Part of COSD pathology user guide v4.1.1

Central Nervous System - Pathology

Pathology chapter on central nervous system data as part of the pathology user guide version 4.1.1

Previous Chapter

Pathology - Breast

Current Chapter

Current chapter – Central Nervous System - Pathology

View all

Next Chapter

Pathology - Colorectal

This is the site specific section for additional central nervous system cancer specific data items to be recorded. These will be aligned within the schema to form a single report.

May be up to one occurrence per pathology report (0..1)

Start of repeating item - Molecular Diagnostics Code

Data Item No	Data Item Name	Format	Schema Specification (M/R/O/X)
pBA3070	Molecular Diagnostics Code	an2	R*

End of repeating item - Molecular Diagnostics Code

Start of repeating item - Immunohistochemistry Hormone Expression Type

Data Item No	Data Item Name	Format	Schema Specification (M/R/O/X)
pBA3150	Immunohistochemistry Hormone Expression Type	an1	R*

End of repeating item - Immunohistochemistry Hormone Expression Type

Molecular Diagnostics Code

Chromosomal or genetic markers associated with the brain tumour. This may involve selection of more than one value for each tumour, as it is a repeating data item.

This table was extensively discussed by the Brain CNS expert group and has been based on the 2016 WHO categories for Molecular Diagnostic Markers.

National Code	National code definition
06	Evidence of ALK rearrangement
07	Evidence of native ALK
08	Evidence of ATRX mutation
09	Evidence of wt ATRX
10	Evidence of BRAF V600E mutation
11	Evidence of wt BRAF
12	Evidence of KIAA1549-BRAF fusion
13	Evidence of BRAF/RAF1 mutations, or fusions involving genes other than KIAA1549
14	Evidence of C11orf95-RELA fusion
15	Evidence of native C11orf95 and RELA
16	Evidence of amplification or fusion of C19MC locus (chr.19q13.42)
17	Evidence of unaltered C19MC locus (chr.19q13.42)
18	Evidence of CDK4/6 amplification
19	Evidence of CDK4/6 normal copy number
20	Evidence of CDKN2A locus homozygous deletion
21	Evidence of CDKN2A locus normal copy number
22	Evidence of CCND1/2/3 amplification
23	Evidence of CCND1/2/3 normal copy number
24	Evidence of CTNNB1 mutation
25	Evidence of wt CTNNB1
26	Evidence of amplification of EGFR
27	Evidence of mutation / rearrangement of EGFR
28	Evidence of unaltered EGFR
29	Evidence of EWSR1-FLI1 fusion
30	Evidence of native EWSR1 and FLI1
31	Evidence of FGFR1 mutation / rearrangement / fusion
32	Evidence of unaltered FGFR1
33	Evidence of H3F3A/H3F3B (H3.3) K27M mutation
34	Evidence of H3F3A/H3F3B (H3.3) wt K27
35	Evidence of H3F3A/H3F3B (H3.3) G34R/V mutation
36	Evidence of H3F3A/H3F3B (H3.3) wt G34
37	Evidence of HIST1H3B K27M mutation
38	Evidence of HIST1H3B wt K27
39	Evidence of HIST1H3C K27M mutation
40	Evidence of HIST1H3C wt K27
41	Evidence of ID2 amplification
42	Evidence of ID2 normal copy number
43	IDH1 (codon 132) or IDH2 (codon 172) mutation identified
44	IDH1 (codon 132) and IDH2 (codon 172) wt confirmed
45	Evidence of KLF4 K409Q and TRAF7 mutations
46	Evidence of wt KLF4 and TRAF7
47	Evidence of MAP2K1 mutation
48	Evidence of wt MAP2K1
49	Evidence of MET amplification
50	Evidence of MET normal copy number
51	Evidence of significant MGMT promoter methylation
52	Evidence of unmethylated MGMT promoter
53	Evidence of MYC/MYCN amplification
54	Evidence of MYC/MYCN normal copy number
55	Evidence of NF1 biallelic loss / mutation
56	Evidence of unaltered NF1
57	Evidence of NF2 biallelic loss / mutation
58	Evidence of unaltered NF2
59	Evidence of NKTR fusions
60	Evidence of native NKTR
61	Evidence of PTEN biallelic loss / mutation
62	Evidence of unaltered PTEN
63	Evidence of SDHB or SDHD mutation
64	Evidence of wt SDHB and SDHD
65	Evidence of SHH pathway activation
66	Evidence of normal SHH pathway
67	Evidence of inactivation of SMARCB1 (INI1)
68	Evidence of wt SMARCB1 (INI1)
69	Evidence of inactivation of SMARCA4
70	Evidence of wt SMARCA4
71	Evidence of TERT promotor mutation
72	Evidence of wt TERT promotor
73	Evidence of TP53 mutation
74	Evidence of wt TP53
75	Evidence of TSC1 or TSC2 mutation
76	Evidence of wt TSC1 and TSC2
77	Evidence of VHL mutation
78	Evidence of wt VHL gene
79	Evidence of WNT pathway activation
80	Evidence of normal WNT pathway
81	Evidence of WWTR1-CAMTA1 fusion
82	Evidence of native WWTR1 and CAMTA1
83	Evidence of codeletion of chr.1p and chr.19q
84	Evidence of total chr.1p loss but normal copy number of chr.19q
85	Evidence of normal copy number of both chr.1p and chr.19q
86	Evidence of monosomy chr.6
87	Evidence of chr.6 normal copy number
88	Evidence of polysomy chr.7
89	Evidence of chr.7 normal copy number
90	Evidence of loss of chr.10 or chr.10q
91	Evidence of chr.10 normal copy number
92	Evidence of loss of chr.22 or chr.22q
93	Evidence of chr.22 or chr.22q normal copy number
98	Other
99	Not Known (Not Recorded)

The old codes (below) can be mapped as follows to enable a seamless transition to v4, where old reports are re-submitted as part of a clinical review.

Old Code	Description	New Code	Description
01	Evidence of IDH1 or IDH2 mutation	43	IDH1 (codon 132) or IDH2 (codon 172) mutation identified
02	Evidence of methylation of the MGMT gene CpG island	51	Evidence of significant MGMT promoter methylation
03	Evidence of total loss of 1p and 19q	83	Evidence of codeletion of chr.1p and chr.19q
04	Evidence of KIAA 1549-BRAF fusion gene	12	Evidence of KIAA1549-BRAF fusion
05	Other	98	Other

Immunohistochemistry Hormone Expression Type

Hormone expression by immunohistochemistry. for pituitary adenomas only. This may involve selection of more than one value, as it is a repeating data item.

National Code	National code definition
0	Non functioning
1	ACTH
2	LH
3	FSH
4	Alpha-subunit
5	TSH
6	Prolactin
7	Growth Hormone

Last edited: 5 January 2023 2:06 pm