MS recommendation line for therapy-determining cases (ATTR vs AL).

  • Prion work requires a segregated workflow, formic-acid protocols, and documented decontamination — plan before offering, not after the first referral.

Last updated